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

BackgroundSparse 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 2020, 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+ decedents. Subsequently, we conducted a longer and far larger follow-on survey using and expanding on the same methodology. MethodsWe 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 lineages. We weighted our results to adjust for enrolment ratios and stratified them by setting (facility vs. community), time of year, age, and location. ResultsFrom 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 the AE.1 lineage and the Beta and Delta variants, respectively. During peak transmission, COVID-19 was detected in [~]90% of all deaths. 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 and overall, only [~]10% of COVID-19+ deaths were identified in life. ConclusionsCOVID-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. What is already known on this topicO_LIPreviously, we reported that COVID-19 was present among 15-19% of all decedents passing through a busy city morgue in Lusaka. C_LIO_LIData documenting the mortal impact of COVID-19 in Africa remain sparse. C_LIO_LISeveral modeling groups have also argued that COVID-19s impact in Africa has been underreported and hence underestimated. C_LI What this study addsO_LIAntemortem testing for COVID-19 captured only [~]10% of COVID-19 positive individuals indicating a substantial gap in surveillance. C_LIO_LIDuring peak transmission periods, [~]90% of all deceased individuals tested positive for COVID-19. C_LIO_LIMost COVID-19 positive deceased adults presented with symptoms typical of COVID-19, arguing that COVID-19 caused their deaths and was not a co-incidental finding. C_LIO_LIDeaths occurred across the age spectrum, including among young children, indicating a different pattern of impact from what has been seen in high income country settings. C_LIO_LIWe document three waves of transmission, attributable to the AE.1 lineage, and the Beta and Delta variants, respectively. C_LI