High Seroprevalence of SARS-CoV-2 Eight Months After Introduction in Nairobi, Kenya

Background: The lower-than-expected COVID-19 morbidity and mortality in Africa has been attributed to multiple factors, including weak surveillance. We set out to estimate the burden of SARS-CoV-2 infections eight months into the epidemic in Nairobi, Kenya. Methods: We conducted a population based cross-sectional survey using multi-stage random sampling to select households within Nairobi in November 2020. Sera from consenting household members were tested for IgM and IgG antibodies to SARS-CoV-2. Seroprevalence was estimated after adjusting for population structure and test performance. Risk factors were determined using logistic regression and Infection fatality ratios (IFRs) calculated by comparing our estimates to reported cases and deaths. Findings: Of 1,164 individuals from 527 households tested, the adjusted seroprevalence was 34·7% (95%CI 31·8-37·6), indicating that approximately 1·5 million Nairobi residents had been infected. Some 261 (49·5%) households had at least one positive participant, and positivity rates increased in more densely populated areas (spearman’s r=0·63; p=0·009). Individuals aged 20-59 years had up to 2-fold higher seropositivity when compared to those aged 0-9 years or ≥60 years. The IFR was 40 per 100,000 infections, with individuals ≥40 years old having higher IFRs. Interpretation: Over one third of Nairobi residents in half of the households were infected by November 2020, indicating extensive transmission in the city, comparable to countries reporting more severe forms of the pandemic. However, the IFR was >10-fold lower than that reported in Europe and the United States, supporting the perceived low morbidity and mortality in sub–Saharan Africa. Funding Statement: Funding was provided by the US National Institutes of Health (NIH), grant number U01AI151799, through the Centre for Research in Emerging Infectious Diseases – East and Central Africa (CREID-ECA). Declaration of Interests: The authors declare that they have no competing interests Ethics Approval Statement: This study was reviewed and approved by the Kenya Medical Research Institute Scientific and Ethical Review Committee (number SSC 4098), National Commission for Science Technology and Innovation (number 827570), U.S. CDC (number CGH-ET-4/12/21-f3b82), and a reliance approval provided by Washington State University Institutional Review Board based on in-country ethical reviews as provided for in Code of Federal Regulations (45 C.F.R part 46 and 21 C.F.R. part 56). Administrative approval was provided by the Kenya MoH and Nairobi City County administration. All participants provided written consent prior to enrollment.