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.

We used publicly available data to describe epidemiology, genomic surveillance, and public health and social measures from the first 3 COVID-19 pandemic waves in southern Africa during April 6, 2020–September 19, 2021. South Africa detected regional waves on average 7.2 weeks before other countries. Average testing volume 244 tests/million/day) increased across waves and was highest in upper-middle-income countries. Across the 3 waves, average reported regional incidence increased (17.4, 51.9, 123.3 cases/1 million population/day), as did positivity of diagnostic tests (8.8%, 12.2%, 14.5%); mortality (0.3, 1.5, 2.7 deaths/1 million populaiton/day); and case-fatality ratios (1.9%, 2.1%, 2.5%). Beta variant (B.1.351) drove the second wave and Delta (B.1.617.2) the third. Stringent implementation of safety measures declined across waves. As of September 19, 2021, completed vaccination coverage remained low (8.1% of total population). Our findings highlight opportunities for strengthening surveillance, health systems, and access to realistically available therapeutics, and scaling up risk-based vaccination.

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Background In December 2015, an outbreak of yellow fever virus (YFV) infection was reported in Angola, characterized by fever and jaundice, with at least one of the following symptoms: headache, asthenia, conjunctivitis, vomiting, with a different type of haemorrhage. Methods A total of 4,618 cases of yellow fever (YF) were referred to the national referral laboratory of the Instituto Nacional de Investigação em Saúde, from December 5, 2015 through December 23, 2016 that were analyzed using ELISA, and subsequently samples were confirmed using consensus primers for RT-PCR assay. Results We detected 884 (4%) cases that were positive on ELISA and RT-PCR assays. Patients were reported from 16 provinces of Angola. The incidence was approximately three times as high among male patients (10.88% per 100,000) than among female patients (2.65% per 100,000) in the 20 to 29 age group. Conclusions This study represents the transmission of YFV human-to-human via the bite of the infected vector. The re-emergence of YFV is a huge concern for a national public health system. Thus, laboratory and public health surveillance systems have to be strengthened to alleviate the risk of re-emerging human infections.