SARS-CoV-2 seroprevalence and implications for population immunity: Evidence from two Health and Demographic Surveillance System sites in Kenya, February-June 2022

Abstract

Background Up-to-date SARS-CoV-2 antibody seroprevalence estimates are important for informing public health planning, including priorities for Coronavirus disease 2019 (COVID-19) vaccination programs. We sought to estimate infection- and vaccination-induced SARS-CoV-2 antibody seroprevalence within representative samples of the Kenyan population approximately two years into the COVID-19 pandemic and approximately one year after rollout of the national COVID-19 vaccination program. Methods We conducted cross-sectional serosurveys within random, age-stratified samples of Kilifi Health and Demographic Surveillance System (HDSS) and Nairobi Urban HDSS residents. Anti-spike (anti-S) immunoglobulin G (IgG) and anti-nucleoprotein (anti-N) IgG were measured using validated in-house ELISAs. Target-specific Bayesian population-weighted seroprevalence was calculated overall, by sex and by age, with adjustment for test performance as appropriate. Anti-S IgG concentrations were estimated with reference to the WHO International Standard (IS) for anti-SARS-CoV-2 immunoglobulin and their reverse cumulative distributions plotted. Results Between February and June 2022, 852 and 851 individuals within the Kilifi HDSS and the Nairobi Urban HDSS, respectively, were sampled. Only 11.0% (95% confidence interval [CI] 9.0-13.3) of all Kilifi HDSS participants and 33.4% (95%CI 30.2-36.6) of all Nairobi Urban HDSS participants had received any doses of COVID-19 vaccine. Population-weighted anti-S IgG seroprevalence was 69.1% (95% credible interval [CrI] 65.8-72.3) within the Kilifi HDSS and 88.5% (95%CrI 86.1-90.6) within the Nairobi Urban HDSS. Among COVID-unvaccinated residents of the Kilifi HDSS and Nairobi Urban HDSS, it was 66.7% (95%CrI 63.3-70.0) and 85.3% (95%CrI 82.1-88.2), respectively. Population-weighted, test-adjusted anti-N IgG seroprevalence within the Kilifi HDSS was 53.5% (95%CrI 46.5-61.1) and 65.5% (95%CrI 56.0-75.6) within the Nairobi Urban HDSS. The prevalence of anti-N antibodies was similar in vaccinated and unvaccinated subgroups in both HDSS populations. Anti-S IgG concentrations were significantly lower among Kilifi HDSS residents than among Nairobi Urban HDSS residents (p< 0.001). Conclusions Approximately, 7 in 10 Kilifi residents and 9 in 10 Nairobi residents were seropositive for anti-S IgG by May 2022 and June 2022, respectively. Given COVID-19 vaccination coverage, anti-S IgG seropositivity among COVID-unvaccinated individuals, and anti-N IgG seroprevalence, population-level anti-S IgG seroprevalence was predominantly derived from infection. Interventions to improve COVID-19 vaccination uptake should be targeted to individuals in rural Kenya who are at high risk of severe COVID-19.

Omicron B.1.1.529 variant infections associated with severe disease are uncommon in a COVID-19 under-vaccinated, high SARS-CoV-2 seroprevalence population in Malawi

“…23 Notwithstanding the reduced number of hospitalisations and deaths in Malawi, the Omicron variant drove a rapid rise in SARS-CoV-2 infections consistent with its high transmissibility 24,25 as observed in other settings. 1,26 Based on previous estimates from our adult blood donor serosurvey, the estimated seroprevalence by July 2021 was >65%, 10 reaching around 80% by November 2021 (unpublished), before the Omicrondominant fourth wave in Malawi, and this is in agreement with other African countries including Kenya, 27 South Africa 1 and Nigeria. 28 In South Africa, a lower rate of hospitalisations and deaths was associated with the high seroprevalence before the onset of the Omicron-dominant wave, driven by both vaccination and infection.…”

Impact of COVID-19 on mortality in coastal Kenya: a longitudinal open cohort study

“…The green line represents the effective reproductive number (scale on right-hand y-axis). The dates of the two anti-SARS-CoV-2 antibody serosurveys in Kilifi HDSS are shown as grey bars 10,11 .…”

“…Seroprevalence among adults was 25% in December 2020 to April 2021 10 and 75% in February to May 2022 11 results in children were lower at 15% and 64%, respectively. Given only 17% of the adult population had been vaccinated in the second survey, this suggests wide dissemination of SARS-CoV-2 in Kilifi, typical of elsewhere in Africa [12][13][14][15][16][17][18][19] .…”

Prospective Clinical Surveillance for Severe Acute Respiratory Illness in Kenyan Hospitals during the COVID-19 pandemic

“…Overall, these VE estimates are lower than those reported elsewhere in sub-Saharan Africa (42, 43, 44, 45, 46). Our estimates, while informative, should be interpreted with caution as they are reported against a backdrop of extensive community spread of COVID-19 before vaccine introduction(47), limited access to and availability of COVID-19 tests and low vaccine coverage with variable availability of the vaccine(14). For example, COVID-19 vaccine coverage among the study participants was 4% compared to a national vaccine coverage of 36%.…”