Comments on “Cross‐species transmission of the newly identified coronavirus 2019‐nCoV”

Dear Editor,

After reading the article speculating that novel coronavirus from Wuhan may be transmitted to humans through snakes, I think the most critical analysis method is the synonymous codon usage analysis, which estimated the relative synonymous codon usage (RSCU) of the 2019‐nCoV (novel coronavirus) and its potential hosts. Here, I would like to make a few comments:

First, there exists a large difference in the number of codons used in potential hosts, which would obviously cause biases and lead to an unreliable conclusion. Only 5381 codons, 9587 codons, and 8081 codons were used in Bungarus multicinctus, Naja atra, and Rhinolophus sinicus. While 16 717 458 codons, 21 090 600 codons, 22 980 491 codons, 36 086 657 codons, and 40 662 582 codons were used in Erinaceus europaeus, Marmota, Manis javanica, Gallus gallus, and human. The genome of Ophiophagus hannah (GCA_000516915.1) and Rhinolophus ferrumequinum (GCA_004115265.2) might be alternatives to estimate the RSCU in snake and bat.

Second, the measure of judgment on putative wildlife reservoir hosts is lacking. I do not think it is appropriate to conclude that Marmota was the reservoir host when B. multicinctus and N. atra were removed from the comparison.

Finally and most importantly, the result of comparison of RSCU between 2019‐nCoV and its putative wildlife reservoir hosts was lacking adequate support (Figure 1). Theoretically, the patterns and factors that affect codon usage of viruses should reflect evolutionary changes that allow them to optimize their codon usage in their hosts. But there is no evidence showing that this rule worked for coronavirus also. To make it more convincing, Middle East respiratory syndrome‐coronavirus (MERS‐CoV) and its host Camelus dromedaries (GCA_000803125.3) should be included as control. While even taking camel into consideration, we can see that it is still far away from these CoVs.

Figure 1.

Comparison of relative synonymous codon usage (RSCU) between 2019‐nCoV and its putative wildlife animal reservoir(s)

In summary, we think the conclusion that the newly identified coronavirus may boost cross‐species transmission from snake to human is inadequate, and it can lead to public misperception.