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

Abstract

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 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.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 variants. 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 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 Lusaka’s 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.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. If typical, these findings contradict assertions that Africa was spared from the COVID-19 pandemic.What is already known on this topicData documenting the mortal impact of COVID-19 in Africa remain sparse.Previously, we reported that COVID-19 was present among 15-19% of all decedents passing through a busy city morgue in Lusaka.Several modeling groups have also argued that COVID-19’s impact in Africa has been underreported and hence underestimated.But this prior analysis was based on a relatively small cohort including only seventy COVID-19 positive deaths.What this study addsFrom data collected among a larger cohort over a longer period, we again document that COVID-19 has had a severe impact in Lusaka, Zambia.Most 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.Deaths 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.We document three waves of transmission, attributable to the AE.1, Beta, and Delta variants, respectively.During peak transmission periods, ∼90% of all deceased individuals tested positive for COVID-19.Antemortem testing for COVID-19 captured only ∼10% of COVID-19 positive individuals indicating a substantial gap in surveillance.If these results are typical, the impact of COVID-19 in Africa has been vastly underestimated.

Regional importation and asymmetric within-country spread of SARS-CoV-2 variants of concern in the Netherlands

“…We aimed to sample 100 sequences each week. To ensure that countries that are underreporting cases ( Gill et al, 2022 ) were included in our analyses, at least one representative sequence was included for each country with reported cases that week. The actual number of sequences sampled each week for each variant may differ because of sequence availability and the requirement to have at least one sequence from each country each week.…”

Leveraging Serosurveillance and Postmortem Surveillance to Quantify the Impact of COVID-19 in Africa

“…To create another set of multiplicative factors, we made use of 2 Zambian postmortem surveillance studies that employed quantitative reverse transcription PCR to detect COVID-19 in decedents: Mwananyanda et al’s (2021) postmortem surveillance study, as well as its preprinted (not yet peer-reviewed) follow-up from Gill et al (2022) [20, 21]. Both studies were performed in a sample from Zambia’s capital, Lusaka, with the first conducted between June and October 2020 following the first wave of infections and the second conducted between January and June 2021 following the second wave of infections [22].…”

“…(not yet peer-reviewed) follow-up from Gill et al (2022) [20,21]. Both studies were performed in a sample from Zambia's capital, Lusaka, with the first conducted between June and October 2020 following the first wave of infections and the second conducted between January and June 2021 following the second wave of infections [22].…”

SARS-CoV-2 diagnostic testing rates determine the sensitivity of genomic surveillance programs

“…We also assumed that all symptomatic individuals who have severe symptoms require hospitalization, and are tested separately from mild symptomatic persons who sought testing. Given that likely only ~10-20% of COVID-19 deaths in Zambia were tested for the disease in life, 19,20 we assumed that 10 only 20% of individuals with severe disease would be tested by Ag-RDT or PCR upon presenting severe symptoms and have specimens collected for sequencing.…”