Prevalence and functional profile of SARS-CoV-2 T cells in asymptomatic Kenyan adults

Abstract

Background. SARS-CoV-2 infection in Africa has been characterized by a less severe disease profile than what has been observed elsewhere but the profile of SARS-CoV-2 specific adaptive immunity in these mainly asymptomatic cases has not been analyzed. Methods. We collected samples of residents of rural Kenya (n=80) who had not experienced any respiratory symptoms nor had contact with COVID-19 cases or received COVID-19 vaccines. We analyzed spike-specific antibodies and T cells specific for SARS-CoV-2 structural (membrane, nucleocapsid and spike) and accessory (ORF3a, ORF7, ORF8) proteins. Pre-pandemic samples collected in Nairobi (n=13) and samples of mild-moderately symptomatic COVID-19 convalescents (n=36) living in the urban environment of Singapore were also studied. Results. Among asymptomatic Africans, we detected anti-spike antibodies in 41.0% and T cell responses against ≥2 SARS-CoV-2 proteins in 82.5%. Such a pattern was absent in pre-pandemic samples. Furthermore, distinct from cellular immunity in European and Asian COVID-19 convalescents, strong T cell immunogenicity was observed against viral accessory proteins (ORF3a, ORF8) and not structural proteins, as well as a higher IL-10/IFN-γ ratio cytokine profile. Conclusions. The high incidence of T cell response against different SARS-CoV-2 proteins in seronegative participants suggests that serosurveys underestimate SARS-CoV-2 prevalence in settings where asymptomatic infections prevail. The functional and antigen-specific profile of SARS-CoV-2 specific T cells in African individuals suggests that environmental factors can play a role in the development of protective antiviral immunity. Fundings. U.S. Centers for Disease Control and Prevention, Division of Global Health Protection; the Singapore Ministry of Health’s National Medical Research Council.