Phylogenetic reconstruction of hCoV-19 (SARS-CoV-2) genomes plays a central role in understanding viral evolution across Europe, where extensive sequencing efforts have generated dense genomic datasets since the earliest phase of the pandemic. A Europe-focused phylogenetic tree captures how viral lineages have emerged, diversified, and been replaced over time, while maintaining global context through the inclusion of selected reference genomes from outside the region.
This time-scaled phylogenetic analysis spans the full duration of the pandemic, from initial European cases in 2020 to the most recently collected genomes. The resulting tree reflects both rapid shifts in dominant lineages and longer-term evolutionary patterns, offering a detailed view of hCoV-19 diversification across successive epidemic periods.
The most recent branches of the phylogenetic tree are primarily composed of viruses assigned to XFG, which currently dominate newly deposited European sequences. These lineages form tight, well-supported clusters near the tree tips, consistent with their ongoing circulation. Alongside XFG, genomes belonging to NB.1.8.1 and BA.3 continue to appear, underscoring sustained evolutionary activity within Omicron-derived lineages.
The branching structure of the tree illustrates the accumulation of genetic changes through time and supports molecular clock-based estimates of lineage divergence. Together, these features provide insight into patterns of lineage turnover and persistence across the European region.
Recent submissions to GISAID indicate that United Kingdom, Germany, and Netherlands are currently the largest contributors of hCoV-19 genome data from Europe. The high volume of sequences from these countries improves phylogenetic resolution and allows fine-scale analysis of transmission dynamics, while also strengthening comparisons with genomes sampled in other parts of the world.
Although centered on Europe, the phylogenetic tree includes a limited number of genomes from other continents to anchor regional patterns within the global evolutionary landscape.
A Europe-focused hCoV-19 phylogenetic tree supports detailed monitoring of viral evolution and provides essential context for interpreting changes in lineage prevalence. By integrating genomic data with evolutionary analysis, this framework contributes to surveillance efforts and enhances understanding of how SARS-CoV-2 continues to evolve across Europe.
