Correlates of Neutralization against SARS-CoV-2 Variants of Concern by Early Pandemic Sera

Abstract

Emerging SARS-CoV-2 variants of concern that overcome natural and vaccine-induced immunity threaten to exacerbate the COVID-19 pandemic. Increasing evidence suggests that neutralizing antibody (NAb) responses are a primary mechanism of protection against infection. However, little is known about the extent and mechanisms by which natural immunity acquired during the early COVID-19 pandemic confers cross-neutralization of emerging variants. In this study, we investigated cross-neutralization of the B.1.1.7 and B.1.351 SARS-CoV-2 variants in a well-characterized cohort of early pandemic convalescent subjects. We observed modestly decreased cross-neutralization of B.1.1.7 but a substantial 4.8-fold reduction in cross-neutralization of B.1.351. Correlates of cross-neutralization included receptor binding domain (RBD) and N-terminal domain (NTD) binding antibodies, homologous NAb titers, and membrane-directed T cell responses. These data shed light on the cross-neutralization of emerging variants by early pandemic convalescent immune responses. IMPORTANCE Widespread immunity to SARS-CoV-2 will be necessary to end the COVID-19 pandemic. NAb responses are a critical component of immunity that can be stimulated by natural infection as well as vaccines. However, SARS-CoV-2 variants are emerging that contain mutations in the spike gene that promote evasion from NAb responses. These variants may therefore delay control of the COVID-19 pandemic. We studied whether NAb responses from early COVID-19 convalescent patients are effective against the two SARS-CoV-2 variants, B.1.1.7 and B.1.351. We observed that the B.1.351 variant demonstrates significantly reduced susceptibility to early pandemic NAb responses. We additionally characterized virological, immunological, and clinical features that correlate with cross-neutralization. These studies increase our understanding of emerging SARS-CoV-2 variants.

Keywords: SARS-CoV-2; T cells; neutralizing antibodies.

FIG 1

SARS-CoV-2 and endemic coronavirus binding antibody responses among early pandemic convalescent COVID-19 inpatients and prepandemic controls. (A) SARS-CoV-2 spike RBD IgG ELISA titers. (B) HKU1, OC43, and 229E spike RBD IgG ELISA titers. (C) Full-length spike, spike RBD, and spike NTD IgG ECLA signals. (D) Spearman correlation between SARS-CoV-2 spike RBD IgG ELISA titer and ECLA signal. Bars represent geometric means. Dotted lines represent limits of detection (LOD) for ELISA and lower limits of detection (LLOD) for ECLA. Convalescent COVID-19 inpatient and prepandemic subjects were compared by Mann-Whitney test.

FIG 2

SARS-CoV2 pseudovirus neutralization among early pandemic convalescent COVID-19 inpatients and correlations with binding antibody titers. (A) Pseudovirus neutralization titers among early pandemic convalescent COVID-19 inpatients and prepandemic controls. (B) Spearman correlations between spike full-length, RBD, NTD, and nucleocapsid IgG ECLA signals and pseudovirus neutralization titers. Bars represent geometric means. Dotted lines represent LOD. Convalescent COVID-19 inpatients and prepandemic controls were compared by Mann-Whitney test.

FIG 3

SARS-CoV-2 T cell responses and correlations with antibody responses among early pandemic convalescent COVID-19 inpatients and prepandemic controls. (A) IFN-γ ELISPOT responses to selected structural and accessory SARS-CoV-2 antigens. (B and C) Spearman correlations between aggregate IFN-γ ELISPOT responses and RBD and NTD binding (B) and pseudovirus Nab responses (C). Bars represent geometric means. Dotted lines represent LOD. Convalescent COVID-19 inpatient and prepandemic and subjects were compared by Mann-Whitney test. *, P < 0.05; **, P < 0.01.

FIG 4

Cross-neutralizing antibody responses to emerging SARS-CoV-2 variants among early pandemic convalescent-phase sera. (A) Grouped comparison of SARS-CoV-2 Wuhan, B.1.1.7, and B.1.351 strain pseudovirus NAb titers. (B) Pairwise comparison of SARS-CoV-2 Wuhan and B.1.351 strain pseudovirus NAb titers. Bars represent geometric means. Dotted lines represent LOD. Multigroup comparisons were performed by Kruskal-Wallis test. Paired comparison was performed by Mann-Whitney test. ns, not significant.

FIG 5

Correlates of emerging variant cross-neutralization by early pandemic convalescent-phase sera. (A) Heat map with unsupervised hierarchical clustering of clinical, virological, and immunological variables as well as patients. (B) Correlogram with unsupervised hierarchical clustering of the same clinical, virological, and immunological variables as in panel A. Red shading depicts positive correlations, blue shading depicts negative correlations, intensity of the shading represents magnitude of the Spearman R statistic, and size of the shading represents significance. *, P < 0.05; **, P < 0.01; ***, P < 0.001. All data include a Benjamini-Hochberg correction for multiple comparisons.