Complete genome sequence of a novel sea otterpox virus
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Members of the Poxviridae family are large, double-stranded DNA viruses that replicate in the cytoplasm of their host cells. The subfamily Chordopoxvirinae contains viruses that infect a wide range of vertebrates including marine mammals within the Balaenidae, Delphinidae, Mustelidae, Odobenidae, Otariidae, Phocidae, and Phocoenidae families. Recently, a novel poxvirus was found in a northern sea otter pup (Enhydra lutris kenyoni) that stranded in Alaska in 2009. The phylogenetic relationships of marine mammal poxviruses are not well established because of the lack of complete genome sequences. The current study sequenced the entire sea otterpox virus Enhydra lutris kenyoni (SOPV-ELK) genome using an Illumina MiSeq sequencer. The SOPV-ELK genome is the smallest poxvirus genome known at 127,879 bp, is 68.7% A+T content, is predicted to encode 132 proteins, and has 2546 bp inverted terminal repeats at each end. Genetic and phylogenetic analyses based on the concatenated amino acid sequences of 7 chorodopoxvirus core genes revealed the SOPV-ELK is 52.5–74.1% divergent from other known chordopoxviruses and is most similar to pteropoxvirus from Australia (PTPV-Aus). SOPV-ELK represents a new chordopoxvirus species and may belong to a novel genus. SOPV-ELK encodes eight unique genes. While the function of six predicted genes remains unknown, two genes appear to function as novel immune-modulators. SOPV-ELK-003 appears to encode a novel interleukin-18 binding protein (IL-18 BP), based on limited sequence and structural similarity to other poxviral IL-18 BPs. SOPV-ELK-035 appears to encode a novel tumor necrosis factor receptor-like (TNFR) protein that may be associated with the depression of the host’s antiviral response. Additionally, SOPV-ELK-036 encodes a tumor necrosis factor-like apoptosis-inducing ligand (TRAIL) protein that has previously only been found in PTPV-Aus. The SOPV-ELK genome is the first mustelid poxvirus and only the second poxvirus from a marine mammal to be fully sequenced. Sequencing of the SOPV-ELK genome is an important step in unraveling the position of marine mammal poxviruses within the larger Poxviridae phylogenetic tree and provides the necessary sequence to develop molecular tools for future diagnostics and epidemiological studies.
KeywordsSea otter Enhydra lutris Next generation sequencing Phylogenetic Poxvirus
We would like to thank the University of Florida Graduate Student Fellowship for providing financial support.
PAT provided the northern sea otter lesion sample. ON isolated the virus using standard cell culture techniques. JMJ, KS, CU, SLT, TBW completed genome assembly and annotation. JMJ, TBW, KS, SLT, CU wrote the manuscript.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
All applicable international, national, and/or institutional guidelines for the care and use of animals were followed.
- 3.Moss B (2007) Poxviridae: the viruses and their replication. In: Knipe DM, Howley PM (eds) Fields virology, 5th edn. Wolters Kluwer Health Lippincott Williams & Wilkins, Philadelphia, pp 2905–2945Google Scholar
- 9.Tuomi PA, Murray MJ, Garner MM, Goertz CEC, Nordhausen RW, Burek-Huntington KA, Getzy DM, Nielsen O, Archer LL, Maness HTD, Wellehan JFS Jr, Waltzek TB (2014) Novel poxvirus infection in northern and southern sea otters (Enhydra lutris kenyoni and Enhydra lutris neiris), Alaska and California. USA J Wildl Dis 50:607–615CrossRefGoogle Scholar
- 14.Van Bressem MF, Van Waerebeek K, Flach L, Reyes JC, de Oliveira Santos MC, Siciliano S, Echgaray M, Viddi F, Felix F, Crespo E, Avila ICS, Fraijia N, Castro C (2008) Skin diseases in cetaceans. In: Scientific Committee document International Whaling Commission SC/60/DW8:1–11Google Scholar
- 22.Kienzel N, Young D, Zehntner S, Bushell G, Sculley TB (1996) DNaseI treatment is a prerequisite for the amplification of cDNA from episomal-based genes. Biotechniques 20:612–616Google Scholar
- 23.Sambrook J, Frisch EF, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, New YorkGoogle Scholar
- 24.Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477CrossRefGoogle Scholar
- 30.Marchler-Bauer A, Bo Y, Han L, He J, Lanczycki CJ, Lu S, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Lu F, Marchler GH, Song JS, Thanki N, Wang Z, Yamashita RA, Zhang D, Zheng C, Geer LY, Bryant SH (2017) CDD/SPARCLE: a functional classification of proteins via subfamily domain architectures. Nucleic Acids Res 45:200–203CrossRefGoogle Scholar