http://www.weizhongli-lab.org/rssgen/?cat=289 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=4730/ Ngô HM, Zhou Y, et al.|-|-| Scientific Reports. 2017 Sep 13; 7. : 11496.|-|-| One third of humans are infected lifelong with the brain-dwelling, protozoan parasite, Toxoplasma gondii. Approximately fifteen million of these have congenital toxoplasmosis. Although neurobehavioral disease is associated with seropositivity, causality is unproven. To better understand what this parasite does to human brains, we performed a comprehensive systems analysis of the infected brain: We identified susceptibility genes for congenital toxoplasmosis in our cohort of infected humans and found these genes are expressed in human brain. Transcriptomic and quantitative proteomic analyses of infected human, primary, neuronal stem and monocytic cells revealed effects on neurodevelopment and plasticity in neural, immune, and endocrine networks. These findings were supported by identification of protein and miRNA biomarkers in sera of ill children reflecting brain damage and T. gondii infection. These data were deconvoluted using three systems biology approaches: "Orbital-deconvolution" elucidated upstream, regulatory pathways interconnecting human susceptibility genes, biomarkers, proteomes, and transcriptomes. "Cluster-deconvolution" revealed visual protein-protein interaction clusters involved in processes affecting brain functions and circuitry, including lipid metabolism, leukocyte migration and olfaction. Finally, "disease-deconvolution" identified associations between the parasite-brain interactions and epilepsy, movement disorders, Alzheimer's disease, and cancer. This "reconstruction-deconvolution" logic provides templates of progenitor cells' potentiating effects, and components affecting human brain parasitism and diseases. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Wed, 13 Sep 2017 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=4731/ Hujer AM, Higgins PG, et al.|-|-| Antimicrobial Agents and Chemotherapy. 2017 Sep 11;. |-|-| Carbapenem antibiotics are among the mainstay for treating infections caused by Acinetobacter baumannii, especially in the Northwest United States where carbapenem resistant A. baumannii remain relatively rare. However, between June 2012 and October 2014, an outbreak of carbapenem-resistant A. baumannii occurred in 16 patients from 5 healthcare facilities in the state of Oregon. All isolates were defined as extensively-drug resistant (XDR). MLST revealed that the isolates belonged to sequence type 2 (international clone 2, IC2), and were greater than 95% similar by rep-PCR analysis. Multiplex PCR revealed the presence of a blaOXA carbapenemase gene, later identified as blaOXA-237 Whole genome sequencing of all isolates revealed a well-supported separate branch within a global A. baumannii phylogeny. Pacific Biosciences (PacBio) SMRT sequencing was also performed on one isolate to gain insight into the genetic location of the carbapenem resistance gene. We discovered that blaOXA-237, flanked on either side by ISAba1 elements in opposite orientations, was carried by a 15,198 bp plasmid designated pORAB01-3, and was present in all 16 isolates. The plasmid also contained genes encoding for: a TonB-dependent receptor, septicolysin, a type IV secretory system conjugative DNA transfer family protein, an integrase, a RepB family plasmid DNA replication initiator protein, an ?/? hydrolase, and a BrnT/BrnA type II toxin-antitoxin system. This is the first reported outbreak associated with this specific carbapenemase. Particularly worrisome is that blaOXA-237 was plasmid encoded and found in the most prominent worldwide clonal group IC2, potentially giving pORAB01-3 great capacity for future widespread dissemination. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Mon, 11 Sep 2017 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=4733/ Buser GL, Cassidy PM, et al.|-|-| Infection Control and Hospital Epidemiology. 2017 Sep 05;. : 1-7.|-|-| OBJECTIVE To determine the scope, source, and mode of transmission of a multifacility outbreak of extensively drug-resistant (XDR) Acinetobacter baumannii. DESIGN Outbreak investigation. SETTING AND PARTICIPANTS Residents and patients in skilled nursing facilities, long-term acute-care hospital, and acute-care hospitals. METHODS A case was defined as the incident isolate from clinical or surveillance cultures of XDR Acinetobacter baumannii resistant to imipenem or meropenem and nonsusceptible to all but 1 or 2 antibiotic classes in a patient in an Oregon healthcare facility during January 2012-December 2014. We queried clinical laboratories, reviewed medical records, oversaw patient and environmental surveillance surveys at 2 facilities, and recommended interventions. Pulsed-field gel electrophoresis (PFGE) and molecular analysis were performed. RESULTS We identified 21 cases, highly related by PFGE or healthcare facility exposure. Overall, 17 patients (81%) were admitted to either long-term acute-care hospital A (n=8), or skilled nursing facility A (n=8), or both (n=1) prior to XDR A. baumannii isolation. Interfacility communication of patient or resident XDR status was not performed during transfer between facilities. The rare plasmid-encoded carbapenemase gene bla OXA-237 was present in 16 outbreak isolates. Contact precautions, chlorhexidine baths, enhanced environmental cleaning, and interfacility communication were implemented for cases to halt transmission. CONCLUSIONS Interfacility transmission of XDR A. baumannii carrying the rare blaOXA-237 was facilitated by transfer of affected patients without communication to receiving facilities. Infect Control Hosp Epidemiol 2017;1-7. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Tue, 05 Sep 2017 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=4727/ Shrivastava S, Puri V, et al.|-|-| Genome Announcements. 2017 Jul 27; 5. |-|-| We report here the complete genome of a Dezidougou virus (DEZV) isolated from a passaged culture of the Zika virus strain DAK AR 41524. The consensus DEZV sequence we recovered shows 99% nucleotide similarity using BLASTN to a previously reported DEZV (accession no. JQ675604.1). The current sequence has additional repeat regions as well as a deleted repeat region, which we confirmed by Sanger sequencing, that were not present in the originally published sequence, JQ675604.1. Thu, 27 Jul 2017 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=4732/ Rojas LJ, Hujer AM, et al.|-|-| Antimicrobial Agents and Chemotherapy. 2017 Jul 01; 61. |-|-| Among Gram-negative bacteria, carbapenem-resistant infections pose a serious and life-threatening challenge. Here, the CRACKLE network reports a sentinel detection and characterization of a carbapenem-resistant Klebsiella pneumoniae ST147 isolate harboring blaNDM-5 and blaOXA-181 from a young man who underwent abdominal surgery in India. blaNDM-5 was located on an IncFII plasmid of ?90 kb, whereas blaOXA-181 was chromosomally encoded. Resistome and genome analysis demonstrated multiple copies of the transposable element IS26 and a "hot-spot region" in the IncFII plasmid. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Sat, 01 Jul 2017 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=4687/ Lee AJ, Bhattacharya R, et al.|-|-| PloS One. 2017 Jun 01; 12. : e0178199.|-|-| Zika virus (ZIKV) is a member of the Flavivirus genus of positive-sense single-stranded RNA viruses, which includes Dengue, West Nile, Yellow Fever, and other mosquito-borne arboviruses. Infection by ZIKV can be difficult to distinguish from infection by other mosquito-borne Flaviviruses due to high sequence similarity, serum antibody cross-reactivity, and virus co-circulation in endemic areas. Indeed, existing serological methods are not able to consistently differentiate ZIKV from other Flaviviruses, which makes it extremely difficult to accurately calculate the incidence rate of Zika-associated Guillain-Barre in adults, microcephaly in newborns, or asymptomatic infections within a geographical area. In order to identify Zika-specific peptide regions that could be used as serology reagents, we have applied comparative genomics and protein structure analyses to identify amino acid residues that distinguish each of 10 Flavivirus species and subtypes from each other by calculating the specificity, sensitivity, and surface exposure of each residue in relevant target proteins. For ZIKV we identified 104 and 116 15-mer peptides in the E glycoprotein and NS1 non-structural protein, respectively, that contain multiple diagnostic sites and are located in surface-exposed regions in the tertiary protein structure. These sensitive, specific, and surface-exposed peptide regions should serve as useful reagents for seroprevalence studies to better distinguish between prior infections with any of these mosquito-borne Flaviviruses. The development of better detection methods and diagnostic tools will enable clinicians and public health workers to more accurately estimate the true incidence rate of asymptomatic infections, neurological syndromes, and birth defects associated with ZIKV infection. Thu, 01 Jun 2017 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=4657/ Brinkac L, Voorhies A, et al.|-|-| Microbial Ecology. 2017 May 11;. |-|-| Ubiquitous in nature, antimicrobial resistance (AMR) has existed long before the golden age of antimicrobials. While antimicrobial agents are beneficial to combat infection, their widespread use contributes to the increase in and emergence of novel resistant microbes in virtually all environmental niches. The human microbiome is an important reservoir of AMR with initial exposure occurring in early life. Once seeded with AMR, commensal organisms may be key contributors to the dissemination of resistance due to the interconnectedness of microbial communities. When acquired by pathogens however, AMR becomes a serious public health threat worldwide. Our ability to combat the threat of emerging resistance relies on accurate AMR detection methods and the development of therapeutics that function despite the presence of antimicrobial resistance. Thu, 11 May 2017 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=4565/ Brinkac LM, Beck E, et al.|-|-| Bioinformatics (Oxford, England). 2017 Jan 27;. |-|-| LOCUST is a custom sequence locus typer tool for classifying microbial genomes. It provides a fully automated opportunity to customize the classification of genome-wide nucleotide variant data most relevant to biological research. Fri, 27 Jan 2017 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=4509/ Sobel Leonard A, McClain MT, et al.|-|-| Journal of Virology. 2016 Dec 15; 90: 11247-11258.|-|-| Knowledge of influenza virus evolution at the point of transmission and at the intrahost level remains limited, particularly for human hosts. Here, we analyze a unique viral data set of next-generation sequencing (NGS) samples generated from a human influenza challenge study wherein 17 healthy subjects were inoculated with cell- and egg-passaged virus. Nasal wash samples collected from 7 of these subjects were successfully deep sequenced. From these, we characterized changes in the subjects' viral populations during infection and identified differences between the virus in these samples and the viral stock used to inoculate the subjects. We first calculated pairwise genetic distances between the subjects' nasal wash samples, the viral stock, and the influenza virus A/Wisconsin/67/2005 (H3N2) reference strain used to generate the stock virus. These distances revealed that considerable viral evolution occurred at various points in the human challenge study. Further quantitative analyses indicated that (i) the viral stock contained genetic variants that originated and likely were selected for during the passaging process, (ii) direct intranasal inoculation with the viral stock resulted in a selective bottleneck that reduced nonsynonymous genetic diversity in the viral hemagglutinin and nucleoprotein, and (iii) intrahost viral evolution continued over the course of infection. These intrahost evolutionary dynamics were dominated by purifying selection. Our findings indicate that rapid viral evolution can occur during acute influenza infection in otherwise healthy human hosts when the founding population size of the virus is large, as is the case with direct intranasal inoculation. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Thu, 15 Dec 2016 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=4505/ Chavda KD, Chen L, et al.|-|-| MBio. 2016 Dec 13; 7|-|-| Knowledge regarding the genomic structure of Enterobacter spp., the second most prevalent carbapenemase-producing Enterobacteriaceae, remains limited. Here we sequenced 97 clinical Enterobacter species isolates that were both carbapenem susceptible and resistant from various geographic regions to decipher the molecular origins of carbapenem resistance and to understand the changing phylogeny of these emerging and drug-resistant pathogens. Of the carbapenem-resistant isolates, 30 possessed blaKPC-2, 40 had blaKPC-3, 2 had blaKPC-4, and 2 had blaNDM-1 Twenty-three isolates were carbapenem susceptible. Six genomes were sequenced to completion, and their sizes ranged from 4.6 to 5.1 Mbp. Phylogenomic analysis placed 96 of these genomes, 351 additional Enterobacter genomes downloaded from NCBI GenBank, and six newly sequenced type strains into 19 phylogenomic groups-18 groups (A to R) in the Enterobacter cloacae complex and Enterobacter aerogenes Diverse mechanisms underlying the molecular evolutionary trajectory of these drug-resistant Enterobacter spp. were revealed, including the acquisition of an antibiotic resistance plasmid, followed by clonal spread, horizontal transfer of blaKPC-harboring plasmids between different phylogenomic groups, and repeated transposition of the blaKPC gene among different plasmid backbones. Group A, which comprises multilocus sequence type 171 (ST171), was the most commonly identified (23% of isolates). Genomic analysis showed that ST171 isolates evolved from a common ancestor and formed two different major clusters; each acquiring unique blaKPC-harboring plasmids, followed by clonal expansion. The data presented here represent the first comprehensive study of phylogenomic interrogation and the relationship between antibiotic resistance and plasmid discrimination among carbapenem-resistant Enterobacter spp., demonstrating the genetic diversity and complexity of the molecular mechanisms driving antibiotic resistance in this genus. Tue, 13 Dec 2016 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=4510/ Patel MC, Wang W, et al.|-|-| PloS One. 2016 Nov 01; 11: e0166336.|-|-| In recent years, there has been a significant increase in detection of Enterovirus D-68 (EV-D68) among patients with severe respiratory infections worldwide. EV-D68 is now recognized as a re-emerging pathogen; however, due to lack of a permissive animal model for EV-D68, a comprehensive understanding of the pathogenesis and immune response against EV-D68 has been hampered. Recently, it was shown that EV-D68 has a strong affinity for ?2,6-linked sialic acids (SAs) and we have shown previously that ?2,6-linked SAs are abundantly present in the respiratory tract of cotton rats (Sigmodon hispidus). Thus, we hypothesized that cotton rats could be a potential model for EV-D68 infection. Here, we evaluated the ability of two recently isolated EV-D68 strains (VANBT/1 and MO/14/49), along with the historical prototype Fermon strain (ATCC), to infect cotton rats. We found that cotton rats are permissive to EV-D68 infection without virus adaptation. The different strains of EV-D68 showed variable infection profiles and the ability to produce neutralizing antibody (NA) upon intranasal infection or intramuscular immunization. Infection with the VANBT/1 resulted in significant induction of pulmonary cytokine gene expression and lung pathology. Intramuscular immunization with live VANBT/1 or MO/14/49 induced strong homologous antibody responses, but a moderate heterologous NA response. We showed that passive prophylactic administration of serum with high content of NA against VANBT/1 resulted in an efficient antiviral therapy. VANBT/1-immunized animals showed complete protection from VANBT/1 challenge, but induced strong pulmonary Th1 and Th2 cytokine responses and enhanced lung pathology, indicating the generation of exacerbated immune response by immunization. In conclusion, our data illustrate that the cotton rat is a powerful animal model that provides an experimental platform to investigate pathogenesis, immune response, anti-viral therapies and vaccines against EV-D68 infection. Tue, 01 Nov 2016 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=4489/ Tran TM, Jones MB, et al.|-|-| Scientific Reports. 2016 Aug 10; 6: 31291.|-|-| Identifying molecular predictors and mechanisms of malaria disease is important for understanding how Plasmodium falciparum malaria is controlled. Transcriptomic studies in humans have so far been limited to retrospective analysis of blood samples from clinical cases. In this prospective, proof-of-principle study, we compared whole-blood RNA-seq profiles at pre-and post-infection time points from Malian adults who were either asymptomatic (n?=?5) or febrile (n?=?3) during their first seasonal PCR-positive P. falciparum infection with those from malaria-naïve Dutch adults after a single controlled human malaria infection (n?=?5). Our data show a graded activation of pathways downstream of pro-inflammatory cytokines, with the highest activation in malaria-naïve Dutch individuals and significantly reduced activation in malaria-experienced Malians. Newly febrile and asymptomatic infections in Malians were statistically indistinguishable except for genes activated by pro-inflammatory cytokines. The combined data provide a molecular basis for the development of a pyrogenic threshold as individuals acquire immunity to clinical malaria. Wed, 10 Aug 2016 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=4355/ McPhillie M, Zhou Y, et al.|-|-| Scientific Reports. 2016 Jul 14; 6: 29179.|-|-| Toxoplasma gondii, the most common parasitic infection of human brain and eye, persists across lifetimes, can progressively damage sight, and is currently incurable. New, curative medicines are needed urgently. Herein, we develop novel models to facilitate drug development: EGS strain T. gondii forms cysts in vitro that induce oocysts in cats, the gold standard criterion for cysts. These cysts highly express cytochrome b. Using these models, we envisioned, and then created, novel 4-(1H)-quinolone scaffolds that target the cytochrome bc1 complex Qi site, of which, a substituted 5,6,7,8-tetrahydroquinolin-4-one inhibits active infection (IC50, 30?nM) and cysts (IC50, 4??M) in vitro, and in vivo (25?mg/kg), and drug resistant Plasmodium falciparum (IC50, Thu, 14 Jul 2016 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=4246/ Wu P, Feldman AS, et al.|-|-| PloS One. 2016 Jul 01; 11: e0151705.|-|-| Environmental exposures that occur in utero and during early life may contribute to the development of childhood asthma through alteration of the human microbiome. The objectives of this study were to estimate the cumulative effect and relative importance of environmental exposures on the risk of childhood asthma. Fri, 01 Jul 2016 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=4265/ Rojas LJ, Wright MS, et al.|-|-| Antimicrobial Agents and Chemotherapy. 2016 Jul 01; 60: 4346-50.|-|-| We report complete genome sequences of four blaNDM-1-harboring Gram-negative multidrug-resistant (MDR) isolates from Colombia. The blaNDM-1 genes were located on 193-kb Inc FIA, 178-kb Inc A/C2, and 47-kb (unknown Inc type) plasmids. Multilocus sequence typing (MLST) revealed that these isolates belong to sequence type 10 (ST10) (Escherichia coli), ST392 (Klebsiella pneumoniae), and ST322 and ST464 (Acinetobacter baumannii and Acinetobacter nosocomialis, respectively). Our analysis identified that the Inc A/C2 plasmid in E. coli contained a novel complex transposon (Tn125 and Tn5393 with three copies of blaNDM-1) and a recombination "hot spot" for the acquisition of new resistance determinants. Fri, 01 Jul 2016 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=4144/ Wright MS, Iovleva A, et al.|-|-| Genome Medicine. 2016 Jun 01; 8. : 26.|-|-| Limited treatment options are available for patients infected with multidrug (MDR)- or pan-drug (PDR)-resistant bacterial pathogens, resulting in infections that can persist for weeks or months. In order to better understand transmission and evolutionary dynamics of MDR Acinetobacter baumannii (Ab) during long-term infection, we analyzed genomes from a series of isolates from individual patients at isolate-specific, patient-specific, and population levels. Wed, 01 Jun 2016 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=4174/ Nelson MI, Wentworth DE, et al.|-|-| The Journal of infectious Diseases. 2016 Jan 15; 213: 173-82.|-|-| The role of exhibition swine in influenza A virus transmission was recently demonstrated by >300 infections with influenza A(H3N2) variant viruses among individuals who attended agricultural fairs. Through active influenza A virus surveillance in US exhibition swine and whole-genome sequencing of 380 isolates, we demonstrate that exhibition swine are actively involved in the evolution of influenza A viruses, including zoonotic strains. First, frequent introduction of influenza A viruses from commercial swine populations provides new genetic diversity in exhibition pigs each year locally. Second, genomic reassortment between viruses cocirculating in exhibition swine increases viral diversity. Third, viral migration between exhibition swine in neighboring states demonstrates that movements of exhibition pigs contributes to the spread of genetic diversity. The unexpected frequency of viral exchange between commercial and exhibition swine raises questions about the understudied interface between these populations. Overall, the complexity of viral evolution in exhibition swine indicates that novel viruses are likely to continually reemerge, presenting threats to humans. Fri, 15 Jan 2016 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3970/ Tan Y, Hassan F, et al.|-|-| Journal of Virology. 2015 Dec 09;|-|-| In August 2014 an outbreak of enterovirus D68 (EV-D68) occurred in North America, causing severe respiratory disease in children. Due to a lack of complete genome sequence data there is only a limited understanding of the molecular evolution and epidemiology of EV-D68 during this outbreak, and it is uncertain whether the differing clinical manifestations of EV-D68 infection are associated with specific viral lineages. We developed a high-throughput complete genome sequencing pipeline for EV-D68 that produced a total of 59 complete genomes from respiratory samples with a 95% success rate, including 57 genomes from Kansas City, Missouri collected during the 2014 outbreak. With these data in-hand we performed phylogenetic analyses of complete genome and VP1 capsid protein sequences. Notably, we observed considerable genetic diversity among EV-D68 isolates in Kansas City, manifest as phylogenetically distinct lineages, indicative of multiple introductions of this virus into the city. In addition, we identified an inter-subclade recombination event within EV-D68, the first recombinant in this virus reported to date. Finally, we found no significant association between EV-D68 genetic variation, either lineages or individual mutations, and a variety of demographic and clinical variables, suggesting that host factors likely play a major role in determining disease severity. Overall, our study revealed the complex pattern of viral evolution within a single geographic locality during a single outbreak, which has implications for the design of effective intervention and prevention strategies. Wed, 09 Dec 2015 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3977/ Bose ME, He J, et al.|-|-| PloS One. 2015 Dec 01; 10: e0120098.|-|-| Human respiratory syncytial virus (RSV) is the leading cause of respiratory tract infections in children globally, with nearly all children experiencing at least one infection by the age of two. Partial sequencing of the attachment glycoprotein gene is conducted routinely for genotyping, but relatively few whole genome sequences are available for RSV. The goal of our study was to sequence the genomes of RSV strains collected from multiple countries to further understand the global diversity of RSV at a whole-genome level. Tue, 01 Dec 2015 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=4003/ Stucker KM, Schobel SA, et al.|-|-| Euro Surveillance : Bulletin Europeì�en Sur Les Maladies Transmissibles = European Communicable Disease Bulletin. 