Identification and complete genome analysis of a novel feline picornavirus from the domestic cat in Hong Kong

Abstract

OBJECTIVES: Picornaviruses are known to infect human and various animals in which they can cause many diseases of varying severity. Since the role and existence of picornaviruses in cats have been largely unkown, we attempted to study the presence of previously undescribed picornaviruses in domestic cats in Hong Kong. METHODS: A cat surveillance study was conducted during a 39-month period, in which samples from 662 stray cats captured from 32 different locations in Hong Kong were collected. Viral RNA extracted from respiratory, fecal, urine and serum samples was used as the template for RT-PCR. Initial picornavirus screening was performed by RT-PCR of 3Dpol gene of picornaviruses using conserved primers. And subsequent screening of novel “feline picornavirus” (“FePV”) was performed by RT-PCR of 2C gene using specific primers, which were designed from the sequence of the first positive sample detected in the initial screening. Five genomes of “FePV” were amplified and sequenced, and the sequences were compared to those of other picornaviruses. RESULTS: “FePV” was detected in fecal samples of 14 cats and urine samples of two cats by RT-PCR among 662 cats. Analysis of five “FePV” genomes revealed distinct phylogenetic position and genomic features. The five “FePV” strains formed a distinct group among known picornaviruses in all three phylogenetic trees constructed using the P1, P2 (excluding 2A) and P3 (excluding 3A) regions. While the high sequence similarity and similar genome organization of the five strains suggested a single species of “FePV”, two potential genotypes may exist based on phylogenetic analysis of VP1 sequences. “FePV” is most closely related to the recently described bat picornaviruses group 1 to 3 and the genus Sapelovirus, while analysis of G+C content and sequences of P1, P2 and P3 regions showed that it is more closely related to bat picornaviruses, especially bat picornavirus group 3, than to sapeloviruses. “FePV” also exhibited other unique genomic features, including a putative type IV IRES instead of type I IRES in bat picornavirus group 3, different protein cleavage sites and H-D-C catalytic triad in 3Cpro, and the shortest leader protein among picornaviruses. CONCLUSION: In this study, we identified a novel feline picornavirus from the domestic cat in Hong Kong. Based on its distinct phylogenetic position and genomic features, we believe “FePV” may be more appropriately classified under a new genus separate from Sapelovirus.