Protein structure and sequence re-analysis of 2019-nCoV genome does not indicate snakes as its intermediate host or the unique similarity between its spike protein insertions and HIV-1

Chengxin Zhang; Wei Zheng; Xiaoqiang Huang; Eric W. Bell; Xiaogen Zhou; Yang Zhang

Here, N=61 is the number of codons that encodes amino acids, thereby excluding the 3 stop codons. X j and X j ' are the RSCU for codon j in the virus and in the vertebrate, respectively. In our report, the codon usages of all vertebrates are taken from the CoCoPUTS 21 database, which was last updated in January 2020. This database was therefore much more recent than the Codon Usage Database 22 last updated in 2007 that was used in the previous research 4 . To obtain the codon usage of coronaviruses, we imported the GenBank annotations of the three coronavirus genomes to SnapGene (GSL Biotech LLC] to export the codon usage table based on the GenBank annotations. CodonW 23 was not used for codon usage calculation as in the previous study because it cannot account for the -1 frameshift translation of the first open reading frame (ORF) in the coronavirus genome.