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Adenoviruses in Avian Hosts: Recent Discoveries Shed New Light on Adenovirus Diversity and Evolution. Viruses 2022; 14:v14081767. [PMID: 36016389 PMCID: PMC9416666 DOI: 10.3390/v14081767] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022] Open
Abstract
While adenoviruses cause infections in a wide range of vertebrates, members of the genus Atadenovirus, Siadenovirus, and Aviadenovirus predominantly infect avian hosts. Several recent studies on avian adenoviruses have encouraged us to re-visit previously proposed adenovirus evolutionary concepts. Complete genomes and partial DNA polymerase sequences of avian adenoviruses were extracted from NCBI and analysed using various software. Genomic analyses and constructed phylogenetic trees identified the atadenovirus origin from an Australian native passerine bird in contrast to the previously established reptilian origin. In addition, we demonstrated that the theories on higher AT content in atadenoviruses are no longer accurate and cannot be considered as a species demarcation criterion for the genus Atadenovirus. Phylogenetic reconstruction further emphasised the need to reconsider siadenovirus origin, and we recommend extended studies on avian adenoviruses in wild birds to provide finer evolutionary resolution.
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Identification and Distribution of Novel Cressdnaviruses and Circular molecules in Four Penguin Species in South Georgia and the Antarctic Peninsula. Viruses 2020; 12:v12091029. [PMID: 32947826 PMCID: PMC7551938 DOI: 10.3390/v12091029] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/26/2022] Open
Abstract
There is growing interest in uncovering the viral diversity present in wild animal species. The remote Antarctic region is home to a wealth of uncovered microbial diversity, some of which is associated with its megafauna, including penguin species, the dominant avian biota. Penguins interface with a number of other biota in their roles as marine mesopredators and several species overlap in their ranges and habitats. To characterize the circular single-stranded viruses related to those in the phylum Cressdnaviricota from these environmental sentinel species, cloacal swabs (n = 95) were obtained from King Penguins in South Georgia, and congeneric Adélie Penguins, Chinstrap Penguins, and Gentoo Penguins across the South Shetland Islands and Antarctic Peninsula. Using a combination of high-throughput sequencing, abutting primers-based PCR recovery of circular genomic elements, cloning, and Sanger sequencing, we detected 97 novel sequences comprising 40 ssDNA viral genomes and 57 viral-like circular molecules from 45 individual penguins. We present their detection patterns, with Chinstrap Penguins harboring the highest number of new sequences. The novel Antarctic viruses identified appear to be host-specific, while one circular molecule was shared between sympatric Chinstrap and Gentoo Penguins. We also report viral genotype sharing between three adult-chick pairs, one in each Pygoscelid species. Sequence similarity network approaches coupled with Maximum likelihood phylogenies of the clusters indicate the 40 novel viral genomes do not fall within any known viral families and likely fall within the recently established phylum Cressdnaviricota based on their replication-associated protein sequences. Similarly, 83 capsid protein sequences encoded by the viruses or viral-like circular molecules identified in this study do not cluster with any of those encoded by classified viral groups. Further research is warranted to expand knowledge of the Antarctic virome and would help elucidate the importance of viral-like molecules in vertebrate host evolution.