2015 Dec 01; 20|-|-| While the early start and higher intensity of the 2012/13 influenza A virus (IAV) epidemic was not unprecedented, it was the first IAV epidemic season since the 2009 H1N1 influenza pandemic where the H3N2 subtype predominated. We directly sequenced the genomes of 154 H3N2 clinical specimens collected throughout the epidemic to better understand the evolution of H3N2 strains and to inform the H3N2 vaccine selection process. Phylogenetic analyses indicated that multiple co-circulating clades and continual antigenic drift in the haemagglutinin (HA) of clades 5, 3A, and 3C, with the evolution of a new 3C subgroup (3C-2012/13), were the driving causes of the epidemic. Drift variants contained HA substitutions and alterations in the potential N-linked glycosylation sites of HA. Antigenic analysis demonstrated that viruses in the emerging subclade 3C.3 and subgroup 3C-2012/13 were not well inhibited by antisera generated against the 3C.1 vaccine strains used for the 2012/13 (A/Victoria/361/2011) or 2013/14 (A/Texas/50/2012) seasons. Our data support updating the H3N2 vaccine strain to a clade 3C.2 or 3C.3-like strain or a subclade that has drifted further. They also underscore the challenges in vaccine strain selection, particularly regarding HA and neuraminidase substitutions derived during laboratory passage that may alter antigenic testing accuracy. Tue, 01 Dec 2015 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=4001/ Stockwell TB, Heberlein-Larson LA, et al.|-|-| Genome Announcements. 2015 Dec 01; 3. |-|-| We report here the first complete sequences of two Keystone virus (KEYV) genomes isolated from Florida in 2005, which include the first two publicly available complete large (L) gene sequences. The sequences of the KEYV L segments show 75.99 to 83.86% nucleotide similarity with those of other viruses in the California (CAL) serogroup of bunyaviruses. Tue, 01 Dec 2015 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=4167/ Lakdawala SS, Jayaraman A, et al.|-|-| Nature. 2015 Oct 01; 526: 122-5.|-|-| Influenza A viruses pose a major public health threat by causing seasonal epidemics and sporadic pandemics. Their epidemiological success relies on airborne transmission from person to person; however, the viral properties governing airborne transmission of influenza A viruses are complex. Influenza A virus infection is mediated via binding of the viral haemagglutinin (HA) to terminally attached ?2,3 or ?2,6 sialic acids on cell surface glycoproteins. Human influenza A viruses preferentially bind ?2,6-linked sialic acids whereas avian influenza A viruses bind ?2,3-linked sialic acids on complex glycans on airway epithelial cells. Historically, influenza A viruses with preferential association with ?2,3-linked sialic acids have not been transmitted efficiently by the airborne route in ferrets. Here we observe efficient airborne transmission of a 2009 pandemic H1N1 (H1N1pdm) virus (A/California/07/2009) engineered to preferentially bind ?2,3-linked sialic acids. Airborne transmission was associated with rapid selection of virus with a change at a single HA site that conferred binding to long-chain ?2,6-linked sialic acids, without loss of ?2,3-linked sialic acid binding. The transmissible virus emerged in experimentally infected ferrets within 24 hours after infection and was remarkably enriched in the soft palate, where long-chain ?2,6-linked sialic acids predominate on the nasopharyngeal surface. Notably, presence of long-chain ?2,6-linked sialic acids is conserved in ferret, pig and human soft palate. Using a loss-of-function approach with this one virus, we demonstrate that the ferret soft palate, a tissue not normally sampled in animal models of influenza, rapidly selects for transmissible influenza A viruses with human receptor (?2,6-linked sialic acids) preference. Thu, 01 Oct 2015 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=4175/ Larkin EK, Gebretsadik T, et al.|-|-| BMC Pulmonary Medicine. 2015 Jun 01; 15: 45.|-|-| Respiratory syncytial virus (RSV) lower respiratory tract infection (LRI) during infancy has been consistently associated with an increased risk of childhood asthma. In addition, evidence supports that this relationship is causal. However, the mechanisms through which RSV contributes to asthma development are not understood. The INSPIRE (Infant Susceptibility to Pulmonary Infections and Asthma Following RSV Exposure) study objectives are to: 1) characterize the host phenotypic response to RSV infection in infancy and the risk of recurrent wheeze and asthma, 2) identify the immune response and lung injury patterns of RSV infection that are associated with the development of early childhood wheezing illness and asthma, and 3) determine the contribution of specific RSV strains to early childhood wheezing and asthma development. This article describes the INSPIRE study, including study aims, design, recruitment results, and enrolled population characteristics. Mon, 01 Jun 2015 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3808/ Magagula NB, Esona MD, et al.|-|-| Journal of Medical Virology. 2015 Jan 01; 87: 79-101.|-|-| Group A rotaviruses (RVAs) are the leading cause of severe gastroenteritis and eventually death among infants and young children worldwide, and disease prevention and management through vaccination is a public health priority. In August 2009, Rotarix™ was introduced in the South African Expanded Programme on Immunisation. As a result, substantial reductions in RVA disease burden have been reported among children younger than 5 years old. Rotavirus strain surveillance post-vaccination is crucial to, inter alia, monitor and study the evolution of vaccine escape strains. Here, full-genome sequence data for the 11 gene segments from 11 South African G1P[8] rotavirus strains were generated, including 5 strains collected from non-vaccinated children during the 2004-2009 rotavirus seasons and 6 strains collected from vaccinated children during the 2010 rotavirus season. These data were analyzed to gain insights into the overall genetic makeup and evolution of South African G1P[8] rotavirus strains and to compare their genetic backbones with those of common human Wa-like RVAs from other countries, as well as with the Rotarix™ and RotaTeq™ G1P[8] vaccine components. All 11 South African G1P[8] strains revealed a complete Wa-like genotype constellation of G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. On the basis of sequence similarities, the South African G1P[8] strains (with the exception of strain RVA/Human-wt/ZAF/1262/2004/G1P[8]) were closely related to each other (96-100% identity in all gene segments). Comparison to the Rotarix™ and RotaTeq™ G1P[8] vaccine components revealed a moderate nucleotide identity of 89-96% and 93-95%, respectively. The results indicated that none of the gene segments of these 11 South African G1P[8] strains were vaccine-derived. This study illustrates that large-scale next generation sequencing will provide crucial information on the influence of the vaccination program on evolution of rotavirus strains. This is the first report to describe full genomic analyses of G1P[8] RVA strains collected from both non-vaccinated and vaccinated children in South Africa. Thu, 01 Jan 2015 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3995/ Dugan VG, Emrich SJ, et al.|-|-| PloS One. 2014 Dec 01; 9: e99979.|-|-| High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium's minimal information (MIxS) and NCBI's BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a consistent representation of these data in the BRC resources and other repositories that leverage these data, allowing investigators to identify relevant genomic sequences and perform comparative genomics analyses that are both statistically meaningful and biologically relevant. Mon, 01 Dec 2014 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3772/ Nyaga MM, Stucker KM, et al.|-|-| Virus Genes. 2014 Oct 01; 49: 196-207.|-|-| Group A rotaviruses (RVAs) with distinct G and P genotype combinations have been reported globally. We report the genome composition and possible origin of seven G8P[4] and five G2P[4] human RVA strains based on the genetic evolution of all 11 genome segments at the nucleotide level. Twelve RVA ELISA positive stool samples collected in the representative countries of Eastern, Southern and West Africa during the 2007-2012 surveillance seasons were subjected to sequencing using the Ion Torrent PGM and Illumina MiSeq platforms. A reference-based assembly was performed using CLC Bio's clc_ref_assemble_long program, and full-genome consensus sequences were obtained. With the exception of the neutralising antigen, VP7, all study strains exhibited the DS-1-like genome constellation (P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2) and clustered phylogenetically with reference strains having a DS-1-like genetic backbone. Comparison of the nucleotide and amino acid sequences with selected global cognate genome segments revealed nucleotide and amino acid sequence identities of 81.7-100 % and 90.6-100 %, respectively, with NSP4 gene segment showing the most diversity among the strains. Bayesian analyses of all gene sequences to estimate the time of divergence of the lineage indicated that divergence times ranged from 16 to 44 years, except for the NSP4 gene where the lineage seemed to arise in the more distant past at an estimated 203 years ago. However, the long-term effects of changes found within the NSP4 genome segment should be further explored, and thus we recommend continued whole-genome analyses from larger sample sets to determine the evolutionary mechanisms of the DS-1-like strains collected in Africa. Wed, 01 Oct 2014 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3743/ Nelson MI, Balmaseda A, et al.|-|-| Virology. 2014 Jun 21; 462: 81-90.|-|-| Despite mounting evidence of the high disease burden of influenza in tropical regions, relatively little viral sequence data is available from tropical countries in the Western hemisphere. To understand the evolutionary dynamics of influenza A and B viruses in Managua, Nicaragua, we performed a phylogenetic analysis of 1956 influenza viruses, including 335 collected for this study during 2007-2010 from a population-based cohort in Managua. North America was consistently identified as the most significant source of influenza virus diversity in Managua, although South America and Mexico were important viral sources during the 2009 A/H1N1 pandemic. The low number of viral introductions of Central American origin may reflect differences in the seasonality of influenza in Nicaragua versus neighboring countries, and underscores the need for additional data in this understudied region. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Sat, 21 Jun 2014 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3688/ Zhou B, Lin X, et al.|-|-| Journal of Clinical Microbiology. 2014 May 01; 52: 1330-7.|-|-| Although human influenza B virus (IBV) is a significant human pathogen, its great genetic diversity has limited our ability to universally amplify the entire genome for subsequent sequencing or vaccine production. The generation of sequence data via next-generation approaches and the rapid cloning of viral genes are critical for basic research, diagnostics, antiviral drugs, and vaccines to combat IBV. To overcome the difficulty of amplifying the diverse and ever-changing IBV genome, we developed and optimized techniques that amplify the complete segmented negative-sense RNA genome from any IBV strain in a single tube/well (IBV genomic amplification [IBV-GA]). Amplicons for >1,000 diverse IBV genomes from different sample types (e.g., clinical specimens) were generated and sequenced using this robust technology. These approaches are sensitive, robust, and sequence independent (i.e., universally amplify past, present, and future IBVs), which facilitates next-generation sequencing and advanced genomic diagnostics. Importantly, special terminal sequences engineered into the optimized IBV-GA2 products also enable ligation-free cloning to rapidly generate reverse-genetics plasmids, which can be used for the rescue of recombinant viruses and/or the creation of vaccine seed stock. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Thu, 01 May 2014 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3687/ Derrick E. Fouts|-|-| Pathogens. 2014 Apr 10; 3: 280-308.|-|-| Leptospirosis, caused by pathogenic spirochetes belonging to the genus Leptospira, is a zoonosis with important impacts on human and animal health worldwide. Research on the mechanisms of Leptospira pathogenesis has been hindered due to slow growth of infectious strains, poor transformability, and a paucity of genetic tools. As a result of second generation sequencing technologies, there has been an acceleration of leptospiral genome sequencing efforts in the past decade, which has enabled a concomitant increase in functional genomics analyses of Leptospira pathogenesis. A pathogenomics approach, by coupling of pan-genomic analysis of multiple isolates with sequencing of experimentally attenuated highly pathogenic Leptospira, has resulted in the functional inference of virulence factors. The global Leptospira Genome Project supported by the U.S. National Institute of Allergy and Infectious Diseases to which key scientific contributions have been made from the international leptospirosis research community has provided a new roadmap for comprehensive studies of Leptospira and leptospirosis well into the future. This review describes functional genomics approaches to apply the data generated by the Leptospira Genome Project towards deepening our knowledge of virulence factors of Leptospira using the emerging discipline of pathogenomics. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Thu, 10 Apr 2014 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3683/ Fries AC, Nolting JM, et al.|-|-| Influenza and Other Respiratory Viruses. 2014 Apr 02;|-|-| The accurate and timely characterization of influenza A viruses (IAV) from natural reservoirs is essential for responses to animal and public health threats. Differences between antigenic and genetic subtyping results for 161 IAV isolates recovered from migratory birds in the central United States during 2010-2011 delayed the recognition of four isolates of interest. Genomic sequencing identified the first reported Eurasian-origin H10 subtype in North America and three additional H14 isolates showing divergence from previously reported H14 isolates. Genomic analyses revealed additional diversity among IAV isolates not detected by antigenic subtyping and provided further insight into interhemispheric spread of avian-origin IAVs. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Wed, 02 Apr 2014 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3684/ Bankamp B, Liu C, et al.|-|-| PloS One. 2014 Apr 01; 9: e95470.|-|-| The length of the single stranded, negative sense RNA genome of measles virus (MeV) is highly conserved at 15,894 nucleotides (nt). MeVs can be grouped into 24 genotypes based on the highly variable 450 nucleotides coding for the carboxyl-terminus of the nucleocapsid protein (N-450). Here, we report the genomic sequences of 2 wild-type viral isolates of genotype D4 with genome lengths of 15,900 nt. Both genomes had a 7 nt insertion in the 3' untranslated region (UTR) of the matrix (M) gene and a 1 nt deletion in the 5' UTR of the fusion (F) gene. The net gain of 6 nt complies with the rule-of-six required for replication competency of the genomes of morbilliviruses. The insertions and deletion (indels) were confirmed in a patient sample that was the source of one of the viral isolates. The positions of the indels were identical in both viral isolates, even though epidemiological data and the 3 nt differences in N-450 between the two genomes suggested that the viruses represented separate chains of transmission. Identical indels were found in the M-F intergenic regions of 14 additional genotype D4 viral isolates that were imported into the US during 2007-2010. Viral isolates with and without indels produced plaques of similar size and replicated efficiently in A549/hSLAM and Vero/hSLAM cells. This is the first report of wild-type MeVs with genome lengths other than 15,894 nt and demonstrates that the length of the M-F UTR of wild-type MeVs is flexible. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Tue, 01 Apr 2014 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3685/ Dusek RJ, Hallgrimsson GT, et al.|-|-| PloS One. 2014 Apr 01; 9: e92075.|-|-| Avian influenza virus (AIV) in wild birds has been of increasing interest over the last decade due to the emergence of AIVs that cause significant disease and mortality in both poultry and humans. While research clearly demonstrates that AIVs can move across the Pacific or Atlantic Ocean, there has been no data to support the mechanism of how this occurs. In spring and autumn of 2010 and autumn of 2011 we obtained cloacal swab samples from 1078 waterfowl, gulls, and shorebirds of various species in southwest and west Iceland and tested them for AIV. From these, we isolated and fully sequenced the genomes of 29 AIVs from wild caught gulls (Charadriiformes) and waterfowl (Anseriformes) in Iceland. We detected viruses that were entirely (8 of 8 genomic segments) of American lineage, viruses that were entirely of Eurasian lineage, and viruses with mixed American-Eurasian lineage. Prior to this work only 2 AIVs had been reported from wild birds in Iceland and only the sequence from one segment was available in GenBank. This is the first report of finding AIVs of entirely American lineage and Eurasian lineage, as well as reassortant viruses, together in the same geographic location. Our study demonstrates the importance of the North Atlantic as a corridor for the movement of AIVs between Europe and North America. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Tue, 01 Apr 2014 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3626/ Karen E. Nelson|-|-| 2014 Mar 01;|-|-| This is a chapter in the book Bioinformatics and Data Analysis in Microbiology for Horizon Press. Sat, 01 Mar 2014 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3634/ Westgeest KB, Russell CA, et al.|-|-| Journal of Virology. 2014 Mar 01; 88: 2844-57.|-|-| Influenza A(H3N2) viruses became widespread in humans during the 1968 H3N2 virus pandemic and have been a major cause of influenza epidemics ever since. These viruses evolve continuously by reassortment and genomic evolution. Antigenic drift is the cause for the need to update influenza vaccines frequently. Using two data sets that span the entire period of circulation of human influenza A(H3N2) viruses, it was shown that influenza A(H3N2) virus evolution can be mapped to 13 antigenic clusters. Here we analyzed the full genomes of 286 influenza A(H3N2) viruses from these two data sets to investigate the genomic evolution and reassortment patterns. Numerous reassortment events were found, scattered over the entire period of virus circulation, but most prominently in viruses circulating between 1991 and 1998. Some of these reassortment events persisted over time, and one of these coincided with an antigenic cluster transition. Furthermore, selection pressures and nucleotide and amino acid substitution rates of all proteins were studied, including those of the recently discovered PB1-N40, PA-X, PA-N155, and PA-N182 proteins. Rates of nucleotide and amino acid substitutions were most pronounced for the hemagglutinin, neuraminidase, and PB1-F2 proteins. Selection pressures were highest in hemagglutinin, neuraminidase, matrix 1, and nonstructural protein 1. This study of genotype in relation to antigenic phenotype throughout the period of circulation of human influenza A(H3N2) viruses leads to a better understanding of the evolution of these viruses. Sat, 01 Mar 2014 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3627/ Karen E.Nelson|-|-| 2014 Feb 01;|-|-| This is a book chapter in Next Generation Sequencing: Current Technologies and Applications. Sat, 01 Feb 2014 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3560/ Madupu R, Szpakowski S, et al.|-|-| Science Progress. 2013 Nov 01; 96: 153-70.|-|-| Metagenomic studies have truly revolutionised biology and medicine, and changed the way we study genomics. As genome sequencing becomes cheaper it is being applied to study complex metagenomes. 'Metagenome' is the genetic material recovered directly from an environmental sample or niche. By delivering fast, cheap, and large volumes of data Next Generation Sequencing (NGS) platforms have facilitated a deeper understanding of the fundamentals of genomes, gene functions and regulation. Metagenomics, also referred to as environmental or community genomics, has brought about radical changes in our ability to analyse complex microbial communities by direct sampling of their natural habitat paving the way for the creation of innovative new areas for biomedical research. Many metagenomic studies involving the 'human microbiome'have been undertaken to date. Samples from of a number of diverse habitats including different human body sites have been subject to metagenomic examinations. Huge national and international projects with the purpose of elucidating the biogeography of microbial communities living within and on the human body, are well underway. The analysis of human microbiome data has brought about a paradigm shift in our understanding of the role of resident microflora in human health and disease and brings non-traditional areas such as gut ecology to the forefront of personalised medicine. In this chapter we present an overview of the state-of-the-art in current literature and projects pertaining to human microbiome studies. Fri, 01 Nov 2013 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3562/ Le MQ, Lam HM, et al.|-|-| Emerging infectious Diseases. 2013 Nov 01; 19: 1756-65.|-|-| Understanding global influenza migration and persistence is crucial for vaccine strain selection. Using 240 new human influenza A virus whole genomes collected in Vietnam during 2001-2008, we looked for persistence patterns and migratory connections between Vietnam and other countries. We found that viruses in Vietnam migrate to and from China, Hong Kong, Taiwan, Cambodia, Japan, South Korea, and the United States. We attempted to reduce geographic bias by generating phylogenies subsampled at the year and country levels. However, migration events in these phylogenies were still driven by the presence or absence of sequence data, indicating that an epidemiologic study design that controls for prevalence is required for robust migration analysis. With whole-genome data, most migration events are not detectable from the phylogeny of the hemagglutinin segment alone, although general migratory relationships between Vietnam and other countries are visible in the hemagglutinin phylogeny. It is possible that virus lineages in Vietnam persisted for >1 year. Fri, 01 Nov 2013 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3559/ Sant'anna FH, Borges LG, et al.|-|-| Archives of Virology. 2013 Oct 10;|-|-| During the 2009 influenza A pH1N1 pandemics in Brazil, the state that was most affected was Rio Grande do Sul (RS), with over 3,000 confirmed cases, including 298 deaths. While no cases were confirmed in 2010, 103 infections with 14 deaths by pH1N1 were reported in 2011. Genomic analysis of the circulating viruses is fundamental for understanding viral evolution and supporting vaccine development against these pathogens. This study investigated whole genomes of six pH1N1 virus isolates from pandemic and post-pandemic periods in RS, Brazil. Phylogenetic analysis using the concatenated genome segments demonstrated that at least two lineages of the virus co-circulated in RS during the 2009 pandemic period. Moreover, our analysis showed that the post-pandemic pH1N1 virus from 2011 constitutes a distinct clade whose ancestor belongs to clade 7. All six isolates contained amino acid substitutions in their proteins when compared to the archetype strains California/04/2009 and California/07/2009. The 2011 isolates contained more amino acid substitutions, and most of their genes were under purifying selection. Based on the amino acid substitutions in HA epitopes from strains isolated in RS, Brazil, in silico analysis predicted a decrease in vaccine efficacy against post-pandemic strains (median 31.562 %) in relation to pandemic ones (median 39.735 %). Thu, 10 Oct 2013 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3268/ Abernathy E, Chen MH, et al.|-|-| Virology Journal. 2013 Sep 01; 10: 32.|-|-| Rubella virus is the causative agent of rubella, a mild rash illness, and a potent teratogenic agent when contracted by a pregnant woman. Global rubella control programs target the reduction and elimination of congenital rubella syndrome. Phylogenetic analysis of partial sequences of rubella viruses has contributed to virus surveillance efforts and played an important role in demonstrating that indigenous rubella viruses have been eliminated in the United States. Sixteen wild-type rubella viruses were chosen for whole genome sequencing. All 16 viruses were collected in the United States from 1961 to 2009 and are from 8 of the 13 known rubella genotypes. Phylogenetic analysis of 30 whole genome sequences produced a maximum likelihood tree giving high bootstrap values for all genotypes except provisional genotype 1a. Comparison of the 16 new complete sequences and 14 previously sequenced wild-type viruses found regions with clusters of variable amino acids. The 5' 250 nucleotides of the genome are more conserved than any other part of the genome. Genotype specific deletions in the untranslated region between the non-structural and structural open reading frames were observed for genotypes 2B and genotype 1G. No evidence was seen for recombination events among the 30 viruses. The analysis presented here is consistent with previous reports on the genetic characterization of rubella virus genomes. Conserved and variable regions were identified and additional evidence for genotype specific nucleotide deletions in the intergenic region was found. Phylogenetic analysis confirmed genotype groupings originally based on structural protein coding region sequences, which provides support for the WHO nomenclature for genetic characterization of wild-type rubella viruses. Sun, 01 Sep 2013 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3254/ Boyce WM, Schobel S, et al.