Background The 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. Methods Combining 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. Results In 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 34% (8–54). As the COVID-19 contact restrictions are nearly fully eased, from December 2020, the probability of a large measles outbreak will increase to 38% (19–54), 46% (30–59), and 54% (43–64) assuming a 15%, 50%, and 100% reduction in measles vaccination coverage. By December 2021, this risk increases further to 43% (25–56), 54% (43–63), and 67% (59–72) for the same coverage scenarios respectively. However, the increased risk of a measles outbreak following the lifting of all restrictions can be overcome by conducting a SIA with ≥ 95% coverage in under-fives. Conclusion While 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 these restrictions are lifted. Implementing delayed SIAs will be critical for prevention of measles outbreaks given the roll-back of contact restrictions in Kenya.

The high proportion of asymptomatic and undetected SARS-CoV-2 infections presents a challenge to tracking the progress of the pandemic and implementing control measures in Kenya. We determined the prevalence of IgG to SARS-CoV-2 in residual blood samples from mothers attending antenatal care services at 2 referral hospitals in Kenya. A total of 196 samples were analysed from Kenyatta National Hospital in Nairobi in August 2020, seroprevalence, adjusted for assay sensitivity and specificity, was 49.8% (95% CI 42.0-57.8). In Kilifi County Hospital in coastal Kenya, 419 samples were analysed between September and November 2020, seroprevalence, adjusted for assay sensitivity and specificity, increased from 1.3% (95% CI 0.03-4.8) in September to 10.9% (95% CI 6.1, 16.8) in November 2020. There has been substantial, unobserved transmission of SARS-CoV-2 in parts of Nairobi and Kilifi Counties.

Policymakers in Africa need robust estimates of the current and future spread of SARS-CoV-2. We used national surveillance PCR test, serological survey and mobility data to develop and fit a county-specific transmission model for Kenya up to the end of September 2020, which encompasses the first wave of SARS-CoV-2 transmission in the country. We estimate that the first wave of the SARS-CoV-2 pandemic peaked before the end of July 2020 in the major urban counties, with 30-50% of residents infected. Our analysis suggests, first, that the reported low COVID-19 disease burden in Kenya cannot be explained solely by limited spread of the virus, and second, that a 30-50% attack rate was not sufficient to avoid a further wave of transmission.