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.

Background Between March and December, 2020, more than 20 000 laboratory-confirmed cases of SARS-CoV-2 infection were reported in Zambia. However, the number of SARS-CoV-2 infections is likely to be higher than the confirmed case counts because many infected people have mild or no symptoms, and limitations exist with regard to testing capacity and surveillance systems in Zambia. We aimed to estimate SARS-CoV-2 prevalence in six districts of Zambia in July, 2020, using a population-based household survey. Methods Between July 4 and July 27, 2020, we did a cross-sectional cluster-sample survey of households in six districts of Zambia. Within each district, 16 standardised enumeration areas were randomly selected as primary sampling units using probability proportional to size. 20 households from each standardised enumeration area were selected using simple random sampling. All members of selected households were eligible to participate. Consenting participants completed a questionnaire and were tested for SARS-CoV-2 infection using real-time PCR (rtPCR) and anti-SARS-CoV-2 antibodies using ELISA. Prevalence estimates, adjusted for the survey design, were calculated for each diagnostic test separately, and combined. We applied the prevalence estimates to census population projections for each district to derive the estimated number of SARS-CoV-2 infections. Findings Overall, 4258 people from 1866 households participated in the study. The median age of participants was 18•2 years (IQR 7•7-31•4) and 50•6% of participants were female. SARS-CoV-2 prevalence for the combined measure was 10•6% (95% CI 7•3-13•9). The rtPCR-positive prevalence was 7•6% (4•7-10•6) and ELISA-positive prevalence was 2•1% (1•1-3•1). An estimated 454 708 SARS-CoV-2 infections (95% CI 312 705-596 713) occurred in the six districts between March and July, 2020, compared with 4917 laboratory-confirmed cases reported in official statistics from the Zambia National Public Health Institute. Interpretation The estimated number of SARS-CoV-2 infections was much higher than the number of reported cases in six districts in Zambia. The high rtPCR-positive SARS-CoV-2 prevalence was consistent with observed community transmission during the study period. The low ELISA-positive SARS-CoV-2 prevalence might be associated with mitigation measures instituted after initial cases were reported in March, 2020. Zambia should monitor patterns of SARS-CoV-2 prevalence and promote measures that can reduce transmission. Funding US Centers for Disease Control and Prevention.

Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time and more regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and shed light on the distinct dispersal dynamics of Variants of Concern, particularly Alpha, Beta, Delta, and Omicron, on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve, while the continent faces many emerging and re-emerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

Highlights Whilst African countries were relatively spared initially when COVID-19 was first reported from China, the frequent travel links between China, Europe and Africa, meant importation of SARS-CoV-2 into Africa was inescapable. In preparation, Zambia had applied a multisectoral national epidemic disease surveillance and response system resulting in the identification of the first case within 48 hours of the individual entering the country by air travel from a trip to France. Phylogenomic analysis showed that the detected SARS-CoV-2 belonged to lineage B.1.1., sharing the last common ancestor with SARS-CoV-2 strains recovered from South Africa. At the African continental level, our analysis showed that lineage B.1 and B.1.1 lineages appear to be predominant in Africa. Whole genome sequence analysis should be part of all surveillance activities to monitor the origin and evolution of SARS-CoV-2 lineages across Africa.

ObjectivesLimited SARS CoV 2 testing in many African countries has constrained availability of data on the impact of COVID-19 (CV19). To address this gap, we conducted a systematic post-mortem surveillance study to directly measure the fatal impact of CV19 in an urban African population.DesignWe enrolled deceased individuals at the University Teaching Hospital (UTH) Morgue in Lusaka, Zambia. We obtained nasopharyngeal swabs for testing via reverse-transcriptase quantitative PCR (RT-qPCR) against the SARS-2 Coronavirus. We stratified deaths by CV19 status, by location, age, sex, and underlying risk factors.SettingUTH is Zambia’s largest tertiary care referral hospital and its morgue registers ∼80% of Lusaka’s deaths.ParticipantsParticipants of all ages were enrolled if within 48 hours of death and if the next of kin or representative provided written informed consent.ResultsWe enrolled 372 participants between June and September 2020, and had PCR results for 364 (99.5%). CV19 was detected in 70/364 (19.2%). The median age for CV19+ deaths was 48 years (IQR 36-72 years) and 70% were male. Most CV19+ deaths (51/70, 72.8%) occurred in the community; none had been tested for CV19 antemortem. Among the 19/70 facility deaths, six were tested antemortem. Among the 52/70 CV19 deaths with symptoms data, 44/52 had typical symptoms of CV19 (cough, fever, shortness of breath), of whom only five were tested antemortem. We identified CV19 among seven children; only one had been tested antemortem. The proportion of CV19+ deaths increased with age, but 75.7% of CV19+ deaths were aged <60 years. The five most common co-morbidities among CV19+ deaths were: tuberculosis (31.4%); hypertension (27.1%); HIV/AIDS (22.9%); alcohol use (17.1%); and diabetes (12.9%).ConclusionsContrary to expectations, CV19+ deaths were common in Lusaka. The majority occurred in the community where testing capacity is lacking. Yet few who died at facilities were tested, despite presenting with typical symptoms of CV19. Therefore, CV19 cases were under reported because testing was rarely done, not because CV19 was rare. If our data are generalizable, the impact of CV19 in Africa has been vastly underestimated.

