Phylogenomics for Tracking the Epidemiology of COVID-19: The Genomic Data Gap for the African Continent

The COVID-19 pandemic has disrupted health systems the world over, resulting in the loss of many lives and destabilising economies. Phylogenomic tracking of the pandemic represents one of the ways to monitor its spread in real-time. However, effective phylogenomic monitoring is dependent on the generation and analysis of rich genomic datasets. In this study, we performed phylogenetic analysis on SARS-CoV-2 genome data for the African continent to illustrate the spread of the pandemic. Africa's contribution to the SARS-CoV-2 genome data stands at just under 2% of the global total, with only seven countries currently represented on the NCBI virus database, and 16 countries on the GISAID database, as of 10 August 2020. A large portion of the data (79%) in NCBI is from Egypt, while sequence data from South Africa (48%) dominates the GISAID collection. Although there exist a massive data gap in terms of geographic coverage and scale across both databases, the inferred phylogeny is consistent with Egypt having the first reported case of COVID-19 on the continent, with multiple independent infections in other parts of Africa. However, we identify significant incongruences in the timing of sampling and placement of sequence on the inferred phylogeny. We surmise that the source of incongruence is a probable discrepancy between sample collection and sequence generation, leading to phylogenetic placements that violate basic rule of molecular evolutionary progression. Consequently, we propose the rapid processing of samples destined for sequencing as soon as they are collected, as Africa gradually increases its SARS-CoV-2 genomic footprint. We also advocate for the release of SARS-CoV-2 genomic sequences to the public domain to facilitate quality research around the virus.