title: A highly divergent picornavirus in a marine mammal.
abstract: Nucleic acids from an unidentified virus from ringed seals (Phoca hispida) were amplified using sequence-independent PCR, subcloned, and then sequenced. The full genome of a novel RNA virus was derived, identifying the first sequence-confirmed picornavirus in a marine mammal. The phylogenetic position of the tentatively named seal picornavirus 1 (SePV-1) as an outlier to the grouping of parechoviruses was found consistently in alignable regions of the genome. A mean protein sequence identity of only 19.3 to 30.0% was found between the 3D polymerase gene sequence of SePV-1 and those of other picornaviruses. The predicted secondary structure of the short 506-base 5'-untranslated region showed some attributes of a type IVB internal ribosome entry site, and the polyprotein lacked an apparent L peptide, both properties associated with the Parechovirus genus. The presence of two SePV-1 2A genes and of the canonical sequence required for cotranslational cleavage resembled the genetic organization of Ljungan virus. Minor genetic variants were detected in culture supernatants derived from 8 of 108 (7.4%) seals collected in 2000 to 2002, indicating a high prevalence of SePV-1 in this hunted seal population. The high level of genetic divergence of SePV-1 compared to other picornaviruses and its mix of characteristics relative to its closest relatives support the provisional classification of SePV-1 as the prototype for a new genus in the family Picornaviridae.
authors.affiliation: Blood Systems Research Institute, 270 Masonic Ave., San Francisco, CA 94118, USA.
authors.forename: A
authors.initials: A
authors.lastname: Kapoor
authors.forename: J
authors.initials: J
authors.lastname: Victoria
authors.forename: P
authors.initials: P
authors.lastname: Simmonds
authors.forename: C
authors.initials: C
authors.lastname: Wang
authors.forename: R W
authors.initials: RW
authors.lastname: Shafer
authors.forename: R
authors.initials: R
authors.lastname: Nims
authors.forename: O
authors.initials: O
authors.lastname: Nielsen
authors.forename: E
authors.initials: E
authors.lastname: Delwart
mesh_terms: D020121:5' Untranslated Regions / Q000737:chemistry; D000818:Animals; D016679:Genome, Viral / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D030061:Parechovirus / Q000235:genetics; D046049:Phoca / Q000821:virology*; D010802:Phylogeny; D010849:Picornaviridae / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D010850:Picornaviridae Infections / Q000821:virology*; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D014764:Viral Proteins / Q000235:genetics
chemical_list: D020121:5' Untranslated Regions; D014764:Viral Proteins