High-Throughput Neutralization and Serology Assays Reveal Correlated but Highly Variable Humoral Immune Responses in a Large Population of Individuals Infected with SARS-CoV-2 in the US between March and August 2020
Shuting Zhang,
Peijun Ma,
Marek Orzechowski,
Allison Lemmer,
Kara Rzasa,
Josephine Bagnall,
Sulyman Barkho,
Michael Chen,
Lorri He,
Raymond Neitupski,
Victoria Tran,
Ross Ackerman,
Emily Gath,
Austin Bond,
Giana Frongillo,
Thomas Cleland,
Aaron Golas,
Anthony Gaca,
Michael Fitzgerald,
Kathleen Kelly,
Kelsey Hazegh,
Larry Dumont,
Corey Hoffman,
Mary Homer,
Peter Marks,
Ann Woolley,
Sharon Wong,
James Gomez,
Jonathan Livny,
Deborah Hung
Affiliations
Shuting Zhang
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Peijun Ma
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Marek Orzechowski
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Allison Lemmer
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Kara Rzasa
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Josephine Bagnall
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Sulyman Barkho
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Michael Chen
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Lorri He
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Raymond Neitupski
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Victoria Tran
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Ross Ackerman
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Emily Gath
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Austin Bond
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Giana Frongillo
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Thomas Cleland
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Aaron Golas
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Anthony Gaca
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Michael Fitzgerald
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Kathleen Kelly
Vitalant Research Institute, Denver, Colorado, USA
Kelsey Hazegh
Vitalant Research Institute, Denver, Colorado, USA
Larry Dumont
Vitalant Research Institute, Denver, Colorado, USA
Corey Hoffman
Biomedical Advanced Research and Development Authority, Administration for Strategic Preparedness and Response, Department of Health and Human Services, Washington, DC, USA
Mary Homer
Biomedical Advanced Research and Development Authority, Administration for Strategic Preparedness and Response, Department of Health and Human Services, Washington, DC, USA
Peter Marks
Center for Biologics Evaluation and Research, US FDA, Silver Spring, Maryland, USA
Ann Woolley
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Sharon Wong
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
James Gomez
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Jonathan Livny
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Deborah Hung
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
ABSTRACT The ability to measure neutralizing antibodies on large scale can be important for understanding features of the natural history and epidemiology of infection, as well as an aid in determining the efficacy of interventions, particularly in outbreaks such as the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Because of the assay’s rapid scalability and high efficiency, serology measurements that quantify the presence rather than function of serum antibodies often serve as proxies of immune protection. Here, we report the development of a high-throughput, automated fluorescence-based neutralization assay using SARS-CoV-2 virus to quantify neutralizing antibody activity in patient specimens. We performed large-scale testing of over 19,000 COVID-19 convalescent plasma (CCP) samples from patients who had been infected with SARS-CoV-2 between March and August 2020 across the United States. The neutralization capacity of the samples was moderately correlated with serological measurements of anti-receptor-binding domain (RBD) IgG levels. The neutralizing antibody levels within these convalescent-phase serum samples were highly variable against the original USA-WA1/2020 strain with almost 10% of individuals who had had PCR-confirmed SARS-CoV-2 infection having no detectable antibodies either by serology or neutralization, and ~1/3 having no or low neutralizing activity. Discordance between neutralization and serology measurements was mainly due to the presence of non-IgG RBD isotypes. Meanwhile, natural infection with the earliest SARS-CoV-2 strain USA-WA1/2020 resulted in weaker neutralization of subsequent B.1.1.7 (alpha) and the B.1.351 (beta) variants, with 88% of samples having no activity against the BA.1 (omicron) variant. IMPORTANCE The ability to directly measure neutralizing antibodies on live SARS-CoV-2 virus in individuals can play an important role in understanding the efficacy of therapeutic interventions or vaccines. In contrast to functional neutralization assays, serological assays only quantify the presence of antibodies as a proxy of immune protection. Here, we have developed a high-throughput, automated neutralization assay for SARS-CoV-2 and measured the neutralizing activity of ~19,000 COVID-19 convalescent plasma (CCP) samples collected across the United States between March and August of 2020. These data were used to support the FDA’s interpretation of CCP efficacy in patients with SARS-CoV-2 infection and their issuance of emergency use authorization of CCP in 2020.
