Coronavirus Research
Overview
The J. Craig Venter Institute (JCVI) has been involved in viral sequencing and analysis for more than 25 years, and coronavirus research for more than 15. This work has aided human health through vaccine development; improved food security by protecting crops and livestock; and provides critical data and analysis to researchers around the world. The Institute has also pioneered a synthetic biology platform which is now integral to fighting current and emerging viral threats.
Following is a summary of our various research projects on the novel coronavirus, SARS-CoV-2.
SARS-CoV-2 Research
COVID-19 Serology Testing
Informatics
JCVI is developing critical resources for the evaluation of antibody reactivity for serology testing. From an informatics perspective, the use of comparative genomics methods and predictive machine learning algorithms are being used to identify the key determinants for immune system recognition and to monitor the impact of virus evolution in immune system evasion. The bioinformatics analyses will aid in developing critical resources for the evaluation of antibody reactivity for serology testing.
Lab
In the laboratory, viral surface proteins are being generated for use as ELISA antigens, pseudotyped recombinant viruses are being constructed for neutralizing assays, and candidate vaccine constructs are being synthetized to define the immunogenicity of the viral proteins and to understand the basis of immune response and protection against SARS-CoV-2.
Funding
Funding for this research is provided through a variety of government and private sources.
We need your support now to continue and to expand upon these critical projects. If you would like to learn more about supporting any of this exciting research, please contact Jill Mullen at jmullen@jcvi.org.
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Your support directly funds novel coronavirus research. This is monumental effort, requiring a wide range of scientific solutions. We need your support.
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Related Research
Publications
Nature communications. 2023-05-25; 14.1: 3026.
A neonatal mouse model characterizes transmissibility of SARS-CoV-2 variants and reveals a role for ORF8
Rodriguez-Rodriguez BA, Ciabattoni GO, Duerr R, Valero-Jimenez AM, Yeung ST, Crosse KM, Schinlever AR, Bernard-Raichon L, Rodriguez Galvan J, McGrath ME, Vashee S, Xue Y, Loomis CA, Khanna KM, Cadwell K, Desvignes L, Frieman MB, Ortigoza MB, Dittmann M
PMID: 37230979
Emerging infectious diseases. 2023-05-01; 29.5:
US National Institutes of Health Prioritization of SARS-CoV-2 Variants
Turner S, Alisoltani A, Bratt D, Cohen-Lavi L, Dearlove BL, Drosten C, Fischer WM, Fouchier RAM, Gonzalez-Reiche AS, Jaroszewski L, Khalil Z, LeGresley E, Johnson M, Jones TC, Mühlemann B, O'Connor D, Sedova M, Shukla M, Theiler J, Wallace ZS, Yoon H, Zhang Y, van Bakel H, DeGrace MM, Ghedin E, Godzik A, Hertz T, Korber B, Lemieux J, Niewiadomska AM, Post DJ, Rolland M, Scheuermann R, Smith DJ
PMID: 37054986
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
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
Frontiers in bioinformatics. 2022-10-24; 2.1020189.
Early detection of emerging SARS-CoV-2 variants of interest for experimental evaluation
Wallace ZS, Davis J, Niewiadomska AM, Olson RD, Shukla M, Stevens R, Zhang Y, Zmasek CM, Scheuermann RH
PMID: 36353215
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
Scientific reports. 2022-10-06; 12.1: 16731.
A novel vaccine based on SARS-CoV-2 CD4+ and CD8+ T cell conserved epitopes from variants Alpha to Omicron
Palatnik-de-Sousa I, Wallace ZS, Cavalcante SC, Ribeiro MPF, Silva JABM, Cavalcante RC, Scheuermann RH, Palatnik-de-Sousa CB
PMID: 36202985
Proceedings of the National Academy of Sciences of the United States of America. 2022-09-13; 119.37: e2204717119.
SARS-CoV-2 variant spike and accessory gene mutations alter pathogenesis
McGrath ME, Xue Y, Dillen C, Oldfield L, Assad-Garcia N, Zaveri J, Singh N, Baracco L, Taylor LJ, Vashee S, Frieman MB
PMID: 36040867
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
Nature. 2022-05-01; 605.7911: 640-652.