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Identification of Circovirus Genome in a Chinstrap Penguin ( Pygoscelis antarcticus) and Adélie Penguin ( Pygoscelis adeliae) on the Antarctic Peninsula. Viruses 2020; 12:v12080858. [PMID: 32781620 PMCID: PMC7472332 DOI: 10.3390/v12080858] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/01/2020] [Accepted: 08/03/2020] [Indexed: 12/21/2022] Open
Abstract
Circoviruses infect a variety of animal species and have small (~1.8–2.2 kb) circular single-stranded DNA genomes. Recently a penguin circovirus (PenCV) was identified associated with an Adélie Penguin (Pygoscelis adeliae) with feather disorder and in the cloacal swabs of three asymptomatic Adélie Penguins at Cape Crozier, Antarctica. A total of 75 cloacal swab samples obtained from adults and chicks of three species of penguin (genus: Pygoscelis) from seven Antarctic breeding colonies (South Shetland Islands and Western Antarctic Peninsula) in the 2015−2016 breeding season were screened for PenCV. We identified new variants of PenCV in one Adélie Penguin and one Chinstrap Penguin (Pygoscelis antarcticus) from Port Charcot, Booth Island, Western Antarctic Peninsula, a site home to all three species of Pygoscelid penguins. These two PenCV genomes (length of 1986 nucleotides) share > 99% genome-wide nucleotide identity with each other and share ~87% genome-wide nucleotide identity with the PenCV sequences described from Adélie Penguins at Cape Crozier ~4400 km away in East Antarctica. We did not find any evidence of recombination among PenCV sequences. This is the first report of PenCV in Chinstrap Penguins and the first detection outside of Ross Island, East Antarctica. Given the limited knowledge on Antarctic animal viral diversity, future samples from Antarctic wildlife should be screened for these and other viruses to determine the prevalence and potential impact of viral infections.
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Vaz FF, Raso TF, Agius JE, Hunt T, Leishman A, Eden JS, Phalen DN. Opportunistic sampling of wild native and invasive birds reveals a rich diversity of adenoviruses in Australia. Virus Evol 2020; 6:veaa024. [PMID: 32411389 PMCID: PMC7211397 DOI: 10.1093/ve/veaa024] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Little is known about the diversity of adenoviruses in wild birds and how they have evolved and are maintained in complex ecosystems. In this study, 409 samples were collected from woodland birds caught for banding (droppings), birds submitted to a wildlife hospital (droppings and tissues), silver gulls (droppings or tissues), and feral pigeons (Columbia livia; oral, cloacal swabs, or tissues) from the Greater Sydney area in NSW, Australia. Additional samples were from native pigeons and doves (swabs) presented to the Healesville Sanctuary, VIC, Australia. Samples were screened for adenovirus DNA using degenerate primers and polymerase chain reaction. Adenovirus sequences were detected in eighty-three samples representing thirty-five novel amino acid sequences. Fourteen novel sequences were atadenoviruses, seven were aviadenoviruses, twelve were siadenoviruses, and one was a mastadenovirus. Sequences from passerine birds were predominately found to form a single lineage within the atadenoviruses, a second lineage in the siadenoviruses, and a third smaller aviadenovirus lineage. These viruses appeared to have co-evolved with a diverse group of woodland birds that share similar habitat. Evidence for host/virus co-evolution in some viruses and a wide host range in others was observed. A high prevalence of adenovirus infection was found in rainbow lorikeets (Trichoglossus haematodus), galahs (Eolophus roseicapilla), and sulphur-crested cockatoos (Cacatua galerita). Sequences were either identical to or mapped to already established lineages in the Aviadenovirus, Siadenovirus, and Atadenovirus genera, suggesting a possible origin of the psittacine adenoviruses in ancestral Australian psittacine birds. The sequences of passerine and psittacine origin provided insight into diversity and structure of the Atadenovirus genus and demonstrated for the first-time viruses of passerine origin in the Aviadenovirus genus. Four unrelated adenovirus sequences were found in silver gull samples (Chroicocephalus novaehollandiae), including one of pigeon origin, suggesting environmental virus exposure. Three pigeon adenovirus types were detected in feral pigeons and infection prevalence was high. Evidence for host switching between invasive species and native species and native species and invasive species was documented. A variant of a murine adenovirus was detected in kidney tissue from two bird species suggesting mouse to bird transmission.
