Viral epitope profiling of COVID-19 patients reveals cross-reactivity and correlates of severity
Open accessAbstract
Profiling coronaviruses: Among the coronaviruses that infect humans, four cause mild common colds, whereas three others, including the currently circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), result in severe infections. Shrock et al. used a technology known as VirScan to probe the antibody repertoires of hundreds of coronavirus disease 2019 (COVID-19) patients and pre–COVID-19 era controls. They identified hundreds of antibody targets, including several antibody epitopes shared by the mild and severe coronaviruses and many specific to SARS-CoV-2. A machine-learning model accurately classified patients infected with SARS-CoV-2 and guided the design of an assay for rapid SARS-CoV-2 antibody detection. The study also looked at how the antibody response and viral exposure history differ in patients with diverging outcomes, which could inform the production of improved vaccine and antibody therapies. Science , this issue p. eabd4250
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COVID-19 severity has been linked to the incidence of CMV.
“COVID-19 severity has been linked to the incidence of CMV, a primary pathogen associated with memory inflation, but more work is needed to establish how CMV and other latent viruses of the elderly affect new memory T cell formation, function, and longevity146.”
From SARS-CoV-2, COVID-19 and the aging immune system (2021) · cites this paper as [146]
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- Authors
- Shrock, E., Fujimura, E., Kula, T., Timms, R. T., Lee, I.-H., Leng, Y., Robinson, M. L., Sie, B. M., Li, M. Z., Chen, Y., Logue, J., Zuiani, A., McCulloch, D., Lelis, F. J. N., Henson, S., Monaco, D. R., Travers, M., Habibi, S., Clarke, W. A., Caturegli, P., Laeyendecker, O., Piechocka-Trocha, A., Li, J. Z., Khatri, A., Chu, H. Y., MGH COVID-19 Collection & Processing Team, Villani, A.-C., Kays, K., Goldberg, M. B., Hacohen, N., Filbin, M. R., Yu, X. G., Walker, B. D., Wesemann, D. R., Larman, H. B., Lederer, J. A., Elledge, S. J., Lavin-Parsons, K., Parry, B., Lilley, B., Lodenstein, C., McKaig, B., Charland, N., Khanna, H., Margolin, J., Gonye, A., Gushterova, I., Lasalle, T., Sharma, N., Russo, B. C., Rojas-Lopez, M., Sade-Feldman, M., Manakongtreecheep, K., Tantivit, J., Thomas, M. F., Abayneh, B. A., Allen, P., Antille, D., Armstrong, K., Boyce, S., Braley, J., Branch, K., Broderick, K., Carney, J., Chan, A., Davidson, S., Dougan, M., Drew, D., Elliman, A., Flaherty, K., Flannery, J., Forde, P., Gettings, E., Griffin, A., Grimmel, S., Grinke, K., Hall, K., Healy, M., Henault, D., Holland, G., Kayitesi, C., LaValle, V., Lu, Y., Luthern, S., Marchewka (Schneider), J., Martino, B., McNamara, R., Nambu, C., Nelson, S., Noone, M., Ommerborn, C., Pacheco, L. C., Phan, N., Porto, F. A., Ryan, E., Selleck, K., Slaughenhaupt, S., Sheppard, K. S., Suschana, E., Wilson, V., Alter, G., Balazs, A., Bals, J., Barbash, M., Bartsch, Y., Boucau, J., Chevalier, J., Chowdhury, F., Einkauf, K., Fallon, J., Fedirko, L., Finn, K., Garcia-Broncano, P., Hartana, C., Jiang, C., Kaplonek, P., Karpell, M., Lam, E. C., Lefteri, K., Lian, X., Lichterfeld, M., Lingwood, D., Liu, H., Liu, J., Ly, N., Michell, A., Millstrom, I., Miranda, N., O’Callaghan, C., Osborn, M., Pillai, S., Rassadkina, Y., Reissis, A., Ruzicka, F., Seiger, K., Sessa, L., Sharr, C., Shin, S., Singh, N., Sun, W., Sun, X., Ticheli, H., Trocha-Piechocka, A., Worrall, D., Zhu, A., Daley, G., Golan, D., Heller, H., Sharpe, A., Jilg, N., Rosenthal, A., & Wong, C.
