Immunophenotypes of anti-SARS-CoV-2 responses associated with fatal COVID-19

BACKGROUND: The relationship between anti-SARS-CoV-2 humoral immune response, pathogenic inflammation, lymphocytes and fatal COVID-19 is poorly understood. METHODS: A longitudinal prospective cohort of hospitalised patients with COVID-19 (n=254) was followed up to 35 days after admission (median, 8 days). We measured early anti-SARS-CoV-2 S1 antibody IgG levels and dynamic (698 samples) of quantitative circulating T-, B- and natural killer lymphocyte subsets and serum interleukin-6 (IL-6) response. We used machine learning to identify patterns of the immune response and related these patterns to the primary outcome of 28-day mortality in analyses adjusted for clinical severity factors. RESULTS: Overall, 45 (18%) patients died within 28 days after hospitalisation. We identified six clusters representing discrete anti-SARS-CoV-2 immunophenotypes. Clusters differed considerably in COVID-19 survival. Two clusters, the anti-S1-IgG(lowest)T(lowest)B(lowest)NK(mod)IL-6(mod,) and the anti-S1-IgG(high)T(low)B(mod)NK(mod)IL-6(highest) had a high risk of fatal COVID-19 (HR 3.36–21.69; 95% CI 1.51–163.61 and HR 8.39–10.79; 95% CI 1.20–82.67; p≤0.03, respectively). The anti-S1-IgG(highest)T(lowest)B(mod)NK(mod)IL-6(mod) and anti-S1-IgG(low)T(highest)B(highest)NK(highest)IL-6(low) cluster were associated with moderate risk of mortality. In contrast, two clusters the anti-S1-IgG(high)T(high)B(mod)NK(mod)IL-6(low) and anti-S1-IgG(highest)T(highest)B(high)NK(high)IL-6(lowest) clusters were characterised by a very low risk of mortality. CONCLUSIONS: By employing unsupervised machine learning we identified multiple anti-SARS-CoV-2 immune response clusters and observed major differences in COVID-19 mortality between these clusters. Two discrete immune pathways may lead to fatal COVID-19. One is driven by impaired or delayed antiviral humoral immunity, independently of hyper-inflammation, and the other may arise through excessive IL-6-mediated host inflammation response, independently of the protective humoral response. Those observations could be explored further for application in clinical practice.