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

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

The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.02.07.939207 doi: bioRxiv preprint from bats to humans 2 , here we present evidence that nCoV-2019 likely arose from yet another recombined coronavirus in an intermediate host. A dataset describing the viral diversity in Malayan pangolins 3 yielded a coronavirus genome that shares 89% nucleotide ( Figure 1A and 1B) and 98% amino acid ( Figure 1C ) identity across the same RBM segment with nCoV-2019. Additionally, the RaTG13 genome only shares one out of five key amino acids involved in receptor binding motif 2 , whereas the pangolin coronavirus shares all five key residues ( Figure 1C) . It therefore appears that the RBM in nCoV-2019 was introduced during a recombination event between the strain of coronavirus found in the pangolin and RaTG13. Given the heavy selective pressure under which the RBM is constrained, it is unlikely that RaTG13 acquired the mutations found in the pangolin coronavirus genome through random chance. We posit that the homology at the RBM between nCoV-2019 and a pangolin coronavirus may have arisen from a recombination event based on sequence analysis presented herein.