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Affiliation(s)
- Frederico F Vaz
- School of Veterinary Medicine and Animal Science, University of São Paulo, Orlando marques de Paiva, 87 05508-270, São Paulo, Brazil
| | - Tânia F Raso
- School of Veterinary Medicine and Animal Science, University of São Paulo, Orlando marques de Paiva, 87 05508-270, São Paulo, Brazil
| | - Jessica E Agius
- Sydney School of Veterinary Science, University of Sydney, Camden, NSW, Australia
| | - Tony Hunt
- 16 Alderson Avenue North Rocks, NSW 2151, Australia
| | - Alan Leishman
- 4/101 Centaur Street, Revesby Heights, NSW 2122, Australia
| | - John-Sebastian Eden
- Sydney Medical School, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW 2145, Australia
| | - David N Phalen
- Sydney School of Veterinary Science, University of Sydney, Camden, NSW, Australia.,Schubot Exotic Bird Health, Texas A&M College of Veterinary Medicine and Biomedical Sciences, College Station, TX 77843-4467, USA
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Sustained RNA virome diversity in Antarctic penguins and their ticks. ISME JOURNAL 2020; 14:1768-1782. [PMID: 32286545 PMCID: PMC7305176 DOI: 10.1038/s41396-020-0643-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/16/2020] [Accepted: 03/20/2020] [Indexed: 01/07/2023]
Abstract
Despite its isolation and extreme climate, Antarctica is home to diverse fauna and associated microorganisms. It has been proposed that the most iconic Antarctic animal, the penguin, experiences low pathogen pressure, accounting for their disease susceptibility in foreign environments. There is, however, a limited understanding of virome diversity in Antarctic species, the extent of in situ virus evolution, or how it relates to that in other geographic regions. To assess whether penguins have limited microbial diversity we determined the RNA viromes of three species of penguins and their ticks sampled on the Antarctic peninsula. Using total RNA sequencing we identified 107 viral species, comprising likely penguin associated viruses (n = 13), penguin diet and microbiome associated viruses (n = 82), and tick viruses (n = 8), two of which may have the potential to infect penguins. Notably, the level of virome diversity revealed in penguins is comparable to that seen in Australian waterbirds, including many of the same viral families. These data run counter to the idea that penguins are subject to lower pathogen pressure. The repeated detection of specific viruses in Antarctic penguins also suggests that rather than being simply spill-over hosts, these animals may act as key virus reservoirs.
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SEROLOGICAL SURVEY FOR SELECT INFECTIOUS AGENTS IN WILD MAGELLANIC PENGUINS (SPHENISCUS MAGELLANICUS) IN ARGENTINA, 1994–2008. J Wildl Dis 2020. [DOI: 10.7589/2019-01-022] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Böszörményi KP, Podgorski II, Vidovszky MZ, Sós E, Benkő M, Harrach B. Full genome sequence analysis of a novel adenovirus from a captive polar bear (Ursus maritimus). Virus Res 2019; 277:197846. [PMID: 31870796 DOI: 10.1016/j.virusres.2019.197846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 12/12/2019] [Accepted: 12/12/2019] [Indexed: 12/23/2022]
Abstract
The presence of a novel adenovirus (AdV) was detected by PCR and sequencing, in the internal organs of a captive polar bear that had died in the Budapest zoo. The virus content of the samples proved to be high enough to allow for conventional Sanger sequencing on PCR-amplified genomic fragments. With this approach, the sequence of the entire genome of the putative polar bear adenovirus 1 (PBAdV-1) was obtained. Although the genome was found to be short, consisting of 27,952 base pairs merely, with a relatively balanced G + C content of 46.3 %, its organisation corresponded largely to that of a typical mastadenovirus. Every genus-common gene could be identified except that of protein IX. The short E3 region of the PBAdV-1 consisted of two novel, supposedly type-specific ORFs only, whereas no homologue of any of the E3 genes, usually conserved in mastadenoviruses, such as for example that of the 12.5 K protein, were present. In the E4 region, only the highly conserved gene of the 34 K protein was found besides two novel ORFs showing no homology to any known E4 ORFs. In silico sequence analysis revealed putative splicing donor and acceptor sites in the genes of the E1A, IVa2, DNA-dependent DNA polymerase, pTP, 33 K proteins, and also of U exon protein, all being characteristic for mastadenoviruses. Phylogenetic calculations, based on various proteins, further supported that the newly-detected PBAdV is the representative of a new species within the genus Mastadenovirus, and may represent the evolutionary lineage of adenoviruses that coevolved with carnivorans.
