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Identification of Two Novel Members of the Tentative Genus Wukipolyomavirus in Wild Rodents.

Nainys J, Timinskas A, Schneider J, Ulrich RG, Gedvilaite A - PLoS ONE (2015)

Bottom Line: Phylogenetic and clustering analysis including all known PyV genomes placed novel bank vole and common vole PyVs amongst members of the tentative Wukipolymavirus genus.The other known four rodent PyVs, Murine PyV and Hamster PyV, and Murine pneumotropic virus and Mastomys PyV belong to different phylogenetic clades, tentatively named Orthopolyomavirus I and Orthopolyomavirus II, respectively.In conclusion, the finding of novel vole-borne PyVs may suggest an evolutionary origin of ancient wukipolyomaviruses in rodents and may offer the possibility to develop a vole-based animal model for human wukipolyomaviruses.

View Article: PubMed Central - PubMed

Affiliation: Department of Eukaryote Genetic Engineering, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.

ABSTRACT
Two novel polyomaviruses (PyVs) were identified in kidney and chest-cavity fluid samples of wild bank voles (Myodes glareolus) and common voles (Microtus arvalis) collected in Germany. All cloned and sequenced genomes had the typical PyV genome organization, including putative open reading frames for early regulatory proteins large T antigen and small T antigen on one strand and for structural late proteins (VP1, VP2 and VP3) on the other strand. Virus-like particles (VLPs) were generated by yeast expression of the VP1 protein of both PyVs. VLP-based ELISA and large T-antigen sequence-targeted polymerase-chain reaction investigations demonstrated signs of infection of these novel PyVs in about 42% of bank voles and 18% of common voles. In most cases only viral DNA, but not VP1-specific antibodies were detected. In additional animals exclusively VP1-specific antibodies, but no viral DNA was detected, indicative for virus clearance. Phylogenetic and clustering analysis including all known PyV genomes placed novel bank vole and common vole PyVs amongst members of the tentative Wukipolymavirus genus. The other known four rodent PyVs, Murine PyV and Hamster PyV, and Murine pneumotropic virus and Mastomys PyV belong to different phylogenetic clades, tentatively named Orthopolyomavirus I and Orthopolyomavirus II, respectively. In conclusion, the finding of novel vole-borne PyVs may suggest an evolutionary origin of ancient wukipolyomaviruses in rodents and may offer the possibility to develop a vole-based animal model for human wukipolyomaviruses.

No MeSH data available.


Related in: MedlinePlus

Relationships between PyV genomes, as shown at various cutoff similarity values.(A) cutoff p = 1x10-10: all PyVs are nested indicating a common nature of all PyVs (not excluding fishpolyomaviruses); (B) cutoff p = 1x10-39: all PyVs are nested, except fishpolyomaviruses; (C) cutoff p = 1x10-56: Avipolyomaviruses are separated; (D) cutoff p = 1x10-69: Wukipolyomaviruses are separated; (E) cutoff p = 1x10-86: Orthopolyomaviruses are divided into 3 main lineages—Orthopolyomavirus I, Orthopolyomavirus II and Malawipolyomavirus. To note, 1x10-86 level indicates closest relationships, while 1x10-10—most distant. Grey lines connect pairs of similar PyV genomes at selected cutoff level of p.
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pone.0140916.g004: Relationships between PyV genomes, as shown at various cutoff similarity values.(A) cutoff p = 1x10-10: all PyVs are nested indicating a common nature of all PyVs (not excluding fishpolyomaviruses); (B) cutoff p = 1x10-39: all PyVs are nested, except fishpolyomaviruses; (C) cutoff p = 1x10-56: Avipolyomaviruses are separated; (D) cutoff p = 1x10-69: Wukipolyomaviruses are separated; (E) cutoff p = 1x10-86: Orthopolyomaviruses are divided into 3 main lineages—Orthopolyomavirus I, Orthopolyomavirus II and Malawipolyomavirus. To note, 1x10-86 level indicates closest relationships, while 1x10-10—most distant. Grey lines connect pairs of similar PyV genomes at selected cutoff level of p.

Mentions: To evaluate the relatedness of PyVs, an alternative algorithm was developed in this study. Novel (global) measure for similarity of genome sequences was introduced by counting pairs of short fragments (of length w) that share higher sequence identity than some predefined value (n identical nucleotides per w) when aligned. This simple measure empowered comparison of any potentially meaningful w-mer pairs, including genomic stretches coding conservative functional domains of proteins, specific regulatory regions of genome, microRNAs or any other important signals within PyVs DNA sequence, without the use of any additional information. Sequence dynamic clustering software CLANS, with the calculated pairwise similarity scores (p) of PyV genomes as input, was used to investigate relatedness between all analyzed genomes (Fig 4).


