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.

selection of seven Sarbecovirus members, the maximum conservation at nucleotide level for gene 1a/b was 85% within a sliding window of 60 bases, compared to 93% for the downstream and 90% for the upstream flank. The longest stretch of conserved nucleotides was 22 in the upstream flank, 33 in the downstream flank and only 20 nucleotides in orf 1ab (results not shown). Only the gene coding for envelope protein E was as strongly conserved as the noncoding flanks (maximum conservation 95% over a window of 60 bases, with a longest conserved stretch of 32 nucleotides) for the seven genomes analysed here. As conservation of coding sequences decreases with third-base variation, it is likely that this degree of conservation in gene E would decrease as more genomes would be included in the comparison. Thus, restricting analyses to only comparing coding regions may reduce the chance a proposed detection target might be able to detect a novel Sarbecovirus species. Instead, we recommend inclusion of the noncoding genome regions in such attempts.