An outbreak of respiratory illness caused by a novel coronavirus (nCoV-2019, NC_045512.2) first identified in Wuhan China has resulted in over seven thousand confirmed cases. So far, the nCoV-2019 has been reported to share 96% sequence identity to the RaTG13 genome (EPI_ISL_402131). However, the S1 Receptor Binding Domain (RBD) of the nCoV-2019 genome was noticeably divergent between the two at amino acid residues 350 to 550 – Figure 1A. We aimed to identity coronaviruses related to nCoV-2019 in viral metagenomics datasets available in the public domain. In a recently published dataset describing viral diversity in Malayan pangolins (PRJNA573298) we used VirMAP to reconstruct a coronavirus genome (approximately 84% complete from samples SRR10168377 and SRR10168378) that shared 97% amino acid identity across the same RBD segment – Figure 1B. This result indicates a potential recombination event for nCoV-2019.
From the coordinates shown in this preprint (Figure 4), it looks like most of the differences between RaTG13 and nCoV-2019 are restricted to loop 2 of the receptor binding motif (positions ~450-500).
Coronavirus.from.Pangolin.fa.gz (7.8 KB)