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Covid-19 deaths in Africa: prospective systematic postmortem surveillance study

BMJ 2021; 372 doi: (Published 17 February 2021) Cite this as: BMJ 2021;372:n334

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Covid-19 in Africa

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  1. Lawrence Mwananyanda, adjunct research professor, chief medical officer*12,
  2. Christopher J Gill, associate professor1*,
  3. William MacLeod, associate professor1,
  4. Geoffrey Kwenda, professor3,
  5. Rachel Pieciak, research fellow1,
  6. Zachariah Mupila, head of ZPRIME Molecular Laboratory4,
  7. Rotem Lapidot, assistant professor5,
  8. Francis Mupeta, clinical professor6,
  9. Leah Forman, statistician7,
  10. Luunga Ziko, registrar6,
  11. Lauren Etter, research fellow1,
  12. Donald Thea, professor1
  1. 1Department of Global Health, Boston University School of Public Health, Boston, MA 02118, USA
  2. 2Right To Care – Zambia
  3. 3Department of Biomedical Sciences, University of Zambia, Lusaka, Zambia
  4. 4ZPRIME Molecular Laboratory, University Teaching Hospital, Lusaka, Zambia
  5. 5Department of Global Health, Boston University School of Public Health, Boston, MA, USA
  6. 6Division of Internal Medicine, Infectious Diseases Section, University Teaching Hospital, Lusaka, Zambia
  7. 7Biostatistics and Epidemiology Data Analytics Center, Boston University School of Public Health, Boston, MA, USA
  8. *Contributed equally
  1. Correspondence to: Christopher J Gill cgill{at} (or @iddocgill on Twitter)
  • Accepted 3 February 2021


Objective To directly measure the fatal impact of coronavirus disease 2019 (covid-19) in an urban African population.

Design Prospective systematic postmortem surveillance study.

Setting Zambia’s largest tertiary care referral hospital.

Participants Deceased people of all ages at the University Teaching Hospital morgue in Lusaka, Zambia, enrolled within 48 hours of death.

Main outcome measure Postmortem nasopharyngeal swabs were tested via reverse transcriptase quantitative polymerase chain reaction (PCR) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Deaths were stratified by covis-19 status, location, age, sex, and underlying risk factors.

Results 372 participants were enrolled between June and September 2020; PCR results were available for 364 (97.8%). SARS-CoV-2 was detected in 58/364 (15.9%) according to the recommended cycle threshold value of <40 and in 70/364 (19.2%) when expanded to any level of PCR detection. The median age at death among people with a positive test for SARS-CoV-2 was 48 (interquartile range 36-72) years, and 69% (n=48) were male. Most deaths in people with covid-19 (51/70; 73%) occurred in the community; none had been tested for SARS-CoV-2 before death. Among the 19/70 people who died in hospital, six were tested before death. Among the 52/70 people with data on symptoms, 44/52 had typical symptoms of covid-19 (cough, fever, shortness of breath), of whom only five were tested before death. Covid-19 was identified in seven children, only one of whom had been tested before death. The proportion of deaths with covid-19 increased with age, but 76% (n=53) of people who died were aged under 60 years. The five most common comorbidities among people who died with covid-19 were tuberculosis (22; 31%), hypertension (19; 27%), HIV/AIDS (16; 23%), alcohol misuse (12; 17%), and diabetes (9; 13%).

Conclusions Contrary to expectations, deaths with covid-19 were common in Lusaka. Most occurred in the community, where testing capacity is lacking. However, few people who died at facilities were tested, despite presenting with typical symptoms of covid-19. Therefore, cases of covid-19 were under-reported because testing was rarely done not because covid-19 was rare. If these data are generalizable, the impact of covid-19 in Africa has been vastly underestimated.


  • Contributors: CJG was the co-principal investigator for the project, secured funding, helped to develop the protocol and data collection tools, contributed to the analysis, wrote the first draft of the paper, and managed the review process. LM was the co-principal investigator on the project, helped to develop the protocol and tools, supervised the field team, ensured data collection, and contributed to the manuscript and its revision. WM was the study statistician, developed the statistical analysis plan, oversaw data collection and warehousing, did the analyses, and contributed the manuscript. GK supervised the PCR laboratory team, contributed to the analysis of data, ensured the quality and fidelity of the PCR testing, and contributed to the manuscript. RP helped to develop the protocol and tools, was the project manager, contributed to data quality control, and contributed to the paper. RL helped to develop the tools and protocol, supported the project as it was being implemented, and contributed to the final manuscript. FM contributed to the analysis and reporting of the paper. LF was the data manager for the team, did analyses for the paper, and contributed to the manuscript. LE contributed to the analysis and reporting of the paper and developed figures for the manuscript. DT contributed to the protocol, tools, analysis, and reporting of the paper. The corresponding author attests that all listed authors meet authorship criteria and that no others meeting the criteria have been omitted. CJG and LM are the guarantors.

  • Funding: The ZPRIME study and the covid-19 expansion were made possible through the generous support of the Bill & Melinda Gates Foundation (OPP 1163027). The funders had no role in designing the study; in the collection and analysis of data; or in the decision to submit the article for publication. An earlier version of the manuscript was shared with the team at the Gates Foundation, and some of their comments were incorporated into the final version.

  • Competing interests: All authors have completed the ICMJE uniform disclosure form at and declare: support from the Bill & Melinda Gates Foundation; no financial relationships with any organizations that might have an interest in the submitted work in the previous three years; no other relationships or activities that could appear to have influenced the submitted work.

  • Ethical approval: Ethical oversight for ZPRIME and the covid-19 expansion were provided by the institutional review boards at Boston University and the University of Zambia. Written informed consent was obtained from the deceased’s family members or representatives.

  • Data sharing: All data from this analysis can be shared on the basis of a reasonable request through a formal data sharing agreement between both parties.

  • The lead authors affirm that the manuscript is an honest, accurate, and transparent account of the study being reported; that no important aspects of the study have been omitted; and that any discrepancies from the study as originally planned (and, if relevant, registered) have been explained.

  • Dissemination plans: To date our results have been disseminated in written, verbal, and electronic formats. Specifically, the results have been presented twice to the Zambian Ministry of Health by co-principal investigator LM. In addition, we have presented our data to the epidemiology working group at the Gates Foundation; to colleagues in Malawi supported by the Wellcome Trust; to colleagues at USAID and CDC; to the epidemiology modeling group at the Institute for Disease Modeling at the Bill & Melinda Gates Foundation; through several media outlets; via a series of web based seminars and a conference at Boston University; and through our own press releases from Boston University. The study has been available as a pre-print version on MedArxiv since Dec 24, 2020.

  • Provenance and peer review: Not commissioned; externally peer reviewed.

  • Publisher’s note: Published maps are provided without any warranty of any kind, either express or implied. The BMJ remains neutral with regard to jurisdictional claims in published maps.

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