Characterization of novel polyomaviruses from Bornean and Sumatran orang-utans

Groenewoud, Marlous J.; Fagrouch, Zahra; Gessel, Sabine van; Niphuis, Henk; Bulavaitė, Aistė; Warren, K.; Heeney, Jonathan L.; Verschoor, Ernst J.

doi:10.1099/vir.0.017673-0

Cited by 27 publications

(22 citation statements)

References 28 publications

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“…Protein sequences associated with the reference genomes for 27 polyomaviruses were obtained from GenBank; these included baboon polyomavirus (NC_007611; SA12) (6), bat polyomavirus (NC_011310; BatPyV) (32), B-lymphotropic polyomavirus (NC_004763; LPyV) (34), BKPyV (NC_001538) (43), Bornean orangutan polyomavirus (NC_013439; OraV1) (17), bovine polyomavirus (NC_001442; BPyV) (41), California sea lion polyomavirus (NC_013796; SLPyV) (8), hamster polyomavirus (NC_001663; HaPyV) (9), JCPyV (NC_001699) (12), MCPyV (HM011557) (40), murine pneumotropic virus (NC_001505; MPtV) (31), murine polyomavirus (NC_001515; MPyV) (16), simian virus 40 (NC_001669; SV40) (27), squirrel monkey polyomavirus (NC_009951; SqPyV) (46), Sumatran orangutan polyomavirus (FN356901; OraV2) (17), TSPyV (NC_014361) (45), HPyV6 (NC_014406) (40), HPyV7 (NC_014407) (40), KIPyV (NC_009238) (2), WUPyV (NC_009539) (13), avian polyomavirus (NC_004764; APyV) (39), canary polyomavirus (GU345044; CaPyV) (19), crow polyomavirus (NC_007922; CPyV) (23), finch polyomavirus (NC_007923; FPyV) (23), goose hemorrhagic polyomavirus (NC_004800; GHV) (22), chimpanzee polyomavirus (NC_014743; ChPyV) (10), and HPyV9 (NC_015150) (42). The predicted open reading frames for MWPyV LTAg, VP1, and VP2 were aligned with the corresponding proteins from the 27 known polyomaviruses using Fast Statistical Alignment (FSA) software, version 1.15.2 (5).…”

Section: Methodsmentioning

confidence: 99%

“…Polyomaviruses also infect a wide variety of mammalian and avian hosts, including the recently described novel polyomaviruses of bats (Myotis species) (32), sea lions (Zalophus californianus) (8,47), multimammate mice (Mastomys species) (33), canaries (Serinus canaria) (19), orangutans (Pongo species) (17), squirrel monkeys (Saimiri species) (46), chimpanzees (Pan troglodytes subsp. verus) (28), and gorillas (Gorilla gorilla) (28).…”

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confidence: 99%

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Identification of MW Polyomavirus, a Novel Polyomavirus in Human Stool

Siebrasse

Reyes

Lim

et al. 2012

J Virol

167

152

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We have discovered a novel polyomavirus present in multiple human stool samples. The virus was initially identified by shotgun pyrosequencing of DNA purified from virus-like particles isolated from a stool sample collected from a healthy child from Malawi. We subsequently sequenced the virus' 4,927-bp genome, which has been provisionally named MW polyomavirus (MWPyV). The virus has genomic features characteristic of the family Polyomaviridae but is highly divergent from other members of this family. It is predicted to encode the large T antigen and small T antigen early proteins and the VP1, VP2, and VP3 structural proteins. A real-time PCR assay was designed and used to screen 514 stool samples from children with diarrhea in St. Louis, MO; 12 specimens were positive for MWPyV. Comparison of the whole-genome sequences of the index Malawi case and one St. Louis case demonstrated that the two strains of MWPyV varied by 5.3% at the nucleotide level. The number of polyomaviruses found in the human body continues to grow, raising the question of how many more species have yet to be identified and what roles they play in humans with and without manifest disease.

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Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Identification of MW Polyomavirus, a Novel Polyomavirus in Human Stool

Siebrasse

Reyes

Lim

et al. 2012

J Virol

167

152

View full text Add to dashboard Cite

show abstract

“…21,99 A number of novel animal polyomaviruses have recently been identified through the use of a nested broad-spectrum PCR assay developed by Johne et al 51 This consensus assay targets the conserved regions of the polyomavirus VP1 gene. With this assay, novel polyomaviruses were detected from fresh tissues, blood, or feces collected from a chimpanzee, 51 a squirrel monkey, 130 bats of Canada, 85 Bornean and Sumatran orangutans, 39 and wild rodents from Zambia. 98 The consensus PCR also worked well for the detection of polyomavirus in FFPE samples, despite the product size target (>600 bp) of the first-round PCR.…”