|-|-| Genome Announcements. 2013 Sep 01; 1|-|-| We report the complete genome sequence of a reassortant H14N2 avian influenza virus isolated in 2011 from a northern shoveler in California. This introduced Eurasian subtype acquired seven segments from North American viruses and circulated in the Pacific Flyway 1 year after its detection in the Mississippi Flyway. Sun, 01 Sep 2013 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3259/ Lindsay LL, Kelly TR, et al.|-|-| Viruses. 2013 Sep 01; 5: 1964-77.|-|-| A high prevalence and diversity of avian influenza (AI) viruses were detected in a population of wild mallards sampled during summer 2011 in California, providing an opportunity to compare results obtained before and after virus culture. We tested cloacal swab samples prior to culture by matrix real-time PCR, and by amplifying and sequencing a 640bp portion of the hemagglutinin (HA) gene. Each sample was also inoculated into embryonated chicken eggs, and full genome sequences were determined for cultured viruses. While low matrix Ct values were a good predictor of virus isolation from eggs, samples with high or undetectable Ct values also yielded isolates. Furthermore, a single passage in eggs altered the occurrence and detection of viral strains, and mixed infections (different HA subtypes) were detected less frequently after culture. There is no gold standard or perfect reference comparison for surveillance of unknown viruses, and true negatives are difficult to distinguish from false negatives. This study showed that sequencing samples prior to culture increases the detection of mixed infections and enhances the identification of viral strains and sequences that may have changed or even disappeared during culture. Sun, 01 Sep 2013 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3554/ Bahl, J., S. Krauss, D. Kuhnert, M. Fourment, G. Raven, S. P. Pryor, L. J. Niles, A. Danner, D. Walker, I. H. Mendenhall, Y. C. Su, V. G. Dugan, R. A. Halpin, T. B. Stockwell, R. J. Webby, D. E. Wentworth, A. J. Drummond, G. J. Smith, R. G. Webster|-|-| 2013 Aug 29; 9: e1003570.|-|-| Wild birds have been implicated in the emergence of human and livestock influenza. The successful prediction of viral spread and disease emergence, as well as formulation of preparedness plans have been hampered by a critical lack of knowledge of viral movements between different host populations. The patterns of viral spread and subsequent risk posed by wild bird viruses therefore remain unpredictable. Here we analyze genomic data, including 287 newly sequenced avian influenza A virus (AIV) samples isolated over a 34-year period of continuous systematic surveillance of North American migratory birds. We use a Bayesian statistical framework to test hypotheses of viral migration, population structure and patterns of genetic reassortment. Our results reveal that despite the high prevalence of Charadriiformes infected in Delaware Bay this host population does not appear to significantly contribute to the North American AIV diversity sampled in Anseriformes. In contrast, influenza viruses sampled from Anseriformes in Alberta are representative of the AIV diversity circulating in North American Anseriformes. While AIV may be restricted to specific migratory flyways over short time frames, our large-scale analysis showed that the long-term persistence of AIV was independent of bird flyways with migration between populations throughout North America. Analysis of long-term surveillance data provides vital insights to develop appropriately informed predictive models critical for pandemic preparedness and livestock protection. Thu, 29 Aug 2013 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3555/ Hauser MJ, Dlugolenski D, et al.|-|-| PloS One. 2013 Jul 01; 8: e70251.|-|-| Swine generate reassortant influenza viruses because they can be simultaneously infected with avian and human influenza; however, the features that restrict influenza reassortment in swine and human hosts are not fully understood. Type I and III interferons (IFNs) act as the first line of defense against influenza virus infection of respiratory epithelium. To determine if human and swine have different capacities to mount an antiviral response the expression of IFN and IFN-stimulated genes (ISG) in normal human bronchial epithelial (NHBE) cells and normal swine bronchial epithelial (NSBE) cells was evaluated following infection with human (H3N2), swine (H1N1), and avian (H5N3, H5N2, H5N1) influenza A viruses. Expression of IFN? and ISGs were substantially higher in NHBE cells compared to NSBE cells following H5 avian influenza virus infection compared to human or swine influenza virus infection. This effect was associated with reduced H5 avian influenza virus replication in human cells at late times post infection. Further, RIG-I expression was lower in NSBE cells compared to NHBE cells suggesting reduced virus sensing. Together, these studies identify key differences in the antiviral response between human and swine respiratory epithelium alluding to differences that may govern influenza reassortment. Mon, 01 Jul 2013 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3191/ Hall JS, Teslaa JL, et al.|-|-| Virology Journal. 2013 Jun 06; 10: 179.|-|-| BACKGROUND: The role of gulls in the ecology of avian influenza (AI) is different than that of waterfowl. Different constellations of subtypes circulate within the two groups of birds and AI viruses isolated from North American gulls frequently possess reassortant genomes with genetic elements from both North America and Eurasian lineages. A 2008 isolate from a Newfoundland Great Black-backed Gull contained a mix of North American waterfowl, North American gull and Eurasian lineage genes. METHODS: We isolated, sequenced and phylogenetically compared avian influenza viruses from 2009 Canadian wild birds. RESULTS: We analyzed six 2009 virus isolates from Canada and found the same phylogenetic lineage had persisted over a larger geographic area, with an expanded host range that included dabbling and diving ducks as well as gulls. All of the 2009 virus isolates contained an internal protein coding set of genes of the same Eurasian lineage genes except PB1 that was from a North American lineage, and these genes continued to evolve by genetic drift. We show evidence that the 2008 Great Black-backed Gull virus was derived from this lineage with a reassortment of a North American PA gene into the more stable core set of internal protein coding genes that has circulated in avian populations for at least 2 years. From this core, the surface glycoprotein genes have switched several times creating H13N6, H13N2, and H16N3 subtypes. These gene segments were from North American lineages except for the H16 and N3 vRNAs. CONCLUSIONS: This process appears similar to genetic shifts seen with swine influenza where a stable "triple reassortant internal gene" core has circulated in swine populations with genetic shifts occurring with hemaggluttinin and neuraminidase proteins getting periodically switched. Thus gulls may serve as genetic mixing vessels for different lineages of avian influenza, similar to the role of swine with regards to human influenza. These findings illustrate the need for continued surveillance in gull and waterfowl populations, both on the Pacific and especially Atlantic coasts of North America, to document virus intercontinental movement and the role of gull species in the evolution and epidemiology of AI. Thu, 06 Jun 2013 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3182/ Zhou B, Pearce MB, et al.|-|-| PloS One. 2013 Jun 01; 8: e67616.|-|-| The 2009/2010 pandemic influenza virus (H1N1pdm) contains an avian-lineage PB2 gene that lacks E627K and D701N substitutions important in the pathogenesis and transmission of avian-origin viruses in humans or other mammals. Previous studies have shown that PB2-627K is not necessary because of a compensatory Q591R substitution. The role that PB2-701N plays in the H1N1pdm phenotype is not well understood. Therefore, PB2-D701N was introduced into an H1N1pdm virus (A/New York/1682/2009 (NY1682)) and analyzed in vitro and in vivo. Mini-genome replication assay, in vitro replication characteristics in cell lines, and analysis in the mouse and ferret models demonstrated that PB2-D701N increased virus replication rates and resulted in more severe pathogenicity in mice and more efficient transmission in ferrets. In addition, compared to the NY1682-WT virus, the NY1682-D701N mutant virus induced less IFN-? and replicated to a higher titer in primary human alveolar epithelial cells. These findings suggest that the acquisition of the PB2-701N substitution by H1N1pdm viruses may result in more severe disease or increase transmission in humans. Sat, 01 Jun 2013 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3184/ Ramanunninair M, Le J, et al.|-|-| PloS One. 2013 Jun 01; 8: e65955.|-|-| Human influenza virus isolates generally grow poorly in embryonated chicken eggs. Hence, gene reassortment of influenza A wild type (wt) viruses is performed with a highly egg adapted donor virus, A/Puerto Rico/8/1934 (PR8), to provide the high yield reassortant (HYR) viral 'seeds' for vaccine production. HYR must contain the hemagglutinin (HA) and neuraminidase (NA) genes of wt virus and one to six 'internal' genes from PR8. Most studies of influenza wt and HYRs have focused on the HA gene. The main objective of this study is the identification of the molecular signature in all eight gene segments of influenza A HYR candidate vaccine seeds associated with high growth in ovo. Sat, 01 Jun 2013 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3171/ Saira K, Lin X, et al.|-|-| Journal of Virology. 2013 May 15;|-|-| Influenza virus defective interfering (DI) particles are naturally occurring non-infectious virions typically generated during in vitro serial passages in cell culture of the virus at high multiplicity of infection. DI particles are recognized for the role they play in inhibiting viral replication, and for the impact they have on the production of infectious virions. To date, influenza virus DI particles have been reported primarily as a phenomenon of cell culture and in experimentally infected embryonated chicken eggs. They have also been isolated from a respiratory infection of chickens. Using a sequencing approach we characterize several subgenomic viral RNAs from human naso-pharyngeal specimens infected with the influenza A (H1N1)pdm09 virus. Distribution of these in vivo-derived DI-like RNAs was similar to that of in vitro DIs, with the majority of the defective RNAs generated from the PB2 (segment 1) of the polymerase complex, followed by PB1 and PA. The in vivo-derived DI-like segments are also of similar length as known in vitro DIs and share internal deletions of the same segments. The presence of identical DI-like RNAs in patients linked by direct contact is compatible with transmission between them. The functional role of DI-like RNAs in natural infections remains to be established. Wed, 15 May 2013 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3153/ Keitel WA, Piedra PA, et al.|-|-| BMC Research Notes. 2013 May 03; 6: 177.|-|-| BACKGROUND: When novel influenza viruses cause human infections, it is critical to characterize the illnesses, viruses, and immune responses to infection in order to develop diagnostics, treatments, and vaccines. The objective of the study was to collect samples from patients with suspected or confirmed A(H1N1)pdm09 infections that could be made available to the scientific community. Respiratory secretions, sera and peripheral blood mononuclear cells (PBMCs) were collected sequentially (when possible) from patients presenting with suspected or previously confirmed A(H1N1)pdm09 infections. Clinical manifestations and illness outcomes were assessed. Respiratory secretions were tested for the presence of A(H1N1)pdm09 virus by means of isolation in tissue culture and real time RT-PCR. Sera were tested for the presence and level of HAI and neutralizing antibodies against the A(H1N1)pdm09 virus.Findings and conclusions: Thirty patients with confirmed A(H1N1)pdm09 infection were enrolled at Baylor College of Medicine (BCM). Clinical manifestations of illness were consistent with typical influenza. Twenty-eight of 30 had virological confirmation of illness; all recovered fully. Most patients had serum antibody responses or high levels of antibody in convalescent samples. Virus-positive samples were sent to J. Craig Venter Institute for sequencing and sequences were deposited in GenBank. Large volumes of sera collected from 2 convalescent adults were used to standardize antibody assays; aliquots of these sera are available from the repository. Aliquots of serum, PBMCs and stool collected from BCM subjects and subjects enrolled at other study sites are available for use by the scientific community, upon request. Fri, 03 May 2013 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3169/ Li K, Bihan M, et al.|-|-| PloS One. 2013 May 01; 8: e63139.|-|-| Analyses of the taxonomic diversity associated with the human microbiome continue to be an area of great importance. The study of the nature and extent of the commonly shared taxa ("core"), versus those less prevalent, establishes a baseline for comparing healthy and diseased groups by quantifying the variation among people, across body habitats and over time. The National Institutes of Health (NIH) sponsored Human Microbiome Project (HMP) has provided an unprecedented opportunity to examine and better define what constitutes the taxonomic core within and across body habitats and individuals through pyrosequencing-based profiling of 16S rRNA gene sequences from oral, skin, distal gut (stool), and vaginal body habitats from over 200 healthy individuals. A two-parameter model is introduced to quantitatively identify the core taxonomic members of each body habitat's microbiota across the healthy cohort. Using only cutoffs for taxonomic ubiquity and abundance, core taxonomic members were identified for each of the 18 body habitats and also for the 4 higher-level body regions. Although many microbes were shared at low abundance, they exhibited a relatively continuous spread in both their abundance and ubiquity, as opposed to a more discretized separation. The numbers of core taxa members in the body regions are comparatively small and stable, reflecting the relatively high, but conserved, interpersonal variability within the cohort. Core sizes increased across the body regions in the order of: vagina, skin, stool, and oral cavity. A number of "minor" oral taxonomic core were also identified by their majority presence across the cohort, but with relatively low and stable abundances. A method for quantifying the difference between two cohorts was introduced and applied to samples collected on a second visit, revealing that over time, the oral, skin, and stool body regions tended to be more transient in their taxonomic structure than the vaginal body region. Wed, 01 May 2013 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3272/ Das SR, Hensley SE, et al.|-|-| Cell Host & Microbe. 2013 Mar 13; 13: 314-23.|-|-| Human influenza A virus (IAV) vaccination is limited by "antigenic drift," rapid antibody-driven escape reflecting amino acid substitutions in the globular domain of hemagglutinin (HA), the viral attachment protein. To better understand drift, we used anti-hemagglutinin monoclonal Abs (mAbs) to sequentially select IAV escape mutants. Twelve selection steps, each resulting in a single amino acid substitution in the hemagglutinin globular domain, were required to eliminate antigenicity defined by monoclonal or polyclonal Abs. Sequential mutants grow robustly, showing the structural plasticity of HA, although several hemagglutinin substitutions required an epistatic substitution in the neuraminidase glycoprotein to maximize growth. Selecting escape mutants from parental versus sequential variants with the same mAb revealed distinct escape repertoires, attributed to contextual changes in antigenicity and the mutation landscape. Since each hemagglutinin mutation potentially sculpts future mutation space, drift can follow many stochastic paths, undermining its unpredictability and underscoring the need for drift-insensitive vaccines. Wed, 13 Mar 2013 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3226/ Haft DH, Selengut JD, et al.|-|-| Nucleic Acids Research. 2013 Jan 01; 41: D387-95.|-|-| TIGRFAMs, available online at http://www.weizhongli-lab.org/tigrfams is a database of protein family definitions. Each entry features a seed alignment of trusted representative sequences, a hidden Markov model (HMM) built from that alignment, cutoff scores that let automated annotation pipelines decide which proteins are members, and annotations for transfer onto member proteins. Most TIGRFAMs models are designated equivalog, meaning they assign a specific name to proteins conserved in function from a common ancestral sequence. Models describing more functionally heterogeneous families are designated subfamily or domain, and assign less specific but more widely applicable annotations. The Genome Properties database, available at http://www.weizhongli-lab.org/genome-properties, specifies how computed evidence, including TIGRFAMs HMM results, should be used to judge whether an enzymatic pathway, a protein complex or another type of molecular subsystem is encoded in a genome. TIGRFAMs and Genome Properties content are developed in concert because subsystems reconstruction for large numbers of genomes guides selection of seed alignment sequences and cutoff values during protein family construction. Both databases specialize heavily in bacterial and archaeal subsystems. At present, 4284 models appear in TIGRFAMs, while 628 systems are described by Genome Properties. Content derives both from subsystem discovery work and from biocuration of the scientific literature. Tue, 01 Jan 2013 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3058/ Krampis K, Booth T, et al.|-|-| BMC bioinformatics. 2012 Dec 01; 13: 42.|-|-| A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottleneck for smaller laboratories and institutes that do not have access to substantial computational resources. Sequencing instruments are typically bundled with only the minimal processing and storage capacity required for data capture during sequencing runs. Given the scale of sequence datasets, scientific value cannot be obtained from acquiring a sequencer unless it is accompanied by an equal investment in informatics infrastructure. Sat, 01 Dec 2012 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3052/ Gilchrist CA, Ali IK, et al.|-|-| BMC microbiology. 2012 Dec 01; 12: 151.|-|-| The outcome of an Entamoeba histolytica infection is variable and can result in either asymptomatic carriage, immediate or latent disease (diarrhea/dysentery/amebic liver abscess). An E. histolytica multilocus genotyping system based on tRNA gene-linked arrays has shown that genetic differences exist among parasites isolated from patients with different symptoms however, the tRNA gene-linked arrays cannot be located in the current assembly of the E. histolytica Reference genome (strain HM-1:IMSS) and are highly variable. Sat, 01 Dec 2012 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3228/ Joardar V, Abrams NF, et al.|-|-| BMC Genomics. 2012 Sep 01; 13: 698.|-|-| The genera Aspergillus and Penicillium include some of the most beneficial as well as the most harmful fungal species such as the penicillin-producer Penicillium chrysogenum and the human pathogen Aspergillus fumigatus, respectively. Their mitochondrial genomic sequences may hold vital clues into the mechanisms of their evolution, population genetics, and biology, yet only a handful of these genomes have been fully sequenced and annotated. Sat, 01 Sep 2012 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2961/ Faix DJ, Hawksworth AW, et al.|-|-| PloS one. 2012 Sep 01; 7: e34581.|-|-| Population-based febrile respiratory illness surveillance conducted by the Department of Defense contributes to an estimate of vaccine effectiveness. Between January and March 2011, 64 cases of 2009 A/H1N1 (pH1N1), including one fatality, were confirmed in immunized recruits at Fort Jackson, South Carolina, suggesting insufficient efficacy for the pH1N1 component of the live attenuated influenza vaccine (LAIV). Sat, 01 Sep 2012 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3738/ de Filippis I, de Lemos AP, et al.|-|-| PloS One. 2012 Jul 01; 7: e33016.|-|-| Neisseria meningitidis serogroup B has been predominant in Brazil, but no broadly effective vaccine is available to prevent endemic meningococcal disease. To understand genetic diversity among serogroup B strains in Brazil, we selected a nationally representative sample of clinical disease isolates from 2004, and a temporally representative sample for the state of São Paulo (1988-2006) for study (n?=?372). This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Sun, 01 Jul 2012 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3204/ Chang HW, Egberink HF, et al.|-|-| Emerging infectious Diseases. 2012 Jul 01; 18: 1089-95.|-|-| Coronaviruses are well known for their potential to change their host or tissue tropism, resulting in unpredictable new diseases and changes in pathogenicity; severe acute respiratory syndrome and feline coronaviruses, respectively, are the most recognized examples. Feline coronaviruses occur as 2 pathotypes: nonvirulent feline enteric coronaviruses (FECVs), which replicate in intestinal epithelium cells, and lethal feline infectious peritonitis viruses (FIPVs), which replicate in macrophages. Evidence indicates that FIPV originates from FECV by mutation, but consistent distinguishing differences have not been established. We sequenced the full genome of 11 viruses of each pathotype and then focused on the single most distinctive site by additionally sequencing hundreds of viruses in that region. As a result, we identified 2 alternative amino acid differences in the putative fusion peptide of the spike protein that together distinguish FIPV from FECV in >95% of cases. By these and perhaps other mutations, the virus apparently acquires its macrophage tropism and spreads systemically. Sun, 01 Jul 2012 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3237/ Wang S, Sundaram JP, et al.|-|-| Nucleic Acids Research. 2012 Jul 01; 40: W186-92.|-|-| A gene prediction program, VIGOR (Viral Genome ORF Reader), was developed at J. Craig Venter Institute in 2010 and has been successfully performing gene calling in coronavirus, influenza, rhinovirus and rotavirus for projects at the Genome Sequencing Center for Infectious Diseases. VIGOR uses sequence similarity search against custom protein databases to identify protein coding regions, start and stop codons and other gene features. Ribonucleicacid editing and other features are accurately identified based on sequence similarity and signature residues. VIGOR produces four output files: a gene prediction file, a complementary DNA file, an alignment file, and a gene feature table file. The gene feature table can be used to create GenBank submission. VIGOR takes a single input: viral genomic sequences in FASTA format. VIGOR has been extended to predict genes for 12 viruses: measles virus, mumps virus, rubella virus, respiratory syncytial virus, alphavirus and Venezuelan equine encephalitis virus, norovirus, metapneumovirus, yellow fever virus, Japanese encephalitis virus, parainfluenza virus and Sendai virus. VIGOR accurately detects the complex gene features like ribonucleicacid editing, stop codon leakage and ribosomal shunting. Precisely identifying the mat_peptide cleavage for some viruses is a built-in feature of VIGOR. The gene predictions for these viruses have been evaluated by testing from 27 to 240 genomes from GenBank. Sun, 01 Jul 2012 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2944/ Vivien G Dugan, Kazima Saira, et al.|-|-| 2012 Jun 01; 0: 563-573.|-|-| RNA virus exploration within the field of medical virology has greatly benefited from technological developments in genomics, deepening our understanding of viral dynamics and emergence. Large-scale first-generation technology sequencing projects have expedited molecular epidemiology studies at an unprecedented scale for two pathogenic RNA viruses chosen as models: influenza A virus and dengue. Next-generation sequencing approaches are now leading to a more in-depth analysis of virus genetic diversity, which is greater for RNA than DNA viruses because of high replication rates and the absence of proofreading activity of the RNA-dependent RNA polymerase. In the field of virus discovery, technological advancements and metagenomic approaches are expanding the catalogs of novel viruses by facilitating our probing into the RNA virus world. Fri, 01 Jun 2012 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=3111/ Fedorova ND, Moktali V, et al.