Gene S. Tan, PhD

Assistant Professor

Gene Tan is an assistant professor at the J. Craig Venter Institute working in the Infectious Disease group. The focus of his research is on virus-host interactions by defining the immunological, molecular and genetic determinants that govern immunity and disease. The aim is to better understand how viruses manipulate the host machinery to replicate and in turn elucidate the mechanisms by which the host counteracts the pathogen. Analyses of virus-host interaction can then facilitate the development of better diagnostic tools, novel therapeutics and vaccines.

Prior to his appointment at JCVI, Dr. Tan was a postdoctoral fellow at the Icahn School of Medicine at Mount Sinai working on characterizing the immunological and structural determinants of protection against influenza virus and Zika virus. He received his doctorate from Thomas Jefferson University and his undergraduate degree from the Philadelphia College of Pharmacy and Science.

Patents

Vaccines for use in the prophylaxis and treatment of influenza virus disease (Pat. No. US20170114103)

Research Priorities

Characterization of the structural and immunological determinants of protection against viral pathogens:

Elucidate the mechanisms by which antibodies neutralize virus and protect in vivo.
Emphasis on developing novel methods in isolating monoclonal antibodies from human peripheral blood mononuclear cell (PBMC) compartment.

Characterization of virus-host interaction by defining the molecular and transcriptional response

Emphasis on respiratory and neurotropic pathogens.

Publications

Nucleic acids research. 2024-08-12; 52.14: e63.

Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing

Espinoza JL, Phillips A, Prentice MB, Tan GS, Kamath PL, Lloyd KG, Dupont CL

PMID: 38909293

Nature immunology. 2023-10-01; 24.10: 1616-1627.

SARS-CoV-2 reservoir in post-acute sequelae of COVID-19 (PASC)

Proal AD, VanElzakker MB, Aleman S, Bach K, Boribong BP, Buggert M, Cherry S, Chertow DS, Davies HE, Dupont CL, Deeks SG, Eimer W, Ely EW, Fasano A, Freire M, Geng LN, Griffin DE, Henrich TJ, Iwasaki A, Izquierdo-Garcia D, Locci M, Mehandru S, Painter MM, Peluso MJ, Pretorius E, Price DA, Putrino D, Scheuermann RH, Tan GS, Tanzi RE, VanBrocklin HF, Yonker LM, Wherry EJ

PMID: 37667052

Nature immunology. 2023-10-01; 24.10: 1778.

Author Correction: SARS-CoV-2 reservoir in post-acute sequelae of COVID-19 (PASC)

PMID: 37723351

Gut pathogens. 2023-09-20; 15.1: 44.

Whole-genome characterization of common rotavirus strains circulating in Vellore, India from 2002 to 2017: emergence of non-classical genomic constellations

Khakha SA, Varghese T, Giri S, Durbin A, Tan GS, Kalaivanan M, Prasad JH, Kang G

PMID: 37730725

Heliyon. 2023-07-04; 9.7: e17958.

Persistent immune and clotting dysfunction detected in saliva and blood plasma after COVID-19

Jang H, Choudhury S, Yu Y, Sievers BL, Gelbart T, Singh H, Rawlings SA, Proal A, Tan GS, Qian Y, Smith D, Freire M

PMID: 37483779

Frontiers in genetics. 2023-05-09; 14.1172048.

Influenza A viruses in gulls in landfills and freshwater habitats in Minnesota, United States

Rasmussen EA, Czaja A, Cuthbert FJ, Tan GS, Lemey P, Nelson MI, Culhane MR

PMID: 37229191

Proceedings of the National Academy of Sciences of the United States of America. 2023-04-25; 120.17: e2208718120.

Epistasis reduces fitness costs of influenza A virus escape from stem-binding antibodies

Lee CY, Raghunathan V, Caceres CJ, Geiger G, Seibert B, Cargnin Faccin F, Gay LC, Ferreri LM, Kaul D, Wrammert J, Tan GS, Perez DR, Lowen AC

PMID: 37068231

Critical care (London, England). 2023-04-20; 27.1: 155.

Major adverse cardiovascular events are associated with necroptosis during severe COVID-19

Wiscovitch-Russo R, Ibáñez-Prada ED, Serrano-Mayorga CC, Sievers BL, Engelbride MA, Padmanabhan S, Tan GS, Vashee S, Bustos IG, Pachecho C, Mendez L, Dube PH, Singh H, Reyes LF, Gonzalez-Juarbe N

PMID: 37081485

Nucleic acids research. 2023-01-06; 51.D1: D678-D689.

Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR

Olson RD, Assaf R, Brettin T, Conrad N, Cucinell C, Davis JJ, Dempsey DM, Dickerman A, Dietrich EM, Kenyon RW, Kuscuoglu M, Lefkowitz EJ, Lu J, Machi D, Macken C, Mao C, Niewiadomska A, Nguyen M, Olsen GJ, Overbeek JC, Parrello B, Parrello V, Porter JS, Pusch GD, Shukla M, Singh I, Stewart L, Tan G, Thomas C, VanOeffelen M, Vonstein V, Wallace ZS, Warren AS, Wattam AR, Xia F, Yoo H, Zhang Y, Zmasek CM, Scheuermann RH, Stevens RL

PMID: 36350631

STAR protocols. 2022-12-16; 3.4: 101835.

A high-throughput SARS-CoV-2 pseudovirus multiplex neutralization assay

Sievers BL, Gelbart T, Tan GS

PMID: 36595901

eLife. 2022-10-14; 11.

Early immune markers of clinical, virological, and immunological outcomes in patients with COVID-19: a multi-omics study

Hu Z, van der Ploeg K, Chakraborty S, Arunachalam PS, Mori DAM, Jacobson KB, Bonilla H, Parsonnet J, Andrews JR, Holubar M, Subramanian A, Khosla C, Maldonado Y, Hedlin H, de la Parte L, Press K, Ty M, Tan GS, Blish C, Takahashi S, Rodriguez-Barraquer I, Greenhouse B, Butte AJ, Singh U, Pulendran B, Wang TT, Jagannathan P

PMID: 36239699

Cell reports. Medicine. 2022-06-21; 3.6: 100640.

TNF-α⁺ CD4⁺ T cells dominate the SARS-CoV-2 specific T cell response in COVID-19 outpatients and are associated with durable antibodies

van der Ploeg K, Kirosingh AS, Mori DAM, Chakraborty S, Hu Z, Sievers BL, Jacobson KB, Bonilla H, Parsonnet J, Andrews JR, Press KD, Ty MC, Ruiz-Betancourt DR, de la Parte L, Tan GS, Blish CA, Takahashi S, Rodriguez-Barraquer I, Greenhouse B, Singh U, Wang TT, Jagannathan P

PMID: 35588734

Molecular therapy : the journal of the American Society of Gene Therapy. 2022-05-04; 30.5: 2024-2047.

A single-shot adenoviral vaccine provides hemagglutinin stalk-mediated protection against heterosubtypic influenza challenge in mice

Bliss CM, Freyn AW, Caniels TG, Leyva-Grado VH, Nachbagauer R, Sun W, Tan GS, Gillespie VL, McMahon M, Krammer F, Hill AV, Hill AVS, Palese P, Coughlan L

PMID: 34999208

Science translational medicine. 2022-03-09; 14.635: eabm7853.

Early non-neutralizing, afucosylated antibody responses are associated with COVID-19 severity

Chakraborty S, Gonzalez JC, Sievers BL, Mallajosyula V, Chakraborty S, Dubey M, Ashraf U, Cheng BY, Kathale N, Tran KQT, Scallan C, Sinnott A, Cassidy A, Chen ST, Gelbart T, Gao F, Golan Y, Ji X, Kim-Schulze S, Prahl M, Gaw SL, Gnjatic S, Marron TU, Merad M, Arunachalam PS, Boyd SD, Davis MM, Holubar M, Khosla C, Maecker HT, Maldonado Y, Mellins ED, Nadeau KC, Pulendran B, Singh U, Subramanian A, Utz PJ, Sherwood R, Zhang S, Jagannathan P, Tan GS, Wang TT

PMID: 35040666

Science translational medicine. 2022-03-02; 14.634: eabn7842.

Antibodies elicited by SARS-CoV-2 infection or mRNA vaccines have reduced neutralizing activity against Beta and Omicron pseudoviruses

Sievers BL, Chakraborty S, Xue Y, Gelbart T, Gonzalez JC, Cassidy AG, Golan Y, Prahl M, Gaw SL, Arunachalam PS, Blish CA, Boyd SD, Davis MM, Jagannathan P, Nadeau KC, Pulendran B, Singh U, Scheuermann RH, Frieman MB, Vashee S, Wang TT, Tan GS

PMID: 35025672

Proceedings of the National Academy of Sciences of the United States of America. 2021-09-07; 118.36:

Influenza A viruses balance ER stress with host protein synthesis shutoff

Mazel-Sanchez B, Iwaszkiewicz J, Bonifacio JPP, Silva F, Niu C, Strohmeier S, Eletto D, Krammer F, Tan G, Zoete V, Hale BG, Schmolke M

PMID: 34479996

Viruses. 2021-07-08; 13.7:

Evaluation of ELISA-Based Multiplex Peptides for the Detection of Human Serum Antibodies Induced by Zika Virus Infection across Various Countries

Martinez Viedma MDP, Panossian S, Gifford K, García K, Figueroa I, Parham L, de Moraes L, Nunes Gomes L, García-Salum T, Perret C, Weiskopf D, Tan GS, Augusto Silva A, Boaventura V, Ruiz-Palacios GM, Sette A, De Silva AD, Medina RA, Lorenzana I, Akrami KM, Khouri R, Olson D, Pickett BE

PMID: 34372525

Advanced drug delivery reviews. 2021-05-01; 172.314-338.

