The T cell immune response against SARS-CoV-2

The emergence of SARS-CoV-2 variants with evidence of antibody escape highlight the importance of addressing whether the total CD4+ and CD8+ T cell recognition is also affected. Here, we compare SARS-CoV-2-specific CD4+ and CD8+ T cells against the B.1.1.7, B.1.351, P.1, and CAL.20C lineages in COVID-19 convalescents and in recipients of the Moderna (mRNA-1273) or Pfizer/BioNTech (BNT162b2) COVID-19 vaccines. The total reactivity against SARS-CoV-2 variants is similar in terms of magnitude and frequency of response, with decreases in the 10%-22% range observed in some assay/VOC combinations. A total of 7% and 3% of previously identified CD4+ and CD8+ T cell epitopes, respectively, are affected by mutations in the various VOCs. Thus, the SARS-CoV-2 variants analyzed here do not significantly disrupt the total SARS-CoV-2 T cell reactivity; however, the decreases observed highlight the importance for active monitoring of T cell reactivity in the context of SARS-CoV-2 evolution.

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Impact of SARS-CoV-2 variants on the total CD4 + and CD8 + T cell reactivity in infected or vaccinated individuals.

Analysis of human blood immune cells provides insights into the coordinated response to viral infections such as severe acute respiratory syndrome coronavirus 2, which causes coronavirus disease 2019 (COVID-19). We performed single-cell transcriptome, surface proteome and T and B lymphocyte antigen receptor analyses of over 780,000 peripheral blood mononuclear cells from a cross-sectional cohort of 130 patients with varying severities of COVID-19. We identified expansion of nonclassical monocytes expressing complement transcripts (CD16+C1QA/B/C+) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19. Early, uncommitted CD34+ hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation. Clonally expanded CD8+ T cells and an increased ratio of CD8+ effector T cells to effector memory T cells characterized severe disease, while circulating follicular helper T cells accompanied mild disease. We observed a relative loss of IgA2 in symptomatic disease despite an overall expansion of plasmablasts and plasma cells. Our study highlights the coordinated immune response that contributes to COVID-19 pathogenesis and reveals discrete cellular components that can be targeted for therapy.

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Single-cell multi-omics analysis of the immune response in COVID-19.

SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity.

Immunogenicity and reactogenicity of BNT162b2 booster in ChAdOx1-S-primed participants (CombiVacS): a multicentre, open-label, randomised, controlled, phase 2 trial.

The efficacy of virus-specific T cells in clearing pathogens involves a fine balance between antiviral and inflammatory features. SARS-CoV-2-specific T cells in individuals who clear SARS-CoV-2 without symptoms could reveal nonpathological yet protective characteristics. We longitudinally studied SARS-CoV-2-specific T cells in a cohort of asymptomatic (n = 85) and symptomatic (n = 75) COVID-19 patients after seroconversion. We quantified T cells reactive to structural proteins (M, NP, and Spike) using ELISpot and cytokine secretion in whole blood. Frequencies of SARS-CoV-2-specific T cells were similar between asymptomatic and symptomatic individuals, but the former showed an increased IFN-γ and IL-2 production. This was associated with a proportional secretion of IL-10 and proinflammatory cytokines (IL-6, TNF-α, and IL-1β) only in asymptomatic infection, while a disproportionate secretion of inflammatory cytokines was triggered by SARS-CoV-2-specific T cell activation in symptomatic individuals. Thus, asymptomatic SARS-CoV-2-infected individuals are not characterized by weak antiviral immunity; on the contrary, they mount a highly functional virus-specific cellular immune response.

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Highly functional virus-specific cellular immune response in asymptomatic SARS-CoV-2 infection.

