Evidence of recombination in coronaviruses implicating pangolin origins of nCoV-2019

Matthew C. Wong; Sara J. Javornik Cregeen; Nadim J. Ajami; Joseph F. Petrosino

After merging, the final Pangolin-CoV draft genome was 90.5% similar to nCoV-2019 (median nucleotide identity). Figure 1 shows the sequence homology of Pangolin-CoV, RaTG13-CoV and Bat-CoV relative to nCoV-2019 ( Figure 1A shows the homology across the entire genome length). The multiple alignments across the RBM segments revealed an 89% nucleotide ( Figure 1B ) and 98% amino acid identity ( Figure 1C ) of the Pangolin-CoV compared to nCoV-2019. The sequence homology plots showed that the Pangolin-CoV was more similar to nCoV-2019 at the RBD region than the RaTG13-CoV and Bat-CoV ( Figure 1B) . The multiple alignment comparing the PRRA insertion region at the S1/S2 junction shows the insertion present in nCoV-2019 and missing in the other three CoV genomes ( Figure 2 ).