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Affiliation(s)
- Kinga P Böszörményi
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, H-1143, Budapest, Hungary.
| | - Iva I Podgorski
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, H-1143, Budapest, Hungary
| | - Márton Z Vidovszky
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, H-1143, Budapest, Hungary
| | - Endre Sós
- Budapest Zoo and Botanical Garden, H-1146, Budapest, Hungary
| | - Mária Benkő
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, H-1143, Budapest, Hungary
| | - Balázs Harrach
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, H-1143, Budapest, Hungary
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de Souza WM, Fumagalli MJ, Martin MC, de Araujo J, Orsi MA, Sanfilippo LF, Modha S, Durigon EL, Proença-Módena JL, Arns CW, Murcia PR, Figueiredo LTM. Pingu virus: A new picornavirus in penguins from Antarctica. Virus Evol 2019; 5:vez047. [PMID: 31850147 PMCID: PMC6908804 DOI: 10.1093/ve/vez047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Picornaviridae family comprises single-stranded, positive-sense RNA viruses distributed into forty-seven genera. Picornaviruses have a broad host range and geographic distribution in all continents. In this study, we applied a high-throughput sequencing approach to examine the presence of picornaviruses in penguins from King George Island, Antarctica. We discovered and characterized a novel picornavirus from cloacal swab samples of gentoo penguins (Pygoscelis papua), which we tentatively named Pingu virus. Also, using RT-PCR we detected this virus in 12.9 per cent of cloacal swabs derived from P. papua, but not in samples from adélie penguins (Pygoscelis adeliae) or chinstrap penguins (Pygoscelis antarcticus). Attempts to isolate the virus in a chicken cell line and in embryonated chicken eggs were unsuccessful. Our results expand the viral diversity, host range, and geographical distribution of the Picornaviridae.
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Affiliation(s)
- William Marciel de Souza
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Avenida dos Bandeirantes 3900, Ribeirão Preto, SP, 14049-900 Brazil
| | - Marcílio Jorge Fumagalli
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Avenida dos Bandeirantes 3900, Ribeirão Preto, SP, 14049-900 Brazil
| | - Matheus Cavalheiro Martin
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255Cidade Universitária "Zeferino Vaz", Campinas, SP, 13083-862 Brazil
| | - Jansen de Araujo
- Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 2415 - Butantã, São Paulo - SP, 05508-900 Brazil
| | - Maria Angela Orsi
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255Cidade Universitária "Zeferino Vaz", Campinas, SP, 13083-862 Brazil
| | - Luiz Francisco Sanfilippo
- Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 2415 - Butantã, São Paulo - SP, 05508-900 Brazil
| | - Sejal Modha
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow G61 1QH, UK
| | - Edison Luiz Durigon
- Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 2415 - Butantã, São Paulo - SP, 05508-900 Brazil
| | - José Luiz Proença-Módena
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255Cidade Universitária "Zeferino Vaz", Campinas, SP, 13083-862 Brazil
| | - Clarice Weis Arns
- Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255Cidade Universitária "Zeferino Vaz", Campinas, SP, 13083-862 Brazil
| | - Pablo Ramiro Murcia
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Rd, Bearsden, Glasgow G61 1QH, UK
| | - Luiz Tadeu Moraes Figueiredo
- Virology Research Center, Ribeirão Preto Medical School, University of São Paulo, Avenida dos Bandeirantes 3900, Ribeirão Preto, SP, 14049-900 Brazil
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Harrach B, Tarján ZL, Benkő M. Adenoviruses across the animal kingdom: a walk in the zoo. FEBS Lett 2019; 593:3660-3673. [PMID: 31747467 DOI: 10.1002/1873-3468.13687] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 11/11/2019] [Accepted: 11/12/2019] [Indexed: 01/14/2023]
Abstract
Adenoviruses (AdVs) infect representatives of numerous species from almost every major vertebrate class, albeit their incidence shows great variability. AdVs infecting birds, reptiles, and bats are the most common and diverse, whereas only one AdV has been so far isolated both from fish and amphibians. The family Adenoviridae is divided into five genera, each corresponding to an independent evolutionary lineage that supposedly coevolved with its respective vertebrate hosts. Members of genera Mastadenovirus and Aviadenovirus seem to infect exclusively mammals and birds, respectively. The genus Ichtadenovirus includes the single known AdV from fish. The majority of AdVs in the genus Atadenovirus originated from squamate reptiles (lizards and snakes), but also certain mammalian and avian AdVs are classified within this genus. The genus Siadenovirus contains the only AdV isolated from frog, along with numerous avian AdVs. In turtles, members of a sixth AdV lineage have been discovered, pending official recognition as an independent genus. The most likely scenario for AdV evolution includes long-term cospeciation with the hosts, as well as occasional switches between closely or, rarely, more distantly related hosts.
