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

To address these issues, we re-implemented the RSCU comparison algorithm proposed by Ji et al. to analyze the codon usage in the 2019-nCoV genome (NCBI accession MN908947.3) and those of all 102,367 vertebrate species in the CoCoPUTS database. To test whether this kind of analysis can recover known hosts of well-studied coronavirus, severe acute respiratory syndrome-related coronavirus (SARS-CoV, NCBI accession NC_004718) and Middle East respiratory syndrome-related coronavirus (MERS-CoV, NCBI accession NC_019843) are also included. Codon usage frequency are converted to squared Euclidean distance of RSCU in two separate analyses: one based on all vertebrates (Figure 4A-C) and the other on the subset of vertebrates with enough statistics, i.e. >2000 known CDSs (Figure 4D-F) , roughly corresponding to 10% of all protein coding genes in a typical vertebrate genome.