Landscape of non-SARS-CoV-2 respiratory virus sequence data in Africa

Background Sequencing capacity in Africa greatly expanded during the COVID-19 pandemic. However, the availability of sequence data for non-SARS-CoV-2 respiratory viruses in the region remains uncertain. We systematically analysed sequence data from GenBank, GISAID and Pathoplexus for 12 non-SARS-CoV-2 respiratory virus groups from Africa and compared Africa's genomic record availability with global genomic datasets. We further examined global genomic sequences to identify virus-specific patterns that could inform respiratory virus monitoring efforts in Africa. Results In Africa, the most sequenced virus was respiratory syncytial virus (RSV) (n=15,452), followed by influenza A virus (IAV) (n=10,900) and rhinovirus (n=4,774), when all sequences, including partial ones, were considered. Kenya and South Africa together contributed more than 60% of African respiratory virus sequences, while 30% of African countries submitted none. Within the global dataset of near-complete genomes, IAV was the most sequenced virus in Africa, consistent with global trends. However, Africa contributed the second-lowest number of genomes per million population among all world regions, exceeding only Asia. Substantial differences in relative genetic diversity were observed across viruses. Cytomegalovirus (94%) and parechovirus (38%) showed high sequence retention after clustering, with their clusters typically comprising sequences from a single region. In contrast, influenza viruses and RSV exhibited lower retention, with most clusters circulating across world regions. Additionally, sequences generated through next-generation sequencing were generally more complete than those obtained using Sanger sequencing. Conclusions Our analysis revealed substantial regional disparities in respiratory virus sequence availability across Africa, along with differences in diversity and geographical distribution patterns observed among viruses. This indicates the need for tailored and virus-specific surveillance strategies. Expanding sequencing capacity in more African nations is crucial for a clearer understanding of respiratory viruses circulating in Africa. Ultimately, this can guide vaccine and diagnostic development as well as performance assessment, aiding pandemic preparedness through the timely detection of emerging respiratory viruses.