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.

DISPATCHESM any key epidemiologic and serologic characteristics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remain unknown. Few seroprevalence studies have been conducted in Africa to better understand the landscape of humoral immunity. In Sudan, 32,846 confirmed cases of coronavirus disease (COVID-19) were recorded during March 13, 2020-April 10, 2021; of those, 72% were registered in the state of Khartoum alone (1). A study of a convenience sample of >1,000 participants from 22 neighborhoods of the city of Khartoum in March-July 2020 found that 35% of participants were positive by real time RT-PCR for SARS-CoV-2, and 18% had SARS-CoV-2 antibodies (2). Similar discrepancies between clinical confirmed cases and infection rates assessed by serology or PCR testing independent of symptoms have been described elsewhere in Africa (3-5).The National Health Review Ethics Committee (no. 3-1-21), Médecins Sans Frontières Ethics Review Board (ID 2089c), and Khartoum State Ministry of Health approved this study. Before field data collection began, we visited the leader of the resistance committee for each block to obtain verbal consent. For the mortality survey, we obtained verbal consent from the head of the household. For the seroprevalence survey, we obtained written informed consent from adults and, for participants <18 years of age, first written informed consent from parents or legal guardians and second, oral assent from the participants themselves. The StudySudan's capital, Khartoum, is a tripartite metropolis comprising Khartoum, Bahri, and Omdurman; it has >8 million inhabitants (6). We chose Omdurman, the largest of the 3 cities, as the study site for 2 surveys conducted in March-July 2020 (Appendix, https:// wwwnc.cdc.gov/EID/article/28/5/21-1951-App1. pdf). One, a retrospective mortality survey, was conducted using a 2-stage cluster sampling methodology based on random geopoints with 2 recall periods, the prepandemic (January 1, 2019-February 29, 2020) and the pandemic period (March 1, 2020-date of survey); an adult representative of the household answered a standardized questionnaire. The second was a nested SARS-CoV-2 antibody prevalence survey; all the members of a subset of the household, regardless of age, were invited to participate in the seroprevalence study.Capillary blood was collected on dried blood spot cards and directly tested with the STANDARD

Background Even after adjusting for the expected lower severity due to the younger age of the population, relatively low SARS–CoV–2 incidence and mortality rates have been reported throughout Africa. For investigating whether this is truly the case, we conducted a survey to estimate the COVID–19 related mortality and cumulative incidence of SARS–CoV–2 infections in Omdurman the most populated city of the tripartite metropolis Khartoum in Sudan. Methods A retrospective, cross–sectional, mortality and seroprevalence survey was conducted in Omdurman, Sudan, from March 1, until April 10 2021. A two–stage cluster sampling method was used to investigate the death rate for the pre–pandemic (January 1, 2019–February 29, 2020) and pandemic (March 1, 2020 – day of the survey) period using questionnaires. The seroprevalence survey was performed in a subset of households and all consenting members were tested with a rapid serological test (SD–Biosensor) and a subgroup additionally with ELISA (EUROIMMUN). Fisher′s exact test was used to assess differences between the pre–and pandemic periods and a random effect and Bayesian latent class model to adjust for test performance. Findings Data from 27315 people (3716 households) for the entire recall period showed a 67% (95% CI 32–110) increase in death rate between the pre–pandemic (0.12 deaths/10000 people/day [95% CI 0.10–0.14]) and pandemic (0.20 [0.16–0.23]) periods. Notably, a 74% (30–133) increase in death was observed among people aged ≥50 years. The adjusted seroprevalence of SARS–CoV–2 was 54.6% (95% CI 51.4–57.8). The seroprevalence was significantly associated with age, increasing up to 80.7% (71.7–89.7) for the oldest age group (≥50 years). Interpretation Our results showed a significant elevated mortality for the pandemic period with a considerable excess mortality in Omdurman, Sudan. The overall high seroprevalence indicated a different age pattern compared to other countries, with a significant increase by age. Funding Medécins Sans Frontières

Background: Antimicrobial resistance (AMR) is becoming a critical public health issue globally. The World Health Organization launched the Global Antimicrobial Resistance and Use Surveillance System (GLASS) to support the strengthening of the AMR evidence base.Objective: The article describes the evolution of national AMR surveillance systems and AMR data reporting of countries in the African continent between 2017 and 2019, and the constraints, perceived impact and value of the participation in GLASS.Methods: Data on implementation of national surveillance systems and AMR rates were submitted to GLASS between 2017 and 2019 and summarised though descriptive statistics. The information on constraints and perceived impact and value in GLASS participation was collected though a set of questionnaires.Results: Between 2017 and 2019, Egypt, Ethiopia, Madagascar, Malawi, Mali, Mozambique, Nigeria, South Africa, Sudan, Tunisia, Uganda and Zambia submitted data to GLASS. The main constraints listed are linked to scarce laboratory capacity and capability, limited staffing, budget issues, and data management. Moreover, while the data are not yet nationally representative, high resistance rates were reported to commonly-used antibiotics, as the emerging resistance to last treatment options.Conclusion: Despite the limitations, more and more countries in the African continent are working towards reaching a status that will enable them to report AMR data in a complete and systematic manner. Future improvements involve the expansion of routine surveillance capacity for several countries and the implementation of surveys that allow to effectively define the magnitude of AMR in the continent.

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