Identification of Two Novel Members of the Tentative Genus Wukipolyomavirus in Wild Rodents.

Nainys J, Timinskas A, Schneider J, Ulrich RG, Gedvilaite A - PLoS ONE (2015)

Relationships between PyV genomes, as shown at various cutoff similarity values.(A) cutoff p = 1x10-10: all PyVs are nested indicating a common nature of all PyVs (not excluding fishpolyomaviruses); (B) cutoff p = 1x10-39: all PyVs are nested, except fishpolyomaviruses; (C) cutoff p = 1x10-56: Avipolyomaviruses are separated; (D) cutoff p = 1x10-69: Wukipolyomaviruses are separated; (E) cutoff p = 1x10-86: Orthopolyomaviruses are divided into 3 main lineages—Orthopolyomavirus I, Orthopolyomavirus II and Malawipolyomavirus. To note, 1x10-86 level indicates closest relationships, while 1x10-10—most distant. Grey lines connect pairs of similar PyV genomes at selected cutoff level of p.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4608572&req=5

pone.0140916.g004: Relationships between PyV genomes, as shown at various cutoff similarity values.(A) cutoff p = 1x10-10: all PyVs are nested indicating a common nature of all PyVs (not excluding fishpolyomaviruses); (B) cutoff p = 1x10-39: all PyVs are nested, except fishpolyomaviruses; (C) cutoff p = 1x10-56: Avipolyomaviruses are separated; (D) cutoff p = 1x10-69: Wukipolyomaviruses are separated; (E) cutoff p = 1x10-86: Orthopolyomaviruses are divided into 3 main lineages—Orthopolyomavirus I, Orthopolyomavirus II and Malawipolyomavirus. To note, 1x10-86 level indicates closest relationships, while 1x10-10—most distant. Grey lines connect pairs of similar PyV genomes at selected cutoff level of p.
Mentions: To evaluate the relatedness of PyVs, an alternative algorithm was developed in this study. Novel (global) measure for similarity of genome sequences was introduced by counting pairs of short fragments (of length w) that share higher sequence identity than some predefined value (n identical nucleotides per w) when aligned. This simple measure empowered comparison of any potentially meaningful w-mer pairs, including genomic stretches coding conservative functional domains of proteins, specific regulatory regions of genome, microRNAs or any other important signals within PyVs DNA sequence, without the use of any additional information. Sequence dynamic clustering software CLANS, with the calculated pairwise similarity scores (p) of PyV genomes as input, was used to investigate relatedness between all analyzed genomes (Fig 4).

Bottom Line: Phylogenetic and clustering analysis including all known PyV genomes placed novel bank vole and common vole PyVs amongst members of the tentative Wukipolymavirus genus.The other known four rodent PyVs, Murine PyV and Hamster PyV, and Murine pneumotropic virus and Mastomys PyV belong to different phylogenetic clades, tentatively named Orthopolyomavirus I and Orthopolyomavirus II, respectively.In conclusion, the finding of novel vole-borne PyVs may suggest an evolutionary origin of ancient wukipolyomaviruses in rodents and may offer the possibility to develop a vole-based animal model for human wukipolyomaviruses.

View Article: PubMed Central - PubMed

Affiliation: Department of Eukaryote Genetic Engineering, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.

ABSTRACT
Two novel polyomaviruses (PyVs) were identified in kidney and chest-cavity fluid samples of wild bank voles (Myodes glareolus) and common voles (Microtus arvalis) collected in Germany. All cloned and sequenced genomes had the typical PyV genome organization, including putative open reading frames for early regulatory proteins large T antigen and small T antigen on one strand and for structural late proteins (VP1, VP2 and VP3) on the other strand. Virus-like particles (VLPs) were generated by yeast expression of the VP1 protein of both PyVs. VLP-based ELISA and large T-antigen sequence-targeted polymerase-chain reaction investigations demonstrated signs of infection of these novel PyVs in about 42% of bank voles and 18% of common voles. In most cases only viral DNA, but not VP1-specific antibodies were detected. In additional animals exclusively VP1-specific antibodies, but no viral DNA was detected, indicative for virus clearance. Phylogenetic and clustering analysis including all known PyV genomes placed novel bank vole and common vole PyVs amongst members of the tentative Wukipolymavirus genus. The other known four rodent PyVs, Murine PyV and Hamster PyV, and Murine pneumotropic virus and Mastomys PyV belong to different phylogenetic clades, tentatively named Orthopolyomavirus I and Orthopolyomavirus II, respectively. In conclusion, the finding of novel vole-borne PyVs may suggest an evolutionary origin of ancient wukipolyomaviruses in rodents and may offer the possibility to develop a vole-based animal model for human wukipolyomaviruses.

No MeSH data available.


Related in: MedlinePlus