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.

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IntroductionIn spite of the extreme importance of an early antenatal care visit, more than 50% of Zambian pregnant women book for antenatal care late. We aimed to determine factors associated with late antenatal care booking in Zambia.MethodsData stem from the 2007 Zambia Demographic and Health Survey where information on socio-demographic, social-economic, obstetrical characteristics and timing of the first antenatal visit were extracted on all women aged 15 to 49 years. A weighted survey analysis using STATA version 12 was applied. Firstly, we explored proportions of ANC booking at 0-3 months, 4-5 month and 6-9 months. Secondly, we investigated the association between predictor variables and late antenatal care booking using univariate and multivariate logistic regression.ResultsOverall (n= 3979), the proportion of late ANC booking (booking between 4th to 9th month) was 81% disaggregated as 56% and 19% at 4 to 5 months and 6 to 9 months respectively. Women who wanted their last child later were more likely to book late than those with wanted pregnancies then (AOR: 1.35 95% CI 1.10-1.66). Women with higher education were 55% less likely to book for ANC late compared to women with no education (AOR: 0.45 95%CI: 0.27-0.74). Women aged 20-34 years were 30% more likely to book earlier than women younger than 20 years (AOR: 0.69 95% CI 0.50-0.97).ConclusionWe found high proportion of late ANC booking associated with presence of unplanned or unwanted pregnancies in this population. The concentration of this problem in lower or no education groups may be an illustration of existing inequalities which might further explain limitations in health promotion messages meant to mitigate this challenge. There is thus urgent need to re-pack health promotion message to specifically target this and related poor groups.

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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.

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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.