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Shuster KA, Yang TS, Snyder KT, Creanza N, Mitchell PK, Goodman LB, Grenier JK, Tataryn NM, Himmel LE, Gibson-Corley KN. Polyomavirus-associated Disseminated T-cell Lymphoma in a Colony of Zebra Finches ( Taeniopygia guttata). Comp Med 2023; 73:383-390. [PMID: 38087403 PMCID: PMC10702165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 12/18/2023]
Abstract
Four zebra finches in a closed research colony presented with variable clinical signs, including masses, skin lesions, shivering, and/or ruffled feathers. These birds were not responsive to treatment efforts; 3 died and one was euthanized. All 4 were submitted for necropsy to determine the cause of the clinical signs. Gross necropsy and histopathologic findings from all birds resulted in a diagnosis of round cell neoplasia in multiple organs, including the skin, liver, kidney, and reproductive tract, with intranuclear inclusion bodies in the neoplastic cells. In all 4 cases, immunohistochemical staining showed strong immunoreactivity for CD3 in 70% to 80% of the neoplastic round cells, with a relatively small subset that were immunopositive for Pax5. These findings supported a diagnosis of T-cell lymphoma. Frozen liver tissue from one case was submitted for next-generation sequencing (NGS), which revealed viral RNA with 100% sequence homology to canary polyomavirus strain 34639 that had originally been identified in a European goldfinch. Formalin-fixed paraffin-embedded scrolls from another case were also submitted for NGS, which revealed viral RNA with 97.2% sequence homology to canary polyomavirus strain 37273 that had originally been identified in a canary. To localize the virus in situ, RNAscope hybridization was performed using a probe designed to target the VP1 gene of the sequenced virus in frozen liver tissue. In all 4 cases, disseminated and robust hybridization signals were detected in neoplastic cells. These findings indicate that polyomaviruses have the potential to be oncogenic in zebra finches.
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Affiliation(s)
- Katherine A Shuster
- Division of Comparative Medicine, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee;,
| | - Tzushan S Yang
- Division of Comparative Medicine, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Kate T Snyder
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee
| | - Nicole Creanza
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee
| | | | - Laura B Goodman
- Cornell University College of Veterinary Medicine, Ithaca, New York
| | - Jennifer K Grenier
- Cornell Institute of Biotechnology, Transcriptional Regulation and Expression Facility, Ithaca, New York
| | - Nicholas M Tataryn
- Division of Comparative Medicine, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lauren E Himmel
- Division of Comparative Medicine, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Katherine N Gibson-Corley
- Division of Comparative Medicine, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
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2
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Nath C, Hossain MS, Ahaduzzaman M. First molecular detection of avian polyomavirus from captive psittacine birds in Bangladesh, together with confirmation of beak and feather disease virus co-infection. Virusdisease 2023; 34:440-445. [PMID: 37780906 PMCID: PMC10533433 DOI: 10.1007/s13337-023-00829-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 06/05/2023] [Indexed: 10/03/2023] Open
Abstract
Avian polyomavirus (APV) is an emerging pathogen in many parts of the world responsible for causing significant mortality in captive psittacine birds. The virus spreads slowly, and transboundary movement of birds is one of the potential risk factors for the virus introduction in the naïve population. Bangladesh allows the import of birds, however there is currently no surveillance to screen for APV. Since we confirmed beak and feather disease virus (BFDV) infection in the captive population in our earlier investigation, we hypothesized that APV may also be circulating in Bangladesh. Feather samples were collected from 100 birds (90 psittacine and 10 non-psittacine). The polymerase chain reaction (PCR) was used to detect viral DNA together with sequencing and phylogenetic analysis. This first pilot study confirmed the presence (7%, 7/100) of APV in captive psittacine birds of Bangladesh and almost half (4%, 4/100) of the APV positive birds had the BFDV co-infection. All the PCR-positive birds were asymptomatic and found in live bird markets (LBMs). No significant variation was observed in the detection rate considering species (P = 0.94), age (P = 0.39) or sex (P = 0.55) of birds. According to the results of the phylogenetic study, the APV isolates found in Bangladesh appear to be unrelated to isolates from other geographical areas. These findings provide an evidence of APV circulating in Bangladesh, with or without the co-infection of BFDV. Additional studies are needed to investigate the occurrence of APV/BFDV co-infection in the larger population of Bangladesh and in countries where transboundary bird interaction with Bangladesh may be possible.
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Affiliation(s)
- Chandan Nath
- Department of Medicine and Surgery, Chattogram Veterinary and Animal Sciences University (CVASU), Chattogram, Bangladesh
| | - Md Saddam Hossain
- Department of Medicine and Surgery, Chattogram Veterinary and Animal Sciences University (CVASU), Chattogram, Bangladesh
| | - Md Ahaduzzaman
- Department of Medicine and Surgery, Chattogram Veterinary and Animal Sciences University (CVASU), Chattogram, Bangladesh
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3
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Styś-Fijoł N, Kozdruń W, Piekarska K, Niczyporuk JS. Molecular analysis Polish isolates of goose hemorrhagic polyomavirus from geese and free-living birds. Heliyon 2023; 9:e17083. [PMID: 37484428 PMCID: PMC10361228 DOI: 10.1016/j.heliyon.2023.e17083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 05/18/2023] [Accepted: 06/07/2023] [Indexed: 07/25/2023] Open
Abstract
Goose haemorrhagic polyomavirus (GHPV) is the viral agent of hemorrhagic nephritis and enteritis of geese (HNEG), a lethal disease of goose. The study describes the results of a molecular analysis Polish isolates of GHPV from geese and free-living birds based on complete VP1 gene and VP2 gene sequences. The sequences were analyzed and aligned with different GHPV isolates sequences accessible in the GenBank database. This study indicates affiliation GHPV isolates from fee-living birds and GHPV isolates circulating in Polish goose flocks and around the world to the same genetic groups, which proves their evolutionary relationship and indicates the potential role of free-living birds as a source of infections for poultry.
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Host diversification is concurrent with linear motif evolution in a Mastadenovirus hub protein. J Mol Biol 2022; 434:167563. [PMID: 35351519 DOI: 10.1016/j.jmb.2022.167563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 02/28/2022] [Accepted: 03/22/2022] [Indexed: 12/23/2022]
Abstract
Over one hundred Mastadenovirus types infect seven orders of mammals. Virus-host coevolution may involve cospeciation, duplication, host switch and partial extinction events. We reconstruct Mastadenovirus diversification, finding that while cospeciation is dominant, the other three events are also common in Mastadenovirus evolution. Linear motifs are fast-evolving protein functional elements and key mediators of virus-host interactions, thus likely to partake in adaptive viral evolution. We study the evolution of eleven linear motifs in the Mastadenovirus E1A protein, a hub of virus-host protein-protein interactions, in the context of host diversification. The reconstruction of linear motif gain and loss events shows fast linear motif turnover, corresponding a virus-host protein-protein interaction turnover orders of magnitude faster than in model host proteomes. Evolution of E1A linear motifs is coupled, indicating functional coordination at the protein scale, yet presents motif-specific patterns suggestive of convergent evolution. We report a pervasive association between Mastadenovirus host diversification events and the evolution of E1A linear motifs. Eight of 17 host switches associate with the gain of one linear motif and the loss of four different linear motifs, while five of nine partial extinctions associate with the loss of one linear motif. The specific changes in E1A linear motifs during a host switch or a partial extinction suggest that changes in the host molecular environment lead to modulation of the interactions with the retinoblastoma protein and host transcriptional regulators. Altogether, changes in the linear motif repertoire of a viral hub protein are associated with adaptive evolution events during Mastadenovirus evolution.
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5
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Oliver-Guimerá A, Hejtmánková A, Jackson K, Pesavento PA. A polyomavirus detected in American black bear (Ursus americanus). Arch Virol 2021; 166:1521-1524. [PMID: 33721099 DOI: 10.1007/s00705-021-05030-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/22/2021] [Indexed: 10/21/2022]
Abstract
Polyomaviruses are ancient DNA viruses that infect several species of animals. While recognition of the family Polyomaviridae has grown rapidly, there are few studies that consider their potential association with disease. Carnivora are a diverse and widespread order affected by polyomaviruses (PyVs) that have co-evolved with their hosts for millions of years. PyVs have been identified in sea lions, raccoons, badgers, Weddell seals, and dogs. We have discovered a polyomavirus, tentatively named "Ursus americanus polyomavirus 1" (UaPyV1) in black bears (Ursus americanus). UaPyV1 was detectable in various tissues of six out of seven bears submitted for necropsy. Based on viral phylogenetic clustering and detection of the virus in multiple individuals, we suggest that black bears are the natural hosts for UaPyV1. In this albeit small group, there is no clear relationship between UaPyV1 infection and any specific disease.
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Affiliation(s)
- Arturo Oliver-Guimerá
- Department of Pathology, Microbiology and Immunology, UC Davis School of Veterinary Medicine, 1044 Haring Hall, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Alžběta Hejtmánková
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Kenneth Jackson
- Department of Pathology, Microbiology and Immunology, UC Davis School of Veterinary Medicine, 1044 Haring Hall, 1 Shields Avenue, Davis, CA, 95616, USA
| | - Patricia A Pesavento
- Department of Pathology, Microbiology and Immunology, UC Davis School of Veterinary Medicine, 1044 Haring Hall, 1 Shields Avenue, Davis, CA, 95616, USA.