- Affiliations
- Brigham and Women's Hospital (US)
- Harvard University (US)
- Johns Hopkins University (US)
- University of Washington (US)
- National Institutes of Health (US)
- Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA.
- Massachusetts General Hospital (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Shrock, Ellen
- Fujimura, Eric
- Kula, Tomasz
- Timms, Richard T.
- Elledge, Stephen J.
- ORCID
- Shrock, Ellen
- Fujimura, Eric
- Kula, Tomasz
- Timms, Richard T.
- Lee, I-Hsiu
- Leng, Yumei
- Robinson, Matthew L.
- Sie, Brandon M.
- Li, Mamie Z.
- Chen, Yuezhou
- Logue, Jennifer
- Zuiani, Adam
- McCulloch, Denise
- Lelis, Felipe J. N.
- Henson, Stephanie
- Travers, Meghan
- Habibi, Shaghayegh
- Clarke, William A.
- Caturegli, Patrizio
- Laeyendecker, Oliver
- Piechocka-Trocha, Alicja
- Li, Jonathan Z.
- Khatri, Ashok
- Chu, Helen Y.
- Villani, Alexandra-Chloé
- Goldberg, Marcia B.
- Hacohen, Nir
- Filbin, Michael R.
- Yu, Xu G.
- Walker, Bruce D.
- Wesemann, Duane R.
- Larman, H. Benjamin
- Elledge, Stephen J.
- Parry, Blair
- Lilley, Brendan
- McKaig, Brenna
- Charland, Nicole
- Khanna, Hargun
- Margolin, Justin
- Gonye, Anna
- Gushterova, Irena
- Russo, Brian C.
- Sade-Feldman, Moshe
- Manakongtreecheep, Kasidet
- Tantivit, Jessica
- Thomas, Molly Fisher
- Dougan, Michael
- Flaherty, Keith
- Hall, Kathryn
- Healy, Meg
- Lu, Yuting
- Martino, Brittani
- Phan, Nicole
- Ryan, Edward
- Suschana, Elizabeth
- Alter, Galit
- Balazs, Alejandro
- Bals, Julia
- Bartsch, Yannic
- Boucau, Julie
- Chowdhury, Fatema
- Einkauf, Kevin
- Hartana, Ciputra
- Jiang, Chenyang
- Lam, Evan C.
- Lian, Xiaodong
- Lichterfeld, Mathias
- Lingwood, Daniel
- Liu, Hang
- Michell, Ashlin
- Osborn, Matthew
- Pillai, Shiv
- Rassadkina, Yelizaveta
- Seiger, Kyra
- Sessa, Libera
- Shin, Sally
- Singh, Nishant
- Sun, Weiwei
- Sun, Xiaoming
- Worrall, Daniel
- Zhu, Alex
- Daley, George
- Heller, Howard
- Sharpe, Arlene
- Jilg, Nikolaus
- Venue
- Science
- Published
- 2020-11-27
- Volume
- 370
- Issue
- 6520
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC7857405
- OpenAlex
- W3091214020
- Cited by
- 678
- References
- 38
- Citations by year
- 2026: 31 · 2025: 44 · 2024: 67 · 2023: 105 · 2022: 156 · 2021: 236 · 2020: 39
- FWCI
- 17.56
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Science (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (AI139538)
- National Cancer Institute (U24)
- MassCPR (No Number)
- U.S. Department of Defense (W81XWH-16-1-0464)
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 detection and testing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Keywords
- SARS-CoV-2, COVID-19 pandemic, humoral immune response, cross-reactive antibodies, neutralizing antibodies, spike protein, nucleocapsid protein, ORF1, pre-existing antibodies, disease severity, cytomegalovirus, herpes simplex virus type 1, sex differences in antibody response, hospitalized patients
- MeSH terms
- Seroconversion, COVID-19, SARS-CoV-2, COVID-19 Serological Testing, Antibody Formation, Epitopes, Cross Reactions, Female, Humans, Male, Protein Conformation, Severity of Illness Index, Epitope Mapping, Cryoelectron Microscopy, Antibodies, Neutralizing
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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