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

Taraz Samandari; Joshua Ongalo; Kimberly McCarthy; Richard K. Biegon; Philister Madiega; Anne Mithika; Joseph Orinda; Grace M. Mboya; Patrick Mwaura; Omu Anzala; Clayton Onyango; Fredrick O. Oluoch; Eric M. Osoro; Charles-Antoine Dutertre; Nicole Tan; Shou Kit Hang; Smrithi Hariharaputran; David C. Lye; Amy Herman-Roloff; Nina Le Bert; Antonio Bertoletti

doi:10.1172/JCI170011

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

Taraz Samandari,¹ Joshua Ongalo,² Kimberly McCarthy,³ Richard K. Biegon,⁴ Philister Madiega,² Anne Mithika,² Joseph Orinda,² Grace M. Mboya,² Patrick Mwaura,⁵ Omu Anzala,⁵ Clayton Onyango,¹ Fredrick O. Oluoch,⁶ Eric M. Osoro,⁷ Charles-Antoine Dutertre,⁸ Nicole Tan,⁹ Shou Kit Hang,⁹ Smrithi Hariharaputran,⁹ David C. Lye,¹⁰ Amy Herman-Roloff,¹ Nina Le Bert,⁹ and Antonio Bertoletti⁹

Published May 23, 2023 - More info

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Abstract

BACKGROUND. SARS-CoV-2 infection in Africa has been characterized by less severe disease than elsewhere but the profile of SARS-CoV-2 specific adaptive immunity in this largely asymptomatic spread has not been studied.

METHODS. We collected blood and nasopharyngeal samples from rural Kenyans (n=80) without respiratory symptoms since 2019, had no contact with COVID-19 cases or received COVID-19 vaccines and were negative for current SARS-CoV-2 infection. 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 urban Nairobi, Kenya (n=13) between 2015-2016 and samples of mild-moderately symptomatic COVID-19 convalescents (n=36) living in the urban environment of Singapore were also studied.

RESULTS. Among asymptomatic Kenyans, we detected anti-spike antibodies in 41.0% and T cell responses against ≥2 SARS-CoV-2 proteins in 82.5%. The pre-pandemic samples from Nairobi had low-level, monospecific responses. 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 responses against different SARS-CoV-2 proteins in largely seronegative participants suggests that serosurveys underestimate SARS-CoV-2 prevalence in settings where asymptomatic infections prevail. Similar observations have been made with other coronavirus infections such as MERS and SARS-CoV-1. The functional and antigen-specific profile of SARS-CoV-2 specific T cells in these African individuals suggests that genetic or environmental factors 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.

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

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