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Extensive Genetic Diversity of Polyomaviruses in Sympatric Bat Communities: Host Switching versus Coevolution. J Virol 2020; 94:JVI.02101-19. [PMID: 32075934 DOI: 10.1128/jvi.02101-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 02/11/2020] [Indexed: 01/17/2023] Open
Abstract
Polyomaviruses (PyVs) are small DNA viruses carried by diverse vertebrates. The evolutionary relationships of viruses and hosts remain largely unclear due to very limited surveillance in sympatric communities. In order to investigate whether PyVs can transmit among different mammalian species and to identify host-switching events in the field, we conducted a systematic study of a large collection of bats (n = 1,083) from 29 sympatric communities across China which contained multiple species with frequent contact. PyVs were detected in 21 bat communities, with 192 PyVs identified in 186 bats from 15 species within 6 families representing at least 28 newly described PyVs. Surveillance results and phylogenetic analyses surprisingly revealed three interfamily PyV host-switching events in these sympatric bat communities: two distinct PyVs were identified in two bat species in restricted geographical locations, while another PyV clustered phylogenetically with PyVs carried by bats from a different host family. Virus-host relationships of all discovered PyVs were also evaluated, and no additional host-switching events were found. PyVs were identified in different horseshoe bat species in sympatric communities without observation of host-switching events, showed high genomic identities, and clustered with each other. This suggested that even for PyVs with high genomic identities in closely related host species, the potential for host switching is low. In summary, our findings revealed that PyV host switching in sympatric bat communities can occur but is limited and that host switching of bat-borne PyVs is relatively rare on the predominantly evolutionary background of codivergence with their hosts.IMPORTANCE Since the discovery of murine polyomavirus in the 1950s, polyomaviruses (PyVs) have been considered highly host restricted in mammals. Sympatric bat communities commonly contain several different bat species in an ecological niche facilitating viral transmission, and they therefore represent a model to identify host-switching events of PyVs. In this study, we screened PyVs in a large number of bats in sympatric communities from diverse habitats across China. We provide evidence that cross-species bat-borne PyV transmission exists, though is limited, and that host-switching events appear relatively rare during the evolutionary history of these viruses. PyVs with close genomic identities were also identified in different bat species without host-switching events. Based on these findings, we propose an evolutionary scheme for bat-borne PyVs in which limited host-switching events occur on the background of codivergence and lineage duplication, generating the viral genetic diversity in bats.
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7
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Evolution and molecular epidemiology of polyomaviruses. INFECTION GENETICS AND EVOLUTION 2019; 79:104150. [PMID: 31870972 DOI: 10.1016/j.meegid.2019.104150] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 02/08/2023]
Abstract
Polyomaviruses (PyVs) are small DNA viruses that infect several species, including mammals, birds and fishes. Their study gained momentum after the report of previously unidentified viral species in the past decade, and especially, since the description of the first polyomavirus clearly oncogenic for humans. The aim of this work was to review the most relevant aspects of the evolution and molecular epidemiology of polyomaviruses, allowing to reveal general evolutionary patterns and to identify some unaddressed issues and future challenges. The main points analysed included: 1) the species and genera assignation criteria; 2) the hypotheses, mechanisms and timescale of the ancient and recent evolutionary history of polyomaviruses; and 3) the molecular epidemiology of human viruses, with special attention to JC, BK and Merkel cell polyomaviruses.
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8
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DuShane JK, Wilczek MP, Crocker MA, Maginnis MS. High-Throughput Characterization of Viral and Cellular Protein Expression Patterns During JC Polyomavirus Infection. Front Microbiol 2019; 10:783. [PMID: 31065251 PMCID: PMC6489551 DOI: 10.3389/fmicb.2019.00783] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 03/27/2019] [Indexed: 01/15/2023] Open
Abstract
JC polyomavirus (JCPyV) is a ubiquitous human pathogen and the causative agent of a fatal demyelinating disease in severely immunocompromised individuals. Due to the lack of successful pharmacological interventions, the study of JCPyV infection strategies in a rapid and highly sensitive manner is critical for the characterization of potential antiviral therapeutics. Conventional methodologies for studying viral infectivity often utilize the detection of viral proteins through immunofluorescence microscopy-based techniques. While these methodologies are well established in the field, they require significant time investments and lack a high-throughput modality. Scanning imager-based detection methods like the In-cell Western (ICW)TM have been previously utilized to overcome these challenges incurred by traditional microscopy-based infectivity assays. This automated technique provides not only rapid detection of viral infection status, but can also be optimized to detect changes in host-cell protein expression during JCPyV challenge. Compared to traditional manual determinations of infectivity through microscopy-based techniques, the ICW provides an expeditious and robust determination of JCPyV infection. The optimization of the ICW for the detection of viral and cellular proteins during JCPyV infection provides significant time and cost savings by diminishing sample preparation time and increasing resource utilization. While the ICW cannot provide single-cell analysis information and is limited in the detection of quantitation of low-expressing proteins, this assay provides a high-throughput system to study JCPyV, previously unavailable to the field. Thus, the high-throughput nature and dynamic experimental range of the ICW can be applied to the study of JCPyV infection.
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Affiliation(s)
- Jeanne K DuShane
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, ME, United States
| | - Michael P Wilczek
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, ME, United States
| | - Mason A Crocker
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, ME, United States
| | - Melissa S Maginnis
- Department of Molecular and Biomedical Sciences, The University of Maine, Orono, ME, United States.,Graduate School in Biomedical Sciences and Engineering, The University of Maine, Orono, ME, United States
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Pena GPA, Mendes GS, Dias HG, Gavazzoni LS, Amorim AR, Santos N. Human polyomavirus KI, WU, BK, and JC in healthy volunteers. Eur J Clin Microbiol Infect Dis 2018; 38:135-139. [PMID: 30338464 DOI: 10.1007/s10096-018-3404-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/12/2018] [Indexed: 12/16/2022]
Abstract
Despite the growing importance of infections caused by the human polyomaviruses (HPyVs), information about their transmission, pathogenesis, and epidemiology is scarce. The objective of this work was to evaluate the excretion and distribution of HPyV (HPyV1-HPyV4 [former BKPyV, JCPyV, KIPyV, and WUPyV, respectively]) among asymptomatic individuals from different geographic regions in Brazil, in order to verify the existence of distinct epidemiologic patterns among the Brazilian population. Saliva samples from 889 healthy volunteers living in nine locations in Brazil were analyzed by real-time polymerase chain reaction (PCR) to detect HPyV1-4. Among 889 participants, 346 (39%) had evidence of infection with one or more HPyV species: 127 (14.3%) had HPyV1 only; 70 (7.9%) had HPyV3 only; 60 (6.7%) had HPyV4 only, and 25 (2.8%) had HPyV2 only. Coinfections were detected in 64 participants (7.3%). Although HPyV excretion was detected in samples from all locations, the frequency and distribution of viral species varied significantly. The epidemiologic findings presented demonstrate that the four HPyV species studied are circulating in five geographic regions of Brazil. Salivary excretion of these viruses appears common among healthy Brazilians. The distribution of viral species varies considerably between regions as well as within regions.
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Affiliation(s)
- Giselle P A Pena
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Gabriella S Mendes
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Helver G Dias
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Lucas S Gavazzoni
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Ariane R Amorim
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Norma Santos
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. .,Departamento de Virologia, Instituto de Microbiologia, Universidade Federal do Rio de Janeiro, Cidade Universitária, CCS - Bl. I, Ilha do Fundão, Rio de Janeiro, RJ, 21941-902, Brazil.
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10
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Carr M, Gonzalez G, Sasaki M, Dool SE, Ito K, Ishii A, Hang'ombe BM, Mweene AS, Teeling EC, Hall WW, Orba Y, Sawa H. Identification of the same polyomavirus species in different African horseshoe bat species is indicative of short-range host-switching events. J Gen Virol 2017; 98:2771-2785. [PMID: 28984241 DOI: 10.1099/jgv.0.000935] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Polyomaviruses (PyVs) are considered to be highly host-specific in different mammalian species, with no well-supported evidence for host-switching events. We examined the species diversity and host specificity of PyVs in horseshoe bats (Rhinolophus spp.), a broadly distributed and highly speciose mammalian genus. We annotated six PyV genomes, comprising four new PyV species, based on pairwise identity within the large T antigen (LTAg) coding region. Phylogenetic comparisons revealed two instances of highly related PyV species, one in each of the Alphapolyomavirus and Betapolyomavirus genera, present in different horseshoe bat host species (Rhinolophus blasii and R. simulator), suggestive of short-range host-switching events. The two pairs of Rhinolophus PyVs in different horseshoe bat host species were 99.9 and 88.8 % identical with each other over their respective LTAg coding sequences and thus constitute the same virus species. To corroborate the species identification of the bat hosts, we analysed mitochondrial cytb and a large nuclear intron dataset derived from six independent and neutrally evolving loci for bat taxa of interest. Bayesian estimates of the ages of the most recent common ancestors suggested that the near-identical and more distantly related PyV species diverged approximately 9.1E4 (5E3-2.8E5) and 9.9E6 (4E6-18E6) years before the present, respectively, in contrast to the divergence times of the bat host species: 12.4E6 (10.4E6-15.4E6). Our findings provide evidence that short-range host-switching of PyVs is possible in horseshoe bats, suggesting that PyV transmission between closely related mammalian species can occur.
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Affiliation(s)
- Michael Carr
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan.,National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Gabriel Gonzalez
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Michihito Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Serena E Dool
- Zoological Institute and Museum, University of Greifswald, Anklamer Street 20, D-17489 Greifswald, Germany
| | - Kimihito Ito
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Akihiro Ishii
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Lusaka, Zambia
| | - Bernard M Hang'ombe
- Department of Para-clinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Aaron S Mweene
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - William W Hall
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan.,Global Virus Network, Baltimore, MD 21201, USA
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Hirofumi Sawa
- Global Virus Network, Baltimore, MD 21201, USA.,Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan.,Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia.,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
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11
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Li YM, Shivas RG, Cai L. Cryptic diversity in Tranzscheliella spp. (Ustilaginales) is driven by host switches. Sci Rep 2017; 7:43549. [PMID: 28256543 PMCID: PMC5335255 DOI: 10.1038/srep43549] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 01/25/2017] [Indexed: 01/19/2023] Open
Abstract
Species of Tranzscheliella have been reported as pathogens of more than 30 genera of grasses (Poaceae). In this study, a combined morphological and molecular phylogenetic approach was used to examine 33 specimens provisionally identified as belonging to the T. hypodytes species complex. The phylogenetic analysis resolved several well-supported clades that corresponded to known and novel species of Tranzscheliella. Four new species are described and illustrated. In addition, a new combination in Tranzscheliella is proposed for Sorosporium reverdattoanum. Cophylogenetic analyses assessed by distance-based and event-cost based methods, indicated host switches are likely the prominent force driving speciation in Tranzscheliella.