|-|-| Methods In Molecular Biology (Clifton, N.J.). 2012 Mar 01; 944: 23-45.|-|-| The accelerating pace of microbial genomics is sparking a renaissance in the field of natural products research. Researchers can now get a preview of the organism's secondary metabolome by analyzing its genomic sequence. Combined with other -omics data, this approach may provide a cost-effective alternative to industrial high-throughput screening in drug discovery. In the last few years, several computational tools have been developed to facilitate this process by identifying genes involved in secondary metabolite biosynthesis in bacterial and fungal genomes. Here, we review seven software programs that are available for this purpose, with an emphasis on antibiotics & Secondary Metabolite Analysis SHell (antiSMASH) and Secondary Metabolite Unknown Regions Finder (SMURF), the only tools that can comprehensively detect complete secondary metabolite biosynthesis gene clusters. We also discuss five related software packages-CLUster SEquence ANalyzer (CLUSEAN), ClustScan, Structure Based Sequence Analysis of Polyketide Synthases (SBSPKS), NRPSPredictor, and Natural Product searcher (NP.searcher)-that identify secondary metabolite backbone biosynthesis genes. This chapter offers detailed protocols, suggestions, and caveats to assist researchers in using these tools most effectively. Thu, 01 Mar 2012 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2733/ Gillespie, J. J., Joardar, V., et al.|-|-| Journal of bacteriology. 2012 Jan 01; 194(2): 376-94.|-|-| We present the draft genome for the Rickettsia endosymbiont of Ixodes scapularis (REIS), a symbiont of the deer tick vector of Lyme disease in North America. Among Rickettsia species (Alphaproteobacteria: Rickettsiales), REIS has the largest genome sequenced to date (>2 Mb) and contains 2,309 genes across the chromosome and four plasmids (pREIS1 to pREIS4). The most remarkable finding within the REIS genome is the extraordinary proliferation of mobile genetic elements (MGEs), which contributes to a limited synteny with other Rickettsia genomes. In particular, an integrative conjugative element named RAGE (for Rickettsiales amplified genetic element), previously identified in scrub typhus rickettsiae (Orientia tsutsugamushi) genomes, is present on both the REIS chromosome and plasmids. Unlike the pseudogene-laden RAGEs of O. tsutsugamushi, REIS encodes nine conserved RAGEs that include F-like type IV secretion systems similar to that of the tra genes encoded in the Rickettsia bellii and R. massiliae genomes. An unparalleled abundance of encoded transposases (>650) relative to genome size, together with the RAGEs and other MGEs, comprise ~35% of the total genome, making REIS one of the most plastic and repetitive bacterial genomes sequenced to date. We present evidence that conserved rickettsial genes associated with an intracellular lifestyle were acquired via MGEs, especially the RAGE, through a continuum of genomic invasions. Robust phylogeny estimation suggests REIS is ancestral to the virulent spotted fever group of rickettsiae. As REIS is not known to invade vertebrate cells and has no known pathogenic effects on I. scapularis, its genome sequence provides insight on the origin of mechanisms of rickettsial pathogenicity. Sun, 01 Jan 2012 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2779/ Klaassen, C. H., Gibbons, J. G., et al.|-|-| Molecular ecology. 2012 Jan 01; 21(1): 57-70.|-|-| As the frequency of antifungal drug resistance continues to increase, understanding the genetic structure of fungal populations, where resistant isolates have emerged and spread, is of major importance. Aspergillus fumigatus is an ubiquitously distributed fungus and the primary causative agent of invasive aspergillosis (IA), a potentially lethal infection in immunocompromised individuals. In the last few years, an increasing number of A. fumigatus isolates has evolved resistance to triazoles, the primary drugs for treating IA infections. In most isolates, this multiple-triazole-resistance (MTR) phenotype is caused by mutations in the cyp51A gene, which encodes the protein targeted by the triazoles. We investigated the genetic differentiation and reproductive mode of A. fumigatus in the Netherlands, the country where the MTR phenotype probably originated, to determine their role in facilitating the emergence and distribution of resistance genotypes. Using 20 genome-wide neutral markers, we genotyped 255 Dutch isolates including 25 isolates with the MTR phenotype. In contrast to previous reports, our results show that Dutch A. fumigatus genotypes are genetically differentiated into five distinct populations. Four of the five populations show significant linkage disequilibrium, indicative of an asexual reproductive mode, whereas the fifth population is in linkage equilibrium, indicative of a sexual reproductive mode. Notably, the observed genetic differentiation among Dutch isolates does not correlate with geography, although all isolates with the MTR phenotype nest within a single, predominantly asexual, population. These results suggest that both reproductive mode and genetic differentiation contribute to the structure of Dutch A. fumigatus populations and are probably shaping the evolutionary dynamics of drug resistance in this potentially deadly pathogen. Sun, 01 Jan 2012 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2860/ Lam, T. T., Ip, H. S., et al.|-|-| Ecology letters. 2012 Jan 01; 15(1): 24-33.|-|-| Despite the importance of migratory birds in the ecology and evolution of avian influenza virus (AIV), there is a lack of information on the patterns of AIV spread at the intra-continental scale. We applied a variety of statistical phylogeographic techniques to a plethora of viral genome sequence data to determine the strength, pattern and determinants of gene flow in AIV sampled from wild birds in North America. These analyses revealed a clear isolation-by-distance of AIV among sampling localities. In addition, we show that phylogeographic models incorporating information on the avian flyway of sampling proved a better fit to the observed sequence data than those specifying homogeneous or random rates of gene flow among localities. In sum, these data strongly suggest that the intra-continental spread of AIV by migratory birds is subject to major ecological barriers, including spatial distance and avian flyway. Sun, 01 Jan 2012 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2859/ Bahl J, Nelson MI, et al.|-|-| Proceedings of the National Academy of Sciences of the United States of America. 2011 Nov 29; 108: 19359-64.|-|-| Populations of seasonal influenza virus experience strong annual bottlenecks that pose a considerable extinction risk. It has been suggested that an influenza source population located in tropical Southeast or East Asia seeds annual temperate epidemics. Here we investigate the seasonal dynamics and migration patterns of influenza A H3N2 virus by analysis of virus samples obtained from 2003 to 2006 from Australia, Europe, Japan, New York, New Zealand, Southeast Asia, and newly sequenced viruses from Hong Kong. In contrast to annual temperate epidemics, relatively low levels of relative genetic diversity and no seasonal fluctuations characterized virus populations in tropical Southeast Asia and Hong Kong. Bayesian phylogeographic analysis using discrete temporal and spatial characters reveal high rates of viral migration between urban centers tested. Although the virus population that migrated between Southeast Asia and Hong Kong persisted through time, this was dependent on virus input from temperate regions and these tropical regions did not maintain a source for annual H3N2 influenza epidemics. We further show that multiple lineages may seed annual influenza epidemics, and that each region may function as a potential source population. We therefore propose that the global persistence of H3N2 influenza A virus is the result of a migrating metapopulation in which multiple different localities may seed seasonal epidemics in temperate regions in a given year. Such complex global migration dynamics may confound control efforts and contribute to the emergence and spread of antigenic variants and drug-resistant viruses. Tue, 29 Nov 2011 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2683/ Myers, C. A., Kasper, M. R., et al.|-|-| The American journal of tropical medicine and hygiene. 2011 Nov 01; 85(5): 961-3.|-|-| During the early months of 2009, a novel influenza A/H1N1 virus (pH1N1) emerged in Mexico and quickly spread across the globe. In October 2009, a 23-year-old male residing in central Cambodia was diagnosed with pH1N1. Subsequently, a cluster of four influenza-like illness cases developed involving three children who resided in his home and the children's school teacher. Base composition analysis of internal genes using reverse transcriptase polymerase chain reaction and electrospray ionization mass spectrometry revealed that specimens from two of the secondary victims were coinfected with influenza A/H3N2 and pH1N1. Phylogenetic analysis of the hemagglutinin genes from these isolated viruses showed that they were closely related to existing pH1N1 and A/H3N2 viruses circulating in the region. Genetic recombination was not evident within plaque-purified viral isolates on full genome sequencing. This incident confirms dual influenza virus infections and highlights the risk of zoonotic and seasonal influenza viruses to coinfect and possibly, reassort where they cocirculate. Tue, 01 Nov 2011 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2625/ McDonald SM, Davis K, et al.|-|-| Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases. 2011 Oct 01; 11: 1586-94.|-|-| Group A human rotaviruses (RVs) remain the most frequently detected viral agents associated with acute gastroenteritis in infants and young children. Despite their medical importance, relatively few complete genome sequences have been determined for commonly circulating G/P-type strains (i.e., G1P[8], G2P[4], G3P[8], G4P[8], and G9P[8]). In the current study, we sequenced the genomes of 11 G4P[8] isolates from stool specimens that were collected in Washington, DC during the years of 1974-1991. We found that the VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5/6-encoding genes of all 11 G4P[8] RVs have the genotypes of G4-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. By constructing phylogenetic trees for each gene, extensive intra-genotypic diversity was revealed among the G4P[8] RVs, and new sub-genotype gene alleles were identified. Several of these alleles are nearly identical to those of G3P[8] isolates previously sequenced from this same Washington, DC collection, strongly suggesting that the RVs underwent gene reassortment. On the other hand, we observed that some G4P[8] RVs exhibit completely different allele-based genome constellations, despite being collected during the same epidemic season; there was no evidence of gene reassortment between these strains. This observation extends our previous findings and supports the notion that stable, genetically-distinct clades of human RVs with the same G/P-type can co-circulate in a community. Interestingly, the sub-genotype gene alleles found in some of the DC RVs share a close evolutionary relationship with genes of more contemporary human strains. Thus, archival human RVs sequenced in this study might represent evolutionary precursors to modern-day strains. Sat, 01 Oct 2011 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2959/ Haft, D. H., Varghese, N., et al.|-|-| PloS one. 2011 Aug 01; 6(12): e28886.|-|-| The rhomboid family of serine proteases occurs in all domains of life. Its members contain at least six hydrophobic membrane-spanning helices, with an active site serine located deep within the hydrophobic interior of the plasma membrane. The model member GlpG from Escherichia coli is heavily studied through engineered mutant forms, varied model substrates, and multiple X-ray crystal studies, yet its relationship to endogenous substrates is not well understood. Here we describe an apparent membrane anchoring C-terminal homology domain that appears in numerous genera including Shewanella, Vibrio, Acinetobacter, and Ralstonia, but excluding Escherichia and Haemophilus. Individual genomes encode up to thirteen members, usually homologous to each other only in this C-terminal region. The domain's tripartite architecture consists of motif, transmembrane helix, and cluster of basic residues at the protein C-terminus, as also seen with the LPXTG recognition sequence for sortase A and the PEP-CTERM recognition sequence for exosortase. Partial Phylogenetic Profiling identifies a distinctive rhomboid-like protease subfamily almost perfectly co-distributed with this recognition sequence. This protease subfamily and its putative target domain are hereby renamed rhombosortase and GlyGly-CTERM, respectively. The protease and target are encoded by consecutive genes in most genomes with just a single target, but far apart otherwise. The signature motif of the Rhombo-CTERM domain, often SGGS, only partially resembles known cleavage sites of rhomboid protease family model substrates. Some protein families that have several members with C-terminal GlyGly-CTERM domains also have additional members with LPXTG or PEP-CTERM domains instead, suggesting there may be common themes to the post-translational processing of these proteins by three different membrane protein superfamilies. Mon, 01 Aug 2011 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2862/ Dwyer, D. E., Dwyer DE|-|-| Vaccine. 2011 Jul 22; 29: B56-62.|-|-| The novel pandemic influenza A (H1H1) 2009 virus spread rapidly around the world in 2009. The paucity of prospective international epidemiologic data on predictors of clinical outcomes with pandemic (H1N1) 2009 virus infection stimulated the INSIGHT network, an international network of community and hospital-based investigators, to commence two worldwide clinical observational studies to describe pandemic (H1N1) 2009 virus activity. The purpose of these two studies was to estimate the percent of adult patients with illness due to laboratory-confirmed pandemic (H1N1) 2009 virus infection that experience clinically significant outcomes and to study factors related to these outcomes. Enrollment commenced in October 2009 and will continue until August 2011: as of the end of 2010, 62 sites in 14 countries in Australasia (12 sites), Europe (37) and North America (13) have enrolled 1365 adult patients, with 1049 enrollments into the FLU 002 outpatient study and 316 into the FLU 003 hospitalization study. These 'in progress' INSIGHT influenza observational studies may act as a model for obtaining epidemiological, clinical and laboratory information in future international disease outbreaks. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Fri, 22 Jul 2011 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2866/ Holmes, E. C., Ghedin, E., et al.|-|-| Journal of virology. 2011 Jul 01; 85(14): 6923-9.|-|-| Despite growing interest in the molecular epidemiology of influenza virus, the pattern of viral spread within individual communities remains poorly understood. To determine the phylogeography of influenza virus in a single population, we examined the spatial diffusion of H1N1/09 influenza A virus within the student body of the University of California, San Diego (UCSD), sampling for a 1-month period between October and November 2009. Despite the highly focused nature of our study, an analysis of complete viral genome sequences revealed between 24 and 33 independent introductions of H1N1/09 into the UCSD community, comprising much of the global genetic diversity in this virus. These data were also characterized by a relatively low level of on-campus transmission as well as extensive spatial mixing, such that there was little geographical clustering by either student residence or city ZIP code. Most notably, students experiencing illness on the same day and residing in the same dorm possessed phylogenetically distinct lineages. H1N1/09 influenza A virus is therefore characterized by a remarkable spatial fluidity, which is likely to impede community-based methods for its control, including class cancellations, quarantine, and chemoprophylaxis. Fri, 01 Jul 2011 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2867/ Vlasova, A. N., Halpin, R., et al.|-|-| The Journal of general virology. 2011 Jun 01; 92(0): 1369-79.|-|-| A coronavirus (CoV) previously shown to be associated with catarrhal gastroenteritis in mink (Mustela vison) was identified by electron microscopy in mink faeces from two fur farms in Wisconsin and Minnesota in 1998. A pan-coronavirus and a genus-specific RT-PCR assay were used initially to demonstrate that the newly discovered mink CoVs (MCoVs) were members of the genus Alphacoronavirus. Subsequently, using a random RT-PCR approach, full-genomic sequences were generated that further confirmed that, phylogenetically, the MCoVs belonged to the genus Alphacoronavirus, with closest relatedness to the recently identified but only partially sequenced (fragments of the polymerase, and full-length spike, 3c, envelope, nucleoprotein, membrane, 3x and 7b genes) ferret enteric coronavirus (FRECV) and ferret systemic coronavirus (FRSCV). The molecular data presented in this study provide the first genetic evidence for a new coronavirus associated with epizootic catarrhal gastroenteritis outbreaks in mink and demonstrate that MCoVs possess high genomic variability and relatively low overall nucleotide sequence identities (91.7 %) between contemporary strains. Additionally, the new MCoVs appeared to be phylogenetically distant from human (229E and NL63) and other alphacoronaviruses and did not belong to the species Alphacoronavirus 1. It is proposed that, together with the partially sequenced FRECV and FRSCV, they comprise a new species within the genus Alphacoronavirus. Wed, 01 Jun 2011 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2868/ Ghedin, E., Laplante, J., et al.|-|-| The Journal of infectious diseases. 2011 Jan 15; 203(2): 168-74.|-|-| Mixed infections with seasonal influenza A virus strains are a common occurrence and an important source of genetic diversity. Prolonged viral shedding, as observed in immunocompromised individuals, can lead to mutational accumulation over extended periods. Recently, drug resistance was reported in immunosuppressed patients infected with the 2009 pandemic influenza A (H1N1) virus within a few days after oseltamivir treatment was initiated. To better understand the evolution and emergence of drug resistance in these circumstances, we used a deep sequencing approach to survey the viral population from an immunosuppressed patient infected with H1N1/2009 influenza and treated with neuraminidase inhibitors. This patient harbored 3 genetic variants from 2 phylogenetically distinct viral clades of pandemic H1N1/2009, strongly suggestive of mixed infection. Strikingly, one of these variants also developed drug resistance de novo in response to oseltamivir treatment. Immunocompromised individuals may, therefore, constitute an important source of genetic and phenotypic diversity, both through mixed infection and de novo mutation. Sat, 15 Jan 2011 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2435/ Donati, C., Hiller, N. L., et al.|-|-| Genome Biol. 2010 Oct 29; 11(10): R107.|-|-| ABSTRACT: BACKGROUND: Streptococcus pneumoniae is one of the most important causes of microbial diseases in humans. The genomes of 44 diverse strains of S. pneumoniae were analyzed and compared with strains of non-pathogenic streptococci of the Mitis group. RESULTS: Despite evidence of extensive recombination, the S. pneumoniae phylogenetic tree revealed six major lineages. With the exception of serotype 1, the tree correlated poorly with capsular serotype, geographical site of isolation and disease outcome. The distribution of dispensable genes, genes present in not all, but more than one strain, was consistent with phylogeny, although horizontal gene transfer events attenuated this correlation in the case of ancient lineages. Homologous recombination, involving short stretches of DNA, was the dominant 13 evolutionary process of the core genome of S. pneumoniae. Genetic exchange occurred both within and across the borders of the species, and S. mitis was the main reservoir of genetic diversity of S. pneumoniae. The pan-genome size of S. pneumoniae increased logarithmically with the number of strains and linearly with the number of polymorphic sites of the sampled genomes, suggesting that acquired genes accumulate proportionately to the age of clones. Most genes associated with pathogenicity were shared by all S. pneumoniae strains, but were also present in S. mitis, S. oralis and S. infantis, indicating that these genes are not sufficient to determine virulence. CONCLUSION: Genetic exchange with related species sharing the same ecological niche is the main mechanism of evolution of S. pneumoniae. The open pan genome guarantees the species a quick and economical response to diverse environments. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Fri, 29 Oct 2010 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2433/ Zhou, B., Li, Y., et al.|-|-| J Virol. 2010 Oct 20;|-|-| Influenza A viruses are human and animal pathogens that cause morbidity and mortality, which ranges from mild-to-severe. The 2009-H1N1 pandemic was caused by the emergence of a reassortant H1N1 subtype (H1N1pdm) influenza A virus containing gene segments that originally circulated in human, avian, and swine virus reservoirs. The molecular determinants of replication and pathogenesis of H1N1pdm viruses in humans and other mammals are poorly understood. Therefore, we set out to elucidate viral determinants critical to the pathogenesis of this novel reassortant using a mouse model. We found that a glutamate to glycine substitution at residue 158 of the PB2 gene (PB2-E158G) increased the morbidity and mortality of the parental H1N1pdm virus. Results from mini-genome replication assays in human cells and virus titration in mouse tissues demonstrate that PB2-E158G is a pathogenic determinant because it significantly increases viral replication rates. The virus load in PB2-E158G infected mouse lungs was 1300-fold higher than the wild type virus. Our data also shows that PB2-E158G had a much stronger influence on RNA replication and pathogenesis of H1N1pdm viruses than PB2-E627K, which is a known pathogenic determinant. Remarkably, PB2-E158G substitutions also altered the pathotype of two avian H5 viruses in mice, indicating that this residue impacts genetically divergent influenza A viruses and suggests that this region of PB2 could be a new antiviral target. Collectively the data presented in this study demonstrates that PB2-E158G is a novel pathogenic determinant of influenza A viruses in the mouse model. We speculate that PB2-E158G may be important in the adaptation of avian PB2 genes to other mammals and BLAST sequence analysis identified a naturally occurring human H1N1pdm isolate that has this substitution. Therefore, future surveillance efforts should include scrutiny in this region of PB2 because of its potential impact on pathogenesis. Wed, 20 Oct 2010 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2411/ Wang, S., Sundaram, J. P., et al.|-|-| BMC Bioinformatics. 2010 Sep 07; 11(1): 451.|-|-| ABSTRACT: BACKGROUND: The decrease in cost for sequencing and improvement in technologies has made it easier and more common for the re-sequencing of large genomes as well as parallel sequencing of small genomes. It is possible to completely sequence a small genome within days and this increases the number of publicly available genomes. Among the types of genomes being rapidly sequenced are those of microbial and viral genomes responsible for infectious diseases. However, accurate gene prediction is a challenge that persists for decoding a newly sequenced genome. Therefore, accurate and efficient gene prediction programs are highly desired for rapid and cost effective surveillance of RNA viruses through full genome sequencing. RESULTS: We have developed VIGOR (Viral Genome ORF Reader), a web application tool for gene prediction in influenza virus, rotavirus, rhinovirus and coronavirus subtypes. VIGOR detects protein coding regions based on sequence similarity searches and can accurately detect genome specific features such as frame shifts, overlapping genes, embedded genes, and can predict mature peptides within the context of a single polypeptide open reading frame. Genotyping capability for influenza is built into the program. We compared VIGOR to previously described gene prediction programs, ZCURVE_V, GeneMarkS and FLAN. The specificity and sensitivity of VIGOR are greater than 99% for the RNA viral genomes tested. CONCLUSIONS: VIGOR is a user friendly web-based genome annotation program for five different viral agents, influenza, rotavirus, rhinovirus, coronavirus and SARS coronavirus. This is the first gene prediction program for rotavirus and rhinovirus for public access. VIGOR is able to accurately predict protein coding genes for the above five viral types and has the capability to assign function to the predicted open reading frames and genotype influenza virus. The prediction software was designed for performing high throughput annotation and closure validation in a post-sequencing production pipeline. Tue, 07 Sep 2010 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2589/ Adams, M. D., Chan, E. R., et al.