Defining the risk of SARS-CoV-2 variants on immune protection
DeGrace MM, Ghedin E, Frieman MB, Krammer F, Grifoni A, Alisoltani A, Alter G, Amara RR, Baric RS, Barouch DH, Bloom JD, Bloyet LM, Bonenfant G, Boon ACM, Boritz EA, Bratt DL, Bricker TL, Brown L, Buchser WJ, Carreño JM, Cohen-Lavi L, Darling TL, Davis-Gardner ME, Dearlove BL, Di H, Dittmann M, Doria-Rose NA, Douek DC, Drosten C, Edara VV, Ellebedy A, Fabrizio TP, Ferrari G, Florence WC, Fischer WM, Fouchier RAM, Franks J, García-Sastre A, Godzik A, Gonzalez-Reiche AS, Gordon A, Haagmans BL, Halfmann PJ, Ho DD, Holbrook MR, Huang Y, James SL, Jaroszewski L, Jeevan T, Johnson RM, Jones TC, Joshi A, Kawaoka Y, Kercher L, Koopmans MPG, Korber B, Koren E, Koup RA, LeGresley EB, Lemieux JE, Liebeskind MJ, Liu Z, Livingston B, Logue JP, Luo Y, McDermott AB, McElrath MJ, Meliopoulos VA, Menachery VD, Montefiori DC, Mühlemann B, Munster VJ, Munt JE, Nair MS, Netzl A, Niewiadomska AM, O'Dell S, Pekosz A, Perlman S, Pontelli MC, Rockx B, Rolland M, Rothlauf PW, Sacharen S, Scheuermann RH, Schmidt SD, Schotsaert M, Schultz-Cherry S, Seder RA, Sedova M, Sette A, Shabman RS, Shen X, Shi PY, Shukla M, Simon V, Stumpf S, Sullivan NJ, Thackray LB, Theiler J, Thomas PG, Trifkovic S, Türeli S, Turner SA, Vakaki MA, van Bakel H, VanBlargan LA, Vincent LR, Wallace ZS, Wang L, Wang M, Wang P, Wang W, Weaver SC, Webby RJ, Weiss CD, Wentworth DE, Weston SM, Whelan SPJ, Whitener BM, Wilks SH, Xie X, Ying B, Yoon H, Zhou B, Hertz T, Smith DJ, Diamond MS, Post DJ, Suthar MS
PMID: 35361968
mSystems. 2022-04-26; 7.2: e0146621.
High-Content Screening and Computational Prediction Reveal Viral Genes That Suppress the Innate Immune Response
Ng TL, Olson EJ, Yoo TY, Weiss HS, Koide Y, Koch PD, Rollins NJ, Mach P, Meisinger T, Bricken T, Chang TZ, Molloy C, Zürcher J, Chang RL, Mitchison TJ, Glass JI, Marks DS, Way JC, Silver PA
PMID: 35319251
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
Journal of leukocyte biology. 2021-12-01; 110.6: 1225-1239.
Corticosteroid treatment in COVID-19 modulates host inflammatory responses and transcriptional signatures of immune dysregulation
Pinski AN, Steffen TL, Zulu MZ, George SL, Dickson A, Tifrea D, Maroney KJ, Tedeschi N, Zhang Y, Scheuermann RH, Pinto AK, Brien JD, Messaoudi I
PMID: 34730254
Journal of virology. 2021-09-27; 95.20: e0101021.
Kinetic Multi-omic Analysis of Responses to SARS-CoV-2 Infection in a Model of Severe COVID-19
Cantwell AM, Singh H, Platt M, Yu Y, Lin YH, Ikeno Y, Hubbard G, Xiang Y, Gonzalez-Juarbe N, Dube PH
PMID: 34319784
Cell reports. Medicine. 2021-07-20; 2.7: 100355.
Impact of SARS-CoV-2 variants on the total CD4+ and CD8+ T cell reactivity in infected or vaccinated individuals
Tarke A, Sidney J, Methot N, Yu ED, Zhang Y, Dan JM, Goodwin B, Rubiro P, Sutherland A, Wang E, Frazier A, Ramirez SI, Rawlings SA, Smith DM, da Silva Antunes R, Peters B, Scheuermann RH, Weiskopf D, Crotty S, Grifoni A, Sette A
PMID: 34230917
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
Nature medicine. 2021-05-01; 27.5: 892-903.
SARS-CoV-2 infection of the oral cavity and saliva
Huang N, Pérez P, Kato T, Mikami Y, Okuda K, Gilmore RC, Conde CD, Gasmi B, Stein S, Beach M, Pelayo E, Maldonado JO, Lafont BA, Jang SI, Nasir N, Padilla RJ, Murrah VA, Maile R, Lovell W, Wallet SM, Bowman NM, Meinig SL, Wolfgang MC, Choudhury SN, Novotny M, Aevermann BD, Scheuermann RH, Cannon G, Anderson CW, Lee RE, Marchesan JT, Bush M, Freire M, Kimple AJ, Herr DL, Rabin J, Grazioli A, Das S, French BN, Pranzatelli T, Chiorini JA, Kleiner DE, Pittaluga S, Hewitt SM, Burbelo PD, Chertow D, NIH COVID-19 Autopsy Consortium, HCA Oral and Craniofacial Biological Network, Frank K, Lee J, Boucher RC, Teichmann SA, Warner BM, Byrd KM
PMID: 33767405
Viruses. 2021-04-01; 13.4:
Rescue of Infectious Sindbis Virus by Yeast Spheroplast-Mammalian Cell Fusion
Ding L, Brown DM, Glass JI
PMID: 33916100
bioRxiv : the preprint server for biology. 2021-03-01;
Negligible impact of SARS-CoV-2 variants on CD4 + and CD8 + T cell reactivity in COVID-19 exposed donors and vaccinees
Tarke A, Sidney J, Methot N, Zhang Y, Dan JM, Goodwin B, Rubiro P, Sutherland A, da Silva Antunes R, Frazier A, Rawlings SA, Smith DM, Peters B, Scheuermann RH, Weiskopf D, Crotty S, Grifoni A, Sette A
PMID: 33688655
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
Scientific data. 2020-06-19; 7.1: 188.