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Affiliation(s)
- Ying-Ming Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Roger G Shivas
- Plant Pathology Herbarium, Department of Agriculture and Forestry, Dutton Park, Queensland, 4102, Australia
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
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12
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Geoghegan JL, Duchêne S, Holmes EC. Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families. PLoS Pathog 2017; 13:e1006215. [PMID: 28178344 PMCID: PMC5319820 DOI: 10.1371/journal.ppat.1006215] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 02/21/2017] [Accepted: 02/02/2017] [Indexed: 01/20/2023] Open
Abstract
The cross-species transmission of viruses from one host species to another is responsible for the majority of emerging infections. However, it is unclear whether some virus families have a greater propensity to jump host species than others. If related viruses have an evolutionary history of co-divergence with their hosts there should be evidence of topological similarities between the virus and host phylogenetic trees, whereas host jumping generates incongruent tree topologies. By analyzing co-phylogenetic processes in 19 virus families and their eukaryotic hosts we provide a quantitative and comparative estimate of the relative frequency of virus-host co-divergence versus cross-species transmission among virus families. Notably, our analysis reveals that cross-species transmission is a near universal feature of the viruses analyzed here, with virus-host co-divergence occurring less frequently and always on a subset of viruses. Despite the overall high topological incongruence among virus and host phylogenies, the Hepadnaviridae, Polyomaviridae, Poxviridae, Papillomaviridae and Adenoviridae, all of which possess double-stranded DNA genomes, exhibited more frequent co-divergence than the other virus families studied here. At the other extreme, the virus and host trees for all the RNA viruses studied here, particularly the Rhabdoviridae and the Picornaviridae, displayed high levels of topological incongruence, indicative of frequent host switching. Overall, we show that cross-species transmission plays a major role in virus evolution, with all the virus families studied here having the potential to jump host species, and that increased sampling will likely reveal more instances of host jumping.
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Affiliation(s)
- Jemma L. Geoghegan
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Sebastián Duchêne
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
- Centre for Systems Genomics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
- * E-mail:
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13
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Assessing Host-Virus Codivergence for Close Relatives of Merkel Cell Polyomavirus Infecting African Great Apes. J Virol 2016; 90:8531-41. [PMID: 27440885 DOI: 10.1128/jvi.00247-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 07/12/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED It has long been hypothesized that polyomaviruses (PyV; family Polyomaviridae) codiverged with their animal hosts. In contrast, recent analyses suggested that codivergence may only marginally influence the evolution of PyV. We reassess this question by focusing on a single lineage of PyV infecting hominine hosts, the Merkel cell polyomavirus (MCPyV) lineage. By characterizing the genetic diversity of these viruses in seven African great ape taxa, we show that they exhibit very strong host specificity. Reconciliation analyses identify more codivergence than noncodivergence events. In addition, we find that a number of host and PyV divergence events are synchronous. Collectively, our results support codivergence as the dominant process at play during the evolution of the MCPyV lineage. More generally, our results add to the growing body of evidence suggesting an ancient and stable association of PyV and their animal hosts. IMPORTANCE The processes involved in viral evolution and the interaction of viruses with their hosts are of great scientific interest and public health relevance. It has long been thought that the genetic diversity of double-stranded DNA viruses was generated over long periods of time, similar to typical host evolutionary timescales. This was also hypothesized for polyomaviruses (family Polyomaviridae), a group comprising several human pathogens, but this remains a point of controversy. Here, we investigate this question by focusing on a single lineage of polyomaviruses that infect both humans and their closest relatives, the African great apes. We show that these viruses exhibit considerable host specificity and that their evolution largely mirrors that of their hosts, suggesting that codivergence with their hosts played a major role in their diversification. Our results provide statistical evidence in favor of an association of polyomaviruses and their hosts over millions of years.
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Concurrence of Iridovirus, Polyomavirus, and a Unique Member of a New Group of Fish Papillomaviruses in Lymphocystis Disease-Affected Gilthead Sea Bream. J Virol 2016; 90:8768-79. [PMID: 27440877 DOI: 10.1128/jvi.01369-16] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 07/15/2016] [Indexed: 01/25/2023] Open
Abstract
UNLABELLED Lymphocystis disease is a geographically widespread disease affecting more than 150 different species of marine and freshwater fish. The disease, provoked by the iridovirus lymphocystis disease virus (LCDV), is characterized by the appearance of papillomalike lesions on the skin of affected animals that usually self-resolve over time. Development of the disease is usually associated with several environmental factors and, more frequently, with stress conditions provoked by the intensive culture conditions present in fish farms. In gilthead sea bream (Sparus aurata), an economically important cultured fish species in the Mediterranean area, a distinct LCDV has been identified but not yet completely characterized. We have used direct sequencing of the virome of lymphocystis lesions from affected S. aurata fish to obtain the complete genome of a new LCDV-Sa species that is the largest vertebrate iridovirus sequenced to date. Importantly, this approach allowed us to assemble the full-length circular genome sequence of two previously unknown viruses belonging to the papillomaviruses and polyomaviruses, termed Sparus aurata papillomavirus 1 (SaPV1) and Sparus aurata polyomavirus 1 (SaPyV1), respectively. Epidemiological surveys showed that lymphocystis disease was frequently associated with the concurrent appearance of one or both of the new viruses. SaPV1 has unique characteristics, such as an intron within the L1 gene, and as the first member of the Papillomaviridae family described in fish, provides evidence for a more ancient origin of this family than previously thought. IMPORTANCE Lymphocystis disease affects marine and freshwater fish species worldwide. It is characterized by the appearance of papillomalike lesions on the skin that contain heavily enlarged cells (lymphocysts). The causative agent is the lymphocystis disease virus (LCDV), a large icosahedral virus of the family Iridoviridae In the Mediterranean area, the gilthead sea bream (Sparus aurata), an important farmed fish, is frequently affected. Using next-generation sequencing, we have identified within S. aurata lymphocystis lesions the concurrent presence of an additional LCDV species (LCDV-Sa) as well as two novel viruses. These are members of polyomavirus and papillomavirus families, and here we report them to be frequently associated with the presence of lymphocysts in affected fish. Because papillomaviruses have not been described in fish before, these findings support a more ancient origin of this virus family than previously thought and evolutionary implications are discussed.
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15
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Buck CB, Van Doorslaer K, Peretti A, Geoghegan EM, Tisza MJ, An P, Katz JP, Pipas JM, McBride AA, Camus AC, McDermott AJ, Dill JA, Delwart E, Ng TFF, Farkas K, Austin C, Kraberger S, Davison W, Pastrana DV, Varsani A. The Ancient Evolutionary History of Polyomaviruses. PLoS Pathog 2016; 12:e1005574. [PMID: 27093155 PMCID: PMC4836724 DOI: 10.1371/journal.ppat.1005574] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/23/2016] [Indexed: 12/21/2022] Open
Abstract
Polyomaviruses are a family of DNA tumor viruses that are known to infect mammals and birds. To investigate the deeper evolutionary history of the family, we used a combination of viral metagenomics, bioinformatics, and structural modeling approaches to identify and characterize polyomavirus sequences associated with fish and arthropods. Analyses drawing upon the divergent new sequences indicate that polyomaviruses have been gradually co-evolving with their animal hosts for at least half a billion years. Phylogenetic analyses of individual polyomavirus genes suggest that some modern polyomavirus species arose after ancient recombination events involving distantly related polyomavirus lineages. The improved evolutionary model provides a useful platform for developing a more accurate taxonomic classification system for the viral family Polyomaviridae. Polyomaviruses are a family of DNA-based viruses that are known to infect various terrestrial vertebrates, including humans. In this report, we describe our discovery of highly divergent polyomaviruses associated with various marine fish. Searches of public deep sequencing databases unexpectedly revealed the existence of polyomavirus-like sequences in scorpion and spider datasets. Our analysis of these new sequences suggests that polyomaviruses have slowly co-evolved with individual host animal lineages through an established mechanism known as intrahost divergence. The proposed model is similar to the mechanisms through with other DNA viruses, such as papillomaviruses, are thought to have evolved. Our analysis also suggests that distantly related polyomaviruses sometimes recombine to produce new chimeric lineages. We propose a possible taxonomic scheme that can account for these inferred ancient recombination events.
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Affiliation(s)
- Christopher B. Buck
- Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America
- * E-mail:
| | | | - Alberto Peretti
- Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America
| | - Eileen M. Geoghegan
- Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America
| | - Michael J. Tisza
- Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America
| | - Ping An
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Joshua P. Katz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - James M. Pipas
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Alison A. McBride
- Lab of Viral Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Alvin C. Camus
- Department of Pathology, University of Georgia, Athens, Georgia, United States of America
| | - Alexa J. McDermott
- Animal Health Department, Georgia Aquarium, Inc., Atlanta, Georgia, United States of America
| | - Jennifer A. Dill
- Department of Pathology, University of Georgia, Athens, Georgia, United States of America
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Terry F. F. Ng
- Blood Systems Research Institute, San Francisco, California, United States of America
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Kata Farkas
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Charlotte Austin
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Simona Kraberger
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - William Davison
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Diana V. Pastrana
- Lab of Cellular Oncology, NCI, NIH, Bethesda, Maryland, United States of America
| | - Arvind Varsani
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
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16
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Complete Genome Sequence of Bovine Polyomavirus Type 1 from Aborted Cattle, Isolated in Belgium in 2014. GENOME ANNOUNCEMENTS 2016; 4:4/2/e01646-15. [PMID: 26941154 PMCID: PMC4777765 DOI: 10.1128/genomea.01646-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The complete and fully annotated genome sequence of a bovine polyomavirus type 1 (BPyV/BEL/1/2014) from aborted cattle was assembled from a metagenomics data set. The 4,697-bp circular dsDNA genome contains 6 protein-coding genes. Bovine polyomavirus is unlikely to be causally related to the abortion cases.
