Fig. 2: Recombination events in the history of SARS-CoV-2.

a Variations in the sequence relatedness of different regions of SARS-CoV-2 in comparison with alternative strains of coronaviruses from pangolins (Pangolin Guangdong 2019), bats (RaTG13, Bat-SL-CoV, Rs3367), palm civets (PC4-13), and humans (Tor2). In region 1 (R1), region 2 (R2), and region 4 (R4), SARS-CoV-2 is most similar to the corresponding regions of the bat coronavirus RaTG13. In region 3 (R3), SARS-CoV-2 and the pangolin strain of coronavirus (Pangolin Guangdong 2019) are more closely related. The pangolin strain consistently clusters within bat coronavirus clades. For regions 1, 2, and 3, phylogenetic relationships were obtained from Lam et al.³²; for region 4, phylogenetic relationships were obtained from Boni et al.²⁸. Regions are colored based on their genomic position in the SARS-CoV-2 genome model (top panel). b Two scenarios hypothesizing the evolutionary timing of the recombination event that may have introduced the pangolin coronavirus sequence (region 3/R3) into SARS-CoV-2. In scenario I, after the divergence of SARS-CoV-2 and RaTG13, recombination between SARS-CoV-2 and Pangolin Guangdong 2019 resulted in the acquisition of the new sequence. In scenario II, recombination occurred between the common ancestral lineage of SARS-CoV-2 and RaTG13 and the pangolin (Pangolin Guangdong 2019) lineage, followed by the accumulation of mutations in the RaTG13 lineage.