|-|-| Antimicrob Agents Chemother. 2010 Sep 01; 54(9): 3569-77.|-|-| Multidrug resistance has emerged as a significant concern with infections caused by Acinetobacter baumannii. Ample evidence supports the involvement of mobile genetic elements in the transfer of antibiotic resistance genes, but the extent of variability and the rate of genetic change associated with the acquisition of antibiotic resistance have not been studied in detail. Whole-genome sequence analysis of six closely related clinical isolates of A. baumannii, including four from the same hospital, revealed extensive divergence of the resistance genotype that correlated with observed differences in antimicrobial susceptibility. Resistance genes associated with insertion sequences, plasmids, and a chromosomal resistance gene island all showed variability. The highly dynamic resistance gene repertoire suggests rapid evolution of drug resistance. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Wed, 01 Sep 2010 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2623/ Xiao, L., Glass, J. I., et al.|-|-| Journal of clinical microbiology. 2010 Aug 01; 48(8): 2715-23.|-|-| We designed primers and probes for the detection and discrimination of Ureaplasma parvum and U. urealyticum and their 14 serovars by real-time PCR. The analytical sensitivity and specificity of the multiplex species-specific PCR were determined by testing corresponding American Type Culture Collection (ATCC) type strains, 47 other microbial species, and human genomic DNA. The limits of the multiplex PCR were 2.8 x 10(-2) CFU/microl PCR mixture for detecting U. parvum and 4.1 x 10(-2) CFU/microl PCR mixture for detecting U. urealyticum. Clinical specificity and sensitivity were proven by comparison with culture and traditional PCR. For the detection of any Ureaplasma species, the clinical sensitivity and specificity of real-time PCR were 96.9% and 79.0%, respectively, using culture as a reference. Multiplex real-time PCR was also more sensitive than traditional PCR in discriminating the two Ureaplasma species in culture-positive subcultures. Each of the 14 monoplex serovar-specific PCR assays was specific for the corresponding ATCC type strain serovar. This new species identification PCR is specific and sensitive in the detection of Ureaplasma species in clinical specimens, and the serovar-specific PCR assays are the first set of complete genotypic assays to differentiate all 14 known Ureaplasma serovars. These assays provide quick and reliable means for investigating the epidemiology and pathogenicity of ureaplasmas at the serovar level. Sun, 01 Aug 2010 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2360/ Bulach, D., Halpin, R., et al.|-|-| J Virol. 2010 Jul 28; 84(19): 9957-66.|-|-| Full genome sequencing of 11 Australian and one New Zealand subtype H7 avian influenza A isolates has enabled the comparison of sequences from each of the genome segments to other subtype H7 avian influenza A. The inference of phylogenetic relationships for each segment has been used to develop a model of the natural history of these viruses in Australia. Phylogenetic analysis of the hemagglutinin segment indicates that the Australian H7 isolates form a monophyletic clade. This pattern is consistent with the long-term, independent evolution that is, in this instance, associated with geographic regions. Based on the analysis of the other H7 hemagglutinin sequences, three other geographic regions for which similar monophyletic clades have been observed were confirmed. These regions are Eurasia plus Africa, North America, and South America. Analysis of neuraminidase from H7N1, H7N3 or H7N7 genomes revealed the same region based relationships. This pattern of independent evolution of Australian isolates is supported by analysis of each of the six remaining genomic segments. These results in conjunction with the occurrence of five different combinations of neuraminidase subtypes (H7N2, H7N3, H7N4, H7N6, H7N7) among the 11 Australian isolates suggest the maintenance host(s) are nearly exclusively associated with Australia. The single lineage of Australian H7 hemagglutinin sequences despite the occurrence of multiple neuraminidase types suggests a genetic pool from which a variety of reassortants arise rather than the presence of a small number of stable viral clones. This pattern of evolution is likely to occur in each of the regions mentioned above. Wed, 28 Jul 2010 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2350/ Lorenzi, H. A., Puiu, D., et al.|-|-| PLoS Negl Trop Dis. 2010 Jun 01; 4(6). : e716.|-|-| BACKGROUND: In order to maintain genome information accurately and relevantly, original genome annotations need to be updated and evaluated regularly. Manual reannotation of genomes is important as it can significantly reduce the propagation of errors and consequently diminishes the time spent on mistaken research. For this reason, after five years from the initial submission of the Entamoeba histolytica draft genome publication, we have re-examined the original 23 Mb assembly and the annotation of the predicted genes. PRINCIPAL FINDINGS: The evaluation of the genomic sequence led to the identification of more than one hundred artifactual tandem duplications that were eliminated by re-assembling the genome. The reannotation was done using a combination of manual and automated genome analysis. The new 20 Mb assembly contains 1,496 scaffolds and 8,201 predicted genes, of which 60% are identical to the initial annotation and the remaining 40% underwent structural changes. Functional classification of 60% of the genes was modified based on recent sequence comparisons and new experimental data. We have assigned putative function to 3,788 proteins (46% of the predicted proteome) based on the annotation of predicted gene families, and have identified 58 protein families of five or more members that share no homology with known proteins and thus could be entamoeba specific. Genome analysis also revealed new features such as the presence of segmental duplications of up to 16 kb flanked by inverted repeats, and the tight association of some gene families with transposable elements. SIGNIFICANCE: This new genome annotation and analysis represents a more refined and accurate blueprint of the pathogen genome, and provides an upgraded tool as reference for the study of many important aspects of E. histolytica biology, such as genome evolution and pathogenesis. Tue, 01 Jun 2010 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2871/ Ghedin, E., Wentworth, D. E., et al.|-|-| Journal of virology. 2010 Jun 01; 84(11). : 5715-8.|-|-| The initial wave of swine-origin influenza A virus (pandemic H1N1/09) in the United States during the spring and summer of 2009 also resulted in an increased vigilance and sampling of seasonal influenza viruses (H1N1 and H3N2), even though they are normally characterized by very low incidence outside of the winter months. To explore the nature of virus evolution during this influenza "off-season," we conducted a phylogenetic analysis of H1N1 and H3N2 sequences sampled during April to June 2009 in New York State. Our analysis revealed that multiple lineages of both viruses were introduced and cocirculated during this time, as is typical of influenza virus during the winter. Strikingly, however, we also found strong evidence for the presence of a large transmission chain of H3N2 viruses centered on the south-east of New York State and which continued until at least 1 June 2009. These results suggest that the unseasonal transmission of influenza A viruses may be more widespread than is usually supposed. Tue, 01 Jun 2010 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2318/ Eckerle, L. D., Becker, M. M., et al.|-|-| PLoS Pathog. 2010 May 06; 6(5): e1000896.|-|-| Most RNA viruses lack the mechanisms to recognize and correct mutations that arise during genome replication, resulting in quasispecies diversity that is required for pathogenesis and adaptation. However, it is not known how viruses encoding large viral RNA genomes such as the Coronaviridae (26 to 32 kb) balance the requirements for genome stability and quasispecies diversity. Further, the limits of replication infidelity during replication of large RNA genomes and how decreased fidelity impacts virus fitness over time are not known. Our previous work demonstrated that genetic inactivation of the coronavirus exoribonuclease (ExoN) in nonstructural protein 14 (nsp14) of murine hepatitis virus results in a 15-fold decrease in replication fidelity. However, it is not known whether nsp14-ExoN is required for replication fidelity of all coronaviruses, nor the impact of decreased fidelity on genome diversity and fitness during replication and passage. We report here the engineering and recovery of nsp14-ExoN mutant viruses of severe acute respiratory syndrome coronavirus (SARS-CoV) that have stable growth defects and demonstrate a 21-fold increase in mutation frequency during replication in culture. Analysis of complete genome sequences from SARS-ExoN mutant viral clones revealed unique mutation sets in every genome examined from the same round of replication and a total of 100 unique mutations across the genome. Using novel bioinformatic tools and deep sequencing across the full-length genome following 10 population passages in vitro, we demonstrate retention of ExoN mutations and continued increased diversity and mutational load compared to wild-type SARS-CoV. The results define a novel genetic and bioinformatics model for introduction and identification of multi-allelic mutations in replication competent viruses that will be powerful tools for testing the effects of decreased fidelity and increased quasispecies diversity on viral replication, pathogenesis, and evolution. Thu, 06 May 2010 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2384/ Eppinger, M., Guo, Z., et al.|-|-| J Bacteriol. 2009 Dec 01; 191(24): 7628-9.|-|-| To gain insights into the evolutionary origin, emergence, and pathogenicity of the etiologic agent of plague, we have sequenced the genomes of four Yersinia pestis strains isolated from the zoonotic rodent reservoir in foci of endemic plague in China. These resources enable in-depth studies of Y. pestis sequence variations and detailed whole-genome comparisons of very closely related genomes from the supposed site of the origin and the emergence of global pandemics of plague. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Tue, 01 Dec 2009 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2164/ Nelson, M., Spiro, D., et al.|-|-| PLoS Curr Influenza. 2009 Dec 01;: RRN1126.|-|-| Background Since its initial detection in April 2009, the A/H1N1pdm influenza virus has spread rapidly in humans, with over 5,700 human deaths. However, little is known about the evolutionary dynamics of H1N1pdm and its geographic and temporal diversification.Methods Phylogenetic analysis was conducted upon the concatenated coding regions of whole-genome sequences from 290 H1N1pdm isolates sampled globally between April 1 - July 9, 2009, including relatively large samples from the US states of Wisconsin and New York. Results At least 7 phylogenetically distinct viral clades have disseminated globally and co-circulated in localities that experienced multiple introductions of H1N1pdm. The epidemics in New York and Wisconsin were dominated by two different clades, both phylogenetically distinct from the viruses first identified in California and Mexico, suggesting an important role for founder effects in determining local viral population structures. Conclusions Determining the global diversity of H1N1pdm is central to understanding the evolution and spatial spread of the current pandemic, and to predict its future impact on human populations. Our results indicate that H1N1pdm has already diversified into distinct viral lineages with defined spatial patterns. Tue, 01 Dec 2009 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2152/ McDonald, S. M., Matthijnssens, J., et al.|-|-| PLoS Pathog. 2009 Oct 01; 5(10): e1000634.|-|-| Group A human rotaviruses (RVs) are a major cause of severe gastroenteritis in infants and young children. Yet, aside from the genes encoding serotype antigens (VP7; G-type and VP4; P-type), little is known about the genetic make-up of emerging and endemic human RV strains. To gain insight into the diversity and evolution of RVs circulating at a single location over a period of time, we sequenced the eleven-segmented, double-stranded RNA genomes of fifty-one G3P[8] strains collected from 1974 to 1991 at Children's Hospital National Medical Center, Washington, D. C. During this period, G1P[8] strains typically dominated, comprising on average 56% of RV infections each year in hospitalized children. A notable exception was in the 1976 and 1991 winter seasons when the incidence of G1P[8] infections decreased dramatically, a trend that correlated with a significant increase in G3P[8] infections. Our sequence analysis indicates that the 1976 season was characterized by the presence of several genetically distinct, co-circulating clades of G3P[8] viruses, which contained minor but significant differences in their encoded proteins. These 1976 lineages did not readily exchange gene segments with each other, but instead remained stable over the course of the season. In contrast, the 1991 season contained a single major clade, whose genome constellation was similar to one of the 1976 clades. The 1991 clade may have gained a fitness advantage after reassorting with as of yet unidentified RV strain(s). This study reveals for the first time that genetically distinct RV clades of the same G/P-type can co-circulate and cause disease. The findings from this study also suggest that, although gene segment exchange occurs, most reassortant strains are replaced over time by lineages with preferred genome constellations. Elucidation of the selective pressures that favor maintenance of RVs with certain sets of genes may be necessary to anticipate future vaccine needs. Thu, 01 Oct 2009 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2393/ Wywial, E., Haven, J., et al.|-|-| Gene. 2009 Sep 15; 445(1): 26-37.|-|-| Microbial pathogens have evolved sophisticated mechanisms for evasion of host innate and adaptive immunities. PFam54 is the largest paralogous gene family in the genomes of Borrelia burgdorferi, the Lyme disease bacterium. One member of PFam54, the complement-regulator acquiring surface proteins 1 (BbCrasp-1), is able to abort the alternative pathway of complement activation via binding human complement-regulator factor H (FH). The gene coding for BbCRASP-1 exists in a tandem array of PFam54 genes in the B. burgdorferi genome, a result apparently of repeated gene duplications. To help elucidate the functions of the large number of PFam54 genes, we performed phylogenomic and structural analyses of the PFam54 gene array from ten B. burgdorferi genomes. Analyses based on gene tree, genome synteny, and structural models revealed rapid adaptive evolution of this array through gene duplication, gene loss, and functional diversification. Individual PFam54 genes, however, do not show high intra-population sequence polymorphisms as genes providing evasion from adaptive immunity generally do. PFam54 members able to bind human FH are not monophyletic, suggesting that human FH affinity, however strong, is an incidental rather than main function of these PFam54 proteins. The large number of PFam54 genes existing in any single B. burgdorferi genome may target different innate-immunity proteins of a single host species or the same immune protein of a variety of host species. Genetic variability of the PFam54 gene array suggests that universally present PFam54 lineages such as BBA64, BBA65, BBA66, and BBA73 may be better candidates for the development of broad-spectrum vaccines or drugs than strain-restricted lineages such as BbCRASP-1. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Tue, 15 Sep 2009 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2385/ Fricke, W. F., McDermott, P. F., et al.|-|-| Appl Environ Microbiol. 2009 Sep 01; 75(18): 5963-71.|-|-| Salmonella enterica, a leading cause of food-borne gastroenteritis worldwide, may be found in any raw food of animal, vegetable, or fruit origin. Salmonella serovars differ in distribution, virulence, and host specificity. Salmonella enterica serovar Kentucky, though often found in the food supply, is less commonly isolated from ill humans. The multidrug-resistant isolate S. Kentucky CVM29188, isolated from a chicken breast sample in 2003, contains three plasmids (146,811 bp, 101,461 bp, and 46,121 bp), two of which carry resistance determinants (pCVM29188_146 [strAB and tetRA] and pCVM29188_101 [bla(CMY-2) and sugE]). Both resistance plasmids were transferable by conjugation, alone or in combination, to S. Kentucky, Salmonella enterica serovar Newport, and Escherichia coli recipients. pCVM29188_146 shares a highly conserved plasmid backbone of 106 kb (>90% nucleotide identity) with two virulence plasmids from avian pathogenic Escherichia coli strains (pAPEC-O1-ColBM and pAPEC-O2-ColV). Shared avian pathogenic E. coli (APEC) virulence factors include iutA iucABCD, sitABCD, etsABC, iss, and iroBCDEN. PCR analyses of recent (1997 to 2005) S. Kentucky isolates from food animal, retail meat, and human sources revealed that 172 (60%) contained similar APEC-like plasmid backbones. Notably, though rare in human- and cattle-derived isolates, this plasmid backbone was found at a high frequency (50 to 100%) among S. Kentucky isolates from chickens within the same time span. Ninety-four percent of the APEC-positive isolates showed resistance to tetracycline and streptomycin. Together, our findings of a resistance-conferring APEC virulence plasmid in a poultry-derived S. Kentucky isolate and of similar resistance/virulence plasmids in most recent S. Kentucky isolates from chickens and, to lesser degree, from humans and cattle highlight the need for additional research in order to examine the prevalence and spread of combined virulence and resistance plasmids in bacteria in agricultural, environmental, and clinical settings. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Tue, 01 Sep 2009 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2386/ Fricke, W. F., Welch, T. J., et al.|-|-| J Bacteriol. 2009 Aug 01; 191(15): 4750-7.|-|-| Multidrug resistance (MDR) plasmids belonging to the IncA/C plasmid family are widely distributed among Salmonella and other enterobacterial isolates from agricultural sources and have, at least once, also been identified in a drug-resistant Yersinia pestis isolate (IP275) from Madagascar. Here, we present the complete plasmid sequences of the IncA/C reference plasmid pRA1 (143,963 bp), isolated in 1971 from the fish pathogen Aeromonas hydrophila, and of the cryptic IncA/C plasmid pRAx (49,763 bp), isolated from Escherichia coli transconjugant D7-3, which was obtained through pRA1 transfer in 1980. Using comparative sequence analysis of pRA1 and pRAx with recent members of the IncA/C plasmid family, we show that both plasmids provide novel insights into the evolution of the IncA/C MDR plasmid family and the minimal machinery necessary for stable IncA/C plasmid maintenance. Our results indicate that recent members of the IncA/C plasmid family evolved from a common ancestor, similar in composition to pRA1, through stepwise integration of horizontally acquired resistance gene arrays into a conserved plasmid backbone. Phylogenetic comparisons predict type IV secretion-like conjugative transfer operons encoded on the shared plasmid backbones to be closely related to a group of integrating conjugative elements, which use conjugative transfer for horizontal propagation but stably integrate into the host chromosome during vegetative growth. A hipAB toxin-antitoxin gene cluster found on pRA1, which in Escherichia coli is involved in the formation of persister cell subpopulations, suggests persistence as an early broad-spectrum antimicrobial resistance mechanism in the evolution of IncA/C resistance plasmids. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Sat, 01 Aug 2009 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2810/ Lefébure T, Stanhope MJ|-|-| Genome research. 2009 Jul 01; 19: 1224-32.|-|-| An open question in bacterial genomics is the role that adaptive evolution of the core genome plays in diversification and adaptation of bacterial species, and how this might differ between groups of bacteria occupying different environmental circumstances. The genus Campylobacter encompasses several important human and animal enteric pathogens, with genome sequence data available for eight species. We estimate the Campylobacter core genome at 647 genes, with 92.5% of the nonrecombinant core genome loci under positive selection in at least one lineage and the same gene frequently under positive selection in multiple lineages. Tests are provided that reject recombination, saturation, and variation in codon usage bias as factors contributing to this high level of selection. We suggest this genome-wide adaptive evolution may result from a Red Queen macroevolutionary dynamic, in which species are involved in competition for resources within the mammalian and/or vertebrate gastrointestinal tract. Much reduced levels of positive selection evident in Streptococcus, as reported by the authors in an earlier work, may be a consequence of these taxa inhabiting less species-rich habitats, and more unique niches. Despite many common loci under positive selection in multiple Campylobacter lineages, we found no evidence for molecular adaptive convergence at the level of the same or adjacent codons, or even protein domains. Taken collectively, these results describe the diversification of a bacterial genus that involves pervasive natural selection pressure across virtually the entire genome, with this adaptation occurring in different ways in different lineages, despite the species tendency toward a common gastrointestinal habitat. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Wed, 01 Jul 2009 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2076/ Ghedin, E., Fitch, A., et al.|-|-| J Virol. 2009 Jun 24;|-|-| The emergence of viral infections with potentially devastating consequences for human health is highly dependent on their underlying evolutionary dynamics. One likely scenario for an avian influenza virus, such as A/H5N1, to evolve human-to-human transmission is through the acquisition of genetic material from the A/H1N1 or A/H3N2 subtypes already circulating in human populations. This would require that viruses of both subtypes co-infect the same cells, generating a mixed infection, and then reassort. Determining the nature and frequency of mixed infection in influenza virus is therefore central to understanding the emergence of pandemic, antigenic and drug resistant strains. To better understand the potential for such events, we explored patterns of intra-host genetic diversity in recently circulating strains of human influenza virus. By analyzing multiple viral genome sequences sampled from individual influenza patients we reveal a high level of mixed infection, including diverse lineages of the same influenza subtype, drug resistant and sensitive strains, those that are likely to differ in antigenicity, and even viruses of different influenza types (A and B). These results reveal individuals can harbor influenza viruses that differ in major phenotypic properties, including those that are antigenically distinct and those that differ in their sensitivity to antiviral agents. Wed, 24 Jun 2009 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2389/ Nelson, M. I., Simonsen, L., et al.|-|-| Virology. 2009 Jun 05; 388(2): 270-8.|-|-| Resistance to the adamantane class of antiviral drugs by human A/H3N2 influenza viruses currently exceeds 90% in the United States and multiple Asian countries. Adamantane resistance is associated with a single amino acid change (S31N) in the M2 protein, which was shown to rapidly disseminate globally in 2005 in association with a genome reassortment event. However, the exact origin of influenza A/H3N2 viruses carrying the S31N mutation has not been characterized, particularly in South-East Asia. We therefore conducted a phylogenetic analysis of the HA, NA, and M1/2 segments of viral isolates collected between 1997 and 2007 from temperate localities in the Northern hemisphere (New York State, United States, 492 isolates) and Southern hemisphere (New Zealand and Australia, 629 isolates) and a subtropical locality in South-East Asia (Hong Kong, 281 isolates). We find that although the S31N mutation was independently introduced at least 11 times, the vast majority of resistant viruses now circulating globally descend from a single introduction that was first detected in the summer of 2003 in Hong Kong. These resistant viruses were continually detected in Hong Kong throughout 2003-2005, acquired a novel HA through reassortment during the first part of 2005, and thereafter spread globally. The emergence and persistence of adamantane resistant viruses in Hong Kong further supports a source-sink model of global influenza virus ecology, in which South-East Asia experiences continuous viral activity and repeatedly seeds epidemics in temperate areas. