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

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.

SARS-CoV-2 Seroprevalence in three Kenyan Health and Demographic Surveillance Sites, December 2020-May 2021 (preprint)

Importance Most of the studies that have informed the public health response to the COVID-19 pandemic in Kenya have relied on samples that are not representative of the general population. Objective To determine the cumulative incidence of infection with SARS-CoV-2, from a randomly selected sample of individuals normally resident at three Health and Demographic Surveillance Systems (HDSSs) in Kenya. Design This was a cross-sectional population-based serosurvey conducted at Kilifi HDSS, Nairobi Urban HDSS, and Manyatta HDSS in Kenya. We selected age-stratified samples at HDSSs in Kilifi, Kisumu and Nairobi, in Kenya. Blood samples were collected from participants between 01 Dec 2020 and 27 May 2021. Setting Kilifi HDSS comprises a predominantly rural population, Manyatta HDSS comprises a predominantly semi-urban population, while Nairobi Urban HDSS comprises an urban population. The total population under regular surveillance at the three sites is ~470,000. Exposure We tested for IgG antibodies to SARS-CoV-2 spike protein using ELISA. Locally validated assay sensitivity and specificity were 93% (95% CI 88-96%) and 99% (95% CI 98-99.5%), respectively. Main Outcome and Measures The primary outcome measure was cumulative incidence of infection with SARS-COV-2 virus as evidenced by seropositivity to SARS-CoV-2 whole spike protein. We adjusted our estimates using classical methods and Bayesian modelling to account for assay performance. We performed multivariable logistic regression to test associations between seropositivity and age category, time period and sex. Results We recruited 2,559 individuals from the three HDSS sites, median age (IQR) 27years (10-78) and 52% were female. Seroprevalence at all three sites rose steadily during the study period. In Kilifi, Kisumu and Nairobi, seroprevalences at the beginning of the study were 14.5 % (9.1-21), 36.0 (28.2-44.4) and 32.4 % (23.1-42.4) respectively; at the end they were 27.6 % (21.4-33.9), 42.0 % (34.7-50.0) and 50.2 % (39.7-61.1), respectively. In multivariable logistic regression models that adjusted for sex and period of sample collections, age category was strongly associated with seroprevalence (p<0.001), with the highest seroprevalences being observed in the 35-44 and [≥]65 year age categories. Conclusion There has been substantial unobserved transmission of SARS-CoV-2 in the general population in Kenya. There is wide variation in cumulative incidence by location and age category.

Seroprevalence of anti-SARS-CoV-2 IgG antibodies among truck drivers and assistants in Kenya (preprint)

In October 2020, anti-SARS-CoV-2 IgG seroprevalence among truck drivers and their assistants (TDA) in Kenya was 42.3%, higher than among other key populations. TDA transport essential supplies during the COVID-19 pandemic, placing them at increased risk of being infected and of transmitting SARS-CoV-2 infection over a wide geographical area.

The importance of supplementary immunisation activities to prevent measles outbreaks during the COVID-19 pandemic in Kenya (preprint)

BackgroundThe COVID-19 pandemic has disrupted routine measles immunisation and supplementary immunisation activities (SIAs) in most countries including Kenya. We assessed the risk of measles outbreaks during the pandemic in Kenya as a case study for the African Region. MethodsCombining measles serological data, local contact patterns, and vaccination coverage into a cohort model, we predicted the age-adjusted population immunity in Kenya and estimated the probability of outbreaks when contact-reducing COVID-19 interventions are lifted. We considered various scenarios for reduced measles vaccination coverage from April 2020. FindingsIn February 2020, when a scheduled SIA was postponed, population immunity was close to the herd immunity threshold and the probability of a large outbreak was 22% (0-46). As the COVID-19 restrictions to physical contact are lifted, from December 2020, the probability of a large measles outbreak increased to 31% (8-51), 35% (16-52) and 43% (31-56) assuming a 15%, 50% and 100% reduction in measles vaccination coverage. By December 2021, this risk increases further to 37% (17-54), 44% (29-57) and 57% (48-65) for the same coverage scenarios respectively. However, the increased risk of a measles outbreak following the lifting of restrictions on contact can be overcome by conducting an SIA with [≥] 95% coverage in under-fives. InterpretationWhile contact restrictions sufficient for SAR-CoV-2 control temporarily reduce measles transmissibility and the risk of an outbreak from a measles immunity gap, this risk rises rapidly once physical distancing is relaxed. Implementing delayed SIAs will be critical for prevention of measles outbreaks once contact restrictions are fully lifted in Kenya. FundingThe United Kingdoms Medical Research Council and the Department for International Development