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de Sales Lima FE, Cibulski SP, Witt AA, Franco AC, Roehe PM. Genomic characterization of two novel polyomaviruses in Brazilian insectivorous bats. Arch Virol 2015; 160:1831-6. [PMID: 25963124 PMCID: PMC7086640 DOI: 10.1007/s00705-015-2447-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 04/30/2015] [Indexed: 01/15/2023]
Abstract
Two novel genomes comprising ≈4.9 kb were identified by next-generation sequencing from pooled organs of Tadarida brasiliensis bats. The overall nucleotide sequence identities between the viral genomes characterized here were less than 80% in comparison to other polyomaviruses (PyVs), members of the family Polyomaviridae. The new genomes display the archetypal organization of PyVs, which includes open reading frames for the regulatory proteins small T antigen (STAg) and large T antigen (LTAg), as well as capsid proteins VP1, VP2 and VP3. In addition, an alternate ORF was identified in the early genome region that is conserved in a large monophyletic group of polyomaviruses. Phylogenetic analysis showed similar clustering with group of PyVs detected in Otomops and Chaerephon bats and some species of monkeys. In this study, the genomes of two novel PyVs were detected in bats of a single species, demonstrating that these mammals can harbor genetically diverse polyomaviruses.
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Affiliation(s)
- Francisco Esmaile de Sales Lima
- Virology Laboratory, Department of Microbiology, Immunology and Parasitology, Institute of Basic Health Sciences, Federal University of Rio Grande do Sul (UFRGS), Rua Sarmento Leite 500, Porto Alegre, Rio Grande do Sul, CEP 90050-170, Brazil,
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18
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Hill SC, Murphy AA, Cotten M, Palser AL, Benson P, Lesellier S, Gormley E, Richomme C, Grierson S, Bhuachalla DN, Chambers M, Kellam P, Boschiroli ML, Ehlers B, Jarvis MA, Pybus OG. Discovery of a polyomavirus in European badgers (Meles meles) and the evolution of host range in the family Polyomaviridae. J Gen Virol 2015; 96:1411-1422. [PMID: 25626684 PMCID: PMC4635489 DOI: 10.1099/vir.0.000071] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 01/23/2015] [Indexed: 12/25/2022] Open
Abstract
Polyomaviruses infect a diverse range of mammalian and avian hosts, and are associated with a variety of symptoms. However, it is unknown whether the viruses are found in all mammalian families and the evolutionary history of the polyomaviruses is still unclear. Here, we report the discovery of a novel polyomavirus in the European badger (Meles meles), which to our knowledge represents the first polyomavirus to be characterized in the family Mustelidae, and within a European carnivoran. Although the virus was discovered serendipitously in the supernatant of a cell culture inoculated with badger material, we subsequently confirmed its presence in wild badgers. The European badger polyomavirus was tentatively named Meles meles polyomavirus 1 (MmelPyV1). The genome is 5187 bp long and encodes proteins typical of polyomaviruses. Phylogenetic analyses including all known polyomavirus genomes consistently group MmelPyV1 with California sea lion polyomavirus 1 across all regions of the genome. Further evolutionary analyses revealed phylogenetic discordance amongst polyomavirus genome regions, possibly arising from evolutionary rate heterogeneity, and a complex association between polyomavirus phylogeny and host taxonomic groups.
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Affiliation(s)
| | - Aisling A Murphy
- School of Biomedical and Healthcare Sciences, Plymouth University, UK
| | | | | | - Phillip Benson
- School of Biomedical and Healthcare Sciences, Plymouth University, UK
| | | | - Eamonn Gormley
- School of Veterinary Medicine, University College Dublin (UCD), Ireland
| | | | | | | | - Mark Chambers
- School of Veterinary Medicine, University of Surrey, UK.,Bacteriology Department, Animal and Plant Health Agency, UK
| | - Paul Kellam
- MRC/UCL Centre for Medical Molecular Virology, University College London, UK.,Wellcome Trust Sanger Institute, UK
| | - María-Laura Boschiroli
- University Paris-Est, ANSES, Laboratory for Animal Health, Bovine Tuberculosis National Reference Laboratory, France
| | - Bernhard Ehlers
- Robert Koch Institute, Division 12 'Measles, Mumps, Rubella and Viruses Affecting Immunocompromised Patients', Germany
| | - Michael A Jarvis
- School of Biomedical and Healthcare Sciences, Plymouth University, UK
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19
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A novel papillomavirus isolated from a nasal neoplasia in an Italian free-ranging chamois (Rupicapra r. rupicapra). Vet Microbiol 2014; 172:108-19. [PMID: 24910075 DOI: 10.1016/j.vetmic.2014.05.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 04/30/2014] [Accepted: 05/04/2014] [Indexed: 11/22/2022]
Abstract
Most amniotes are the hosts of many, distantly related papillomaviruses (PVs). Infection by PVs can be asymptomatic, or lead instead to benign or malignant lesions. However, PVs infecting animals and associated with malignancies are still largely understudied. In the present study, we communicate the complete genome of a novel PV found in a nasal neoplasia of a free-ranging alpine chamois (Rupicapra r. rupicapra) in an Italian national park. Long-PCR and cloning approaches followed for Sanger sequencing were used to identify the first PV found in chamois. The genome of the novel virus - RrupPV1 - of 7256 bp in length, presents the classical PV structure, and lacks the interE2-L2 region that hosts the E5 gene in AlphaPVs and in DeltaPVs. The nucleotide identity percentage of the L1 ORF, places RrupPV1 together with OaPV3 in the same genus. The latter is a PV isolated from a squamous cell carcinoma in sheep in Sardinia. Full-genome phylogenetic reconstructions suggest that these two viruses are sister taxa, and that both of them are very distantly related to any other known PV. Many cetartiodactyl species are infected by non-monophyletic PVs. Our results exemplify further the multiple links between the infection by certain, distantly related PVs and the development of diverse cancers in animals and highlight the need of a systematic search of oncogenic and non-oncogenic animal PVs.
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20
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Bellec L, Clerissi C, Edern R, Foulon E, Simon N, Grimsley N, Desdevises Y. Cophylogenetic interactions between marine viruses and eukaryotic picophytoplankton. BMC Evol Biol 2014; 14:59. [PMID: 24669847 PMCID: PMC3983898 DOI: 10.1186/1471-2148-14-59] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 03/20/2014] [Indexed: 01/10/2023] Open
Abstract
Background Numerous studies have investigated cospeciation (or cophylogeny) in various host-symbiont systems, and different patterns were inferred, from strict cospeciation where symbiont phylogeny mirrors host phylogeny, to complete absence of correspondence between trees. The degree of cospeciation is generally linked to the level of host specificity in the symbiont species and the opportunity they have to switch hosts. In this study, we investigated cophylogeny for the first time in a microalgae-virus association in the open sea, where symbionts are believed to be highly host-specific but have wide opportunities to switch hosts. We studied prasinovirus-Mamiellales associations using 51 different viral strains infecting 22 host strains, selected from the characterisation and experimental testing of the specificities of 313 virus strains on 26 host strains. Results All virus strains were restricted to their host genus, and most were species-specific, but some of them were able to infect different host species within a genus. Phylogenetic trees were reconstructed for viruses and their hosts, and their congruence was assessed based on these trees and the specificity data using different cophylogenetic methods, a topology-based approach, Jane, and a global congruence method, ParaFit. We found significant congruence between virus and host trees, but with a putatively complex evolutionary history. Conclusions Mechanisms other than true cospeciation, such as host-switching, might explain a part of the data. It has been observed in a previous study on the same taxa that the genomic divergence between host pairs is larger than between their viruses. It implies that if cospeciation predominates in this algae-virus system, this would support the hypothesis that prasinoviruses evolve more slowly than their microalgal hosts, whereas host switching would imply that these viruses speciated more recently than the divergence of their host genera.
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Affiliation(s)
| | | | | | | | | | | | - Yves Desdevises
- Integrative Biology of Marine Organisms, Observatoire Océanologique, Sorbonne Universités, UPMC Univ Paris 06, UMR 7232, F-66650 Banyuls-sur-Mer, France.
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21
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Millanes AM, Truong C, Westberg M, Diederich P, Wedin M. Host switching promotes diversity in host-specialized mycoparasitic fungi: uncoupled evolution in the Biatoropsis-usnea system. Evolution 2014; 68:1576-93. [PMID: 24495034 DOI: 10.1111/evo.12374] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 01/24/2014] [Indexed: 12/15/2022]
Abstract
Fungal mycoparasitism-fungi parasitizing other fungi-is a common lifestyle in some basal lineages of the basidiomycetes, particularly within the Tremellales. Relatively nonaggressive mycoparasitic fungi of this group are in general highly host specific, suggesting cospeciation as a plausible speciation mode in these associations. Species delimitation in the Tremellales is often challenging because morphological characters are scant. Host specificity is therefore a great aid to discriminate between species but appropriate species delimitation methods that account for actual diversity are needed to identify both specialist and generalist taxa and avoid inflating or underestimating diversity. We use the Biatoropsis-Usnea system to study factors inducing parasite diversification. We employ morphological, ecological, and molecular data-methods including genealogical concordance phylogenetic species recognition (GCPSR) and the general mixed Yule-coalescent (GMYC) model-to assess the diversity of fungi currently assigned to Biatoropsis usnearum. The degree of cospeciation in this association is assessed with two cophylogeny analysis tools (ParaFit and Jane 4.0). Biatoropsis constitutes a species complex formed by at least seven different independent lineages and host switching is a prominent force driving speciation, particularly in host specialists. Combining ITS and nLSU is recommended as barcode system in tremellalean fungi.