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Affiliation(s)
- Balázs Harrach
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Zoltán L Tarján
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Mária Benkő
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
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Needle DB, Wise AG, Gregory CR, Maes RK, Sidor IF, Ritchie BW, Agnew D. Necrotizing Ventriculitis in Fledgling Chimney Swifts ( Chaetura Pelagica) Associated With a Novel Adenovirus, Chimney Swift Adenovirus-1 (CsAdV-1). Vet Pathol 2019; 56:907-914. [PMID: 31331256 DOI: 10.1177/0300985819861717] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Five chimney swift fledglings died following a progressive loss of appetite and condition while being cared for by an experienced wildlife rehabilitator. All animals had severe necrotizing and heterophilic ventriculitis, with myriad epithelial cells characterized by karyomegaly with intranuclear inclusion bodies. Transmission electron microscopy showed distention of epithelial cell nuclei and chromatin peripheralization by nonenveloped, icosahedral, 75- to 85-nm-diameter virions. Degenerate nested PCR for a highly conserved region of the adenovirus DNA polymerase gene was positive. BLAST analysis of the amplicon sequence indicated the presence of a novel adenovirus, with 74% homology to Antarctic penguin adenoviruses and 72% homology to a bat adenovirus, at low query coverages of only 65% and 63%, respectively. BLAST analysis of the predicted amino acid sequence generated the highest scores for squamate adenoviruses at 100% query coverage. Based on phylogenetic analysis of the partial amino acid sequence of the DNA polymerase, the chimney swift virus was a novel adenovirus most closely related to the Atadenovirus genus. Using a probe based on the novel viral sequence, DNA in situ hybridization identified viral nucleic acid in the nucleus. While the tentatively named chimney swift adenovirus-1 (CsAdV-1) is so far classified with the Atadenoviruses, it is relatively divergent from other members of that genus and may represent the first identified member of a new genus of Adenoviruses.