Introduction Healthcare workers (HCWs) in Zambia have become infected with SARS-CoV-2, the virus that causes coronavirus disease (COVID-19). However, SARS-CoV-2 prevalence among HCWs is not known in Zambia. Methods We conducted a cross-sectional SARS-CoV-2 prevalence survey among Zambian HCWs in twenty health facilities in six districts in July 2020. Participants were tested for SARS-CoV-2 infection using polymerase chain reaction (PCR) and for SARS-CoV-2 antibodies using enzyme-linked immunosorbent assay (ELISA). Prevalence estimates and 95% confidence intervals (CIs), adjusted for health facility clustering, were calculated for each test separately and a combined measure for those who had PCR and ELISA performed. Results In total, 660 HCWs participated in the study, with 450 (68.2%) providing nasopharyngeal swab for PCR and 575 (87.1%) providing a blood specimen for ELISA. Sixty-six percent of participants were females and the median age was 31.5 years (interquartile range 26.2–39.8 years). The overall prevalence of the combined measure was 9.3% (95% CI 3.8%–14.7%). PCR-positive prevalence of SARS-CoV-2 was 6.6% (95% CI 2.0%–11.1%) and ELISA-positive prevalence was 2.2% (95% CI 0.5%–3.9%). Conclusions SARS-CoV-2 prevalence among HCWs was similar to a population-based estimate (10.6%) during a period of community transmission in Zambia. Public health measures such as establishing COVID-19 treatment centers before the first cases, screening for COVID-19 symptoms among patients accessing health facilities, infection prevention and control trainings, and targeted distribution of personal protective equipment based on exposure risk might have prevented increased SARS-CoV-2 transmission among Zambian HCWs.

IntroductionDuring March-December 2020, Zambia recorded 20,725 confirmed COVID-19 cases, with the first wave peaking between July and August. Of the 388 COVID-19-related deaths occurring nationwide, most occurred in the community. We report findings from COVID-19 mortality surveillance among community deaths brought to the University Teaching Hospital (UTH) mortuary in Lusaka.MethodsIn Zambia, when a person dies in the community, and is brought into a health facility mortuary, they are recorded as ‘brought in dead’ (BID). The UTH mortuary accepts persons BID for Lusaka District, the most populated district in Zambia. We analyzed data for persons BID at UTH during 2020. We analyzed two data sources: weekly SARS-CoV-2 test results for persons BID and monthly all-cause mortality numbers among persons BID. For all-cause mortality among persons BID, monthly deaths during 2020 that were above the upper bound of the 95% confidence interval for the historic mean (2017-2019) were considered significant. Spearman’s rank test was used to correlate the overall percent positivity in Zambia with all-cause mortality and SARS-CoV-2 testing among persons BID at UTH mortuary.ResultsDuring 2020, 7,756 persons were BID at UTH (monthly range 556-810). SARS-CoV-2 testing began in April 2020, and through December 3,131 (51.9%) of 6,022 persons BID were tested. Of these, 212 (6.8%) were SARS-CoV-2 positive with weekly percent test positivity ranging from 0-32%, with the highest positivity occurring during July 2020. There were 1,139 excess persons BID from all causes at UTH mortuary in 2020 compared to the 2017-2019 mean. The monthly number of persons BID from all causes was above the upper bound of the 95% confidence interval during June-September and December.ConclusionIncreases in all-cause mortality and SARS-CoV-2 test positivity among persons BID at UTH mortuary corresponded with the first peak of the COVID-19 epidemic in June and August 2020, indicating possible increased mortality related to the COVID-19 epidemic in Zambia. Combining all-cause mortality and SARS-CoV-2 testing for persons BID provides useful information about the severity of the epidemic in Lusaka and should be implemented throughout Zambia.

Pernicious anemia (PA) is a rarely considered cause of anemia in HIV-infected population and is seldom on the list of differential diagnoses. However, PA can have serious consequences if misdiagnosed or left untreated. We present the case of a 38-year-old HIV-positive man who was diagnosed with PA, which was preceded by a one-year history of vitiligo. Our case is a reminder for clinicians to have a high index of suspicion for an autoimmune process as a potential cause of anemia in HIV-infected individuals.