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Affiliation(s)
- Ana M Millanes
- Departamento de Biología y Geología, Universidad Rey Juan Carlos, E-28933 Móstoles, Spain.
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22
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Bhattacharjee S. Role of genomic and proteomic tools in the study of host-virus interactions and virus evolution. INDIAN JOURNAL OF VIROLOGY : AN OFFICIAL ORGAN OF INDIAN VIROLOGICAL SOCIETY 2013; 24:306-11. [PMID: 24426292 PMCID: PMC3832694 DOI: 10.1007/s13337-013-0150-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 07/24/2013] [Indexed: 01/05/2023]
Abstract
Viruses have short replication cycles and produce genomic variants within a host, a process that seems to adapt to their specific host and also enable them to infect new hosts. The recent emergence of viral genomic variants from the circulating pool within the host population and re-emergence of the old ones are posing serious threat to agriculture, animal husbandry and humanity as a whole. This review assesses the potential role of genomic and proteomic tools that can monitor not only the course of infection and pathogenesis, but also predict the pandemic or zoonotic epidemic potential of a virus in a previously exposed or immunologically naive biological population.
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Affiliation(s)
- Soumen Bhattacharjee
- Cell and Molecular Biology Laboratory, Department of Zoology, University of North Bengal, Raja Rammohunpur, P.O. North Bengal University, Siliguri, 734 013 District Darjeeling, West Bengal India
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23
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Tao Y, Shi M, Conrardy C, Kuzmin IV, Recuenco S, Agwanda B, Alvarez DA, Ellison JA, Gilbert AT, Moran D, Niezgoda M, Lindblade KA, Holmes EC, Breiman RF, Rupprecht CE, Tong S. Discovery of diverse polyomaviruses in bats and the evolutionary history of the Polyomaviridae. J Gen Virol 2013; 94:738-748. [PMID: 23239573 PMCID: PMC7346582 DOI: 10.1099/vir.0.047928-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 12/09/2012] [Indexed: 12/18/2022] Open
Abstract
Polyomaviruses (PyVs) have been identified in a wide range of avian and mammalian species. However, little is known about their occurrence, genetic diversity and evolutionary history in bats, even though bats are important reservoirs for many emerging viral pathogens. This study screened 380 specimens from 35 bat species from Kenya and Guatemala for the presence of PyVs by semi-nested pan-PyV PCR assays. PyV DNA was detected in 24 of the 380 bat specimens. Phylogenetic analysis revealed that the bat PyV sequences formed 12 distinct lineages. Full-genome sequences were obtained for seven representative lineages and possessed similar genomic features to known PyVs. Strikingly, this evolutionary analysis revealed that the bat PyVs were paraphyletic, suggestive of multiple species jumps between bats and other mammalian species, such that the theory of virus-host co-divergence for mammalian PyVs as a whole could be rejected. In addition, evidence was found for strong heterogeneity in evolutionary rate and potential recombination in a number of PyV complete genomes, which complicates both phylogenetic analysis and virus classification. In summary, this study revealed that bats are important reservoirs of PyVs and that these viruses have a complex evolutionary history.
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Affiliation(s)
- Ying Tao
- Division of Viral Diseases, Centers for Disease Control and
Prevention, Atlanta, GA 30333, USA
| | - Mang Shi
- Sydney Emerging Infections and Biosecurity Institute, School of
Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW
2006, Australia
| | - Christina Conrardy
- Division of Viral Diseases, Centers for Disease Control and
Prevention, Atlanta, GA 30333, USA
| | - Ivan V. Kuzmin
- Division of High Consequence Pathogens and Pathology, Centers for
Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Sergio Recuenco
- Division of High Consequence Pathogens and Pathology, Centers for
Disease Control and Prevention, Atlanta, GA 30333, USA
| | | | - Danilo A. Alvarez
- Center for Health Studies, Universidad del Valle de Guatemala,
Guatemala City, Guatemala
| | - James A. Ellison
- Division of High Consequence Pathogens and Pathology, Centers for
Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Amy T. Gilbert
- Division of High Consequence Pathogens and Pathology, Centers for
Disease Control and Prevention, Atlanta, GA 30333, USA
| | - David Moran
- Center for Health Studies, Universidad del Valle de Guatemala,
Guatemala City, Guatemala
| | - Michael Niezgoda
- Division of High Consequence Pathogens and Pathology, Centers for
Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Kim A. Lindblade
- Centers for Disease Control and Prevention Central America and
Panama, Guatemala
| | - Edward C. Holmes
- Sydney Emerging Infections and Biosecurity Institute, School of
Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW
2006, Australia
- Fogarty International Center, National Institutes of Health,
Bethesda, MD 20892, USA
| | | | - Charles E. Rupprecht
- Division of High Consequence Pathogens and Pathology, Centers for
Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Suxiang Tong
- Division of Viral Diseases, Centers for Disease Control and
Prevention, Atlanta, GA 30333, USA
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de Vienne DM, Refrégier G, López-Villavicencio M, Tellier A, Hood ME, Giraud T. Cospeciation vs host-shift speciation: methods for testing, evidence from natural associations and relation to coevolution. THE NEW PHYTOLOGIST 2013; 198:347-385. [PMID: 23437795 DOI: 10.1111/nph.12150] [Citation(s) in RCA: 259] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 12/19/2012] [Indexed: 05/26/2023]
Abstract
Hosts and their symbionts are involved in intimate physiological and ecological interactions. The impact of these interactions on the evolution of each partner depends on the time-scale considered. Short-term dynamics - 'coevolution' in the narrow sense - has been reviewed elsewhere. We focus here on the long-term evolutionary dynamics of cospeciation and speciation following host shifts. Whether hosts and their symbionts speciate in parallel, by cospeciation, or through host shifts, is a key issue in host-symbiont evolution. In this review, we first outline approaches to compare divergence between pairwise associated groups of species, their advantages and pitfalls. We then consider recent insights into the long-term evolution of host-parasite and host-mutualist associations by critically reviewing the literature. We show that convincing cases of cospeciation are rare (7%) and that cophylogenetic methods overestimate the occurrence of such events. Finally, we examine the relationships between short-term coevolutionary dynamics and long-term patterns of diversification in host-symbiont associations. We review theoretical and experimental studies showing that short-term dynamics can foster parasite specialization, but that these events can occur following host shifts and do not necessarily involve cospeciation. Overall, there is now substantial evidence to suggest that coevolutionary dynamics of hosts and parasites do not favor long-term cospeciation.
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Affiliation(s)
- D M de Vienne
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - G Refrégier
- Université Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, 91405, Orsay, France
- CNRS, UMR8621, 91405, Orsay, France
| | - M López-Villavicencio
- Muséum National d'Histoire Naturelle, 57 rue Cuvier, F-75231, Paris Cedex 05, France
| | - A Tellier
- Section of Population Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, D-85354, Freising, Germany
| | - M E Hood
- Department of Biology, Amherst College, Amherst, MA, USA
| | - T Giraud
- Université Paris-Sud, Ecologie, Systématique et Evolution, UMR 8079, 91405, Orsay, France
- CNRS, UMR8079, 91405, Orsay, France
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Abstract
During the past 6 years, focused virus hunting has led to the discovery of nine new human polyomaviruses, including Merkel cell polyomavirus, which has been linked to Merkel cell carcinoma, a lethal skin cell cancer. The discovery of so many new and highly divergent human polyomaviruses raises key questions regarding their evolution, tropism, latency, reactivation, immune evasion and contribution to disease. This Review describes the similarities and differences among the new human polyomaviruses and discusses how these viruses might interact with their human host.
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Affiliation(s)
- James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.
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Feltkamp MCW, Kazem S, van der Meijden E, Lauber C, Gorbalenya AE. From Stockholm to Malawi: recent developments in studying human polyomaviruses. J Gen Virol 2013; 94:482-496. [DOI: 10.1099/vir.0.048462-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Until a few years ago the polyomavirus family (Polyomaviridae) included a dozen viruses identified in avian and mammalian hosts. Two of these, the JC and BK-polyomaviruses isolated a long time ago, are known to infect humans and cause severe illness in immunocompromised hosts. Since 2007 an unprecedented number of eight novel polyomaviruses were discovered in humans. Among them are the KI- and WU-polyomaviruses identified in respiratory samples, the Merkel cell polyomavirus found in skin carcinomas and the polyomavirus associated with trichodysplasia spinulosa, a skin disease of transplant patients. Another four novel human polyomaviruses were identified, HPyV6, HPyV7, HPyV9 and the Malawi polyomavirus, so far not associated with any disease. In the same period several novel mammalian polyomaviruses were described. This review summarizes the recent developments in studying the novel human polyomaviruses, and touches upon several aspects of polyomavirus virology, pathogenicity, epidemiology and phylogeny.
