A highly divergent picornavirus in a marine mammal.
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.
Kapoor
A
A
Blood Systems Research Institute, 270 Masonic Ave., San Francisco, CA 94118, USA.
Victoria
J
J
Simmonds
P
P
Wang
C
C
Shafer
R W
RW
Nims
R
R
Nielsen
O
O
Delwart
E
E
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
D020121:5' Untranslated Regions; D014764:Viral Proteins