Longitudinal cohort study of SARS-CoV2 sero-conversion in a malaria-endemic community in Western Kenya

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In many developing countries, the Covid-19 pandemic has had limited direct impact, including Kenya, which as of 5 March 2021, has recorded only 107,329 cases and 1,870 deaths owing to Covid19. Although this limited clinical impact is in part the result of strict travel and movement restrictions and under-reporting, these low numbers contrast with seroprevalences of 4-8% in Kenyan blood donors, suggesting that a large number of Covid19 cases in Kenya are subclinical. A further consideration in such settings is the potential for interactions between SARS-CoV2 and endemic pathogens such as Plasmodium falciparum, which in Western Kenya is transmitted perennially and intensely. These asymptomatic infections shape the risk of subsequent malaria and have differential impact on hosts. In this sero-epidemiologic study, our specific objective is to investigate the spread of SARS-CoV2 in a large, densely-sampled community cohort in rural Kenya. Our longitudinal cohort consists of Kenyan household members of all ages enrolled since January 2020 in an observational study of malaria transmission in the rural district of Webuye (parent study R01 AI146849, MPI: O’Meara/Taylor). From 550 people, we have collected blood from all participants during both i) monthly surveillance visits as well as ii) at febrile sick visits, and collection will be ongoing through 2023. The SARS-CoV2 antibody Prevalence and Acquisition in Rural Kenya (SPARK) study will be a sub-study of this parent cohort, in which we will test monthly specimens collected prior to and during the Covid19 pandemic using an ELISA detecting neutralizing antibodies to the SARS-CoV2 spike protein. Baseline sero-positivity will be measured in Jan 2020 specimens, and sero-conversion as the appearance of neutralizing antibodies in a previously-negative person. Monthly questionnaires will capture recent travel and illness not previously reported to the study team. We will then, using P. falciparum detection and genotype data from the parent study, estimate the impact of P. falciparum infection on the risk of SARS-CoV2 acquisition using longitudinal statistical modelling of the effect of cumulative malaria infections and of specific parasite genotypes on the risk of sero-conversion and the risk of acute illness during sero-conversion. Our multidisciplinary team will use samples and data from a large, separately-funded, densely-sampled longitudinal community cohort to describe the community spread and sero-epidemiology of SARS-CoV2 in a rural Kenyan setting and investigate its associated with P. falciparum malaria.