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. 2025 Mar 12;25(1):345.
doi: 10.1186/s12879-025-10692-1.

The vast majority of SARS-CoV-2 infections were asymptomatic in a clinic-based cohort of people with and without HIV in four African countries

Rither Langat  1 , Natalie Burns  2   3 , Ibrahim Daud  4 , Hannah Kibuuka  5 , John Owuoth  6 , Valentine Sing'oei  6 , Jonah Maswai  4 , Zahra Parker  7   3 , Abdulwasiu Tiamiyu  8 , Emmanuel Bahemana  9 , Reginald Gervas  9 , Nicole F Dear  2   3 , Seth Frndak  2   3 , Ajay P Parikh  2   3 , Emma R Duff  2   3 , Michelle Imbach  2   3 , Badryah Omar  2   3 , Jaclyn Hern  2   3 , Neha Shah  2 , Julie A Ake  2 , Trevor A Crowell  2   3 , Matthew L Romo  2   3 ; AFRICOS Study Group
Collaborators, Affiliations

The vast majority of SARS-CoV-2 infections were asymptomatic in a clinic-based cohort of people with and without HIV in four African countries

Rither Langat et al. BMC Infect Dis. .

Abstract

Background: Persons living with HIV (PLWH) were prioritized for SARS-CoV-2 vaccination in sub-Saharan Africa, however, SARS-CoV-2 infection and COVID-19 symptomatology have not been well characterized among PLWH. We described SARS-CoV-2 infection prevalence and symptomatology, and examined factors associated with nasal swab RT-PCR positivity in Kenya, Uganda, Tanzania, and Nigeria.

Methods: The ongoing African Cohort Study (AFRICOS) follows PLWH and people living without HIV (PLWoH) in four African countries. All participants undergo clinical assessment and socio-behavioral questionnaire administration at enrollment and each six-monthly visits, with CD4 count and viral load collected for PLWH. Optional nasal swabs were collected for SARS-CoV-2 rapid RT-PCR testing at visits after 19 July 2022. Participants were asked if they had experienced COVID-19 symptoms. We used the Agresti-Coull method to estimate the prevalence of SARS-CoV-2 infection at each participant's first nasal swab collection. Adjusted prevalence ratios (aPRs) and 95% confidence intervals (CIs) for factors potentially associated with SARS-CoV-2 infection were estimated using multivariable robust Poisson regression.

Results: Between 19 July 2022 and 1 March 2024, 1,187 participants underwent nasal swab collection with a valid SARS-CoV-2 RT-PCR result; 1,032 (86.9%) were PLWH and 155 (13.1%) were PLWoH. A majority were female (57.2%), and the median age was 44.6 (interquartile range 34.4-52.2) years. Prevalence at first nasal swab of SARS-CoV-2 was 6.8% (95%CI 5.5%-8.4%). Most participants with positive SARS-CoV-2 RT-PCR were asymptomatic (97.5%). SARS-CoV-2 was marginally more common among PLWoH as compared to PLWH (10.3% vs. 6.3%; p = 0.093). In the multivariable model, SARS-CoV-2 was significantly more common among participants who received at least one dose of a COVID-19 vaccine as compared to participants who received no doses (aPR 1.66; 95%CI 1.05-2.62; p = 0.031) and during the omicron wave as compared to non-wave periods (aPR 2.15; 95%CI 1.42-3.25; p < 0.001). Among PLWH, CD4 and viral load were not associated with SARS-CoV-2 prevalence.

Conclusion: The vast majority of people with positive SARS-CoV-2 RT-PCR were asymptomatic. Universal screening may be needed to fully understand the epidemiology of SARS-CoV-2 and future outbreaks of similar respiratory viruses, capture early infection, and plan for intervention.

Keywords: AFRICOS; HIV; Omicron; RT-PCR; SARS-CoV-2.

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Conflict of interest statement

Declarations. Ethics approval and consent to participate: The African Cohort Study was approved by institutional review boards of the Walter Reed Army Institute of Research Silver Spring, MD, USA; Makerere University School of Public Health, Kampala, Uganda; Kenya Medical Research Institute, Nairobi, Kenya; Tanzania National Institute of Medical Research, Mbeya, Tanzania; Nigerian Ministry of Defence, Abuja, Nigeria; and all collaborating institutions. All participants provided written informed consent prior to any study procedures. All work was conducted in accordance with the Declaration of Helsinki. Consent for publication: Not Applicable. Competing interests: The authors declare no competing interests.

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