title: Chickens host diverse picornaviruses originated from potential interspecies transmission with recombination.
abstract: While chickens are an important reservoir for emerging pathogens such as avian influenza viruses, little is known about the diversity of picornaviruses in poultry. We discovered a previously unknown diversity of picornaviruses in chickens in Hong Kong. Picornaviruses were detected in 87 cloacal and 7 tracheal samples from 93 of 900 chickens by reverse transcription-PCR, with their partial 3D(pol) gene sequences forming five distinct clades (I to V) among known picornaviruses. Analysis of eight genomes from different clades revealed seven different picornaviruses, including six novel picornavirus species (ChPV1 from clade I, ChPV2 and ChPV3 from clade II, ChPV4 and ChPV5 from clade III, ChGV1 from clade IV) and one existing species (Avian encephalomyelitis virus from clade V). The six novel chicken picornavirus genomes exhibited distinct phylogenetic positions and genome features different from related picornaviruses, supporting their classification as separate species. Moreover, ChPV1 may potentially belong to a novel genus, with low sequence homologies to related picornaviruses, especially in the P1 and P2 regions, including the predicted L and 2A proteins. Nevertheless, these novel picornaviruses were most closely related to picornaviruses of other avian species (ChPV1 related to Passerivirus A, ChPV2 and ChPV3 to Avisivirus A and Duck hepatitis A virus, ChPV4 and ChPV5 to Melegrivirus A, ChGV1 to Gallivirus A). Furthermore, ChPV5 represented a potential recombinant picornavirus, with its P2 and P3 regions possibly originating from Melegrivirus A. Chickens are an important reservoir for diverse picornaviruses that may cross avian species barriers through mutation or recombination.
authors.affiliation: Carol Yu Centre for Infection, University of Hong Kong, Hong Kong, PR China.|State Key Laboratory of Emerging Infectious Diseases, University of Hong Kong, Hong Kong, PR China.|Department of Microbiology, University of Hong Kong, Hong Kong, PR China.|Research Centre of Infection and Immunology, University of Hong Kong, Hong Kong, PR China.
authors.forename: Susanna K P
authors.initials: SKP
authors.lastname: Lau
authors.affiliation: Research Centre of Infection and Immunology, University of Hong Kong, Hong Kong, PR China.|Carol Yu Centre for Infection, University of Hong Kong, Hong Kong, PR China.|State Key Laboratory of Emerging Infectious Diseases, University of Hong Kong, Hong Kong, PR China.|Department of Microbiology, University of Hong Kong, Hong Kong, PR China.
authors.forename: Patrick C Y
authors.initials: PCY
authors.lastname: Woo
authors.affiliation: Department of Microbiology, University of Hong Kong, Hong Kong, PR China.
authors.forename: Cyril C Y
authors.initials: CCY
authors.lastname: Yip
authors.affiliation: Department of Microbiology, University of Hong Kong, Hong Kong, PR China.
authors.forename: Kenneth S M
authors.initials: KSM
authors.lastname: Li
authors.affiliation: Department of Microbiology, University of Hong Kong, Hong Kong, PR China.
authors.forename: Rachel Y Y
authors.initials: RYY
authors.lastname: Fan
authors.affiliation: Department of Microbiology, University of Hong Kong, Hong Kong, PR China.
authors.forename: Ru
authors.initials: R
authors.lastname: Bai
authors.affiliation: Department of Microbiology, University of Hong Kong, Hong Kong, PR China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Huang
authors.affiliation: Department of Microbiology, University of Hong Kong, Hong Kong, PR China.
authors.forename: Kwok-Hung
authors.initials: KH
authors.lastname: Chan
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases, University of Hong Kong, Hong Kong, PR China.|Research Centre of Infection and Immunology, University of Hong Kong, Hong Kong, PR China.|Carol Yu Centre for Infection, University of Hong Kong, Hong Kong, PR China.|Department of Microbiology, University of Hong Kong, Hong Kong, PR China.
authors.forename: Kwok-Yung
authors.initials: KY
authors.lastname: Yuen
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D044822:Biodiversity; D005075:Biological Evolution; D002645:Chickens / Q000821:virology*; D014644:Genetic Variation; D016678:Genome / Q000235:genetics; D016679:Genome, Viral; D008969:Molecular Sequence Data; D010802:Phylogeny; D010849:Picornaviridae / Q000145:classification* / Q000235:genetics*; D010850:Picornaviridae Infections / Q000635:transmission / Q000821:virology; D011201:Poultry Diseases / Q000821:virology*; D012367:RNA, Viral / Q000235:genetics; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000662:veterinary
chemical_list: D012367:RNA, Viral