Section: Polyomavirusesmentioning

confidence: 99%

Beyond H&E

et al. 2013

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Veterinary pathology of infectious, particularly viral, and neoplastic diseases has advanced significantly with the advent of newer molecular methodologies that can detect nucleic acid of infectious agents within microscopic lesions, differentiate neoplastic from nonneoplastic cells, or determine the suitability of a targeted therapy by detecting specific mutations in certain cancers. Polymerase chain reaction-based amplification of DNA or RNA and in situ hybridization are currently the most commonly used methods for nucleic acid detection. In contrast, the main methodology used for protein detection within microscopic lesions is immunohistochemistry. Other methods that allow for analysis of nucleic acids within a particular cell type or individual cells, such as laser capture microdissection, are also available in some laboratories. This review gives an overview of the factors that influence the accurate analysis of nucleic acids in formalin-fixed tissues, as well as of different approaches to detect such targets. Keywords cancer, ISH, IHC, nucleic acid analysis, molecular pathology, PCR, virology Technical ConsiderationsTissue Handling, Fixation, and Embedding Fixation of tissues in 10% neutral buffered formalin, followed by paraffin embedding (FFPE), has long been the standard approach of tissue preparation for microscopic evaluation. The chemical principle of formalin fixation is based on the crosslinking of proteins. Formalin has been used extensively because it is inexpensive and excellently preserves morphological detail in histological sections. However, the relatively recent development and increasing use of both protein and nucleic acid detection methods have revealed some significant shortcomings associated with the formalin-based fixation process. The effects of formalin fixation on DNA are chemical modification, DNA trapping, and potentially DNA fragmentation. Chemical modification, considered the main effect, results from the direct cross-linking of proteins to DNA. 68 In addition, extensive protein-protein cross-linking and the formation of protein networks result in DNA trapping. The combination of these effects makes it much more difficult to extract DNA from FFPE tissue than from unfixed tissue, especially when methods used for extraction from fresh tissues are used on FFPE tissue without any modifications. 60,83 In addition to interfering with the ability to extract nucleic acid, formalin fixation also causes DNA fragmentation, especially when the formalin used is inadequately buffered, which then leads to formic acid formation during the fixation process. This, in turn, results in depurination of the DNA, which then becomes susceptible to cleavage by hydroxyl ions and results in the formation of single-stranded breaks.60 Similar to DNA, RNA is also degraded and chemically modified as the result of formalin fixation. The most important chemical effect of formalin on RNA is the formation of monomethylol groups with purine bases. 77 This has a significant effect on reverse transcription ...

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“…SV40 has been detected in human tissues, but its prevalence and relationship to human cancer are still controversial. Using a broad-spectrum PCR approach, recent studies discovered new polyomaviruses in zoo animals or wild animals such as chimpanzees, squirrel monkeys, bats and orang-utans (Johne et al, 2005;Verschoor et al, 2008;Misra et al, 2009;Groenewoud et al, 2010). These studies indicate that there could still be many unknown polyomaviruses in wild animals.…”

Section: Introductionmentioning

confidence: 99%

“…At present, eight human and 18 non-human polyomaviruses are known (Groenewoud et al, 2010;Krumbholz et al, 2009;Misra et al, 2009;Schowalter et al, 2010;van der Meijden et al, 2010). Most mammalian polyomaviruses cause subclinical infections with life-long persistence in their natural immunocompetent hosts.…”

Section: Introductionmentioning

confidence: 99%

Detection and characterization of a novel polyomavirus in wild rodents

Orba

Kobayashi

Nakamura

et al. 2010

Journal of General Virology

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To investigate polyomavirus infection in wild rodents, we analysed DNA samples from the spleens of 100 wild rodents from Zambia using a broad-spectrum PCR-based assay. A previously unknown polyomavirus genome was identified in a sample from a multimammate mouse (Mastomys species) and the entire viral genome of 4899 bp was subsequently sequenced. This viral genome contained potential ORFs for the capsid proteins, VP1, VP2 and VP3, and early proteins, small t antigen and large T antigen. Phylogenetic analysis showed that it was a novel member of the family Polyomaviridae, and thus the virus was tentatively named mastomys polyomavirus. After transfection of the viral genome into several mammalian cell lines, transient expression of the VP1 and large T antigen proteins was confirmed by immunoblotting and immunocytochemical analyses. Comparison of large T antigen function in mastomys polyomavirus with that in rhesus monkey polyomavirus SV40 and human polyomavirus JC virus revealed that the large T antigen from mastomys polyomavirus interacted with the tumour suppressor protein pRb, but not with p53.

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Characterization of novel polyomaviruses from Bornean and Sumatran orang-utans

Cited by 27 publications

References 28 publications

Identification of MW Polyomavirus, a Novel Polyomavirus in Human Stool

Identification of MW Polyomavirus, a Novel Polyomavirus in Human Stool

Beyond H&E

Detection and characterization of a novel polyomavirus in wild rodents

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