Sustained high prevalence of COVID-19 deaths from a systematic post-mortem study in Lusaka, Zambia: one year later
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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.
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SciScore for 10.1101/2022.03.08.22272087: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: The research was conducted with the approval of the ethical review boards from Boston University and the University of Zambia; written informed consent was obtained from the next of kin or family representative in all cases.
Consent: The research was conducted with the approval of the ethical review boards from Boston University and the University of Zambia; written informed consent was obtained from the next of kin or family representative in all cases.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Complementary DNA was synthesized using LunaScript® RT … SciScore for 10.1101/2022.03.08.22272087: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Ethics IRB: The research was conducted with the approval of the ethical review boards from Boston University and the University of Zambia; written informed consent was obtained from the next of kin or family representative in all cases.
Consent: The research was conducted with the approval of the ethical review boards from Boston University and the University of Zambia; written informed consent was obtained from the next of kin or family representative in all cases.Sex as a biological variable not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Table 2: Resources
Software and Algorithms Sentences Resources Complementary DNA was synthesized using LunaScript® RT SuperMix Kit (New England Biolabs, Ipswich, Massachusetts, USA) according to the manufacturer’s protocol and multiplex PCR was conducted using custom primers, which were designed using Geneious software version 10.0.9, as used previously to sequence the first COVID-19 case in Zambia using the Sanger method. Geneioussuggested: (Geneious, RRID:SCR_010519)The data generated through the MinION was processed using the standard ARTIC bioinformatic pipeline (https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html). MinIONsuggested: (MinION, RRID:SCR_017985)For the geospatial analyses, we used ArcGIS software (ESRI, Redlands, California, USA). ArcGISsuggested: (ArcGIS for Desktop Basic, RRID:SCR_011081)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Strengths and limitations: A strength was that our data were collected prospectively, capturing a wide spectrum of ages in community and facility settings and without prior knowledge of clinical presentation or antemortem testing results. And while all came from the UTH morgue, 80% of all deaths in the city transit this facility, making it highly representative. Additionally, we were able to combine multiple data elements on the same individual: clinical presentation, molecular testing, geography, and viral genotype, to provide an overall picture of the mortal impact of the COVID-19 pandemic in Lusaka over time. Limitations include that there was a three-month gap in surveillance between Rounds 1 and 2, and that Round 2 ended prior to the resolution of Wave 3 caused by the Delta variant. Our adjudications were necessarily limited by the completeness of clinical data for the facility deaths and by the accuracy of recall from non-medical persons through the verbal autopsy for community deaths. That could lead to some misclassification that might affect causal inferences. Our data describe impact but cannot directly provide a case fatality rate since we lack concurrent incidence data. Lastly, while Round 2 data confirm the surprisingly high proportion of pediatric deaths with COVID-19 and again show that gastrointestinal symptoms are common in children <5 years, we are no closer to inferring causality. In our judgement, resolving this question requires a higher gold standard. Th...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
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- No protocol registration statement was detected.
Results from scite Reference Check: We found no unreliable references.
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