A highly divergent picornavirus in a marine mammal.

• Main Authors: Nielsen O, Delwart E
• Other Authors: The Pennsylvania State University CiteSeerX Archives
• Format: Text
• Language: English
• Subjects: Phoca hispida
• Online Access: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.483.7369; http://jvi.asm.org/content/early/2007/10/17/JVI.01240-07.full.pdf

Nucleic acids from an unidentified virus from ringed seals (Phoca hispida) were amplified using a 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 19.3-30.0 % 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’-UTR showed some attributes of a type-IVB IRES 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 co-translational cleavage resembled the genetic organization of the Ljungan virus. Minor genetic variants were detected in culture supernatants derived from eight of 108 (7.4%) seals collected in 2000-2002 indicating a high prevalence of SePV-1 in this hunted seal population. The high level of genetic divergence of SePV-1 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 Picornaviridae family.