COVID-19 pandemic reveals the peril of ignoring metadata standards
Schriml LM, Chuvochina M, Davies N, Eloe-Fadrosh EA, Finn RD, Hugenholtz P, Hunter CI, Hurwitz BL, Kyrpides NC, Meyer F, Mizrachi IK, Sansone SA, Sutton G, Tighe S, Walls R
PMID: 32561801
Proceedings of the National Academy of Sciences of the United States of America. 2020-06-09; 117.23: 12522-12523.
Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable
Mavian C, Pond SK, Marini S, Magalis BR, Vandamme AM, Dellicour S, Scarpino SV, Houldcroft C, Villabona-Arenas J, Paisie TK, Trovão NS, Boucher C, Zhang Y, Scheuermann RH, Gascuel O, Lam TT, Suchard MA, Abecasis A, Wilkinson E, de Oliveira T, Bento AI, Schmidt HA, Martin D, Hadfield J, Faria N, Grubaugh ND, Neher RA, Baele G, Lemey P, Stadler T, Albert J, Crandall KA, Leitner T, Stamatakis A, Prosperi M, Salemi M
PMID: 32381734
Cell host & microbe. 2020-04-08; 27.4: 671-680.e2.
A Sequence Homology and Bioinformatic Approach Can Predict Candidate Targets for Immune Responses to SARS-CoV-2
Grifoni A, Sidney J, Zhang Y, Scheuermann RH, Peters B, Sette A
PMID: 32183941
Scientific data. 2014-10-14; 1.140033.
A comprehensive collection of systems biology data characterizing the host response to viral infection
Aevermann BD, Pickett BE, Kumar S, Klem EB, Agnihothram S, Askovich PS, Bankhead A, Bolles M, Carter V, Chang J, Clauss TR, Dash P, Diercks AH, Eisfeld AJ, Ellis A, Fan S, Ferris MT, Gralinski LE, Green RR, Gritsenko MA, Hatta M, Heegel RA, Jacobs JM, Jeng S, Josset L, Kaiser SM, Kelly S, Law GL, Li C, Li J, Long C, Luna ML, Matzke M, McDermott J, Menachery V, Metz TO, Mitchell H, Monroe ME, Navarro G, Neumann G, Podyminogin RL, Purvine SO, Rosenberger CM, Sanders CJ, Schepmoes AA, Shukla AK, Sims A, Sova P, Tam VC, Tchitchek N, Thomas PG, Tilton SC, Totura A, Wang J, Webb-Robertson BJ, Wen J, Weiss JM, Yang F, Yount B, Zhang Q, McWeeney S, Smith RD, Waters KM, Kawaoka Y, Baric R, Aderem A, Katze MG, Scheuermann RH
PMID: 25977790
The Journal of general virology. 2014-04-01; 95.Pt 4: 836-848.
Isolation, propagation, genome analysis and epidemiology of HKU1 betacoronaviruses
Dominguez SR, Shrivastava S, Berglund A, Qian Z, Góes LGB, Góes LG, Halpin RA, Fedorova N, Ransier A, Weston PA, Durigon EL, Jerez JA, Robinson CC, Town CD, Holmes KV
PMID: 24394697
Viruses. 2012-11-19; 4.11: 3209-26.
Virus pathogen database and analysis resource (ViPR): a comprehensive bioinformatics database and analysis resource for the coronavirus research community
Pickett BE, Greer DS, Zhang Y, Stewart L, Zhou L, Sun G, Gu Z, Kumar S, Zaremba S, Larsen CN, Jen W, Klem EB, Scheuermann RH
PMID: 23202522
The Journal of general virology. 2012-11-01; 93.Pt 11: 2387-2398.
Genomic analysis of 16 Colorado human NL63 coronaviruses identifies a new genotype, high sequence diversity in the N-terminal domain of the spike gene and evidence of recombination
Dominguez SR, Sims GE, Wentworth DE, Halpin RA, Robinson CC, Town CD, Holmes KV
PMID: 22837419
Virology. 2012-09-01; 430.2: 90-9.