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Fri, 05 Jun 2009 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2033/ Fedorova, N. D., Harris, S., et al.|-|-| Med Mycol. 2009 Mar 17;: 1-8.|-|-| We have examined the feasibility of using array comparative genomic hybridization (aCGH) to explore intraspecific genetic variability at the genomic level in two pathogenic molds, Aspergillus fumigatus and Aspergillus flavus. Our analysis showed that strain-specific genes may comprise up to 2% of their genomes in comparison to isolates from different vegetative (heterokaryon) compatibility groups (VCGs). In contrast, isolates with the same VCG affiliations have almost identical gene content. Most isolate-specific genes are annotated as 'hypothetical' and located in a few large subtelomeric indels. The list includes highly polymorphic loci that contain putative het (heterokaryon compatibility) loci, which determine the individual's VCG during parasexual crossing. Incidentally, VCGs in both species seem to be significantly associated with either alpha or HMG mating type (Chi-square test, P=0.05). In conclusion CGH can be used to effectively to identify isolate-specific genes in Aspergillus species. Preliminary evidence suggests that gene flow in both species is largely constrained by VCG boundaries, although further VCG sampling is required to confirm this observation. Tue, 17 Mar 2009 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2060/ Song, H., Hwang, J., et al.|-|-| Mol Cells. 2009 Feb 01; 27(2): 237-41.|-|-| Pathogens Burkholderia pseudomallei (Bp) and Burkholderia mallei (Bm) contain a large number (> 12,000) of Simple Sequence Repeats (SSRs). To study the extent to which these features have contributed to the diversification of genes, we have conducted comparative studies with nineteen genomes of these bacteria. We found 210 genes with characteristic types of SSR variations. SSRs with nonamer repeat units were the most abundant, followed by hexamers and trimers. Amino acids with smaller and nonpolar R-groups are preferred to be encoded by the variant SSRs, perhaps due to their minimal impacts to protein functionality. A majority of these genes appears to code for surface or secreted proteins that may directly interact with the host factors during pathogenesis or other environmental factors. There also are others that encode diverse functions in the cytoplasm, and this protein variability may reflect an extensive involvement of phase variation in survival and adaptation of these pathogens. Sun, 01 Feb 2009 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2382/ Beare, P. A., Unsworth, N., et al.|-|-| Infect Immun. 2009 Feb 01; 77(2): 642-56.|-|-| Genetically distinct isolates of Coxiella burnetii, the cause of human Q fever, display different phenotypes with respect to in vitro infectivity/cytopathology and pathogenicity for laboratory animals. Moreover, correlations between C. burnetii genomic groups and human disease presentation (acute versus chronic) have been described, suggesting that isolates have distinct virulence characteristics. To provide a more-complete understanding of C. burnetii's genetic diversity, evolution, and pathogenic potential, we deciphered the whole-genome sequences of the K (Q154) and G (Q212) human chronic endocarditis isolates and the naturally attenuated Dugway (5J108-111) rodent isolate. Cross-genome comparisons that included the previously sequenced Nine Mile (NM) reference isolate (RSA493) revealed both novel gene content and disparate collections of pseudogenes that may contribute to isolate virulence and other phenotypes. While C. burnetii genomes are highly syntenous, recombination between abundant insertion sequence (IS) elements has resulted in genome plasticity manifested as chromosomal rearrangement of syntenic blocks and DNA insertions/deletions. The numerous IS elements, genomic rearrangements, and pseudogenes of C. burnetii isolates are consistent with genome structures of other bacterial pathogens that have recently emerged from nonpathogens with expanded niches. The observation that the attenuated Dugway isolate has the largest genome with the fewest pseudogenes and IS elements suggests that this isolate's lineage is at an earlier stage of pathoadaptation than the NM, K, and G lineages. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Sun, 01 Feb 2009 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2150/ Djikeng, A., Spiro, D.|-|-| Future Virol. 2009 Jan 01; 4(1): 47-53.|-|-| In the face of numerous emerging and re-emerging viral threats, large-scale genome sequencing efforts are underway to monitor viral evolution in real-time. To fully appreciate the mechanisms of viral adaptation and evolution, and to also develop reagents and resources for a better molecular diagnosis of emerging and re-emerging viral infections, there has been an increasing effort toward producing full length viral genome sequences. To date, high-throughput platforms have been developed using traditional Sanger-based sequencing and there are currently prospects to apply next generation sequencing methods to develop an ultra high-throughput strategy for viral genome sequencing and analysis. Thu, 01 Jan 2009 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2387/ Mabey Gilsenan, J. E., Atherton, G., et al.|-|-| Nucleic Acids Res. 2009 Jan 01; 37(0): D509-14.|-|-| Aspergillus Genomes is a public resource for viewing annotated genes predicted by various Aspergillus sequencing projects. It has arisen from the union of two significant resources: the Aspergillus/Aspergillosis website and the Central Aspergillus Data REpository (CADRE). The former has primarily served the medical community, providing information about Aspergillus and associated diseases to medics, patients and scientists; the latter has focused on the fungal genomic community, providing a central repository for sequences and annotation extracted from Aspergillus Genomes. By merging these databases, genomes benefit from extensive cross-linking with medical information to create a unique resource, spanning genomics and clinical aspects of the genus. Aspergillus Genomes is accessible from http://www.aspergillus-genomes.org.uk. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Thu, 01 Jan 2009 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2007/ Lorenzi, H., Thiagarajan, M., et al.|-|-| BMC Genomics. 2008 Dec 10; 9(1): 595.|-|-| ABSTRACT: BACKGROUND: Identification and mapping of repetitive elements is a key step for accurate gene prediction and overall structural annotation of genomes. During the assembly and annotation of three highly repetitive amoeba genomes, Entamoeba histolytica, Entamoeba dispar, and Entamoeba invadens, we performed comparative sequence analysis to identify and map all class I and class II transposable elements in their sequences. RESULTS: Here, we report the identification of two novel Entamoeba-specific repeats: ERE1 and ERE2; ERE1 is spread across the three genomes and associated with different repeats in a species-specific manner, while ERE2 is unique to E. histolytica. We also report the identification of two novel subfamilies of LINE and SINE retrotransposons in E. dispar and provide evidence for how the different LINE and SINE subfamilies evolved in these species. Additionally, we found a putative transposase-coding gene in E. histolytica and E. dispar related to the mariner transposon Hydargos from E. invadens. The distribution of transposable elements in these genomes is markedly skewed with a tendency of forming clusters. More than 70% of the three genomes have a repeat density below their corresponding average value indicating that transposable elements are not evenly distributed. We show that repeats and repeat-clusters are found at syntenic break points between E. histolytica and E. dispar and hence, could work as recombination hot spots promoting genome rearrangements. CONCLUSIONS: The mapping of all transposable elements found in these parasites shows that repeat coverage is up to three times higher than previously reported. LINE, ERE1 and mariner elements were present in the common ancestor to the three Entamoeba species while ERE2 was likely acquired by E. histolytica after its separation from E. dispar. We demonstrate that E. histolytica and E. dispar share their entire repertoire of LINE and SINE retrotransposons and that Eh_SINE3/Ed_SINE1 originated as a chimeric SINE from Eh/Ed_SINE2 and Eh_SINE1/Ed_SINE3. Our work shows that transposable elements are organized in clusters, frequently found at syntenic break points providing insights into their contribution to chromosome instability and therefore, to genomic variation and speciation in these parasites. Wed, 10 Dec 2008 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=1966/ Alekseev, K. P., Vlasova, A. N., et al.|-|-| J Virol. 2008 Oct 08; 82(24): 12422-31.|-|-| We sequenced and analyzed the full-length genomes of four coronaviruses (CoVs) each from a distinct wild ruminant species in Ohio: sambar deer (Cervus unicolor), a waterbuck (Kobus ellipsiprymnus), a sable antelope (Hippotragus niger) and a white-tailed deer (Odocoileus virginianus). The fecal samples from sambar deer, waterbuck and white-tailed deer were collected during winter dysentery outbreaks and sporadic diarrhea cases in 1993-1994 (Tsunemitsu, H., Z. R. el-Kanawati, D. R. Smith, H. H. Reed, and L. J. Saif. 1995. J. Clin. Microbiol. 33:3264-9). A fecal sample from a sable antelope was collected in 2003 from an Ohio wild animal habitat, during the same outbreak when a bovine-like CoV from a giraffe (GiCoV) was isolated (Hasoksuz, M., K. Alekseev, A. Vlasova, X. Zhang, D. Spiro, R. Halpin, S. Wang, E. Ghedin, and L. J. Saif. 2007. J. Virol. 81:4981-4990). For two of the CoVs (sambar deer and waterbuck), complete genomes from both the cell culture-adapted and gnotobiotic calf-passaged strains were also sequenced and analyzed. Phylogenetically, wild ruminant CoVs belong to group 2a CoVs with the closest relatedness to the recent BCoV strains. High nucleotide identities (99.4-99.6%) among the wild ruminant strains and the recent BCoV strains (BCoV-LUN and BCoV-ENT, 1998) further comfirm the close relatedness. Comparative genetic analysis of captive wild ruminant CoVs with BCoV strains suggests that no specific genomic markers are present that allow discrimination between the bovine strains and bovine-like CoVs from captive wild ruminants; furthermore, no specific genetic markers were identified that defined cell culture or calf-passaged strains, or host origin of strains. This study confirms prior biologic and antigenic similarities reported between bovine and wild ruminant CoVs and suggests that cattle may be reservoirs for CoVs that infect captive wild ruminants or vice versa and that these CoVs may represent host range variants of an ancestral CoV. Wed, 08 Oct 2008 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=1664/ Rasko, D. A., Rosovitz, M. J., et al.|-|-| J Bacteriol. 2008 Aug 01; 190(20): 6881-93.|-|-| Whole genome sequencing has been skewed towards bacterial pathogens as a consequence of the prioritization of medical and veterinary diseases. However, it is becoming clear that in order to accurately measure genetic variation within and between pathogenic groups, multiple isolates, as well as commensal species must be sequenced. This study examines the pan-genomic content of E. coli. Six distinct E. coli pathovars can be distinguished using molecular or phenotypic markers, but only two of the six pathovars had been subjected to any genome sequencing. As such, this report is the seminal description of the genomic content and unique features of three unsequenced pathovars, ETEC, EPEC and EAEC. We have also determined the first genome sequence of a human commensal E. coli isolate, E. coli HS, which will undoubtedly provide a new baseline from which one can examine the evolution of pathogenic E. coli. Comparison of 17 E. coli genomes, eight of which are new, identified approximately 2200 genes conserved in all isolates. We were also able to identify genes that were isolate- and pathovar-specific. Fewer pathovar-specific genes were identified than anticipated, suggesting that each isolate may have independently developed virulence capabilities. Pan-genome calculations indicate that E. coli genomic diversity represents an open pan-genome model containing a reservoir of greater than 13000 genes, many of which may be uncharacterized but important virulence factors. This comparative study of the E. coli species, while descriptive in nature, will provide the basis for future functional work on this important group of pathogens. Fri, 01 Aug 2008 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=1689/ Nelson, M. I., Edelman, L., et al.|-|-| PLoS Pathog. 2008 Aug 01; 4(8): e1000133.|-|-| To determine the spatial and temporal dynamics of influenza A virus during a single epidemic, we examined whole-genome sequences of 284 A/H1N1 and 69 A/H3N2 viruses collected across the continental United States during the 2006-2007 influenza season, representing the largest study of its kind undertaken to date. A phylogenetic analysis revealed that multiple clades of both A/H1N1 and A/H3N2 entered and co-circulated in the United States during this season, even in localities that are distant from major metropolitan areas, and with no clear pattern of spatial spread. In addition, co-circulating clades of the same subtype exchanged genome segments through reassortment, producing both a minor clade of A/H3N2 viruses that appears to have re-acquired sensitivity to the adamantane class of antiviral drugs, as well as a likely antigenically distinct A/H1N1 clade that became globally dominant following this season. Overall, the co-circulation of multiple viral clades during the 2006-2007 epidemic season revealed patterns of spatial spread that are far more complex than observed previously, and suggests a major role for both migration and reassortment in shaping the epidemiological dynamics of human influenza A virus. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Fri, 01 Aug 2008 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2448/ Margos, G., Gatewood, A. G., et al.|-|-| Proc Natl Acad Sci U S A. 2008 Jun 24; 105(25): 8730-5.|-|-| Lyme borreliosis, caused by the tick-borne bacterium Borrelia burgdorferi, has become the most common vector-borne disease in North America over the last three decades. To understand the dynamics of the epizootic spread and to predict the evolutionary trajectories of B. burgdorferi, accurate information on the population structure and the evolutionary relationships of the pathogen is crucial. We, therefore, developed a multilocus sequence typing (MLST) scheme for B. burgdorferi based on eight chromosomal housekeeping genes. We validated the MLST scheme on B. burgdorferi specimens from North America and Europe, comprising both cultured isolates and infected ticks. These data were compared with sequences for the commonly used genetic markers rrs-rrlA intergenic spacer (IGS) and the gene encoding the outer surface protein C (ospC). The study demonstrates that the concatenated sequences of the housekeeping genes of B. burgdorferi provide highly resolved phylogenetic signals and that the housekeeping genes evolve differently compared with the IGS locus and ospC. Using sequence data, the study reveals that North American and European populations of B. burgdorferi correspond to genetically distinct populations. Importantly, the MLST data suggest that B. burgdorferi originated in Europe rather than in North America as proposed previously. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Tue, 24 Jun 2008 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=1624/ Dugan, V.G., Chen, R., et al.|-|-| PLoS Pathog. 2008 May 30; 4(5): e1000076.|-|-| We surveyed the genetic diversity among avian influenza virus (AIV) in wild birds, comprising 167 complete viral genomes from 14 bird species sampled in four locations across the United States. These isolates represented 29 type A influenza virus hemagglutinin (HA) and neuraminidase (NA) subtype combinations, with up to 26% of isolates showing evidence of mixed subtype infection. Through a phylogenetic analysis of the largest data set of AIV genomes compiled to date, we were able to document a remarkably high rate of genome reassortment, with no clear pattern of gene segment association and occasional inter-hemisphere gene segment migration and reassortment. From this, we propose that AIV in wild birds forms transient "genome constellations," continually reshuffled by reassortment, in contrast to the spread of a limited number of stable genome constellations that characterizes the evolution of mammalian-adapted influenza A viruses. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Fri, 30 May 2008 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2390/ Rambaut, A., Pybus, O. G., et al.|-|-| Nature. 2008 May 29; 453(7195): 615-9.|-|-| The evolutionary interaction between influenza A virus and the human immune system, manifest as 'antigenic drift' of the viral haemagglutinin, is one of the best described patterns in molecular evolution. However, little is known about the genome-scale evolutionary dynamics of this pathogen. Similarly, how genomic processes relate to global influenza epidemiology, in which the A/H3N2 and A/H1N1 subtypes co-circulate, is poorly understood. Here through an analysis of 1,302 complete viral genomes sampled from temperate populations in both hemispheres, we show that the genomic evolution of influenza A virus is characterized by a complex interplay between frequent reassortment and periodic selective sweeps. The A/H3N2 and A/H1N1 subtypes exhibit different evolutionary dynamics, with diverse lineages circulating in A/H1N1, indicative of weaker antigenic drift. These results suggest a sink-source model of viral ecology in which new lineages are seeded from a persistent influenza reservoir, which we hypothesize to be located in the tropics, to sink populations in temperate regions. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Thu, 29 May 2008 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2383/ Boni, M. F., Zhou, Y., et al.|-|-| J Virol. 2008 May 01; 82(10): 4807-11.|-|-| To determine the extent of homologous recombination in human influenza A virus, we assembled a data set of 13,852 sequences representing all eight segments and both major circulating subtypes, H3N2 and H1N1. Using an exhaustive search and a nonparametric test for mosaic structure, we identified 315 sequences (approximately 2%) in five different RNA segments that, after a multiple-comparison correction, had statistically significant mosaic signals compatible with homologous recombination. Of these, only two contained recombinant regions of sufficient length (>100 nucleotides [nt]) that the occurrence of homologous recombination could be verified using phylogenetic methods, with the rest involving very short sequence regions (15 to 30 nt). Although this secondary analysis revealed patterns of phylogenetic incongruence compatible with the action of recombination, neither candidate recombinant was strongly supported. Given our inability to exclude the occurrence of mixed infection and template switching during amplification, laboratory artifacts provide an alternative and likely explanation for the occurrence of phylogenetic incongruence in these two cases. We therefore conclude that, if it occurs at all, homologous recombination plays only a very minor role in the evolution of human influenza A virus. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Thu, 01 May 2008 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=385/ Tumapa, S., Holden, M. T., et al.|-|-| BMC Genomics. 2008 Apr 25; 9(1): 190.|-|-| ABSTRACT: BACKGROUND: Burkholderia pseudomallei is a soil-dwelling saprophyte and the cause of melioidosis. Horizontal gene transfer contributes to the genetic diversity of this pathogen and may be an important determinant of virulence potential. The genome contains genomic island (GI) regions that encode a broad array of functions. Although there is some evidence for the variable distribution of genomic islands in B. pseudomallei isolates, little is known about the extent of variation between related strains or their association with disease or environmental survival. RESULTS: Five islands from B. pseudomallei strain K96243 were chosen as representatives of different types of genomic islands present in this strain, and their presence investigated in other B. pseudomallei. In silico analysis of 10 B. pseudomallei genome sequences provided evidence for the variable presence of these regions, together with microevolutionary changes that generate GI diversity. The diversity of GIs in 186 isolates from NE Thailand (83 environmental and 103 clinical isolates) was investigated using multiplex PCR screening. The proportion of all isolates positive by PCR ranged from 12% for a prophage-like island (GI 9), to 76% for a metabolic island (GI 16). The presence of each of the five GIs did not differ between environmental and disease-associated isolates (p>0.05 for all five islands). The cumulative number of GIs per isolate for the 186 isolates ranged from 0 to 5 (median 2, IQR 1 to 3). The distribution of cumulative GI number did not differ between environmental and disease-associated isolates (p=0.27). The presence of GIs was defined for the three largest clones in this collection (each defined as a single sequence type, ST, by multilocus sequence typing); these were ST 70 (n=15 isolates), ST 54 (n=11), and ST 167 (n=9). The rapid loss and/or acquisition of gene islands was observed within individual clones. Comparisons were drawn between isolates obtained from the environment and from patients with melioidosis in order to examine the role of genomic islands in virulence and clinical associations. There was no reproducible association between the individual or cumulative presence of five GIs and a range of clinical features in 103 patients with melioidosis. CONCLUSIONS: Horizontal gene transfer of mobile genetic elements can rapidly alter the gene repertoire of B. pseudomallei. This study confirms the utility of a range of approaches in defining the presence and significance of genomic variation in natural populations of B. pseudomallei. Fri, 25 Apr 2008 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2447/ Kraiczy, P., Seling, A., et al.|-|-| Clin Vaccine Immunol. 2008 Mar 01; 15(3): 484-91.|-|-| Serological diagnosis of Lyme disease may be complicated by antigenic differences between infecting organisms and those used as test references. Accordingly, it would be helpful to include antigens whose sequences are well conserved by a broad range of Lyme disease spirochetes. In the present study, line blot analyses were performed using recombinant complement regulator-acquiring surface protein 2 (BbCRASP-2) from Borrelia burgdorferi sensu stricto strain B31 and serum samples from human Lyme disease patients from throughout the United States and Germany. The results indicated that a large proportion of the patients had produced antibodies recognizing recombinant BbCRASP-2. In addition, Lyme disease spirochetes isolated from across North America and Europe were found to contain genes encoding proteins with high degrees of similarity to the B. burgdorferi type strain B31 BbCRASP-2, consistent with the high percentage of serologically positive patients. These data indicate that BbCRASP-2 may be valuable for use in a widely effective serological assay. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Sat, 01 Mar 2008 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=1605/ Nelson, M. I., Viboud, C., et al.|-|-| PLoS Pathog. 2008 Feb 15; 4(2): e1000012.|-|-| The H1N1 subtype of influenza A virus has caused substantial morbidity and mortality in humans, first documented in the global pandemic of 1918 and continuing to the present day. Despite this disease burden, the evolutionary history of the A/H1N1 virus is not well understood, particularly whether there is a virological basis for several notable epidemics of unusual severity in the 1940s and 1950s. Using a data set of 71 representative complete genome sequences sampled between 1918 and 2006, we show that segmental reassortment has played an important role in the genomic evolution of A/H1N1 since 1918. Specifically, we demonstrate that an A/H1N1 isolate from the 1947 epidemic acquired novel PB2 and HA genes through intra-subtype reassortment, which may explain the abrupt antigenic evolution of this virus. Similarly, the 1951 influenza epidemic may also have been associated with reassortant A/H1N1 viruses. Intra-subtype reassortment therefore appears to be a more important process in the evolution and epidemiology of H1N1 influenza A virus than previously realized. Fri, 15 Feb 2008 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=1462/ Fedorova, N.D., Nierman, W.C., et al.|-|-| The Aspergilli Genomics, Medical Aspects, Biotechnology, and Research Methods. 2008 Feb 01;: 25-42.|-|-| Fri, 01 Feb 2008 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2381/ Bao, Y., Bolotov, P., et al.