SARS-CoV-2 vaccines in advanced clinical trials: Where do we stand?

Chakraborty S, Mallajosyula V, Tato CM, Tan GS, Wang TT

PMID: 33482248

Viruses. 2021-01-28; 13.2:

Influenza A Viruses in Whistling Ducks (Subfamily Dendrocygninae)

Carter DL, Link P, Tan G, Stallknecht DE, Poulson RL

PMID: 33525360

Nature immunology. 2021-01-01; 22.1: 67-73.

Proinflammatory IgG Fc structures in patients with severe COVID-19

Chakraborty S, Gonzalez J, Edwards K, Mallajosyula V, Buzzanco AS, Sherwood R, Buffone C, Kathale N, Providenza S, Xie MM, Andrews JR, Blish CA, Singh U, Dugan H, Wilson PC, Pham TD, Boyd SD, Nadeau KC, Pinsky BA, Zhang S, Memoli MJ, Taubenberger JK, Morales T, Schapiro JM, Tan GS, Jagannathan P, Wang TT

PMID: 33169014

Nature microbiology. 2020-09-01; 5.9: 1158-1169.

Collective interactions augment influenza A virus replication in a host-dependent manner

Phipps KL, Ganti K, Jacobs NT, Lee CY, Carnaccini S, White MC, Manandhar M, Pickett BE, Tan GS, Ferreri LM, Perez DR, Lowen AC

PMID: 32632248

Nature communications. 2020-06-16; 11.1: 3132.

Author Correction: Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection

Kaul D, Rathnasinghe R, Ferres M, Tan GS, Barrera A, Pickett BE, Methe BA, Das SR, Budnik I, Halpin RA, Wentworth D, Schmolke M, Mena I, Albrecht RA, Singh I, Nelson KE, García-Sastre A, Dupont CL, Medina RA

PMID: 32546784

Nature communications. 2020-05-21; 11.1: 2537.

Microbiome disturbance and resilience dynamics of the upper respiratory tract during influenza A virus infection

Kaul D, Rathnasinghe R, Ferres M, Tan GS, Barrera A, Pickett BE, Methe BA, Das SR, Das S, Budnik I, Halpin RA, Wentworth D, Schmolke M, Mena I, Albrecht RA, Singh I, Nelson KE, García-Sastre A, Dupont CL, Medina RA

PMID: 32439901

mBio. 2020-03-24; 11.2:

Neutralizing Monoclonal Antibodies against the Gn and the Gc of the Andes Virus Glycoprotein Spike Complex Protect from Virus Challenge in a Preclinical Hamster Model

Duehr J, McMahon M, Williamson B, Amanat F, Durbin A, Hawman DW, Noack D, Uhl S, Tan GS, Feldmann H, Krammer F

PMID: 32209676

Journal of virology. 2019-10-15; 93.20:

Innate Immune Response to Influenza Virus at Single-Cell Resolution in Human Epithelial Cells Revealed Paracrine Induction of Interferon Lambda 1

Ramos I, Smith G, Ruf-Zamojski F, Martínez-Romero C, Fribourg M, Carbajal EA, Hartmann BM, Nair VD, Marjanovic N, Monteagudo PL, DeJesus VA, Mutetwa T, Zamojski M, Tan GS, Jayaprakash C, Zaslavsky E, Albrecht RA, Sealfon SC, García-Sastre A, Fernandez-Sesma A

PMID: 31375585

Nature communications. 2018-10-11; 9.1: 4223.

Non-neutralizing antibodies elicited by recombinant Lassa-Rabies vaccine are critical for protection against Lassa fever

Abreu-Mota T, Hagen KR, Cooper K, Jahrling PB, Tan G, Wirblich C, Johnson RF, Schnell MJ

PMID: 30310067

Journal of visualized experiments : JoVE. 2018-02-23; 132:

A Method to Assess Fc-mediated Effector Functions Induced by Influenza Hemagglutinin Specific Antibodies

Bailey MJ, Broecker F, Leon PE, Tan GS

PMID: 29553549

Nature communications. 2017-10-10; 8.1: 846.

