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

Another early study attempting to understanding the infection of 2019-nCoV was performed by Ji et al. 4 . In this study, the authors analyzed the Relative Synonymous Codon Usage (RSCU) of 2019-nCoV and 8 vertebrates, including two species of snakes (Bungarus multicinctus and Naja atra), hedgehog (Erinaceus europaeus), bat (Rhinolophus sinicus), marmot (Marmota), pangolin (manis javanica), chicken (Gallus gallus), and human (Homo sapiens). Among these vertebrates, snakes have the smallest codon usage difference (squared Euclidiean distance of RSCU) from 2019-nCoV and were therefore proposed by Ji et al. as the intermediate hosts of 2019-nCoV. This conclusion is controversial among virologists, mainly due to the lack of prior biological evidence that coronavirus can infect animals other than mammals and birds 15 . In this report, we further scrutinize the bioinformatics approach and the underlying biological assumptions by a large-scale replication of the RSCU analysis.