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Affiliation(s)
- David B Needle
- New Hampshire Veterinary Diagnostic Laboratory, University of New Hampshire, College of Life Sciences and Agriculture, Durham, NH, USA
| | - Annabel G Wise
- Veterinary Diagnostic Laboratory, Michigan State University, East Lansing MI, USA
| | - Christopher R Gregory
- Emerging Diseases Research Group and Infectious Diseases Laboratory, University of Georgia, Athens, GA, USA
| | - Roger K Maes
- Veterinary Diagnostic Laboratory, Michigan State University, East Lansing MI, USA
| | - Inga F Sidor
- New Hampshire Veterinary Diagnostic Laboratory, University of New Hampshire, College of Life Sciences and Agriculture, Durham, NH, USA
| | - Branson W Ritchie
- Emerging Diseases Research Group and Infectious Diseases Laboratory, University of Georgia, Athens, GA, USA
| | - Dalen Agnew
- Veterinary Diagnostic Laboratory, Michigan State University, East Lansing MI, USA
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Wernike K, Wylezich C, Höper D, Schneider J, Lurz PWW, Meredith A, Milne E, Beer M, Ulrich RG. Widespread occurrence of squirrel adenovirus 1 in red and grey squirrels in Scotland detected by a novel real-time PCR assay. Virus Res 2018; 257:113-118. [PMID: 30237072 DOI: 10.1016/j.virusres.2018.09.007] [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: 06/19/2018] [Revised: 08/13/2018] [Accepted: 09/17/2018] [Indexed: 01/12/2023]
Abstract
The Eurasian Red Squirrel (Sciurus vulgaris) is distributed throughout large parts of Europe and Asia. However, its distribution in certain regions of Europe is endangered by the invasive, non-native Grey Squirrel (Sciurus carolinensis). Adenoviruses were already described in squirrels in Great Britain almost two decades ago. In 2013, a squirrel adenovirus (SqAdV-1) was additionally found in a red squirrel from Germany, which suffered from acute diffuse catarrhal enteritis, and the complete genome sequence was determined. Here, samples from dead red (n = 25) and grey (n = 12) squirrels collected in Scotland, UK, were analysed for the presence of this squirrel-associated virus. By using a newly developed real-time PCR targeting the adenoviral polymerase gene, viral DNA was detected in at least one of four tissue samples tested per animal in 64.0% of the red squirrels and 41.7% of the grey squirrels. Exceptionally high viral genome loads were detected in the intestine and liver, but SqAdV-1 DNA was also present in lung and kidney samples of affected animals. Almost complete genome sequence determination of a red squirrel-derived SqAdV-1 strain from Scotland indicated a very high degree of identity to the first German strain. Sequence analysis of the hexon gene, which encodes one of the major antigens of the virion, revealed an identity of 100% between viruses found in red and grey squirrels from Scotland. In conclusion, SqAdV-1 appears to be widespread in the Scottish red and grey squirrel population, which highlights the necessity for continuous wildlife surveillance. The novel real-time PCR assay offers a highly sensitive and robust method for SqAdV-1 surveillance.
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Affiliation(s)
- Kerstin Wernike
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany.
| | - Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany.
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany.
| | - Julia Schneider
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany; NMI TT Pharmaservices, c/o CoLaborator, Müllerstraße 178, 13353, Berlin, Germany.
| | - Peter W W Lurz
- Royal (Dick) School of Veterinary Studies, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Roslin, Midlothian, EH25 9RG, UK.
| | - Anna Meredith
- Royal (Dick) School of Veterinary Studies, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Roslin, Midlothian, EH25 9RG, UK; Melbourne Veterinary School, The University of Melbourne, Royal Parade Parkville 3010, Melbourne, Australia.
| | - Elspeth Milne
- Royal (Dick) School of Veterinary Studies, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Roslin, Midlothian, EH25 9RG, UK.
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany.
| | - Rainer G Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Südufer 10, 17493, Greifswald-Insel Riems, Germany.
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12
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Crane A, Goebel ME, Kraberger S, Stone AC, Varsani A. Novel anelloviruses identified in buccal swabs of Antarctic fur seals. Virus Genes 2018; 54:719-723. [DOI: 10.1007/s11262-018-1585-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/29/2018] [Indexed: 11/27/2022]
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13
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Smeele ZE, Burns JM, Van Doorsaler K, Fontenele RS, Waits K, Stainton D, Shero MR, Beltran RS, Kirkham AL, Berngartt R, Kraberger S, Varsani A. Diverse papillomaviruses identified in Weddell seals. J Gen Virol 2018; 99:549-557. [PMID: 29469687 DOI: 10.1099/jgv.0.001028] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Papillomaviridae is a diverse family of circular, double-stranded DNA (dsDNA) viruses that infect a broad range of mammalian, avian and fish hosts. While papillomaviruses have been characterized most extensively in humans, the study of non-human papillomaviruses has contributed greatly to our understanding of their pathogenicity and evolution. Using high-throughput sequencing approaches, we identified 7 novel papillomaviruses from vaginal swabs collected from 81 adult female Weddell seals (Leptonychotes weddellii) in the Ross Sea of Antarctica between 2014-2017. These seven papillomavirus genomes were amplified from seven individual seals, and six of the seven genomes represented novel species with distinct evolutionary lineages. This highlights the diversity of papillomaviruses among the relatively small number of Weddell seal samples tested. Viruses associated with large vertebrates are poorly studied in Antarctica, and this study adds information about papillomaviruses associated with Weddell seals and contributes to our understanding of the evolutionary history of papillomaviruses.
