2019_nCoV/SARS-CoV-2: rapid classification of betacoronaviruses and identification of Traditional Chinese Medicine as potential origin of zoonotic coronaviruses

Wassenaar, T.M.; Zou, Y.

This lack of homologous DNA sequences was a bit surprising, as Lu et al. (2020) recently published a phylogenetic tree based on 50 genome sequences (including 10 2019_nCoV isolates) with high bootstrap values, which can only be obtained with sufficient degrees of conservation between members of the data set. Their analysis was based on complete genomes (presumably, nucleotide sequences), whereas in our pilot analysis only protein-coding nucleotide sequences were compared. This initiated an analysis to identify how much of the phylogenetic signal and conservation was actually present in noncoding regions of the viral genomes. In case of coronavirus these are mostly restricted to the 5'-and 3-'end flanks, as all open reading frames are tightly packed. Therefore, a more extensive comparison was performed, this time with either the 5'-or the 3'-end noncoding flanks, obtained from 31 whole genome sequences covering all subspecies of Betacoronavirus (Table 1) . This selection included the most variable genomes identified by Lu and colleagues, complemented with other members of the subgenera, while genomes with high similarity to another genome were discarded to remove redundancy. The phylogenetic trees obtained with these two noncoding regions are shown in Fig. 1 . Both fragments could separate the four subspecies, and an unclassified bat isolate from Cameroon could be identified as a member of the Nobecovirus. Another unclassified virus isolated from a Nigerian bat showed high similarity with the only other fully sequenced member of Hibecovirus, at least for its 5'-flank (Fig. 1a) .