Phylogenetic analysis of hCoV-19 (SARS-CoV-2) genome has become a cornerstone of genomic epidemiology, enabling researchers to visualize how viral lineages evolve and spread over time.An Africa-focused hCoV-19 (SARS-CoV-2) phylogenetic tree offers critical insight into the continent’s role in the global pandemic, while still placing African sequences in a broader international context through the inclusion of selected genomes from other regions of the world.
This phylodynamics reconstruction spans the full temporal range of the pandemic, from the earliest African detections in 2020 through to the most recently collected genomes. By incorporating time-resolved sequencing data, the tree highlights both long-term evolutionary trends and recent lineage expansions, providing a dynamic view of how hCoV-19 diversity has changed across multiple epidemic waves.
The most recent portion of the phylogenetic tree is dominated by lineages belonging to XFG+XFG.*, which represent the prevailing genetic background among newly deposited African genomes. These lineages form distinct clusters near the tips of the tree, reflecting their ongoing circulation and recent emergence. Following XFG+XFG.*-related viruses, BA.3.2.2 and JN.1+JN.1.* remain well represented, illustrating continued diversification within Omicron-derived lineages.
The phylogenetic structure clearly shows how these lineages branch from earlier variants, capturing the accumulation of mutations over time and reinforcing the role of molecular clock models in dating divergence events. This evolutionary context is essential for interpreting lineage replacement, persistence, and regional spread.
Recent GISAID submissions reveal that South Africa, Egypt, and Zambia are the leading contributors of hCoV-19 (SARS-CoV-2) genome data from Africa in the current period. These three countries account for the highest number of newly deposited sequences, strengthening the resolution of phylogenetic clusters and improving regional surveillance. Their dense sampling enables more accurate inference of local transmission chains while also supporting comparisons with genomes sampled outside Africa.
Although the phylogenetic tree is Africa-centric, a limited number of sequences from other continents are intentionally included. These external genomes provide global reference points that help identify introductions into Africa, exportation events, and shared ancestry with lineages circulating elsewhere, without diluting the African focus of the analysis.
An Africa-centered hCoV-19 (SARS-CoV-2) phylogenetic tree bridges genomics and epidemiology by revealing how viral evolution aligns with geography and time. It supports genomic surveillance efforts, improves understanding of lineage turnover, and helps contextualize Africa’s viral diversity within the global pandemic landscape. As sequencing efforts continue and new lineages emerge, such phylogenetic analyses remain essential for tracking hCoV-19 (SARS-CoV-2) evolution and informing public health strategies across the continent and beyond.