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Affiliation(s)
- Zoe E Smeele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.,School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Jennifer M Burns
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA
| | - Koenraad Van Doorsaler
- School of Animal and Comparative Biomedical Sciences, Cancer Biology Graduate Interdisciplinary Program, Genetics Graduate Interdisciplinary Program, and Bio5, University of Arizona, 1657 E Helen St., Tucson, AZ 85721, USA
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Kara Waits
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Daisy Stainton
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Michelle R Shero
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA
| | - Roxanne S Beltran
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA.,Department of Biology and Wildlife, University of Alaska Fairbanks, PO Box 756100, Fairbanks, AK 99775, USA
| | - Amy L Kirkham
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA.,College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 17101 Point Lena Loop Rd Juneau, Alaska 99801, USA
| | | | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA
| | - Arvind Varsani
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand.,The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Rondebosch, 7701, Cape Town, South Africa
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14
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Viruses associated with Antarctic wildlife: From serology based detection to identification of genomes using high throughput sequencing. Virus Res 2017; 243:91-105. [PMID: 29111456 PMCID: PMC7114543 DOI: 10.1016/j.virusres.2017.10.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/24/2017] [Accepted: 10/24/2017] [Indexed: 11/30/2022]
Abstract
Summary of identified viruses associated with Antarctic animals. Genomes of Antarctic animals viruses have only been determine in the last five years. Limited knowledge of animal virology relative to environmental virology in Antarctica.
The Antarctic, sub-Antarctic islands and surrounding sea-ice provide a unique environment for the existence of organisms. Nonetheless, birds and seals of a variety of species inhabit them, particularly during their breeding seasons. Early research on Antarctic wildlife health, using serology-based assays, showed exposure to viruses in the families Birnaviridae, Flaviviridae, Herpesviridae, Orthomyxoviridae and Paramyxoviridae circulating in seals (Phocidae), penguins (Spheniscidae), petrels (Procellariidae) and skuas (Stercorariidae). It is only during the last decade or so that polymerase chain reaction-based assays have been used to characterize viruses associated with Antarctic animals. Furthermore, it is only during the last five years that full/whole genomes of viruses (adenoviruses, anelloviruses, orthomyxoviruses, a papillomavirus, paramyoviruses, polyomaviruses and a togavirus) have been sequenced using Sanger sequencing or high throughput sequencing (HTS) approaches. This review summaries the knowledge of animal Antarctic virology and discusses potential future directions with the advent of HTS in virus discovery and ecology.
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15
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Walker D, Gregory WF, Turnbull D, Rocchi M, Meredith AL, Philbey AW, Sharp CP. Novel adenoviruses detected in British mustelids, including a unique Aviadenovirus in the tissues of pine martens ( Martes martes). J Med Microbiol 2017; 66:1177-1182. [PMID: 28749327 PMCID: PMC5817191 DOI: 10.1099/jmm.0.000546] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Several adenoviruses are known to cause severe disease in veterinary species. Recent evidence suggests that canine adenovirus type 1 (CAV-1) persists in the tissues of healthy red foxes (Vulpes vulpes), which may be a source of infection for susceptible species. It was hypothesized that mustelids native to the UK, including pine martens (Martes martes) and Eurasian otters (Lutra lutra), may also be persistently infected with adenoviruses. Based on high-throughput sequencing and additional Sanger sequencing, a novel Aviadenovirus, tentatively named marten adenovirus type 1 (MAdV-1), was detected in pine marten tissues. The detection of an Aviadenovirus in mammalian tissue has not been reported previously. Two mastadenoviruses, tentatively designated marten adenovirus type 2 (MAdV-2) and lutrine adenovirus type 1 (LAdV-1), were also detected in tissues of pine martens and Eurasian otters, respectively. Apparently healthy free-ranging animals may be infected with uncharacterized adenoviruses with possible implications for translocation of wildlife.
