The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, Infectious Diseases Institute, College of Health Sciences, Makerere University, P.O. Box 22418, Kampala, Uganda
The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, Infectious Diseases Institute, College of Health Sciences, Makerere University, P.O. Box 22418, Kampala, Uganda
The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, Infectious Diseases Institute, College of Health Sciences, Makerere University, P.O. Box 22418, Kampala, Uganda
Natasha Patience Akwii
Department of Plant Sciences, Microbiology and Biotechnology, College of Natural Sciences, Makerere University, Kampala, Uganda
Esther Nakafu
College of Veterinary Medicine, Animal Resources and Bio-security (COVAB), Makerere University, Kampala, Uganda
The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, Infectious Diseases Institute, College of Health Sciences, Makerere University, P.O. Box 22418, Kampala, Uganda
Grace Kebirungi
The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, Infectious Diseases Institute, College of Health Sciences, Makerere University, P.O. Box 22418, Kampala, Uganda
Alisen Ayitewala
National Health Laboratories and Diagnostics Services, Central Public Health Laboratories, Ministry of Health, P.O Box 7272, Kampala, Uganda
Mike Nsubuga
The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, Infectious Diseases Institute, College of Health Sciences, Makerere University, P.O. Box 22418, Kampala, Uganda
Department of Biochemistry and Molecular Biology, Weill Bugando School of Medicine, Catholic University of Health and Allied Sciences, Mwanza, Tanzania
Stephen Tukwasibwe
School of Medicine, Uganda Christian University, Kampala, Uganda
The routine genomic surveillance of pathogens in diverse geographical settings and equitable data sharing are critical to inform effective infection control and therapeutic development. The coronavirus disease 2019 (COVID-19) pandemic highlighted the importance of routine genomic surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to detect emerging variants of concern. However, the majority of high-income countries sequenced >0.5% of their COVID-19 cases, unlike low- and middle-income countries. By the end of 2022, many countries around the world had managed to establish capacity for pathogen genomic surveillance. Notably, Beta and Omicron; 2 of the 5 current SARS-CoV-2 variants of concern were first discovered in Africa through an aggressive sequencing campaign led by African scientists. To sustain such infrastructure and expertise beyond this pandemic, other endemic pathogens should leverage this investment. Therefore, countries are establishing multi-pathogen genomic surveillance strategies. Here we provide a catalog of the current landscape of sequenced and publicly shared pathogens in different countries in Africa. Drawing upon our collective knowledge and expertise, we review the ever-evolving challenges and propose innovative recommendations.