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Affiliation(s)
- Mariet C. W. Feltkamp
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Siamaque Kazem
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Els van der Meijden
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Chris Lauber
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alexander E. Gorbalenya
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119899 Moscow, Russia
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
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27
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Nims RW, Plavsic M. Polyomavirus inactivation – A review. Biologicals 2013; 41:63-70. [DOI: 10.1016/j.biologicals.2012.09.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 09/10/2012] [Accepted: 09/30/2012] [Indexed: 11/25/2022] Open
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28
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Lim ES, Reyes A, Antonio M, Saha D, Ikumapayi UN, Adeyemi M, Stine OC, Skelton R, Brennan DC, Mkakosya RS, Manary MJ, Gordon JI, Wang D. Discovery of STL polyomavirus, a polyomavirus of ancestral recombinant origin that encodes a unique T antigen by alternative splicing. Virology 2013; 436:295-303. [PMID: 23276405 PMCID: PMC3693558 DOI: 10.1016/j.virol.2012.12.005] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 10/08/2012] [Accepted: 12/05/2012] [Indexed: 12/12/2022]
Abstract
The family Polyomaviridae is comprised of circular double-stranded DNA viruses, several of which are associated with diseases, including cancer, in immunocompromised patients. Here we describe a novel polyomavirus recovered from the fecal microbiota of a child in Malawi, provisionally named STL polyomavirus (STLPyV). We detected STLPyV in clinical stool specimens from USA and The Gambia at up to 1% frequency. Complete genome comparisons of two STLPyV strains demonstrated 5.2% nucleotide divergence. Alternative splicing of the STLPyV early region yielded a unique form of T antigen, which we named 229T, in addition to the expected large and small T antigens. STLPyV has a mosaic genome and shares an ancestral recombinant origin with MWPyV. The discovery of STLPyV highlights a novel alternative splicing strategy and advances our understanding of the complex evolutionary history of polyomaviruses.
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MESH Headings
- Adolescent
- Adult
- Alternative Splicing
- Antigens, Viral, Tumor/genetics
- Child
- Child, Preschool
- Cluster Analysis
- DNA, Viral/chemistry
- DNA, Viral/genetics
- Evolution, Molecular
- Feces/virology
- Female
- Gambia
- Gene Expression Regulation, Viral
- Genome, Viral
- Humans
- Infant
- Malawi
- Male
- Molecular Sequence Data
- Phylogeny
- Polyomavirus/classification
- Polyomavirus/genetics
- Polyomavirus/isolation & purification
- Polyomavirus Infections/epidemiology
- Polyomavirus Infections/virology
- Prevalence
- Recombination, Genetic
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- United States
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Affiliation(s)
- Efrem S. Lim
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, Missouri, USA
| | - Alejandro Reyes
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, Missouri, USA
| | - Martin Antonio
- Medical Research Council Unit, PO Box 273, Banjul, The Gambia
| | - Debasish Saha
- Medical Research Council Unit, PO Box 273, Banjul, The Gambia
| | | | | | - O. Colin Stine
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, 660 W Redwood St., Baltimore, Maryland, USA
| | - Rebecca Skelton
- Department of Internal Medicine, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, Missouri, USA
| | - Daniel C. Brennan
- Department of Internal Medicine, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, Missouri, USA
| | - Rajhab S. Mkakosya
- Department of Pathology, University of Malawi College of Medicine, Private Bag 360, Chichiri, Blantyre 3, Malawi
| | - Mark J. Manary
- Department of Pediatrics, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, Missouri, USA
- Department of Community Health, University of Malawi College of Medicine, Private Bag 360, Chichiri, Blantyre 3, Malawi
| | - Jeffrey I. Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, Missouri, USA
| | - David Wang
- Departments of Molecular Microbiology and Pathology & Immunology, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, Missouri, USA
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29
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Wong K, Fong TT, Bibby K, Molina M. Application of enteric viruses for fecal pollution source tracking in environmental waters. ENVIRONMENT INTERNATIONAL 2012; 45:151-64. [PMID: 22537583 DOI: 10.1016/j.envint.2012.02.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 02/27/2012] [Accepted: 02/28/2012] [Indexed: 05/22/2023]
Abstract
Microbial source tracking (MST) tools are used to identify sources of fecal pollution for accurately assessing public health risk and implementing best management practices (BMPs). This review focuses on the potential of enteric viruses for MST applications. Following host infection, enteric viruses replicate and are excreted in high numbers in the hosts' feces and urine. Due to the specificity in host infection, enteric viruses have been considered one of the most accurate library-independent culture-independent MST tools. In an assessment of molecular viral assays based on sensitivity, specificity and the density of the target virus in fecal-impacted samples, human adenovirus and human polyomavirus were found to be the most promising human-specific viral markers. However, more research is needed to identify promising viral markers for livestock because of cross-reactions that were observed among livestock species or the limited number of samples tested for specificity. Other viral indicators of fecal origin, F+ RNA coliphage and pepper mild mottle virus, have also been proposed as potential targets for developing MST markers. Enhancing the utility of enteric viruses for MST applications through next generation sequencing (NGS) and virus concentration technology is discussed in the latter part of this review. The massive sequence databases generated by shotgun and gene-targeted metagenomics enable more efficient and reliable design of MST assays. Finally, recent studies revealed that alternative virus concentration methodologies may be more cost-effective than standard technologies such as 1MDS; however, improvements in the recovery efficiency and consistency are still needed. Overall, developments in metagenomic information combined with efficient concentration methodologies, as well as high host-specificity, make enteric viruses a promising tool in MST applications.
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Affiliation(s)
- Kelvin Wong
- United States Environmental Protection Agency, Ecosystems Research Division, 960 College Station Road, Athens, GA, USA.
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30
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Gao Y, Luo L. Genome-based phylogeny of dsDNA viruses by a novel alignment-free method. Gene 2011; 492:309-14. [PMID: 22100880 DOI: 10.1016/j.gene.2011.11.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2011] [Revised: 09/19/2011] [Accepted: 11/01/2011] [Indexed: 12/25/2022]
Abstract
Sequence alignment is not directly applicable to whole genome phylogeny since several events such as rearrangements make full length alignments impossible. Here, a novel alignment-free method derived from the standpoint of information theory is proposed and used to construct the whole-genome phylogeny for a population of viruses from 13 viral families comprising 218 dsDNA viruses. The method is based on information correlation (IC) and partial information correlation (PIC). We observe that (i) the IC-PIC tree segregates the population into clades, the membership of each is remarkably consistent with biologist's systematics only with little exceptions; (ii) the IC-PIC tree reveals potential evolutionary relationships among some viral families; and (iii) the IC-PIC tree predicts the taxonomic positions of certain "unclassified" viruses. Our approach provides a new way for recovering the phylogeny of viruses, and has practical applications in developing alignment-free methods for sequence classification.
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Affiliation(s)
- Yang Gao
- Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China
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31
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Stobbe AH, Melcher U, Palmer MW, Roossinck MJ, Shen G. Co-divergence and host-switching in the evolution of tobamoviruses. J Gen Virol 2011; 93:408-418. [PMID: 22049092 DOI: 10.1099/vir.0.034280-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The proposed phylogenetic structure of the genus Tobamovirus supports the idea that these viruses have codiverged with their hosts since radiation of the hosts from a common ancestor. The determinations of genome sequence for two strains of Passion fruit mosaic virus (PafMV), a tobamovirus from plants of the family Passifloraceae (order Malpighiales) from which only one other tobamovirus (Maracuja mosaic virus; MarMV) has been characterized, combined with the development of Bayesian analysis methods for phylogenetic inference, provided an opportunity to reassess the co-divergence hypothesis. The sequence of one PafMV strain, PfaMV-TGP, was discovered during a survey of plants of the Tallgrass Prairie Preserve for their virus content. Its nucleotides are only 73 % identical to those of MarMV. A conserved ORF not found in other tobamovirus genomes, and encoding a cysteine-rich protein, was found in MarMV and both PafMV strains. Phylogenetic tree construction, using an alignment of the nucleotide sequences of PafMV-TGP and other tobamoviruses resulted in a major clade containing isolates exclusively from rosid plants. Asterid-derived viruses were exclusively found in a second major clade that also contained an orchid-derived tobamovirus and tobamoviruses infecting plants of the order Brassicales. With a few exceptions, calibrating the virus tree with dates of host divergence at two points resulted in predictions of divergence times of family specific tobamovirus clades that were consistent with the times of divergence of the host plant orders.
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Affiliation(s)
- Anthony H Stobbe
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Ulrich Melcher
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Michael W Palmer
- Department of Botany, Oklahoma State University, Stillwater, OK 74078, USA
| | - Marilyn J Roossinck
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA
| | - Guoan Shen
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA
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32
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Zhuang Q, Chen J, Mushtaq MH, Chen J, Liu S, Hou G, Li J, Huang B, Jiang W. Prevalence and genetic characterization of avian polyomavirus and psittacine beak and feather disease virus isolated from budgerigars in Mainland China. Arch Virol 2011; 157:53-61. [DOI: 10.1007/s00705-011-1138-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 09/28/2011] [Indexed: 11/25/2022]
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33
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Yan XY, Wu ZH, Jian JC, Lu YS, Sun XQ. Analysis of the genetic diversity of the lymphocystis virus and its evolutionary relationship with its hosts. Virus Genes 2011; 43:358-66. [DOI: 10.1007/s11262-011-0646-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Accepted: 07/12/2011] [Indexed: 01/05/2023]
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34
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Chen PL, Hsu PH, Fang CY, Chang CF, Ou WC, Wang M, Chang D. Phosphorylation of Ser-80 of VP1 and Ser-254 of VP2 is essential for human BK virus propagation in tissue culture. J Gen Virol 2011; 92:2637-2645. [PMID: 21752965 DOI: 10.1099/vir.0.033282-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
BK virus (BKV) infection may cause polyomavirus-associated nephropathy in patients with renal transplantation. Recently, the phosphorylated amino acids on the structural proteins VP1, VP2 and VP3 of BKV have been identified by liquid chromatography-tandem mass spectrometry in our laboratory. In this study, we further analysed the biological effects of these phosphorylation events. Phosphorylation of the BKV structural proteins was demonstrated by [(32)P]orthophosphate labelling in vivo. Site-directed mutagenesis was performed to replace all of the phosphorylated amino acids. The mutated BKV genomes were transfected into Vero cells for propagation analysis. The results showed that expression of the early protein LT and of the late protein VP1 by the mutants VP1-S80A, VP1-S80-133A, VP1-S80-327A, VP1-S80-133-327A and VP2-S254A was abolished. However, propagation of other mutants was similar to that of wild-type BKV. The results suggest that phosphorylation of Ser-80 of VP1 and Ser-254 of VP2 is crucial for BKV propagation.
