Fig. 5: Recombination landscape.

A Phylogenetic network of full-length genomes of lineage 8, using the SplitsTree5 software with the Kimura 2-parameter model. Isolates in the red shaded region corresponding to the intralineage recombination within lineage 8, the green shaded region corresponds to the interlineage recombination with lineage8, with a statistically significant difference using Phi Test (p < 0.0001). B Overview of interlineage recombination patterns. The relative size of linkages from the upper part to the lower part correlates to the recombination frequency of each lineage as minor parent specific to the recombined region. For example, lineage 1 is more likely recombined as minor parent in ORF4-ORF7. C Overview of intralineage recombination patterns. The relative thickness of curve in the upper part correlates to the recombination frequency of each region as minor parent. For example, most intra-lineage recombination events result in a new doner in non-structural region. D Cumulative number of interlineage recombination events per year with color corresponding to different lineages. E Cumulative number of interlineage recombination events per year with color corresponding to different regions. F Cumulative number of intralineage recombination events per year with color corresponding to different regions. G Cumulative proportion of interlineage recombination events relating to each lineage in specific region of ORF1a (top panel) and ORF1b (bottom). H Cumulative proportion of interlineage recombination events relating to each year in specific region of ORF1a (top panel) and ORF1b (bottom). I Cumulative proportion of intralineage recombination events relating to each year in ORF1a (top panel) and ORF1b (bottom).