Characterization of a recombinant canine coronavirus with a distinct receptor-binding (S1) domain
Regan AD, Millet JK, Tse LP, Chillag Z, Rinaldi VD, Licitra BN, Dubovi EJ, Town CD, Whittaker GR
PMID: 22609354
Nucleic acids research. 2012-07-01; 40.Web Server issue: W186-92.
VIGOR extended to annotate genomes for additional 12 different viruses
Wang S, Sundaram JP, Stockwell TB
PMID: 22669909
Emerging infectious diseases. 2012-07-01; 18.7: 1089-95.
Spike protein fusion peptide and feline coronavirus virulence
Chang HW, Egberink HF, Halpin R, Spiro DJ, Rottier PJ
PMID: 22709821
The Journal of general virology. 2011-06-01; 92.Pt 6: 1369-79.
Molecular characterization of a new species in the genus Alphacoronavirus associated with mink epizootic catarrhal gastroenteritis
Vlasova AN, Halpin R, Wang S, Ghedin E, Spiro DJ, Saif LJ
PMID: 21346029
PLoS pathogens. 2010-05-06; 6.5: e1000896.
Infidelity of SARS-CoV Nsp14-exonuclease mutant virus replication is revealed by complete genome sequencing
Eckerle LD, Becker MM, Halpin RA, Li K, Venter E, Lu X, Scherbakova S, Graham RL, Baric RS, Stockwell TB, Spiro DJ, Denison MR
PMID: 20463816
Journal of virology. 2008-12-01; 82.24: 12422-31.
Bovine-like coronaviruses isolated from four species of captive wild ruminants are homologous to bovine coronaviruses, based on complete genomic sequences
Alekseev KP, Vlasova AN, Jung K, Hasoksuz M, Zhang X, Halpin R, Wang S, Ghedin E, Spiro D, Saif LJ
PMID: 18842722
Virology. 2007-06-20; 363.1: 1-10.
Quasispecies of bovine enteric and respiratory coronaviruses based on complete genome sequences and genetic changes after tissue culture adaptation
Zhang X, Hasoksuz M, Spiro D, Halpin R, Wang S, Vlasova A, Janies D, Jones LR, Ghedin E, Saif LJ
PMID: 17434558
Virology. 2007-02-20; 358.2: 424-35.
Complete genomic sequences, a key residue in the spike protein and deletions in nonstructural protein 3b of US strains of the virulent and attenuated coronaviruses, transmissible gastroenteritis virus and porcine respiratory coronavirus
Zhang X, Hasoksuz M, Spiro D, Halpin R, Wang S, Stollar S, Janies D, Hadya N, Tang Y, Ghedin E, Saif L
PMID: 17023013
01-Jun-2023
Collaborator Release
Family resemblance: How T cells could fight many coronaviruses at once
LJI researchers work to head off future pandemics by uncovering key similarities between SARS-CoV-2 and common cold coronaviruses
29-Mar-2023
Collaborator Release
Scientists aim to develop vaccine against all deadly coronaviruses
$8 million NIH grant supports effort to avert next pandemic
08-Sep-2022
Reuters
Top scientists join forces to study leading theory behind long COVID
Several JCVI scientists will be contributing to the newly launched Long Covid Research Initiative — a collaboration of researchers, clinicians, and patients working to rapidly study and treat long Covid.
13-Jan-2022
Press Release
Omicron and Beta variants evade antibodies elicited by vaccines and previous infections, but boosters help
Pregnancy also contributes to a reduced COVID-19 antibody response
03-Mar-2021
Blog
SARS-CoV-2 Mutation Tracking
27-Jan-2021
Press Release
Influenza A Virus Discovered in Heart Muscle Tissue Causing Damage Long After It Has Cleared from the Lungs
Strategies to inhibit necrotic cell death or to prevent mitochondrial damage should be pursued as possible therapies to reduce cardiac damage during influenza infections
24-Dec-2020
The San Diego Union Tribune
Scientists rush to determine if mutant strain of coronavirus will deepen pandemic
U.S. researchers have been slow to perform the genetic sequencing that will help clarify the situation
23-Nov-2020
Blog
Unique Antibody Pattern Discovered in COVID-19 ICU Patients May Be Key to Predicting Severe Outcomes
29-Oct-2020
Blog
COVID-19 Further Complicating Flu Season
27-Oct-2020
Collaborator Release
Study reveals mouth as primary source of COVID-19 infection, spread
UNC-Chapel Hill, NIH identify sites in the oral cavity where coronavirus can take hold
25-Mar-2020
Blog
Online Education Resources to Help With Your New “Normal”
17-Mar-2020
Blog
Coronavirus Pandemic: Putting Comprehensive Genomic Data in the Hands of Frontline Researchers Worldwide is Paramount
12-Mar-2020
Collaborator Release