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

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

R.R. is a member of the SAB of AimedBio in a project unrelated to the current manuscript. . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.10.942748 doi: bioRxiv preprint The copyright holder for this preprint (which was not peer-reviewed) is the . https: //doi.org/10.1101 //doi.org/10. /2020 Sliding window analysis shows (blue curve) the distribution of recombination breakpoints (either start or end) in 800 nucleotide (nt) length windows upstream (namely, in the 5' to 3' direction) of every nt position along the viral genome. The spike protein, and the RBD in particular, overlap with widows that are enriched in recombination breakpoints. Binomial test p-values (red curve) and the 5% significance level are shown (dotted line). The SARS-CoV membrane protein is highlighted (dark gray); it also shows an enrichment of recombination breakpoints.