title: Comparative analysis of six genome sequences of three novel picornaviruses, turdiviruses 1, 2 and 3, in dead wild birds, and proposal of two novel genera, Orthoturdivirus and Paraturdivirus, in the family Picornaviridae.
abstract: In this territory-wide molecular epidemiology study of picornaviruses, involving 6765 dead wild birds from 201 species in 50 families over a 12 month period, three novel picornaviruses, turdiviruses 1, 2 and 3 (TV1, TV2 and TV3), were identified from birds of different genera in the family Turdidae. In contrast to many other viruses in birds of the family Turdidae or viruses of the family Picornaviridae, TV1, TV2 and TV3 were found exclusively in the autumn and winter months. Two genomes each of TV1, TV2 and TV3 were sequenced. Regions P1, P2 and P3 of the three turdiviruses possessed, respectively, <40, <40 and <50 % amino acid identities with those of other picornaviruses. Moreover, P1, P2 and P3 of TV1 also possessed, respectively, <40, <40 and <50 % amino acid identities with those of TV2 and TV3. Phylogenetic analysis revealed that TV1, TV2 and TV3 were distantly related to members of the genus Kobuvirus. Among the three turdiviruses, TV2 and TV3 were always clustered together, with high bootstrap supports of 1000. The genomic features of TV2 and TV3 were also distinct from TV1, including lower G+C contents, shorter leader protein and a preference for codon sequence NNT rather than NNC for amino acids that can use either NNT or NNC as codons (P<0.001 by χ(2)-test). Based on our results we propose two novel genera, Orthoturdivirus for TV1, and Paraturdivirus for TV2 and TV3, in the family Picornaviridae. The type of internal ribosomal entry site for TV1, TV2 and TV3 remains to be determined.
authors.affiliation: State Key Laboratory of Emerging Infectious Diseases, Hong Kong Special Administration Region, Hong Kong SAR.
authors.forename: Patrick C Y
authors.initials: PC
authors.lastname: Woo
authors.forename: Susanna K P
authors.initials: SK
authors.lastname: Lau
authors.forename: Yi
authors.initials: Y
authors.lastname: Huang
authors.forename: Carol S F
authors.initials: CS
authors.lastname: Lam
authors.forename: Rosana W S
authors.initials: RW
authors.lastname: Poon
authors.forename: Hoi-Wah
authors.initials: HW
authors.lastname: Tsoi
authors.forename: Paul
authors.initials: P
authors.lastname: Lee
authors.forename: Herman
authors.initials: H
authors.lastname: Tse
authors.forename: Allen S L
authors.initials: AS
authors.lastname: Chan
authors.forename: Geraldine
authors.initials: G
authors.lastname: Luk
authors.forename: Kwok-Hung
authors.initials: KH
authors.lastname: Chan
authors.forename: Kwok-Yung
authors.initials: KY
authors.lastname: Yuen
mesh_terms: D000818:Animals; D001715:Bird Diseases / Q000453:epidemiology* / Q000821:virology*; D016000:Cluster Analysis; D016679:Genome, Viral; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D010849:Picornaviridae / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D012621:Seasons; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D020308:Songbirds / Q000821:virology; D015678:Viral Structural Proteins / Q000235:genetics*
chemical_list: D015678:Viral Structural Proteins