Bioinformatics analysis of the 2019 novel coronavirus genome

ABSTRACT

In December 2019, a pneumonia outbreak caused by a human coronavirus was reported in Wuhan (China). This virus was predicted as a new coronavirus, named the 2019 novel coronavirus (2019-nCoV), as it caused clinical symptoms different from Severe Acute Respiratory Syndrome (SARS) during the 2003 outbreak. Currently, most of the researchers simply use the complete genome or specific structural gene sequences to investigate coronavirus (e. g. phylogenetic analysis) without considering the functions of the products from coronavirus genes. To overcome this shortcoming, we proposed the joint analysis of the molecular function and phylogeny, and applied it in our previous study of genomes of Betacoronavirus subgroup B(BB coronavirus). In that study, we identified a 22-bp complemented palindrome from a highly conserved Coding Sequence (CDS). Both the 22-bp complemented palindrome (named Nankai complemented palindrome) and the CDS (named Nankai CDS), evolutionary conserved in BB coronavirus genomes, were identified as genomic features associated to the molecular functions of BB coronavirus. In the present study, we used these two genomic features to trace the origin of 2019-nCoV (GenBank MN908947) and conduct a preliminary study of the mechanisms in the cross-species infection and host adaption of BB coronavirus. Our analytical results show that 2019-nCoV with large differences from the SARS coronavirus, may originate from BB coronaviruses in bats. The most important finding is that the alternative translation of Nankai CDS could produce more than 17 putative proteins, which may be responsible for the host adaption. The genotyping of 13 viruses using the 17 putative proteins revealed the high mutation rate and diversity of BB coronavirus. Our study, for the first time, aimed to explain the reason for the high host adaptability of the multi-host BB coronavirus at the molecular level using large amounts of genomic data. The findings in the present study laid foundations for the rapid detection, genotyping, vaccine development and drug design of, but not limited to BB coronavirus.