Recombination and lineage-specific mutations led to the emergence of SARS-CoV-2

Juan Angel Patino-Galindo; Ioan Filip; Mohammed AlQuraishi; Raul Rabadan

To trace back the potential time of the recombination event involving ancestral lineages of SARS-CoV and SARS-CoV-2, we used a Bayesian Phylogenetic approach 14 in the recombinant region (codons 200-500 in the Spike gene) and compared with the whole genome phylogeny ( Figure 3b ). As in the full genome phylogeny, SARS-CoV-2 and RaTG13 were in the same clade, with human SARS-CoV as an outgroup. In light of these results, there two possible scenarios to consider. The first is that SARS-CoV-2 derives from a recombination event between human SARS-CoV and another (unsampled) SARS-like CoV. The second is that there occurred at least two different recombination events, one leading to human SARS-CoV and another one leading to SARS-CoV-2. In either of these two scenarios, the inferred the time to the most recent common ancestor in the recombinant region of the clade leading to RaTG13 and SARS-CoV-2 is no later than 2009 (2003-2013, 95% HPD limit).