Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times 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 illuminate 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 reemerging 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.

SARS-CoV-2 across Africa: The impact of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been hard to track in African countries, largely because of patchy data. Wilkinson et al . curated viral genomes collected in 2021 from several countries across the continent. Outbreaks during 2020 in each African country were initiated by imported cases, mostly from Europe. As the pandemic developed, case numbers in African countries were likely many times higher than reported, and subsequent waves of the pandemic appear to have been more severe. Consequently, high-transmission variants have emerged that have spread within the continent, and African countries must be included in global control efforts. —CA

The World Health Organization African region has the greatest infectious disease burden in the world. However, many African countries have limited capacity to rapidly detect, report, and respond to public health events. The Centre for Epidemic Response and Innovation (CERI), KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP) in South Africa, and global Climate Amplified Diseases and Epidemics (CLIMADE) consortium are investing in building the capacity of African scientists in pathogen genomics and bioinformatics. A two-week long (11–21 April 2023) intensive training in wet-laboratory genomic data production, bioinformatics, and phylogenetic analyses of viral and bacterial pathogens was held in Cape Town, South Africa. Training was provided to 36 fellows with diverse backgrounds from 16 countries, 14 of which were low- and middle-income African countries. In this report, we, the fellows, share our collective experiences and describe how the learnt skills have been integrated into the operations of our home institutions to advance genomic surveillance capabilities. We identified the in-person and hands-on learning format of the training, taught by genomics experts and field application specialists, as the most impactful elements of this training event. Adaptation and miniaturisation of protocols to detect other pathogens is a great enhancement over the traditional method of using a single protocol for a pathogen. We note the duration of the training as the largest limiting factor, particularly for the computationally intensive bioinformatics sessions. We recommend this programme continue to build pathogen genomics capacity in Africa.

Background: Data on the true burden of histoplasmosis in Uganda are limited, largely due to the scarcity of epidemiological studies. We aimed to describe the nationwide burden of histoplasmosis among persons with advanced HIV disease (AHD), highlighting the major challenges in diagnosis and treatment under routine HIV care. Methods: This was a prospective longitudinal study conducted at nine health facilities in Uganda. Persons with AHD (CD4 < 200 cells/mm3) were included and followed up for 2 years. Urine samples were sent to the Central Public Health Laboratories and tested using the Histoplasma galactomannan enzyme immunoassay in batches. Histoplasmosis was defined using standard criteria. Results: We enrolled 332 participants with AHD, and 66.6% were newly diagnosed with HIV. Over half were female (51.5%), with a median age of 35 years (interquartile range [IQR] = 29–42) for all participants. The median CD4 T-cell count was 73 cells/µL (IQR = 30.5–126.5). Eight (2.4%) participants were diagnosed with probable histoplasmosis. None of the cases received the recommended antifungals because they were not available in the country. After 2 years, 5 cases were still alive, 2 were lost to follow-up, and 1 died. Major challenges included missed diagnosis, low index of clinical suspicion, overlap of symptoms with those of pulmonary TB, high cost, limited access to antifungals such as voriconazole and itraconazole, radiology and laboratory investigations, and lack of knowledge about treatment guidelines. Conclusions: Histoplasmosis occurs at a low frequency among persons with AHD in Uganda. Numerous challenges hinder a definite diagnosis and treatment. However, despite these challenges, survival among persons with AHD in Uganda who have untreated histoplasmosis is relatively good.