Divergent trajectories of antiviral memory after SARS-Cov-2 infection

doi:10.21203/rs.3.rs-612205/v1

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Divergent trajectories of antiviral memory after SARS-Cov-2 infection

https://doi.org/10.21203/rs.3.rs-612205/v1

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published 10 Mar, 2022

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Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is normally controlled by effective host immunity including innate, humoral and cellular responses. However, the trajectories and correlates of acquired immunity, and the capacity of memory responses months after infection to neutralise variants of concern - which has important public health implications - is not fully understood. To address this, we studied a cohort of 78 UK healthcare workers who presented in April to June 2020 with symptomatic PCR-confirmed infection or who tested positive during an asymptomatic screening programme and tracked virus-specific B and T cell responses longitudinally at 5-6 time points each over 6 months, prior to vaccination. We observed a highly variable range of responses, some of which - T cell interferon-gamma (IFN-γ) ELISpot, N-specific antibody waned over time across the cohort, while others (spike-specific antibody, B cell memory ELISpot) were stable. In such cohorts, antiviral antibody has been linked to protection against re-infection. We used integrative analysis and a machine-learning approach (SIMON - Sequential Iterative Modeling Over Night) to explore this heterogeneity and to identify predictors of sustained immune responses. Hierarchical clustering defined a group of high and low antibody responders, which showed stability over time regardless of clinical presentation. These antibody responses correlated with IFN-γ ELISpot measures of T cell immunity and represent a subgroup of patients with a robust trajectory for longer term immunity. Importantly, this immune-phenotype associates with higher levels of neutralising antibodies not only against the infecting (Victoria) strain but also against variants B.1.1.7 (alpha) and B.1.351 (beta). Overall memory responses to SARS-CoV-2 show distinct trajectories following early priming, that may define subsequent protection against infection and severe disease from novel variants.

* These authors contributed equally.

# These authors jointly supervised this work and contributed equally.

Corresponding authors: Eleanor Barnes, email: [email protected] Adriana Tomic, email: [email protected]

Immunology

SARS-CoV-2

T cells

B cells

Antibodies

Durability

Healthcare workers

Longevity

variants of concern

COVID-19

Suppfig1.tiff
Fig S1. Comparison of humoral immune responses in individuals with PCR confirmed SARS-CoV-2 asymptomatic (blue), mild (purple) or severe (red) infection. 
Comparison of total IgG specific to the SARS-CoV-2 (A) nucleocapsid and (B) spike glycoprotein, quantification of (C) IgG memory B cells specific to the spike glycoprotein, and (D) pseudoneutralisating antibody titres. Anti-SARS-CoV-2 spike antibody (E-F) isotypes, (G-H) subclasses and (I-L) Fc-mediated effector functions were also compared. See Table S1 for number of individuals evaluated per assay.
Suppfig2.tiff
Fig S2. Further characterisation of longitudinal humoral immune responses to SARS-CoV-2 and non-SARS-CoV-2 coronaviruses in individuals with PCR confirmed SARS-CoV-2 asymptomatic (blue), mild (purple) or severe (red) infection. 
SARS-CoV-2 spike glycoprotein-specific (A) IgA memory B cells and (B) IgG2 subclass antibodies. Meso Scale Discovery (MSD) multiplexed immunoassay (MIA) platform measurements of antibody levels specific to (C) non-SARS-CoV-2 coronaviruses spike glycoproteins compared across the diseases cohorts at each sampling timepoint, and (D) SARS-CoV-2 spike glycoprotein over time. See Table S1 for number of individuals evaluated per assay.
Suppfig3.tiff
Fig S3. Analysis of T cell responses by clinical disease status, and representative gating strategies
(A) Comparison of ex vivo IFN-γ ELISpot responses in healthcare workers post asymptomatic (n=12) vs mild (n=66) SARS-CoV-2 infection. T cell responses to summed SARS-CoV-2 peptide pools spanning spike, accessory and structural proteins (summed total of SARS-CoV-2 proteins, S1, S2, NSP3B, M, NP, ORF 3, ORF8, and the CEFT positive control peptides for T cell responses) at 28, 90 and 180 days post onset of symptoms for mild cases, PCR positive test for asymptomatic participants. Comparison by Mann-Whitney test. (B) to (D) PBMC were stimulated with 1ug/ml of peptide pools or 2ug/ml of PHA and 0.2% DMSO for proliferation assay (B and C) or 2ug/mL of peptide pool for ICS assay (D). Representative gating strategy is shown in for T cell proliferation assay (B) . FECT control responses in the proliferation assay is shown in (C) and Representative ICS plots are shown in (D) for both CD4+ and CD8+ T cell responses.
Suppfig4.tiff
Fig S4 Longitudinal ICS analysis of SARS-CoV-2 T cell responses.
Individuals with ELISpot levels >100 spots/106 PBMC for a particular peptide pool at timepoint 2 were studied longitudinally at two timepoints using ICS. A total of n=18 individuals were studied with n=15 providing paired analysis. 16 frozen PBMC were stimulated with 2ug/mL of the listed peptide along with 1ug/mL CD28 and CD49d antibodies for 6 hours. Expression levels of IFN-γ, IL-2, and TNF in CD4+ T cells (black) and CD8+ T cells (grey) are shown at two timepoints for S1 (A), S2 (C), M (E), NP (G) and NSP3B (I). A paired Friedman test was performed with the two-stage step-up method of Benjamini, Kriegar and Yekutieli correction for multiple comparisons. P values <0.1 are shown. Polyfunctional analysis was performed on both timepoints for individuals with sufficient cell populations for polyfunctional analysis. Data for CD4+ T cells are shown at two timepoints for S1 (B) (n=7, n=8 timepoints 1 and 2 respectively), S2 (D) (n= 5, n=6), M (F) (n=4, n=4), and NP pools (H) (n= 6, n=5). Data for CD8+ T cells are shown at two timepoints for NSP3B pools (J) (n=3, n=5).
Suppfig5.tiff
Fig S5. Polyfunctional T cell responses for NP and NSP3B pools.
Polyfunctional analysis was performed as in Supplemental Figure X. A) shows CD8+ T cell polyfunctional analysis for the NP pool at day 28 (n=3). B) shows CD4+ T cell polyfunctional analysis for the NSP3V pool at day 180 (n=5).
AppendixSupplementaryFiguresandAdditionalMethods.pdf

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Divergent trajectories of antiviral memory after SARS-Cov-2 infection

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