|-|-| J Virol. 2008 Jan 01; 82(2): 596-601.|-|-| Tue, 01 Jan 2008 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2446/ Boyd, E. F., Cohen, A. L., et al.|-|-| BMC Microbiol. 2008 Jan 01; 8: 110.|-|-| BACKGROUND: Vibrio parahaemolyticus is abundant in the aquatic environment particularly in warmer waters and is the leading cause of seafood borne gastroenteritis worldwide. Prior to 1995, numerous V. parahaemolyticus serogroups were associated with disease, however, in that year an O3:K6 serogroup emerged in Southeast Asia causing large outbreaks and rapid hospitalizations. This new highly virulent strain is now globally disseminated. RESULTS: We performed a four-way BLAST analysis on the genome sequence of V. parahaemolyticus RIMD2210633, an O3:K6 isolate from Japan recovered in 1996, versus the genomes of four published Vibrio species and constructed genome BLAST atlases. We identified 24 regions, gaps in the genome atlas, of greater than 10 kb that were unique to RIMD2210633. These 24 regions included an integron, f237 phage, 2 type III secretion systems (T3SS), a type VI secretion system (T6SS) and 7 Vibrio parahaemolyticus genomic islands (VPaI-1 to VPaI-7). Comparative genomic analysis of our fifth genome, V. parahaemolyticus AQ3810, an O3:K6 isolate recovered in 1983, identified four regions unique to each V. parahaemolyticus strain. Interestingly, AQ3810 did not encode 8 of the 24 regions unique to RMID, including a T6SS, which suggests an additional virulence mechanism in RIMD2210633. The distribution of only the VPaI regions was highly variable among a collection of 42 isolates and phylogenetic analysis of these isolates show that these regions are confined to a pathogenic clade. CONCLUSION: Our data show that there is considerable genomic flux in this species and that the new highly virulent clone arose from an O3:K6 isolate that acquired at least seven novel regions, which included both a T3SS and a T6SS. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Tue, 01 Jan 2008 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=443/ Patron, N. J., Waller, R. F., et al.|-|-| BMC Evol Biol. 2007 Sep 26; 7(1): 174.|-|-| ABSTRACT: BACKGROUND: Genes responsible for biosynthesis of fungal secondary metabolites are usually tightly clustered in the genome and co-regulated with metabolite production. Epipolythiodioxopiperazines (ETPs) are a class of secondary metabolite toxins produced by disparate ascomycete fungi and implicated in several animal and plant diseases. Gene clusters responsible for their production have previously been defined in only two fungi. Fungal genome sequence data have been surveyed for the presence of putative ETP clusters and cluster data have been generated from several fungal taxa where genome sequences are not available. Phylogenetic analysis of cluster genes has been used to investigate the assembly and heredity of these gene clusters. RESULTS: Putative ETP gene clusters are present in 14 ascomycete taxa, but absent in numerous other ascomycetes examined. These clusters are discontinuously distributed in ascomycete lineages. Gene content is not absolutely fixed, however, common genes are identified and phylogenies of six of these are separately inferred. In each phylogeny almost all cluster genes form monophyletic clades with non-cluster fungal paralogues being the nearest outgroups. This relatedness of cluster genes suggests that a progenitor ETP gene cluster assembled within an ancestral taxon. Within each of the cluster clades, the cluster genes group together in consistent subclades, however, these relationships do not always reflect the phylogeny of ascomycetes. Micro-synteny of several of the genes within the clusters provides further support for these subclades. CONCLUSION: ETP gene clusters appear to have a single origin and have been inherited relatively intact rather than assembling independently in the different ascomycete lineages. This progenitor cluster has given rise to a small number of distinct phylogenetic classes of clusters that are represented in a discontinuous pattern throughout ascomycetes. The disjunct heredity of these clusters is discussed with consideration to multiple instances of independent cluster loss and lateral transfer of gene clusters between lineages. Wed, 26 Sep 2007 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2388/ Nelson, M. I., Simonsen, L., et al.|-|-| PLoS Pathog. 2007 Sep 14; 3(9): 1220-8.|-|-| The winter seasonality of influenza A virus in temperate climates is one of the most widely recognized, yet least understood, epidemiological patterns in infectious disease. Central to understanding what drives the seasonal emergence of this important human pathogen is determining what becomes of the virus during the non-epidemic summer months. Herein, we take a step towards elucidating the seasonal emergence of influenza virus by determining the evolutionary relationship between populations of influenza A virus sampled from opposite hemispheres. We conducted a phylogenetic analysis of 487 complete genomes of human influenza A/H3N2 viruses collected between 1999 and 2005 from Australia and New Zealand in the southern hemisphere, and a representative sub-sample of viral genome sequences from 413 isolates collected in New York state, United States, representing the northern hemisphere. We show that even in areas as relatively geographically isolated as New Zealand's South Island and Western Australia, global viral migration contributes significantly to the seasonal emergence of influenza A epidemics, and that this migration has no clear directional pattern. These observations run counter to suggestions that local epidemics are triggered by the climate-driven reactivation of influenza viruses that remain latent within hosts between seasons or transmit at low efficiency between seasons. However, a complete understanding of the seasonal movements of influenza A virus will require greatly expanded global surveillance, particularly of tropical regions where the virus circulates year-round, and during non-epidemic periods in temperate climate areas. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Fri, 14 Sep 2007 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=406/ Eppinger, M., Rosovitz, M. J., et al.|-|-| PLoS Genet. 2007 Aug 31; 3(8): e142.|-|-| The first reported Far East scarlet-like fever (FESLF) epidemic swept the Pacific coastal region of Russia in the late 1950s. Symptoms of the severe infection included erythematous skin rash and desquamation, exanthema, hyperhemic tongue, and a toxic shock syndrome. The term FESLF was coined for the infection because it shares clinical presentations with scarlet fever caused by group A streptococci. The causative agent was later identified as Yersinia pseudotuberculosis, although the range of morbidities was vastly different from classical pseudotuberculosis symptoms. To understand the origin and emergence of the peculiar clinical features of FESLF, we have sequenced the genome of the FESLF-causing strain Y. pseudotuberculosis IP31758 and compared it with that of another Y. pseudotuberculosis strain, IP32953, which causes classical gastrointestinal symptoms. The unique gene pool of Y pseudotuberculosis IP31758 accounts for more than 260 strain-specific genes and introduces individual physiological capabilities and virulence determinants, with a significant proportion horizontally acquired that likely originated from Enterobacteriaceae and other soil-dwelling bacteria that persist in the same ecological niche. The mobile genome pool includes two novel plasmids phylogenetically unrelated to all currently reported Yersinia plasmids. An icm/dot type IVB secretion system, shared only with the intracellular persisting pathogens of the order Legionellales, was found on the larger plasmid and could contribute to scarlatinoid fever symptoms in patients due to the introduction of immunomodulatory and immunosuppressive capabilities. We determined the common and unique traits resulting from genome evolution and speciation within the genus Yersinia and drew a more accurate species border between Y. pseudotuberculosis and Y. pestis. In contrast to the lack of genetic diversity observed in the evolutionary young descending Y. pestis lineage, the population genetics of Y. pseudotuberculosis is more heterogenous. Both Y. pseudotuberculosis strains IP31758 and the previously sequenced Y. pseudotuberculosis strain IP32953 have evolved by the acquisition of specific plasmids and by the horizontal acquisition and incorporation of different genetic information into the chromosome, which all together or independently seems to potentially impact the phenotypic adaptation of these two strains. Fri, 31 Aug 2007 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=389/ Auerbach, R. K., Tuanyok, A., et al.|-|-| PLoS ONE. 2007 Aug 22; 2(1): e770.|-|-| BACKGROUND: Yersinia pestis, the etiologic agent of plague, was responsible for several devastating epidemics throughout history and is currently of global importance to current public heath and biodefense efforts. Y. pestis is widespread in the Western United States. Because Y. pestis was first introduced to this region just over 100 years ago, there has been little time for genetic diversity to accumulate. Recent studies based upon single nucleotide polymorphisms have begun to quantify the genetic diversity of Y. pestis in North America. METHODOLOGY/PRINCIPAL FINDINGS: To examine the evolution of Y. pestis in North America, a gapped genome sequence of CA88-4125 was generated. Sequence comparison with another North American Y. pestis strain, CO92, identified seven regions of difference (six inversions, one rearrangement), differing IS element copy numbers, and several SNPs. CONCLUSIONS/SIGNIFICANCE: The relatively large number of inverted/rearranged segments suggests that North American Y. pestis strains may be undergoing inversion fixation at high rates over a short time span, contributing to higher-than-expected diversity in this region. These findings will hopefully encourage the scientific community to sequence additional Y. pestis strains from North America and abroad, leading to a greater understanding of the evolutionary history of this pathogen. Wed, 22 Aug 2007 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=1532/ Zhang, X., Hasoksuz, M., et al.|-|-| Virology. 2007 Jun 20; 363(1): 1-10.|-|-| The genetic diversity of 2 pairs (AH65 and AH187) of wild type bovine coronaviruses (BCoV) sequenced directly from nasal (respiratory) and rectal (enteric) swabs of two feedlot calves with respiratory and enteric symptoms [Hasoksuz, M., Sreevatsan, S., Cho, K.O., Hoet, A.E., Saif, L.J., 2002b. Molecular analysis of the S1 subunit of the spike glycoprotein of respiratory and enteric bovine coronavirus isolates. Virus Res. 84 (1-2), 101-109.]. was analyzed. Sequence analysis of the complete genomes revealed differences at 123 and 149 nucleotides (nt) throughout the entire genome between the respiratory and enteric strains for samples AH65 and AH187, respectively, indicating the presence of intra-host BCoV quasispecies. In addition, significant numbers of sequence ambiguities were found in the genomes of some BCoV-R and BCoV-E strains, suggesting intra-isolate quasispecies. The tissue culture (TC) passaged counterparts of AH65 respiratory BCoV (AH65-R-TC) and enteric BCoV (AH65-E-TC) were also sequenced after 14 and 15 passages and 1 plaque purification in human rectal tumor cells (HRT-18), respectively. Compared to the parental wild type strains, tissue culture passage generated 104 nt changes in the AH65-E-TC isolate but only 8 nt changes in the AH65-R-TC isolate. Particularly noteworthy, the majority of nucleotide changes in the AH65-E-TC isolate occurred at the identical positions as the mutations occurring in the AH65-R strain from the same animal. These data suggest that BCoV evolves through quasispecies development, and that enteric BCoV isolates are more prone to genetic changes and may mutate to resemble respiratory BCoV strains after tissue culture passage. Wed, 20 Jun 2007 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2445/ Allan, G., Williams, A., Rabinowicz, P., Chan, A., Ravel, J., Keim, P.|-|-| Genet Resour Crop Evol.. 2007 Jun 01; 55(3): 365-378.|-|-| Fri, 01 Jun 2007 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=1686/ Salzberg, S. L., Kingsford, C., et al.|-|-| Emerg Infect Dis. 2007 May 01; 13(5): 713-8.|-|-| To better understand the ecology and epidemiology of the highly pathogenic avian influenza virus in its transcontinental spread, we sequenced and analyzed the complete genomes of 36 recent influenza A (H5N1) viruses collected from birds in Europe, northern Africa, and southeastern Asia. These sequences, among the first complete genomes of influenza (H5N1) viruses outside Asia, clearly depict the lineages now infecting wild and domestic birds in Europe and Africa and show the relationships among these isolates and other strains affecting both birds and humans. The isolates fall into 3 distinct lineages, 1 of which contains all known non-Asian isolates. This new Euro-African lineage, which was the cause of several recent (2006) fatal human infections in Egypt and Iraq, has been introduced at least 3 times into the European-African region and has split into 3 distinct, independently evolving sublineages. One isolate provides evidence that 2 of these sublineages have recently reassorted. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Tue, 01 May 2007 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=1505/ Hasoksuz, M., Alekseev, K., et al.|-|-| J Virol. 2007 May 01; 81(10): 4981-90.|-|-| Coronaviruses (CoVs) possess large RNA genomes and exist as quasispecies, which increases the possibility of adaptive mutations and interspecies transmission. Recently, CoVs were recognized as important pathogens in captive wild ruminants. This is the first report of the isolation and detailed genetic, biologic, and antigenic characterization of a bovine-like CoV from a giraffe (Giraffa camelopardalis) in a wild-animal park in the United States. CoV particles were detected by immune electron microscopy in fecal samples from three giraffes with mild-to-severe diarrhea. From one of the three giraffe samples, a CoV (GiCoV-OH3) was isolated and successfully adapted to serial passage in human rectal tumor 18 cell cultures. Hemagglutination assays, receptor-destroying enzyme activity, hemagglutination inhibition, and fluorescence focus neutralization tests revealed close biological and antigenic relationships between the GiCoV-OH3 isolate and selected respiratory and enteric bovine CoV (BCoV) strains. When orally inoculated into a BCoV-seronegative gnotobiotic calf, GiCoV-OH3 caused severe diarrhea and virus shedding within 2 to 3 days. Sequence comparisons and phylogenetic analyses were performed to assess its genetic relatedness to other CoVs. Molecular characterization confirmed that the new isolate belongs to group 2a of the mammalian CoVs and revealed closer genetic relatedness between GiCoV-OH3 and the enteric BCoVs BCoV-ENT and BCoV-DB2, whereas BCoV-Mebus was more distantly related. Detailed sequence analysis of the GiCoV-OH3 spike gene demonstrated the presence of a deletion in the variable region of the S1 subunit (from amino acid 543 to amino acid 547), which is a region associated with pathogenicity and tissue tropism for other CoVs. The point mutations identified in the structural proteins (by comparing GiCoV-OH3, BCoV-ENT, BCoV-DB2, and BCoV-Mebus) were most conserved among GiCoV-OH3, BCoV-ENT, and BCoV-DB2, whereas most of the point mutations in the nonstructural proteins were unique to GiCoV-OH3. Our results confirm the existence of a bovine-like CoV transmissible to cattle from wild ruminants, namely, giraffes, but with certain genetic properties different from those of BCoVs. Tue, 01 May 2007 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=460/ Tiyawisutsri, R., Holden, M. T., et al.|-|-| BMC Microbiol. 2007 Mar 15; 7(1): 19.|-|-| ABSTRACT: BACKGROUND: The bacterial biothreat agents Burkholderia mallei and Burkholderia pseudomallei are the cause of glanders and melioidosis, respectively. Genomic and epidemiological studies have shown that B. mallei is a recently emerged, host restricted clone of B. pseudomallei. RESULTS: Using bacteriophage-mediated immunoscreening we identified genes expressed in vivo during experimental equine glanders infection. A family of immunodominant antigens were identified that share protein domain architectures with hemagglutinins and invasins. These have been designated Burkholderia Hep_Hag autotransporter (BuHA) proteins. A total of 110/207 positive clones (53%) of a B. mallei expression library screened with sera from two infected horses belonged to this family. This contrasted with 6/189 positive clones (3%) of a B. pseudomallei expression library screened with serum from 21 patients with culture-proven melioidosis. CONCLUSIONS: Members of the BuHA proteins are found in other Gram-negative bacteria and have been shown to have important roles related to virulence. Compared with other bacterial species, the genomes of both B. mallei and B. pseudomallei contain a relative abundance of this family of proteins. The domain structures of these proteins suggest that they function as multimeric surface proteins that modulate interactions of the cell with the host and environment. Their effect on the cellular immune response to B. mallei and their potential as diagnostics for glanders requires further study. Thu, 15 Mar 2007 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2391/ Welch, T. J., Fricke, W. F., et al.|-|-| PLoS One. 2007 Mar 01; 2(3): e309.|-|-| Antimicrobial resistance in Yersinia pestis is rare, yet constitutes a significant international public health and biodefense threat. In 1995, the first multidrug resistant (MDR) isolate of Y. pestis (strain IP275) was identified, and was shown to contain a self-transmissible plasmid (pIP1202) that conferred resistance to many of the antimicrobials recommended for plague treatment and prophylaxis. Comparative analysis of the DNA sequence of Y. pestis plasmid pIP1202 revealed a near identical IncA/C plasmid backbone that is shared by MDR plasmids isolated from Salmonella enterica serotype Newport SL254 and the fish pathogen Yersinia ruckeri YR71. The high degree of sequence identity and gene synteny between the plasmid backbones suggests recent acquisition of these plasmids from a common ancestor. In addition, the Y. pestis pIP1202-like plasmid backbone was detected in numerous MDR enterobacterial pathogens isolated from retail meat samples collected between 2002 and 2005 in the United States. Plasmid-positive strains were isolated from beef, chicken, turkey and pork, and were found in samples from the following states: California, Colorado, Connecticut, Georgia, Maryland, Minnesota, New Mexico, New York and Oregon. Our studies reveal that this common plasmid backbone is broadly disseminated among MDR zoonotic pathogens associated with agriculture. This reservoir of mobile resistance determinants has the potential to disseminate to Y. pestis and other human and zoonotic bacterial pathogens and therefore represents a significant public health concern. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Thu, 01 Mar 2007 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2394/ Zhang, X., Hasoksuz, M., et al.|-|-| Virology. 2007 Feb 20; 358(2): 424-35.|-|-| Transmissible gastroenteritis virus (TGEV) isolates that have been adapted to passage in cell culture maintain their infectivity in vitro but may lose their pathogenicity in vivo. To better understand the genomic mechanisms for viral attenuation, we sequenced the complete genomes of two virulent TGEV strains and their attenuated counterparts: virulent TGEV Miller M6 and attenuated TGEV Miller M60 and virulent TGEV Purdue and attenuated TGEV Purdue P115, together with the ISU-1 strain of porcine respiratory coronavirus (PRCV-ISU-1), a naturally occurring TGEV deletion mutant with an altered respiratory tropism and reduced virulence. Pairwise comparison at both the nucleotide (nt) and amino acid (aa) levels between virulent and attenuated TGEV strains identified a common change in nt 1753 of the spike gene, resulting in a serine to alanine mutation at aa position 585 of the spike proteins of the attenuated TGEV strains. Alanine was also present in this protein in PRCV-ISU-1. Particularly noteworthy, the serine to alanine mutation resides in the region of the major antigenic site A/B (aa 506-706) that elicits neutralizing antibodies and within the domain mediating the cell surface receptor aminopeptidase N binding (aa 522-744). Comparison of the predicted polypeptide products of ORF3b showed significant deletions in the naturally attenuated PRCV-ISU-1 and TGEV Miller M60; these deletions occurred at a common break point, suggesting a related mechanism of recombination that may affect viral virulence or tropism. Sequence comparisons at both genomic and protein levels indicated that PRCV-ISU-1 had a closer relationship with TGEV Miller strains than Purdue strains. Phylogenetic analyses showed that virulence is an evolutionarily labile trait in TGEV and that TGEV strains as a group share a common ancestor with PRCV. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Tue, 20 Feb 2007 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=394/ Carlton, J. M., Hirt, R. P., et al.|-|-| Science. 2007 Jan 12; 315(5809): 207-12.|-|-| We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the approximately 160-megabase genome, reflecting a recent massive expansion of genetic material. This expansion, in conjunction with the shaping of metabolic pathways that likely transpired through lateral gene transfer from bacteria, and amplification of specific gene families implicated in pathogenesis and phagocytosis of host proteins may exemplify adaptations of the parasite during its transition to a urogenital environment. The genome sequence predicts previously unknown functions for the hydrogenosome, which support a common evolutionary origin of this unusual organelle with mitochondria. Fri, 12 Jan 2007 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=1523/ Rasko, D. A., Rosovitz, M. J., et al.|-|-| J Bacteriol. 2007 Jan 01; 189(1): 52-64.|-|-| The plasmids of the members of the Bacillus cereus sensu lato group of organisms are essential in defining the phenotypic traits associated with pathogenesis and ecology. For example, Bacillus anthracis contains two plasmids, pXO1 and pXO2, encoding toxin production and encapsulation, respectively, that define this species pathogenic potential, whereas the presence of a Bt toxin-encoding plasmid defines Bacillus thuringiensis isolates. In this study the plasmids from B. cereus isolates that produce emetic toxin or are linked to periodontal disease were sequenced and analyzed. Two periodontal isolates examined contained almost identical approximately 272-kb plasmids, named pPER272. The emetic toxin-producing isolate contained one approximately 270-kb plasmid, named pCER270, encoding the cereulide biosynthesis gene cluster. Comparative sequence analyses of these B. cereus plasmids revealed a high degree of sequence similarity to the B. anthracis pXO1 plasmid, especially in a putative replication region. These plasmids form a newly defined group of pXO1-like plasmids. However, these novel plasmids do not contain the pXO1 pathogenicity island, which in each instance is replaced by plasmid specific DNA. Plasmids pCER270 and pPER272 share regions that are not found in any other pXO1-like plasmids. Evolutionary studies suggest that these plasmids are more closely related to each other than to other identified B. cereus plasmids. Screening of a population of B. cereus group isolates revealed that pXO1-like plasmids are more often found in association with clinical isolates. This study demonstrates that the pXO1-like plasmids may define pathogenic B. cereus isolates in the same way that pXO1 and pXO2 define the B. anthracis species. Mon, 01 Jan 2007 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=1524/ Rokas, A., Payne, G., et al.|-|-| Stud Mycol. 2007 Jan 01; 59: 11-7.|-|-| Understanding the nature of species" boundaries is a fundamental question in evolutionary biology. The availability of genomes from several species of the genus Aspergillus allows us for the first time to examine the demarcation of fungal species at the whole-genome level. Here, we examine four case studies, two of which involve intraspecific comparisons, whereas the other two deal with interspecific genomic comparisons between closely related species. These four comparisons reveal significant variation in the nature of species boundaries across Aspergillus. For example, comparisons between A. fumigatus and Neosartorya fischeri (the teleomorph of A. fischerianus) and between A. oryzae and A. flavus suggest that measures of sequence similarity and species-specific genes are significantly higher for the A. fumigatus - N. fischeri pair. Importantly, the values obtained from the comparison between A. oryzae and A. flavus are remarkably similar to those obtained from an intra-specific comparison of A. fumigatus strains, giving support to the proposal that A. oryzae represents a distinct ecotype of A. flavus and not a distinct species. We argue that genomic data can aid Aspergillus taxonomy by serving as a source of novel and unprecedented amounts of comparative data, as a resource for the development of additional diagnostic tools, and finally as a knowledge database about the biological differences between strains and species. Mon, 01 Jan 2007 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=533/ Nelson, M. I., Simonsen, L., et al.