Sustained high prevalence of COVID-19 deaths from a systematic post-mortem study in Lusaka, Zambia: one year later

Abstract

Background. Sparse data documenting the impact of COVID-19 in Africa has fostered the belief that COVID-19 skipped Africa. We previously published results from a systematic postmortem surveillance at a busy inner-city morgue in Lusaka, Zambia. Between June-October 2021, we detected COVID-19 in 15-19% of all deaths and concentrated in community settings where testing for COVID-19 was absent. Yet these conclusions rested on a small cohort of 70 COVID-19+ individuals. Subsequently, we conducted a longer and far larger follow-on survey using the same methodology. Methods We obtained a nasopharyngeal swab from each enrolled decedent and tested these using reverse transcriptase quantitative PCR (RT-qPCR). A subset of samples with a PCR cycle threshold <30 underwent genotyping to identify viral variants. We weighted our results to adjust for enrolment ratios and stratified them by setting (facility vs. community), time of year, age, and location. Results From 1,118 enrolled decedents, COVID-19 was detected among 32.0% (358/1,116). We observed three waves of transmission that peaked in July 2020, January 2021, and ~June 2021 (end of surveillance). These were dominated by viral variants AE.1, Beta, and Delta, respectively. During peak transmission, COVID-19 was detected in ~90% of all deaths. COVID-19 deaths clustered in Lusakas poorest city wards. Roughly four COVID-19 deaths occurred in the community for every facility death. Antemortem testing occurred for 52.6% (302/574) of facility deaths but only 1.8% (10/544) of community deaths; overall, only ~10% of COVID-19+ deaths were identified in life. Conclusions COVID-19 had a devastating impact in Lusaka. COVID-19+ deaths occurred in all age groups and was the leading cause of death during peak transmission periods. Testing was rarely done for the vast majority of COVID-19 deaths that occurred in the community, yielding a substantial undercount. If typical, these findings contradict assertions that Africa was spared from the COVID-19 pandemic.