Single-cell profiling of dysfunctional NK cells in COVID-19: from immunization to acute infection and beyond

Abstract

Vaccination and natural infection with Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) confer immune protection through distinct mechanisms, however, their effects on Natural Killer (NK) cell responses remain poorly understood, particularly in relation to COVID-19 disease severity. NK cells, key mediators of anti-viral immunity, have been implicated in coronavirus disease 2019 (COVID-19) pathogenesis, where severe disease is associated with hyperactivated yet dysfunctional NK-cell states that likely impair viral control and contribute to tissue damage. To define how vaccination and infection shape NK-cell biology, we performed longitudinal single-cell RNA sequencing (scRNA-seq) of NK cells from SARS-CoV-2-naïve individuals receiving two doses of the BNT162b2mRNA vaccine. These longitudinal vaccine profiles were integrated with cross-sectional scRNA-seq datasets from unvaccinated patients with acute COVID-19 and from independent convalescent individuals, all enrolled before vaccine introduction. We identified distinct NK cell transcriptional programs associated with vaccination, acute infection and convalescence, with the most pronounced infection-related alterations observed in the severe form of the disease. These diverging transcriptional signatures correlate with differences in NK-cell subset composition and activation markers between vaccinated and infected individuals. Taken together, these findings provide a rationale for future studies examining whether vaccine-associated NK-cell transcriptional programs contribute to durable immune protection.