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

• Published in: The Journal of clinical investigation Vol. 133; no. 13; pp. 1 - 12
• Main Authors: Samandari, Taraz, Ongalo, Joshua B, McCarthy, Kimberly D, Biegon, Richard K, Madiega, Philister A, Mithika, Anne, Orinda, Joseph, Mboya, Grace M, Mwaura, Patrick, Anzala, Omu, Onyango, Clayton, Oluoch, Fredrick O, Osoro, Eric, Dutertre, Charles-Antoine, Tan, Nicole, Hang, Shou Kit, Hariharaputran, Smrithi, Lye, David C, Herman-Roloff, Amy, Le Bert, Nina, Bertoletti, Antonio
• Format: Journal Article
• Language: English
• Published: United States American Society for Clinical Investigation 03.07.2023
• Subjects: Adaptive immunity; Antibodies; Asymptomatic; Biomedical research; Blood & organ donations; Cell-mediated immunity; Cells; Clinical Medicine; COVID-19; COVID-19 vaccines; Cytokines; Environmental factors; Health aspects; HIV; Human immunodeficiency virus; Immune response; Immunity; Immunogenicity; Infections; Infectious disease; Interleukin 10; Lymphocytes; Lymphocytes T; Medical research; Nucleocapsids; Pandemics; Peptides; Physiological aspects; Proteins; Public health; Rural areas; Serology; Severe acute respiratory syndrome coronavirus 2; Structural proteins; T cells; Urban environments; γ-Interferon; Kenya; Singapore; United States > US; Africa; COVID-19; T cells; Infectious disease
• ISSN: 1558-8238; 0021-9738; 1558-8238
• DOI: 10.1172/JCI170011

BackgroundSARS-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 patients has not, to our knowledge, been analyzed.MethodsWe collected blood samples from residents of rural Kenya (n = 80), who had not experienced any respiratory symptoms or had contact with individuals with COVID-19 and had not 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 blood samples collected in Nairobi (n = 13) and blood samples from mild-to-moderately symptomatic COVID-19 convalescent patients (n = 36) living in the urban environment of Singapore were also studied.ResultsAmong asymptomatic Africans, we detected anti-spike antibodies in 41.0% of the samples and T cell responses against 2 or more SARS-CoV-2 proteins in 82.5% of samples examined. Such a pattern was absent in the pre-pandemic samples. Furthermore, distinct from cellular immunity in European and Asian COVID-19 convalescents, we observed strong T cell immunogenicity against viral accessory proteins (ORF3a, ORF8) but not structural proteins, as well as a higher IL-10/IFN-γ cytokine ratio profile.ConclusionsThe high incidence of T cell responses 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.FundingUS Centers for Disease Control and Prevention, Division of Global Health Protection; the Singapore Ministry of Health's National Medical Research Council (COVID19RF3-0060, COVID19RF-001, COVID19RF-008, MOH-StaR17Nov-0001).