Molecular Evolutionary Analyses And Detection On Genes Of Feline Coronavirus

Feline coronavirus(FCo V)is a virus widespread in cats,which contain two biotypes called Feline infectious peritonitis virus(FIPV)and Feline enteric coronavirus(FECV),FECV always cause mild enteritis,however,FIPV is the pathogeny of Feline infectious peritonitis(FIP)which cause domestic and feral cats to die.In order to investigate if the selection pressure of FCo V sequences from different regions existed,we analyzed the key genes of FCo V sequences from domestic and other countries,providing a basis for the study of the molecular evolution mechanism and pathogenesis of FCo V.S proteins are membrane glycoproteins with signaling peptides,which are used for receptor binding and virus entry;ORF1ab encodes replicase polyproteins,which are associated with viral replication;the N protein is the nucleocapsid protein of the virus;7b gene is associated with the virulence of the virus.Therefore,we amplified and sequenced the above genes of FCo V,and phylogenetic analysis was conducted with FCo V sequences from other countries in NCBI,the results showed that all FCo V sequences from China mainland were clustered together into a single clade and some sequences from Netherlands were also clustered together with them,other sequences from Belgium,America,and Netherlands clustered together into a different clade,and only the sequences from the United Kingdom clustered together into a separate clade,which did not include sequences from any other country,therefore,the evolutionary tree reconstructed by FCo V gene sequences from above countries did not show significant regionalism.Due to the recombination of virus can affect the selection pressure analysis of sequences,we first conduct recombination analysis of virus sequence using GARD method,and the results showed that there was no obvious evidence of recombination,and it had little impact on the analysis of selection pressure.The selection pressure analysis of the sequences using PAML showed that the evolution rate of the sequences in the United Kingdom was different from that in other countries,and the evolution rate of the sequences from the United Kingdom was slightly lower.After selection pressure analysis of sites with PAML and Data Monkey,we detected 4 positive selection sites in nsp12-14 gene,10 positive selection sites in S gene,4 positive selection sites in N gene and 4 positive selection sites in 7b gene,in addition,the 245 site of S gene previously reported that can distinguish 96% FIPV from FECV strain sequences is also a positive selection site.The FEL and REL methods in the Data Monkey detected the same negative selection sites in different genes.These sites may be relatively stable and critical to the virus.106 negative selection sites were detected in nsp12-14 gene,which may be necessary for viral genome replication.168 negative selection sites were detected in S gene,which may be necessary for the virus to bind to or enter the host cell.25 negative selection sites were detected in the N gene,which may be the key to the nucleocapsid protein of the virus.17 negative selection sites were detected in the 7b gene,which may be the key to viral virulence.In all the genes we analyzed,negative selection sites we detected were more than positive selection sites,which indicated that these genes are relatively conserved.A small number of positive selection sites may help these viruses adapt to and survive in new or harmful conditions,245 site in S gene that can distinguish 96% FIPV from FECV was under positive selection,which suggested that these positive selection sites might be related to the occurrence of FIPV.