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Affiliation(s)
- Pei-Lain Chen
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, Taiwan, ROC.,Department of Chemistry and Biochemistry, National Chung Cheng University, Chia-Yi, Taiwan, ROC.,Institute of Molecular Biology, National Chung Cheng University, Chia-Yi, Taiwan, ROC
| | - Pang-Hung Hsu
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan, ROC.,Department of Life Science, National Taiwan Ocean University, Keelung, Taiwan, ROC
| | - Chiung-Yao Fang
- Institute of Molecular Biology, National Chung Cheng University, Chia-Yi, Taiwan, ROC
| | - Chi-Fang Chang
- Institute of Molecular Biology, National Chung Cheng University, Chia-Yi, Taiwan, ROC
| | - Wei-Chih Ou
- Department of Medical Laboratory Science and Biotechnology, Central Taiwan University of Science and Technology, Taichung, Taiwan, ROC
| | - Meilin Wang
- Department of Microbiology and Immunology, Chung Shan Medical University, Taichung, Taiwan, ROC
| | - Deching Chang
- Institute of Molecular Biology, National Chung Cheng University, Chia-Yi, Taiwan, ROC
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35
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Wellehan JF, Rivera R, Archer LL, Benham C, Muller JK, Colegrove KM, Gulland FM, St. Leger JA, Venn-Watson SK, Nollens HH. Characterization of California sea lion polyomavirus 1: Expansion of the known host range of the Polyomaviridae to Carnivora. INFECTION GENETICS AND EVOLUTION 2011; 11:987-96. [DOI: 10.1016/j.meegid.2011.03.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 02/11/2011] [Accepted: 03/17/2011] [Indexed: 11/29/2022]
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36
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Taxonomical developments in the family Polyomaviridae. Arch Virol 2011; 156:1627-34. [PMID: 21562881 DOI: 10.1007/s00705-011-1008-x] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 04/20/2011] [Indexed: 01/01/2023]
Abstract
The Polyomaviridae Study Group of the International Committee on Taxonomy of Viruses (ICTV) has recommended several taxonomical revisions, as follows: The family Polyomaviridae, which is currently constituted as a single genus (Polyomavirus), will be comprised of three genera: two containing mammalian viruses and one containing avian viruses. The two mammalian genera will be designated Orthopolyomavirus and Wukipolyomavirus, and the avian genus will be named Avipolyomavirus. These genera will be created by the redistribution of species from the current single genus (Polyomavirus) and by the inclusion of several new species. In addition, the names of several species will be changed to reflect current usage.
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37
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Shen PS, Enderlein D, Nelson CDS, Carter WS, Kawano M, Xing L, Swenson RD, Olson NH, Baker TS, Cheng RH, Atwood WJ, Johne R, Belnap DM. The structure of avian polyomavirus reveals variably sized capsids, non-conserved inter-capsomere interactions, and a possible location of the minor capsid protein VP4. Virology 2011; 411:142-52. [PMID: 21239031 DOI: 10.1016/j.virol.2010.12.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2010] [Revised: 11/18/2010] [Accepted: 12/06/2010] [Indexed: 10/18/2022]
Abstract
Avian polyomavirus (APV) causes a fatal, multi-organ disease among several bird species. Using cryogenic electron microscopy and other biochemical techniques, we investigated the structure of APV and compared it to that of mammalian polyomaviruses, particularly JC polyomavirus and simian virus 40. The structure of the pentameric major capsid protein (VP1) is mostly conserved; however, APV VP1 has a unique, truncated C-terminus that eliminates an intercapsomere-connecting β-hairpin observed in other polyomaviruses. We postulate that the terminal β-hairpin locks other polyomavirus capsids in a stable conformation and that absence of the hairpin leads to the observed capsid size variation in APV. Plug-like density features were observed at the base of the VP1 pentamers, consistent with the known location of minor capsid proteins VP2 and VP3. However, the plug density is more prominent in APV and may include VP4, a minor capsid protein unique to bird polyomaviruses.
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Affiliation(s)
- Peter S Shen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA
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38
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African great apes are naturally infected with polyomaviruses closely related to Merkel cell polyomavirus. J Virol 2010; 85:916-24. [PMID: 21047967 DOI: 10.1128/jvi.01585-10] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The oncogenic Merkel cell polyomavirus (MCPyV) infects humans worldwide, but little is known about the occurrence of viruses related to MCPyV in the closest phylogenetic relatives of humans, great apes. We analyzed samples from 30 wild chimpanzees and one captive gorilla and identified two new groups of polyomaviruses (PyVs). These new viruses are by far the closest relatives to MCPyV described to date, providing the first evidence of the natural occurrence of PyVs related to MCPyV in wild great apes. Similar to MCPyV, the prevalence of these viruses is relatively high (>30%). This, together with the fact that humans in West and Central Africa frequently hunt and butcher primates, may point toward further MCPyV-like strains spreading to, or already existing in, our species.
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39
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Firth C, Kitchen A, Shapiro B, Suchard MA, Holmes EC, Rambaut A. Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses. Mol Biol Evol 2010; 27:2038-51. [PMID: 20363828 PMCID: PMC3107591 DOI: 10.1093/molbev/msq088] [Citation(s) in RCA: 219] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Double-stranded (ds) DNA viruses are often described as evolving through long-term codivergent associations with their hosts, a pattern that is expected to be associated with low rates of nucleotide substitution. However, the hypothesis of codivergence between dsDNA viruses and their hosts has rarely been rigorously tested, even though the vast majority of nucleotide substitution rate estimates for dsDNA viruses are based upon this assumption. It is therefore important to estimate the evolutionary rates of dsDNA viruses independent of the assumption of host-virus codivergence. Here, we explore the use of temporally structured sequence data within a Bayesian framework to estimate the evolutionary rates for seven human dsDNA viruses, including variola virus (VARV) (the causative agent of smallpox) and herpes simplex virus-1. Our analyses reveal that although the VARV genome is likely to evolve at a rate of approximately 1 x 10(-5) substitutions/site/year and hence approaching that of many RNA viruses, the evolutionary rates of many other dsDNA viruses remain problematic to estimate. Synthetic data sets were constructed to inform our interpretation of the substitution rates estimated for these dsDNA viruses and the analysis of these demonstrated that given a sequence data set of appropriate length and sampling depth, it is possible to use time-structured analyses to estimate the substitution rates of many dsDNA viruses independently from the assumption of host-virus codivergence. Finally, the discovery that some dsDNA viruses may evolve at rates approaching those of RNA viruses has important implications for our understanding of the long-term evolutionary history and emergence potential of this major group of viruses.
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Affiliation(s)
- Cadhla Firth
- Department of Biology, The Pennsylvania State University, USA.
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40
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Halami MY, Dorrestein GM, Couteel P, Heckel G, Müller H, Johne R. Whole-genome characterization of a novel polyomavirus detected in fatally diseased canary birds. J Gen Virol 2010; 91:3016-22. [PMID: 20797969 DOI: 10.1099/vir.0.023549-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Polyomaviruses of birds are aetiological agents of acute inflammatory diseases in non-immunocompromised hosts, which is in contrast to mammalian polyomaviruses. VP4, an additional structural protein encoded by the viral genomes of the known avian polyomaviruses, has been suggested to contribute to pathogenicity through loss of cells following induction of apoptosis. Four distinct bird polyomaviruses have been identified so far, which infect crows, finches, geese and parrots. Using broad-spectrum PCR, a novel polyomavirus, tentatively designated canary polyomavirus (CaPyV), was detected in diseased canary birds (Serinus canaria) that died at an age of about 40 days. Intranuclear inclusion bodies were found in the liver, spleen and kidneys. The entire viral genome was amplified from a tissue sample using rolling-circle amplification. Phylogenetic analysis of the genome sequence indicated a close relationship between CaPyV and other avian polyomaviruses. Remarkably, an ORF encoding VP4 could not be identified in the CaPyV genome. Therefore, the mechanism of pathogenicity of CaPyV may be different from that of the other avian polyomaviruses.
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Affiliation(s)
- Mohammad Yahya Halami
- Institute for Virology, Faculty of Veterinary Medicine, University of Leipzig, Leipzig, Germany.
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41
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Nakamichi K, Takayama-Ito M, Nukuzuma S, Kurane I, Saijo M. Long-term infection of adult mice with murine polyomavirus following stereotaxic inoculation into the brain. Microbiol Immunol 2010; 54:475-82. [PMID: 20646213 DOI: 10.1111/j.1348-0421.2010.00247.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Murine polyomavirus is used in various models of persistent virus infection. This study was undertaken to assess the spatial and temporal patterns of MPyV infection in the brains of immunocompetent (BALB/c) and immunocompromised (KSN nude) mice. MPyV was stereotaxically microinfused into the brain parenchyma, and the kinetics of infection were examined by quantitative PCR. In BALB/c mice, the amount of viral DNA in the brain peaked at 4 days p.i. and then rapidly diminished. In contrast, MPyV DNA levels increased up to 4 days and then gradually decreased over the 30-day observation period in the brain of KSN mice. In both mouse strains, viral DNA was readily detected around the sites of inoculation from 2 to 6 days p.i., and continued to be detected for up to 30 days p.i. In addition, MPyV infection did not lead to a drastic induction of innate immune response in the brains, nor did MPyV-inoculated mice show any signs of disease. These results indicate that MPyV establishes an asymptomatic long-term infection in the mouse brain.
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Affiliation(s)
- Kazuo Nakamichi
- Department of Virology 1, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku, Tokyo 162-8640, Japan.
