GENOME ANNOUNCEMENT
Complete Genome Sequence of a Polyomavirus Isolated from Horses Randall W. Renshaw,a Annabel G. Wise,b Roger K. Maes,b and Edward J. Dubovia Animal Health Diagnostic Center, Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA,a and Diagnostic Center for Population and Animal Health, Michigan State University, Lansing, Michigan, USAb
A polyomavirus was isolated from the eyes of horses, and the sequence was determined. A nearly identical VP1 sequence was amplified from the kidney of another animal. We report the complete genome sequence of the first polyomavirus to be isolated from a horse. Analysis shows it to be most closely related overall to human and nonhuman primate polyomaviruses.
T
he Polyomaviridae family comprises a relatively small group of viruses with circular, double-stranded DNA genomes. The type species is simian virus 40 (SV40). Thirteen species are officially listed as polyomaviruses by the International Committee on Taxonomy of Viruses (ICTV), but a new proposal increases that number to 28 and divides the family into three genera (pdf at http://talk.ictvonline.org/files/proposals/taxonomy_proposals _vertebrate1/m/vert01/3394.aspx). Disease associations of the mammalian polyomaviruses are limited; infections are usually subclinical and thus escape detection. Noted exceptions are JC virus-induced progressive multifocal leukoencephalopathy and BK virus nephropathy in immunocompromised human patients (1, 2). In contrast, the avian polyomaviruses can cause acute disease with high mortality (3, 4). The previously unrecognized virus described here was isolated in equine kidney cell cultures inoculated with eye tissue and aqueous humor collected from 3 of 13 unrelated horses. All samples were from animals with clinical uveitis, although no presumptive disease etiology can be ascribed at this time. Virion DNA was fragmented and cloned into a plasmid vector, sequenced by primer walking using dye terminator chemistry on an ABI Prism 3730 sequencer (Applied Biosystems), and assembled with SeqMan software (DNAStar Inc.). Independently, in another laboratory, a VP1 gene sequence was amplified directly from equine kidney and differed from the eye isolate sequence at only a single nucleotide with a synonymous substitution. The finding of the virus in several horses and the historical observation that polyomaviruses are highly species specific suggests that an appropriate name for this virus is equine polyomavirus (EPyV). The EPyV genome is 4,987 bp with a GC content of 44.64%. The genome organization is typical of polyomaviruses, including a regulatory region flanked by early small- and large-Tantigen genes and the late genes VP1, VP2, and VP3. Analysis of EPyV did not point to a predominant relationship with any other individual polyomavirus, but overall, it appears most closely related to human and nonhuman primate polyomaviruses. Full-genome nucleotide similarity was highest with simian virus 12 (SV12) at 57%, which is less than the proposed classification criterion of ⬍81% to denote a new species (pdf at http://talk.ictvonline.org/files/proposals/taxonomy_proposals _vertebrate1/m/vert01/3394.aspx). Amino acid identity with the large T antigens of the SV12, SV40, BK, and JC viruses was approximately 58%, while identities with all other large-T-antigen sequences were 31 to 55%. Small-T-antigen identity was
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highest at 43 to 45% with the SV12, SV40, JC, and BK viruses. A complete association with the human and nonhuman primate viruses was less clear for the late-gene products. For VP1, some of the highest amino acid identities were with the avian polyomaviruses (GenBank accession numbers NC_004764, GU345044, NC_007922, NC_007923, and NC_004800), for which all identities were ⬎59%, although the highest identity was with Mastomys polyomavirus (DDBJ accession number AB588640) at 61.9%. The highest amino acid identities in VP2/ VP3 were with trichodysplasia spinulosa-associated polyomavirus (GenBank accession number NC_014361), orangutan polyomaviruses 1 and 2 (EMBL accession numbers FN356900 and FN356901), and bat polyomavirus (GenBank accession number NC_011310) and were all 43 to 45%. Availability of the EPyV genome sequence will further the understanding of the phylogenetic relationships between polyomaviruses and allow for development of new diagnostic procedures. Nucleotide sequence accession number. The complete genome sequence of EPyV CU03 was deposited in GenBank under accession number JQ412134. ACKNOWLEDGMENTS This work was supported by departmental funding from the Animal Health Diagnostic Center at Cornell University. We thank Sam Jennings and Keith Linder, College of Veterinary Medicine, North Carolina State University, for sharing the horse renal tissue sample.
REFERENCES 1. Brew BJ, Davies NW, Cinque P, Clifford DB, Nath A. 2010. Progressive multifocal leukoencephalopathy and other forms of JC virus disease. Nat. Rev. Neurol. 6:667– 679. 2. Cimbaluk D, Pitelka L, Kluskens L, Gattuso P. 2009. Update on human polyomavirus BK nephropathy. Diagn. Cytopathol. 37:773–779. 3. Corrand L, et al. 2011. Pathological and epidemiological significance of goose haemorrhagic polyomavirus infection in ducks. Avian Pathol. 40: 355–360. 4. Halami MY, et al. 2010. Whole-genome characterization of a novel polyomavirus detected in fatally diseased canary birds. J. Gen. Virol. 91:3016 – 3022.
Received 21 May 2012 Accepted 24 May 2012 Address correspondence to Edward J. Dubovi,
[email protected], or Randall W. Renshaw,
[email protected]. Copyright © 2012, American Society for Microbiology. All Rights Reserved. doi:10.1128/JVI.01261-12
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