The efficacy of virus-specific T cells in clearing pathogens involves a fine balance between their antiviral and inflammatory features. SARS-CoV-2-specific T cells in individuals who clear SARS-CoV-2 infection without symptoms or disease could reveal non-pathological yet protective characteristics. We therefore compared the quantity and function of SARS-CoV-2-specific T cells in a cohort of asymptomatic individuals (n=85) with that of symptomatic COVID-19 patients (n=76), at different time points after antibody seroconversion. We quantified T cells reactive to structural proteins (M, NP and Spike) using ELISpot assays, and measured the magnitude of cytokine secretion (IL-2, IFN-{gamma}, IL-4, IL-6, IL-1{beta}, TNF- and IL-10) in whole blood following T cell activation with SARS-CoV-2 peptide pools as a functional readout. Frequencies of T cells specific for the different SARS-CoV-2 proteins in the early phases of recovery were similar between asymptomatic and symptomatic individuals. However, we detected an increased IFN-{gamma} and IL-2 production in asymptomatic compared to symptomatic individuals after activation of SARS-CoV-2-specific T cells in blood. This was associated with a proportional secretion of IL-10 and pro-inflammatory cytokines (IL-6, TNF- and IL-1{beta}) only in asymptomatic infection, while a disproportionate secretion of inflammatory cytokines was triggered by SARS-CoV-2-specific T cell activation in symptomatic individuals. Thus, asymptomatic SARS-CoV-2 infected individuals are not characterized by a weak antiviral immunity; on the contrary, they mount a robust and highly functional virus-specific cellular immune response. Their ability to induce a proportionate production of IL-10 might help to reduce inflammatory events during viral clearance.

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Highly functional virus-specific cellular immune response in asymptomatic SARS-CoV-2 infection

Young children are at increased risk of severe illness from influenza and pneumococcal infections. The World Health Organization (WHO) recommends vaccination with influenza and pneumococcal conjugate vaccine (PCV). However, in Singapore, vaccine uptake remains suboptimal relative to other routine childhood immunisations. Limited information exists regarding determinants of influenza and pneumococcal vaccine uptake in children. We estimated vaccine uptake and investigated factors associated with influenza and pneumococcal vaccination status by age group using data from a cohort study on acute respiratory infections in children attending preschools in Singapore. We recruited children aged two to six years at 24 participating preschools from June 2017 to July 2018. We determined the proportion of children immunised with influenza vaccine and PCV, and investigated socio-demographic factors associated with vaccine uptake using logistic regression models. Among 505 children, 77.5% were of Chinese ethnicity, and 53.1% were male. History of influenza vaccination was 27.5% of which 11.7% had been vaccinated within the past 12 months. In multivariable analyses, factors associated with influenza vaccine uptake were ‘children living in landed property’ (aOR = 2.25, 95% CI [1.07–4.67]) and ‘history of hospitalisation due to cough’ (aOR = 1.85, 95% CI [1.00–3.36]). Nearly three-quarters of participants (70.7% 95%CI: [66.6–74.5]) reported prior PCV vaccination. PCV uptake was higher for younger children. ‘Higher parental education’ (OR = 2.83, 95% CI [1.51,5.32]), ‘household income’ (OR = 1.26, 95% CI [1.08,1.48]) and ‘smokers in household’ (OR = 0.48, 95% CI [0.31,0.74]) were significantly associated with PCV uptake in univariable analyses. Only ‘smokers in household’ remained significantly associated with PCV uptake (aOR = 0.55, 95% CI [0.33,0.91]) in the adjusted model. Our results indicate that episodes of severe respiratory illness are a cue to influenza vaccination suggesting that doctors are more likely to recommend influenza vaccines to high-risk children. For PCV, our findings suggest overall greater awareness and education on the benefit of PCV vaccination is required.

https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0285561&type=printable

Marina Zahari

Papers

Highly functional virus-specific cellular immune response in asymptomatic SARS-CoV-2 infection.

Highly functional virus-specific cellular immune response in asymptomatic SARS-CoV-2 infection

Determinants of influenza and pneumococcal vaccine uptake among preschool children in Singapore