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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

Sliding window analysis of genome sequences specific to CVPyV and BVPyV compared to other PyVs (%).The short fragments of a length w = 50 nt of BVPyV and CVPyV genomes were compared with w-mers of all PyV genomes by means of a sliding-window procedure. Only pairs of w-mers which had higher count of identical nucleotides in their alignment than some predefined critical value n = 30 when aligned were determined as similar. VP1, VP2, VP3, LTag, and STag genes are labeled with different colors. The nucleotide positions in genome are indicated at the bottom.
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pone.0140916.g005: Sliding window analysis of genome sequences specific to CVPyV and BVPyV compared to other PyVs (%).The short fragments of a length w = 50 nt of BVPyV and CVPyV genomes were compared with w-mers of all PyV genomes by means of a sliding-window procedure. Only pairs of w-mers which had higher count of identical nucleotides in their alignment than some predefined critical value n = 30 when aligned were determined as similar. VP1, VP2, VP3, LTag, and STag genes are labeled with different colors. The nucleotide positions in genome are indicated at the bottom.

Mentions: Additional investigation of whole genome comparisons were also performed by analyzing PyV genomes for the DNA sequence features conserved between all PyVs and highlighting sequence features that are specific for CVPyV and BVPyV (Fig 5). The VP2 gene sequence carries little similarity among all PyVs (including WUPyV) except for a short region encoding the N-terminal end where a myristoylation target sequence is located. However, this gene of both vole PyVs is highly similar (88% identical). There could be several explanations: a recent branching event in the evolutionary history and/or presence of conserved specific VP2 function of vole PyVs. VP1 gene contains a few conserved sequence features (overall identity of BVPyV and CVPyV VP1 gene sequences is 82%). Notably the highest similarity between the VP1-coding sequences of all PyVs is seen in a region in the middle of the gene that encodes part of the core β-barrel structure. While both of the late region genes show little similarity among all PyVs, the LTag gene sequence is much more conserved. Conserved sequence features can be linked with known domain locations. All three main domains: ATPase, DnaJ domains and origin binding domain (OBD) retain similarity between all PyVs and the new ones as well (Fig 5) [79]. The largest conserved 350 bp length region encode Walker A and B boxes as well as the Surface Loop motif of the AAA+ ATPase domain [79]. Thus, this additional analysis on whole genome comparison algorithm fully confirms the current knowledge of the PyV genome regions and conservation of highly similar domains and motifs and strengthens the results of the CLANS analyses.


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)

Sliding window analysis of genome sequences specific to CVPyV and BVPyV compared to other PyVs (%).The short fragments of a length w = 50 nt of BVPyV and CVPyV genomes were compared with w-mers of all PyV genomes by means of a sliding-window procedure. Only pairs of w-mers which had higher count of identical nucleotides in their alignment than some predefined critical value n = 30 when aligned were determined as similar. VP1, VP2, VP3, LTag, and STag genes are labeled with different colors. The nucleotide positions in genome are indicated at the bottom.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0140916.g005: Sliding window analysis of genome sequences specific to CVPyV and BVPyV compared to other PyVs (%).The short fragments of a length w = 50 nt of BVPyV and CVPyV genomes were compared with w-mers of all PyV genomes by means of a sliding-window procedure. Only pairs of w-mers which had higher count of identical nucleotides in their alignment than some predefined critical value n = 30 when aligned were determined as similar. VP1, VP2, VP3, LTag, and STag genes are labeled with different colors. The nucleotide positions in genome are indicated at the bottom.
Mentions: Additional investigation of whole genome comparisons were also performed by analyzing PyV genomes for the DNA sequence features conserved between all PyVs and highlighting sequence features that are specific for CVPyV and BVPyV (Fig 5). The VP2 gene sequence carries little similarity among all PyVs (including WUPyV) except for a short region encoding the N-terminal end where a myristoylation target sequence is located. However, this gene of both vole PyVs is highly similar (88% identical). There could be several explanations: a recent branching event in the evolutionary history and/or presence of conserved specific VP2 function of vole PyVs. VP1 gene contains a few conserved sequence features (overall identity of BVPyV and CVPyV VP1 gene sequences is 82%). Notably the highest similarity between the VP1-coding sequences of all PyVs is seen in a region in the middle of the gene that encodes part of the core β-barrel structure. While both of the late region genes show little similarity among all PyVs, the LTag gene sequence is much more conserved. Conserved sequence features can be linked with known domain locations. All three main domains: ATPase, DnaJ domains and origin binding domain (OBD) retain similarity between all PyVs and the new ones as well (Fig 5) [79]. The largest conserved 350 bp length region encode Walker A and B boxes as well as the Surface Loop motif of the AAA+ ATPase domain [79]. Thus, this additional analysis on whole genome comparison algorithm fully confirms the current knowledge of the PyV genome regions and conservation of highly similar domains and motifs and strengthens the results of the CLANS analyses.

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