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42
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Fang CY, Chen HY, Wang M, Chen PL, Chang CF, Chen LS, Shen CH, Ou WC, Tsai MD, Hsu PH, Chang D. Global analysis of modifications of the human BK virus structural proteins by LC-MS/MS. Virology 2010; 402:164-76. [PMID: 20381826 DOI: 10.1016/j.virol.2010.03.029] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Revised: 03/03/2010] [Accepted: 03/17/2010] [Indexed: 10/19/2022]
Abstract
BK virus, a human polyomavirus, may cause nephritis and urological disorders in patients who have undergone renal transplantation. Little is known about the characteristics of the BK viral proteins. In the current study, BK viral proteins were characterized by immunoblotting and LC-MS/MS. The results revealed that BK virus is composed of three structural proteins, VP1, VP2, and VP3 and four cellular histones, H2A, H2B, H3, and H4. The major structural protein, VP1, can be divided into 16 subspecies by two-dimensional gel electrophoresis. Modifications of VP1, VP2, and VP3 were comprehensively identified by LC-MS/MS. The presence of acetylation, cysteinylation, carboxymethylation, carboxyethylation, formylation, methylation, methylthiolation, oxidation, dioxidation, and phosphorylation could be identified. This is the first report providing an analysis of the global modifications present on polyomavirus structural proteins. The identification of these modifications of VP1, VP2, and VP3 should facilitate an understanding of the physiology of BKV during its life cycle.
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Affiliation(s)
- Chiung-Yao Fang
- Institute of Molecular Biology, National Chung Cheng University, Chia-Yi, Taiwan
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43
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Yogo Y, Sugimoto C, Zhong S, Homma Y. Evolution of the BK polyomavirus: epidemiological, anthropological and clinical implications. Rev Med Virol 2009; 19:185-99. [PMID: 19530118 DOI: 10.1002/rmv.613] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BK polyomavirus (BKV) is essentially ubiquitous in all human populations worldwide. Asymptomatic infection with this virus occurs during early childhood, leading to life-long persistence in the kidney. BKV has four subtypes that can be identified using serological and genotyping methods. The evolutionary aspects of BKV have remained poorly understood due to the limited availability of BKV genomes, since urinary excretion of BKV DNA is detected primarily in immunocompromised individuals. However, we have found that BKV DNA sequences can often be amplified from non-immunocompromised elderly individuals, using a highly sensitive polymerase chain reaction (PCR) with highly concentrated urinary DNA as the source of viral DNA. Using this approach, we have PCR-amplified and sequenced a large number of partial and complete BKV genomes from various human populations worldwide and conducted a series of evolutionary studies using these sequences. We have shown that subtypes I and IV evolved into four and six subgroups, respectively, with each having a close relationship with a particular human population. In addition, we have provided evidence supporting the hypothesis that BKV strains with the archetypal transcriptional control region (TCR) circulate in the human population. In this review, we describe these findings and discuss their epidemiological, anthropological and clinical implications.
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Affiliation(s)
- Yoshiaki Yogo
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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Woolford L, Bennett MD, Sims C, Thomas N, Friend JA, Nicholls PK, Warren KS, O'Hara AJ. Prevalence, emergence, and factors associated with a viral papillomatosis and carcinomatosis syndrome in wild, reintroduced, and captive western barred bandicoots (Perameles bougainville). ECOHEALTH 2009; 6:414-425. [PMID: 19898897 DOI: 10.1007/s10393-009-0258-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2008] [Revised: 07/23/2009] [Accepted: 09/14/2009] [Indexed: 05/28/2023]
Abstract
Once widespread across western and southern Australia, wild populations of the western barred bandicoot (WBB) are now only found on Bernier and Dorre Islands, Western Australia. Conservation efforts to prevent the extinction of the WBB are presently hampered by a papillomatosis and carcinomatosis syndrome identified in captive and wild bandicoots, associated with infection with the bandicoot papillomatosis carcinomatosis virus type 1 (BPCV1). This study examined the prevalence and distribution of BPCV1 and the associated syndrome in two island and four mainland (reintroduced and captive) WBB populations in Western Australia, and factors that may be associated with susceptibility to this syndrome. BPCV1 and the syndrome were found in the wild WBB population at Red Cliff on Bernier Island, and in mainland populations established from all or a proportion of founder WBBs from Red Cliff. BPCV1 and the syndrome were not found in the wild population on Dorre Island or in the mainland population founded by animals exclusively from Dorre Island. Findings suggested that BPCV1 and the syndrome were disseminated into mainland WBB populations through the introduction of affected WBBs from Red Cliff. No difference in susceptibility to the syndrome was found between Dorre Island, Bernier Island, and island-cross individuals. Severity of lesions and the number of affected animals observed in captivity was greater than that observed in wild populations. This study provided epidemiological evidence to support the pathological and molecular association between BPCV1 infection and the papillomatosis and carcinomatosis syndrome and revealed increasing age as an additional risk factor for this disease.
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Affiliation(s)
- Lucy Woolford
- School of Veterinary and Biomedical Sciences, Murdoch University, South Street, Murdoch, WA, Australia.
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Katoh H, Ohya K, Une Y, Yamaguchi T, Fukushi H. Molecular characterization of avian polyomavirus isolated from psittacine birds based on the whole genome sequence analysis. Vet Microbiol 2009; 138:69-77. [DOI: 10.1016/j.vetmic.2009.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 02/16/2009] [Accepted: 03/02/2009] [Indexed: 10/21/2022]
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Mes THM, van Doornum GJJ, Schutten M. Population genetic tests suggest that the epidemiologies of JCV and BKV are strikingly different. INFECTION GENETICS AND EVOLUTION 2009; 10:397-403. [PMID: 19379842 DOI: 10.1016/j.meegid.2009.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Revised: 02/18/2009] [Accepted: 04/06/2009] [Indexed: 11/30/2022]
Abstract
The JCV and BKV viruses have been used as markers for the study of human evolution by assuming that these viruses coevolved with their host. However, it is currently unclear whether the details of the population expansion of these viruses and humans agree. To study this in more detail, large numbers of complete genomes were used for population genetic tests to detect evidence for population expansion. Relative to the neutral expectation of no selective forces and no demographic changes, the JCV data set contained a striking excess of synonymous and non-synonymous mutations that occur only once in the data set. The same was found for non-synonymous mutations of BKV, but not at all for synonymous mutations of BKV. The different frequency spectra of mutations in JCV and BKV do not result from the inclusion of patients with clinical symptoms associated with BKV and JCV, such as nephropathy or progressive multifocal leucoencefalopathy, nor from the different numbers of genomes available for JCV and BKV. Instead, the distribution of unique mutations and population genetic models that use older mutation classes indicate a striking difference of the historical demographies of JCV and BKV with only the former virus exhibiting the evidence of demographic expansion. Our analyses expand on recent population genetic analyses that document a global population expansion of JCV by taking into account the impact of deleterious mutations and by comparing both human viruses. The striking difference between the demographics of BKV and JCV suggests that important aspects of their epidemiology remain to be discovered.
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Affiliation(s)
- Ted H M Mes
- Department of Virology, CA Rotterdam, The Netherlands.
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47
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Evolution of four BK virus subtypes. INFECTION GENETICS AND EVOLUTION 2008; 8:632-43. [DOI: 10.1016/j.meegid.2008.05.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 05/27/2008] [Accepted: 05/30/2008] [Indexed: 11/21/2022]
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Cui J, Han N, Streicker D, Li G, Tang X, Shi Z, Hu Z, Zhao G, Fontanet A, Guan Y, Wang L, Jones G, Field HE, Daszak P, Zhang S. Evolutionary relationships between bat coronaviruses and their hosts. Emerg Infect Dis 2008; 13:1526-32. [PMID: 18258002 PMCID: PMC2851503 DOI: 10.3201/eid1310.070448] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Host shifting has occurred among Rhinolophus spp., with potential implications for emergence of SARS. Recent studies have suggested that bats are the natural reservoir of a range of coronaviruses (CoVs), and that rhinolophid bats harbor viruses closely related to the severe acute respiratory syndrome (SARS) CoV, which caused an outbreak of respiratory illness in humans during 2002–2003. We examined the evolutionary relationships between bat CoVs and their hosts by using sequence data of the virus RNA-dependent RNA polymerase gene and the bat cytochrome b gene. Phylogenetic analyses showed multiple incongruent associations between the phylogenies of rhinolophid bats and their CoVs, which suggested that host shifts have occurred in the recent evolutionary history of this group. These shifts may be due to either virus biologic traits or host behavioral traits. This finding has implications for the emergence of SARS and for the potential future emergence of SARS-CoVs or related viruses.
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Affiliation(s)
- Jie Cui
- East China Normal University, Shanghai, People's Republic of China
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Gibbs AJ, Ohshima K, Phillips MJ, Gibbs MJ. The prehistory of potyviruses: their initial radiation was during the dawn of agriculture. PLoS One 2008; 3:e2523. [PMID: 18575612 PMCID: PMC2429970 DOI: 10.1371/journal.pone.0002523] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Accepted: 05/19/2008] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Potyviruses are found world wide, are spread by probing aphids and cause considerable crop damage. Potyvirus is one of the two largest plant virus genera and contains about 15% of all named plant virus species. When and why did the potyviruses become so numerous? Here we answer the first question and discuss the other. METHODS AND FINDINGS We have inferred the phylogenies of the partial coat protein gene sequences of about 50 potyviruses, and studied in detail the phylogenies of some using various methods and evolutionary models. Their phylogenies have been calibrated using historical isolation and outbreak events: the plum pox virus epidemic which swept through Europe in the 20th century, incursions of potyviruses into Australia after agriculture was established by European colonists, the likely transport of cowpea aphid-borne mosaic virus in cowpea seed from Africa to the Americas with the 16th century slave trade and the similar transport of papaya ringspot virus from India to the Americas. CONCLUSIONS/SIGNIFICANCE Our studies indicate that the partial coat protein genes of potyviruses have an evolutionary rate of about 1.15x10(-4) nucleotide substitutions/site/year, and the initial radiation of the potyviruses occurred only about 6,600 years ago, and hence coincided with the dawn of agriculture. We discuss the ways in which agriculture may have triggered the prehistoric emergence of potyviruses and fostered their speciation.
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