Response to comments on "Cross‐species Transmission of the Newly Identified Coronavirus 2019‐nCoV” and “Codon bias analysis may be insufficient for identifying host(s) of a novel virus”

To the Editor,

We have recently reported for the first time that severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) maybe a bat‐originated coronavirus with a recombination occurred within the spike (S) protein gene based on phylogenetic and simplot analyses. ¹ These two conclusions are supported by findings recently reported by others and are well accepted in the field of SARS‐CoV‐2 research. ² , ³ , ⁴ In addition, we speculated that snake may serve as a potential reservoir for cross‐species transmission of SARS‐CoV‐2 to humans based on limited information obtained from relative synonymous codon usage (RSCU) bias among different animal species. This later speculation was questioned by Yuzhou Gong et al and Jiating Qian et al in the preceding letters to editors. We concur with the argument that SARS‐CoV‐2 genomes used in the study were inconsistent. In fact, we used several SARS‐CoV‐2 sequences released at the time for phylogenetic analysis. However, we only included 2019 novel coronavirus (2019‐nCoV)‐MN908947 sequence in the article as usage right of the other viral genome sequences from GASID were debatable, which are similar to 2019‐nCoV‐MN908947. Regarding the inconsistent codons used for calculation of RSCU bias among different animal species, we could only use those genome reference complementary DNA (cDNAs) available from Entrez Assembly of GeneBank database. Few animal's genome reference cDNAs were not available, so we have to use all available cDNAs from Entrez Nucleotide of GeneBank database. It should be noted that some of the coding sequences from GeneBank database do not have the initiation codon ATG and multiple of three nucleotides characteristics and therefore were not included. If these sequences were incorporated into the final poly coding sequence, RSCU results would be affected by artificial frameshift mutation. The speculation that snake may serve as a potential animal reservoir was purely based on the most similar codon usage bias between SARS‐CoV‐2 andsnake, which is supported by CAI value from another study. ⁵ Besides, ENC‐plot analysis demonstrated that codon choices of SARS‐CoV‐2 can be affected not only mutation pressure but also natural selection, ⁵ which indicate that forecasting host reservoir only by RSCU are questionable. The true animal reservoir for SARS‐CoV‐2 remains controversial at present time and is warranted for further investigation.