Alveolar macrophages are critical for broadly-reactive antibody-mediated protection against influenza A virus in mice

He W, Chen CJ, Mullarkey CE, Hamilton JR, Wong CK, Leon PE, Uccellini MB, Chromikova V, Henry C, Hoffman KW, Lim JK, Wilson PC, Miller MS, Krammer F, Palese P, Tan GS

PMID: 29018261

Proceedings of the National Academy of Sciences of the United States of America. 2016-10-18; 113.42: 11931-11936.

Epitope specificity plays a critical role in regulating antibody-dependent cell-mediated cytotoxicity against influenza A virus

He W, Tan GS, Mullarkey CE, Lee AJ, Lam MM, Krammer F, Henry C, Wilson PC, Ashkar AA, Palese P, Miller MS

PMID: 27698132

Proceedings of the National Academy of Sciences of the United States of America. 2016-10-04; 113.40: E5944-E5951.

Optimal activation of Fc-mediated effector functions by influenza virus hemagglutinin antibodies requires two points of contact

Leon PE, He W, Mullarkey CE, Bailey MJ, Miller MS, Krammer F, Palese P, Tan GS

PMID: 27647907

Cell host & microbe. 2016-06-08; 19.6: 800-13.

Both Neutralizing and Non-Neutralizing Human H7N9 Influenza Vaccine-Induced Monoclonal Antibodies Confer Protection

Henry Dunand CJ, Leon PE, Huang M, Choi A, Chromikova V, Ho IY, Tan GS, Cruz J, Hirsh A, Zheng NY, Mullarkey CE, Ennis FA, Terajima M, Treanor JJ, Topham DJ, Subbarao K, Palese P, Krammer F, Wilson PC

PMID: 27281570

PLoS pathogens. 2016-04-01; 12.4: e1005578.

Broadly-Reactive Neutralizing and Non-neutralizing Antibodies Directed against the H7 Influenza Virus Hemagglutinin Reveal Divergent Mechanisms of Protection

Tan GS, Leon PE, Albrecht RA, Margine I, Hirsh A, Bahl J, Krammer F

PMID: 27081859

Journal of virology. 2016-01-13; 90.7: 3789-93.

Influenza A Viruses Expressing Intra- or Intergroup Chimeric Hemagglutinins

Chen CJ, Ermler ME, Tan GS, Krammer F, Palese P, Hai R

PMID: 26764009

Antimicrobial agents and chemotherapy. 2015-07-01; 59.7: 4162-72.

Direct administration in the respiratory tract improves efficacy of broadly neutralizing anti-influenza virus monoclonal antibodies

Leyva-Grado VH, Tan GS, Leon PE, Yondola M, Palese P

PMID: 25941218

The Journal of clinical investigation. 2015-03-02; 125.3: 1255-68.

Preexisting human antibodies neutralize recently emerged H7N9 influenza strains

Henry Dunand CJ, Leon PE, Kaur K, Tan GS, Zheng NY, Andrews S, Huang M, Qu X, Huang Y, Salgado-Ferrer M, Ho IY, Taylor W, Hai R, Wrammert J, Ahmed R, García-Sastre A, Palese P, Krammer F, Wilson PC

PMID: 25689254

Journal of virology. 2014-12-01; 88.23: 13580-92.

Characterization of a broadly neutralizing monoclonal antibody that targets the fusion domain of group 2 influenza A virus hemagglutinin

Tan GS, Lee PS, Hoffman RM, Mazel-Sanchez B, Krammer F, Leon PE, Ward AB, Wilson IA, Palese P

PMID: 25210195

Nature medicine. 2014-02-01; 20.2: 143-51.

Broadly neutralizing hemagglutinin stalk-specific antibodies require FcγR interactions for protection against influenza virus in vivo

DiLillo DJ, Tan GS, Palese P, Ravetch JV

PMID: 24412922

Journal of virology. 2012-06-01; 86.11: 6179-88.

A pan-H1 anti-hemagglutinin monoclonal antibody with potent broad-spectrum efficacy in vivo

Tan GS, Krammer F, Eggink D, Kongchanagul A, Moran TM, Palese P

PMID: 22491456

Proceedings of the National Academy of Sciences of the United States of America. 2007-04-24; 104.17: 7229-34.

22-Feb-2024

Collaborator Release

New LongCOVID research launched by PolyBio’s global consortium of scientists

Funding will deepen research on the persistence of the SARS-CoV-2 virus in LongCOVID patients and launch new clinical trials

30-Jan-2024

Press Release

J. Craig Venter Institute contracted by the Centers for Disease Control and Prevention to rapidly construct synthetic influenza genes

Genes will be used to help develop seasonal and pandemic vaccines, improving response time and vaccine efficacy

04-Sep-2023