Detection Of Feline Coronavirus And Phylogenetic Analysis Of S Gene From 2015 To 2018 In Partial Regions Of China

Feline coronavirus(FCoV)is prevalent in cats all over the world.Cats infected with FCoV can suffer from feline infectious peritonitis(FIP).FIP is one of the major infectious diseases causing cat death.There are few molecular epidemiological investigations on FCoV in China.In this study,the samples collected from 2015 to 2018 were detected for FCoV,and the partial S gene sequence and the whole genome sequence of positive samples were analyzed for genetic evolution,which increased the information of genetic evolution of FCoV strains in China and provided a basis for further research on FCoV.To clarify the infection status of FCoV among cats in China,54 fecal samples of healthy cats and 115 ascites samples of FIP suspected cats were collected from 10 areas of China from November 2015 to January 2018.Samples were detected by nested PCR,and then the correlation between clinical symptoms,geographical location,living environment,gender,breed,age and FCoV infection were analyzed.Nested PCR results showed that 126 of 169 samples were positive,positive rate of FCoV was 74.6%(126/169),75.7%(87/115)in suspected FIP cats were positive for FCoV and 72.2%(39/54)in healthy cats were positive for FCoV.The results of correlation analysis showed that infection of FCoV was related to the environment(p=0.006)and age(p=0.008).To clarify the epidemic and genetic evolution of type ? FCoV and type ? FCoV strains in China,partial S gene of FCoV-positive samples were amplified by nested PCR,and the amplified sequences were sequenced and analyzed for the genetic evolution.Then the whole genome sequences and genetic evolution of FCoV were sequenced by next-generation sequencing.Nested PCR results showed that 95 of 126 FCoV positive samples were typed,of which 91 were type ? FCoV(95.8%,91/95)and 4 were type ? FCoV(4.2%,4/95).95 partial S genes were sequenced.The sequence analysis of the partial S gene revealed that the 91 type ? FCoV strains identified had nucleotide homology of 80.4%~100.0% and amino acid homology of 78.6%~100.0%,while nucleotide and amino acid homologies of 97.6%~99.4% and96.4%~100.0% were observed among the 4 type ? FCoV strains,respectively;three type ? FCoV strains(BJ/2017/27,BJ/2018/22,and XM/2018/04)exhibited a six-nucleotide deletion(C4035AGCTC4 040)of partial S gene sequence.The partial S gene-based phylogenetic tree revealedthe genetic diversity of the 91 type ? FCoV strains,4 type ? FCoV strains identified in our study formed one clade which exhibiting a close relationship with the strains from Taiwan.Four genome sequences of type ? FCoV strains were obtained.Three FCoV strains(HLJ/HRB/2016/10,HLJ/HRB/2016/11 and HLJ/HRB/2016/13)formed a potentially new cluster,and the strain HLJ/DQ/2016/01 also formed another clade in the phylogenetic tree based on the complete genome.The complete genome nucleotide and amino acid similarity of 4 type ? FCoV strains in this study with the type ? FCoV Black strain ranged from 91.7%~92.2% and81.6%~82.6%,respectively.This study revealed that type ? and type ? FCoV strains co-circulate in the FIP suspected cats in China.Type ? FCoV strains exhibited high prevalence and genetic diversity in both FIP suspected and clinically healthy cats,and a multi-cat environment and age(<six months)were significantly associated with FCoV infection.