Circulation and genetic diversity of Feline coronavirus type I and II from clinically healthy and FIP‐suspected cats in China

Li, Chunqiu; Liu, Qiujin; Kong, Fanzhi; Guo, Donghua; Zhai, Junjun; Su, Mingjun; Sun, Dongbo

Feline infectious peritonitis (FIP) is a fatal infectious disease of wild and domestic cats, and the occurrence of FIP is frequently reported in China. To trace the evolution of type I and II feline coronavirus in China, 115 samples of ascetic fluid from FIP‐suspected cats and 54 fecal samples from clinically healthy cats were collected from veterinary hospitals in China. The presence of FCoV in the samples was detected by RT‐PCR targeting the 6b gene. The results revealed that a total of 126 (74.6%, 126/169) samples were positive for FCoV: 75.7% (87/115) of the FIP‐suspected samples were positive for FCoV, and 72.2% (39/54) of the clinically healthy samples were positive for FCoV. Of the 126 FCoV‐positive samples, 95 partial S genes were successfully sequenced. The partial S gene‐based genotyping indicated that type I FCoV and type II FCoV accounted for 95.8% (91/95) and 4.2% (4/95), respectively. The partial S gene‐based phylogenetic analyses showed that the 91 type I FCoV strains exhibited genetic diversity; the four type II FCoV strains exhibited a close relationship with type II FCoV strains from Taiwan. Three type I FCoV strains, HLJ/HRB/2016/10, HLJ/HRB/2016/11 and HLJ/HRB/2016/13, formed one potential new clade in the nearly complete genome‐based phylogenetic trees. Further analysis revealed that FCoV infection appeared to be significantly correlated with a multi‐cat environment (p < 0.01) and with age (p < 0.01). The S gene of the three type I FCoV strains identified in China, BJ/2017/27, BJ/2018/22 and XM/2018/04, exhibited a six nucleotide deletion (C(4035) AGCTC (4040)). Our data provide evidence that type I and type II FCoV strains co‐circulate in the FIP‐affected cats in China. Type I FCoV strains exhibited high prevalence and genetic diversity in both FIP‐affected cats and clinically healthy cats, and a multi‐cat environment and age (<6 months) were significantly associated with FCoV infection.