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Journal of Virology, January 2008, p. 311-320, Vol. 82, No. 1
0022-538X/08/$08.00+0     doi:10.1128/JVI.01240-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

A Highly Divergent Picornavirus in a Marine Mammal{triangledown}

A. Kapoor,1,2 J. Victoria,1,2 P. Simmonds,3 C. Wang,4 R. W. Shafer,4 R. Nims,5 O. Nielsen,6 and E. Delwart1,2*

Blood Systems Research Institute, San Francisco, California 94118,1 University of California, San Francisco, San Francisco, California,2 Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, United Kingdom,3 Division of Infection Diseases, Stanford University, Stanford, California,4 BioReliance Corporation, 14920 Broschart Road, Rockville, Maryland 20850,5 Department of Fisheries and Oceans, Central and Arctic Region, 501 University Crescent, Winnipeg, Manitoba R3T 2N6, Canada6

Received 6 June 2007/ Accepted 6 October 2007

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.

* Corresponding author. Mailing address: Blood Systems Research Institute, 270 Masonic Ave., San Francisco, CA 94118. Phone: (415) 923-5763. Fax: (415) 276-2311. E-mail: delwarte{at}medicine.ucsf.edu

{triangledown} Published ahead of print on 17 October 2007.

Journal of Virology, January 2008, p. 311-320, Vol. 82, No. 1
0022-538X/08/$08.00+0     doi:10.1128/JVI.01240-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.



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