Prevalence and functional profile of SARS-CoV-2 T cells in asymptomatic Kenyan adults
Taraz Samandari, Joshua B. Ongalo, Kimberly D. McCarthy, Richard K. Biegon, Philister A. Madiega, Anne Mithika, Joseph Orinda, Grace M. Mboya, Patrick Mwaura, Omu Anzala, Clayton Onyango, Fredrick O. Oluoch, Eric Osoro, Charles-Antoine Dutertre, Nicole Tan, Shou Kit Hang, Smrithi Hariharaputran, David C. Lye, Amy Herman-Roloff, Nina Le Bert, Antonio Bertoletti
Taraz Samandari, Joshua B. Ongalo, Kimberly D. McCarthy, Richard K. Biegon, Philister A. Madiega, Anne Mithika, Joseph Orinda, Grace M. Mboya, Patrick Mwaura, Omu Anzala, Clayton Onyango, Fredrick O. Oluoch, Eric Osoro, Charles-Antoine Dutertre, Nicole Tan, Shou Kit Hang, Smrithi Hariharaputran, David C. Lye, Amy Herman-Roloff, Nina Le Bert, Antonio Bertoletti
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Clinical Research and Public Health Infectious disease

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 patients has not, to our knowledge, been analyzed.Methods We 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.Results Among 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.Conclusions The 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.Funding US 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).

Authors

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

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Figure 4

Immunodominance hierarchy of T cell responses to structural and accessory proteins of SARS-CoV-2.

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Immunodominance hierarchy of T cell responses to structural and accessor...
(A) Schematic representation of the relative length of the 6 different SARS-CoV-2 proteins tested (left) and their number of amino acids (right). (B) The SARS-CoV-2 T cell response composition in each responding asymptomatic participant from Kenya (n = 44) is shown as a percentage of the total detected response (structural proteins are shown in shades of blue; accessory proteins are shown in shades of red). The dotted line represents the relative length of the structural (77%) and accessory proteins (23%) tested. (C) The composition of the SARS-CoV-2 response in convalescent symptomatic COVID-19 patients from Singapore (n = 36) is shown as a percentage of the total detected response. The number of participants with a dominant T cell response to the indicated SARS-CoV-2 proteins is shown for samples from asymptomatic participants from Kenya (D) and symptomatic convalescent COVID-19 patients from Singapore (E).