|-|-| PLoS Pathog. 2006 Dec 01; 2(12): e125.|-|-| Understanding the evolutionary dynamics of influenza A virus is central to its surveillance and control. While immune-driven antigenic drift is a key determinant of viral evolution across epidemic seasons, the evolutionary processes shaping influenza virus diversity within seasons are less clear. Here we show with a phylogenetic analysis of 413 complete genomes of human H3N2 influenza A viruses collected between 1997 and 2005 from New York State, United States, that genetic diversity is both abundant and largely generated through the seasonal importation of multiple divergent clades of the same subtype. These clades cocirculated within New York State, allowing frequent reassortment and generating genome-wide diversity. However, relatively low levels of positive selection and genetic diversity were observed at amino acid sites considered important in antigenic drift. These results indicate that adaptive evolution occurs only sporadically in influenza A virus; rather, the stochastic processes of viral migration and clade reassortment play a vital role in shaping short-term evolutionary dynamics. Thus, predicting future patterns of influenza virus evolution for vaccine strain selection is inherently complex and requires intensive surveillance, whole-genome sequencing, and phenotypic analysis. Fri, 01 Dec 2006 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=578/ Wortman, J. R., Fedorova, N., et al.|-|-| Med Mycol. 2006 Sep 01; 44: 3-7.|-|-| The availability of the genome sequences of multiple Aspergillus spp. presents the research community with an unprecedented opportunity for discovery. The genomes of Neosartorya fischeri and Aspergillus clavatus have been sequenced in order to extend our knowledge of Aspergillus fumigatus, the primary cause of invasive aspergillosis. Through comparative genomic analysis, we hope to elucidate both obvious and subtle differences between genomes, developing new hypotheses that can be tested in the laboratory. A preliminary examination of the genomes and their predicted proteomes reveals extensive conservation between protein sequences and significant synteny, or conserved gene order. Comparative genomic analysis at the level of these closely related aspergilli should provide important insight into the evolutionary forces at play and their effect on gene content, regulation and expression. Fri, 01 Sep 2006 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=556/ Salzberg, S., Ghedin, E., et al.|-|-| Nature. 2006 Mar 30; 440(7084): 605.|-|-| Thu, 30 Mar 2006 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=2392/ Wolf, Y. I., Viboud, C., et al.|-|-| Biol Direct. 2006 Feb 01; 1: 34.|-|-| BACKGROUND: The interpandemic evolution of the influenza A virus hemagglutinin (HA) protein is commonly considered a paragon of rapid evolutionary change under positive selection in which amino acid replacements are fixed by virtue of their effect on antigenicity, enabling the virus to evade immune surveillance. RESULTS: We performed phylogenetic analyses of the recently obtained large and relatively unbiased samples of the HA sequences from 1995-2005 isolates of the H3N2 and H1N1 subtypes of influenza A virus. Unexpectedly, it was found that the evolution of H3N2 HA includes long intervals of generally neutral sequence evolution without apparent substantial antigenic change ("stasis" periods) that are characterized by an excess of synonymous over nonsynonymous substitutions per site, lack of association of amino acid replacements with epitope regions, and slow extinction of coexisting virus lineages. These long periods of stasis are punctuated by shorter intervals of rapid evolution under positive selection during which new dominant lineages quickly displace previously coexisting ones. The preponderance of positive selection during intervals of rapid evolution is supported by the dramatic excess of amino acid replacements in the epitope regions of HA compared to replacements in the rest of the HA molecule. In contrast, the stasis intervals showed a much more uniform distribution of replacements over the HA molecule, with a statistically significant difference in the rate of synonymous over nonsynonymous substitution in the epitope regions between the two modes of evolution. A number of parallel amino acid replacements - the same amino acid substitution occurring independently in different lineages - were also detected in H3N2 HA. These parallel mutations were, largely, associated with periods of rapid fitness change, indicating that there are major limitations on evolutionary pathways during antigenic change. The finding that stasis is the prevailing modality of H3N2 evolution suggests that antigenic changes that lead to an increase in fitness typically result from epistatic interactions between several amino acid substitutions in the HA and, perhaps, other viral proteins. The strains that become dominant due to increased fitness emerge from low frequency strains thanks to the last amino acid replacement that completes the set of replacements required to produce a significant antigenic change; no subset of substitutions results in a biologically significant antigenic change and corresponding fitness increase. In contrast to H3N2, no clear intervals of evolution under positive selection were detected for the H1N1 HA during the same time span. Thus, the ascendancy of H1N1 in some seasons is, most likely, caused by the drop in the relative fitness of the previously prevailing H3N2 lineages as the fraction of susceptible hosts decreases during the stasis intervals. CONCLUSION: We show that the common view of the evolution of influenza virus as a rapid, positive selection-driven process is, at best, incomplete. Rather, the interpandemic evolution of influenza appears to consist of extended intervals of stasis, which are characterized by neutral sequence evolution, punctuated by shorter intervals of rapid fitness increase when evolutionary change is driven by positive selection. These observations have implications for influenza surveillance and vaccine formulation; in particular, the possibility exists that parallel amino acid replacements could serve as a predictor of new dominant strains. REVIEWERS: Ron Fouchier (nominated by Andrey Rzhetsky), David Krakauer, Christopher Lee. This publication is listed for reference purposes only. It may be included to present a more complete view of a JCVI employee's body of work, or as a reference to a JCVI sponsored project. Wed, 01 Feb 2006 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=726/ Seshadri, R., Samuel, J.|-|-| Ann N Y Acad Sci. 2005 Dec 01; 1063: 442-50.|-|-| Coxiella burnetii, the etiological agent of Q fever, is a class B biodefense agent. We are continuing the momentum of discovery generated by the first Coxiella genome sequences by extending the breadth of genomics to include four additional heterogeneous C. burnetii strains. We are also sequencing the genome of Rickettsiella grylli, an intracellular parasite of grasshoppers and the closest known phylogenetic relative to the Coxiella group. These data will enable the investigation of fundamental questions about Coxiella pathogenicity and virulence as well as broader evolutionary questions about the transition to obligate intracellular life. Specifically, sequence comparisons will permit examination of genetic differences, allowing us to address key questions: What core genes are necessary for an obligate intracellular lifestyle and developmental cycle of the genus? What specific genetic determinants can be linked to virulence properties such as host preference, disease severity, and pathology (i.e., acute vs. chronic disease)? What are the frequencies of mutation and intragenomic recombination, and levels of genome reduction? What specific factors are relevant to colonization and virulence in human hosts (based on comparisons with R. grylli)? From a public health and biodefense perspective, exposure to different strains, either natural or due to illegitimate release, may have different outcomes. With extensive genomic-level information from diverse strains, investigators can determine effective drug and vaccine targets and design methods to accurately type Coxiella based on a subset of genes, opening the way for cost-effective targeted PCR- or antibody-based tests. Thu, 01 Dec 2005 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=631/ Ghedin, E., Sengamalay, N. A., et al.|-|-| Nature. 2005 Oct 05; 437(7062): 1162-6.|-|-| Influenza viruses are remarkably adept at surviving in the human population over a long timescale. The human influenza A virus continues to thrive even among populations with widespread access to vaccines, and continues to be a major cause of morbidity and mortality. The virus mutates from year to year, making the existing vaccines ineffective on a regular basis, and requiring that new strains be chosen for a new vaccine. Less-frequent major changes, known as antigenic shift, create new strains against which the human population has little protective immunity, thereby causing worldwide pandemics. The most recent pandemics include the 1918 'Spanish' flu, one of the most deadly outbreaks in recorded history, which killed 30-50 million people worldwide, the 1957 'Asian' flu, and the 1968 'Hong Kong' flu. Motivated by the need for a better understanding of influenza evolution, we have developed flexible protocols that make it possible to apply large-scale sequencing techniques to the highly variable influenza genome. Here we report the results of sequencing 209 complete genomes of the human influenza A virus, encompassing a total of 2,821,103 nucleotides. In addition to increasing markedly the number of publicly available, complete influenza virus genomes, we have discovered several anomalies in these first 209 genomes that demonstrate the dynamic nature of influenza transmission and evolution. This new, large-scale sequencing effort promises to provide a more comprehensive picture of the evolution of influenza viruses and of their pattern of transmission through human and animal populations. All data from this project are being deposited, without delay, in public archives. Wed, 05 Oct 2005 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=659/ Lal, K., Field, M. C., et al.|-|-| Mol Biochem Parasitol. 2005 Oct 01; 143(2): 226-35.|-|-| Rab proteins are pivotal components of the membrane trafficking machinery in all eukaryotes. Distinct Rab proteins locate to specific endomembrane compartments and genomic studies suggest that Rab gene diversity correlates with endomembrane system complexity; for example unicellular organisms generally possess 5-20 Rab family members and the size of the repertoire increases to 25-60 in multicellular systems. Here we report 65 open reading frames from the unicellular protozoan Trichomonas vaginalis that encode distinct Rab proteins (TvRabs), indicating a family with complexity that rivals Homo sapiens in number. The detection of gene transcripts for the majority of these genes and conservation of functional motifs strongly suggests that TvRabs retain functionality and likely roles in membrane trafficking. The T. vaginalis Rab family includes orthologues of the conserved subfamilies, Rab1, Rab5, Rab6, Rab7 and Rab11, but the majority of TvRabs are not represented by orthologues in other systems and includes six novel T. vaginalis specific Rab subfamilies (A-F). The extreme size of the T. vaginalis Rab family, the presence of novel subfamilies plus the divergent nature of many TvRab sequences suggest both the presence of a highly complex endomembrane system within Trichomonas and potentially novel Rab functionality. A family of more than 65 Rab genes in a unicellular genome is unexpected, but may be a requirement for progression though an amoeboid life-cycle phase as both Dictyostelium discoideum and Entamoeba histolytica share with T. vaginalis both an amoeboid life cycle stage and very large Rab gene families. Sat, 01 Oct 2005 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=638/ Hall, N., Carlton, J.|-|-| Curr Opin Genet Dev. 2005 Sep 20; 15(6): 609-13.|-|-| In the past few years, the area of comparative genomics of malaria parasites has begun to come of age, with the completion of genome sequencing projects of four Plasmodium species, and several functional genomics studies. A picture is emerging of a parasite genome that is highly adapted to its mammalian and vector hosts, and which uses post-transcriptional gene-silencing as one method for the control of gene expression. The genome is compartmentalized into a core of conserved housekeeping genes, sandwiched between subtelomerically located genes encoding surface antigens. Species-specific gene families shape the preference of the parasite for host cells, in addition to determining interactions with the host immune-system. Recent research has led to the description of a motif that is conserved across Plasmodium species and which plays a central role in protein export into the host cell. Tue, 20 Sep 2005 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=669/ Loftus, B. J., Hall, N.|-|-| Trends Parasitol. 2005 Aug 11; 21(10): 453.|-|-| Thu, 11 Aug 2005 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=611/ Cui, L., Fan, Q., et al.|-|-| Mol Biochem Parasitol. 2005 Aug 04; 144(1): 1-9.|-|-| Despite the significance of Plasmodium vivax as the most widespread human malaria parasite and a major public health problem, gene expression in this parasite is poorly understood. To accelerate gene discovery and facilitate the annotation phase of the P. vivax genome project, we have undertaken a transcriptome approach to study gene expression in the mixed blood stages of a P. vivax field isolate. Using a cDNA library constructed from purified blood stages, we have obtained single-pass sequences for approximately 21,500 expressed sequence tags (ESTs), the largest number of transcript tags obtained so far for this species. Cluster analysis revealed that the library is highly redundant, resulting in 5407 clusters. Clustered ESTs were searched against public protein databases for functional annotation, and more than one-third showed a significant match, the majority of these to Plasmodium falciparum proteins. The most abundant clusters were to genes encoding ribosomal proteins and proteins involved in metabolism, consistent with the predominance of trophozoites in the field isolate sample. In spite of the scarcity of other parasite stages in the field isolate, we could identify genes that are expressed in rings, schizonts and gametocytes. This study should facilitate our understanding of the gene expression in P. vivax asexual stages and provide valuable data for gene prediction and annotation of the P. vivax genome sequence. Thu, 04 Aug 2005 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=643/ Holmes, E. C., Ghedin, E., et al.|-|-| PLoS Biol. 2005 Jul 26; 3(9): e300.|-|-| Understanding the evolution of influenza A viruses in humans is important for surveillance and vaccine strain selection. We performed a phylogenetic analysis of 156 complete genomes of human H3N2 influenza A viruses collected between 1999 and 2004 from New York State, United States, and observed multiple co-circulating clades with different population frequencies. Strikingly, phylogenies inferred for individual gene segments revealed that multiple reassortment events had occurred among these clades, such that one clade of H3N2 viruses present at least since 2000 had provided the hemagglutinin gene for all those H3N2 viruses sampled after the 2002-2003 influenza season. This reassortment event was the likely progenitor of the antigenically variant influenza strains that caused the A/Fujian/411/2002-like epidemic of the 2003-2004 influenza season. However, despite sharing the same hemagglutinin, these phylogenetically distinct lineages of viruses continue to co-circulate in the same population. These data, derived from the first large-scale analysis of H3N2 viruses, convincingly demonstrate that multiple lineages can co-circulate, persist, and reassort in epidemiologically significant ways, and underscore the importance of genomic analyses for future influenza surveillance. Tue, 26 Jul 2005 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=738/ Wang, R., Arevalo-Herrera, M., et al.|-|-| Eur J Immunol. 2005 May 02; 35(6): 1859-1868.|-|-| Duffy antigen is the receptor used by Plasmodium vivax to invade erythrocytes. Consequently, individuals lacking Duffy antigen [Fy(-)] do not develop blood-stage infections. We hypothesized that naturally exposed Fy(-) humans may develop immune responses mainly to pre-erythrocytic stages and could be used to study acquired immunity to P. vivax and to identify liver-stage antigens. We report here that antibody and IFN-gamma responses to known sporozoite antigens were significantly induced by natural exposure in Fy(-) humans, whereas responses to blood-stage antigens were significantly induced in Fy(+) humans. IFN-gamma responses to sporozoite antigens were lower in Fy(+) than in Fy(-) humans, indicating that in Fy(+) humans blood-stage infections may have suppressed T cell responses to pre-erythrocytic stages. We evaluated the immune responses to 18 novel P. vivax homologs of P. falciparum sporozoite proteins identified from the P. vivax genome sequence. Eight proteins recalled IFN-gamma responses in P. vivax-exposed but not in unexposed individuals. Of these, 3 antigens elicited IFN-gamma responses in Fy(-) but not in Fy(+) individuals. These results suggest that differential immune responses observed in naturally exposed Fy(-) and Fy(+) individuals can be exploited to identify P. vivax stage-specific antigens. Mon, 02 May 2005 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=736/ Vanacova, S., Yan, W., et al.|-|-| Proc Natl Acad Sci U S A. 2005 Mar 22; 102(12): 4430-5.|-|-| Eukaryotes have evolved elaborate splicing mechanisms to remove introns that would otherwise destroy the protein-coding capacity of genes. Nuclear premRNA splicing requires sequence motifs in the intron and is mediated by a ribonucleoprotein complex, the spliceosome. Here we demonstrate the presence of a splicing apparatus in the protist Trichomonas vaginalis and show that RNA motifs found in yeast and metazoan introns are required for splicing. We also describe the first introns in this deep-branching lineage. The positions of these introns are often conserved in orthologous genes, indicating they were present in a common ancestor of trichomonads, yeast, and metazoa. All examined T. vaginalis introns have a highly conserved 12-nt 3' splice-site motif that encompasses the branch point and is necessary for splicing. This motif is also found in the only described intron in a gene from another deep-branching eukaryote, Giardia intestinalis. These studies demonstrate the conservation of intron splicing signals across large evolutionary distances, reveal unexpected motif conservation in deep-branching lineages that suggest a simplified mechanism of splicing in primitive unicellular eukaryotes, and support the presence of introns in the earliest eukaryote. Tue, 22 Mar 2005 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=667/ Loftus, B., Anderson, I., et al.|-|-| Nature. 2005 Feb 24; 433(7028): 865-8.|-|-| Entamoeba histolytica is an intestinal parasite and the causative agent of amoebiasis, which is a significant source of morbidity and mortality in developing countries. Here we present the genome of E. histolytica, which reveals a variety of metabolic adaptations shared with two other amitochondrial protist pathogens: Giardia lamblia and Trichomonas vaginalis. These adaptations include reduction or elimination of most mitochondrial metabolic pathways and the use of oxidative stress enzymes generally associated with anaerobic prokaryotes. Phylogenomic analysis identifies evidence for lateral gene transfer of bacterial genes into the E. histolytica genome, the effects of which centre on expanding aspects of E. histolytica's metabolic repertoire. The presence of these genes and the potential for novel metabolic pathways in E. histolytica may allow for the development of new chemotherapeutic agents. The genome encodes a large number of novel receptor kinases and contains expansions of a variety of gene families, including those associated with virulence. Additional genome features include an abundance of tandemly repeated transfer-RNA-containing arrays, which may have a structural function in the genome. Analysis of the genome provides new insights into the workings and genome evolution of a major human pathogen. Thu, 24 Feb 2005 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=608/ Carlton, J., Silva, J., et al.|-|-| Curr Issues Mol Biol. 2005 Jan 01; 7(1): 23-37.|-|-| The field of comparative genomics of malaria parasites has recently come of age with the completion of the whole genome sequences of the human malaria parasite Plasmodium falciparum and a rodent malaria model, Plasmodium yoelii yoelii. With several other genome sequencing projects of different model and human malaria parasite species underway, comparing genomes from multiple species has necessitated the development of improved informatics tools and analyses. Results from initial comparative analyses reveal striking conservation of gene synteny between malaria species within conserved chromosome cores, in contrast to reduced homology within subtelomeric regions, in line with previous findings on a smaller scale. Genes that elicit a host immune response are frequently found to be species-specific, although a large variant multigene family is common to many rodent malaria species and Plasmodium vivax. Sequence alignment of syntenic regions from multiple species has revealed the similarity between species in coding regions to be high relative to non-coding regions, and phylogenetic footprinting studies promise to reveal conserved motifs in the latter. Comparison of non-synonymous substitution rates between orthologous genes is proving a powerful technique for identifying genes under selection pressure, and may be useful for vaccine design. This is a stimulating time for comparative genomics of model and human malaria parasites, which promises to produce useful results for the development of antimalarial drugs and vaccines. Sat, 01 Jan 2005 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=729/ Silva, J. C., Bastida, F., et al.|-|-| Mol Biol Evol. 2005 Jan 01; 22(1): 126-34.|-|-| Mariner transposable elements encoding a D,D34D motif-bearing transposase are characterized by their pervasiveness among, and exclusivity to, animal phyla. To date, several hundred sequences have been obtained from taxa ranging from cnidarians to humans, only two of which are known to be functional. Related transposons have been identified in plants and fungi, but their absence among protists is noticeable. Here, we identify and characterize Tvmar1, the first representative of the mariner family to be found in a species of protist, the human parasite Trichomonas vaginalis. This is the first D,D34D element to be found outside the animal kingdom, and its inclusion in the mariner family is supported by both structural and phylogenetic analyses. Remarkably, Tvmar1 has all the hallmarks of a functional element and has recently expanded to several hundred copies in the genome of T. vaginalis. Our results show that a new potentially active mariner has been found that belongs to a distinct mariner lineage and has successfully invaded a nonanimal, single-celled organism. The considerable genetic distance between Tvmar1 and other mariners may have valuable implications for the design of new, high-efficiency vectors to be used in transfection studies in protists. Sat, 01 Jan 2005 00:00:00 -0500 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=831/ Lyons, E. J., Carlton, J. M.|-|-| Trends Parasitol. 2004 May 01; 20(5): 204-7.|-|-| As is often the case in the study of infectious diseases, there are those interested in the basic biology of the organism and those primarily concerned with the clinical aspects of infection, disease and treatment. Although it is not uncommon for these two sets of researchers to remain essentially separate, the modern era of genomics is increasingly bringing them together. Such is the case with the community of scientists studying Trichomonas vaginalis, a human protozoan parasite of the urogenital tract that causes the sexually transmitted disease trichomoniasis. Sat, 01 May 2004 00:00:00 -0400 http://www.weizhongli-lab.org/cms/index.php?id=629&no_cache=1&tx_ttnews[tt_news]=920/ Carlton, J.|-|-| Trends Parasitol. 2003 May 01; 19(5): 227-31.|-|-| With the successful completion of the project to sequence the Plasmodium falciparum genome, researchers are now turning their attention to other malaria parasite species. Here, an update on the Plasmodium vivax genome sequencing project is presented, as part of the Trends in Parasitology series of reviews expanding on various aspects of P. vivax research. Thu, 01 May 2003 00:00:00 -0400