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Affiliation(s)
- David Walker
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
- *Correspondence: David Walker,
| | - William F. Gregory
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | - Dylan Turnbull
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh EH26 0PZ, UK
| | - Mara Rocchi
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Edinburgh EH26 0PZ, UK
| | - Anna L. Meredith
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | - Adrian W. Philbey
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
| | - Colin P. Sharp
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh EH25 9RG, UK
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16
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Fahsbender E, Burns JM, Kim S, Kraberger S, Frankfurter G, Eilers AA, Shero MR, Beltran R, Kirkham A, McCorkell R, Berngartt RK, Male MF, Ballard G, Ainley DG, Breitbart M, Varsani A. Diverse and highly recombinant anelloviruses associated with Weddell seals in Antarctica. Virus Evol 2017; 3:vex017. [PMID: 28744371 PMCID: PMC5518176 DOI: 10.1093/ve/vex017] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The viruses circulating among Antarctic wildlife remain largely unknown. In an effort to identify viruses associated with Weddell seals (Leptonychotes weddellii) inhabiting the Ross Sea, vaginal and nasal swabs, and faecal samples were collected between November 2014 and February 2015. In addition, a Weddell seal kidney and South Polar skua (Stercorarius maccormicki) faeces were opportunistically sampled. Using high throughput sequencing, we identified and recovered 152 anellovirus genomes that share 63–70% genome-wide identities with other pinniped anelloviruses. Genome-wide pairwise comparisons coupled with phylogenetic analysis revealed two novel anellovirus species, tentatively named torque teno Leptonychotes weddellii virus (TTLwV) -1 and -2. TTLwV-1 (n = 133, genomes encompassing 40 genotypes) is highly recombinant, whereas TTLwV-2 (n = 19, genomes encompassing three genotypes) is relatively less recombinant. This study documents ubiquitous TTLwVs among Weddell seals in Antarctica with frequent co-infection by multiple genotypes, however, the role these anelloviruses play in seal health remains unknown.
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Affiliation(s)
- Elizabeth Fahsbender
- College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA
| | - Jennifer M Burns
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA
| | - Stacy Kim
- Moss Landing Marine Laboratories, Moss Landing, CA 95039, USA
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life sciences, Arizona State University, Tempe, AZ 85287-5001, USA.,School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Greg Frankfurter
- Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
| | | | - Michelle R Shero
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA
| | - Roxanne Beltran
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA.,Department of Biology and Wildlife, University of Alaska Fairbanks, PO Box 756100, Fairbanks, AK 99775, USA
| | - Amy Kirkham
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK 99508, USA.,College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 17101 Point Lena Loop Rd, Juneau, Alaska 99801, USA
| | - Robert McCorkell
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | | | - Maketalena F Male
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand.,School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Grant Ballard
- Point Blue Conservation Science, Petaluma, CA 94954, USA
| | | | - Mya Breitbart
- College of Marine Science, University of South Florida, Saint Petersburg, FL 33701, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life sciences, Arizona State University, Tempe, AZ 85287-5001, USA.,School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand.,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa
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17
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Varsani A, Frankfurter G, Stainton D, Male MF, Kraberger S, Burns JM. Identification of a polyomavirus in Weddell seal (Leptonychotes weddellii) from the Ross Sea (Antarctica). Arch Virol 2017; 162:1403-1407. [PMID: 28124141 DOI: 10.1007/s00705-017-3239-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 12/23/2016] [Indexed: 11/25/2022]
Abstract
Viruses are ubiquitous in nature, however, very few have been identified that are associated with Antarctic animals. Here we report the identification of a polyomavirus in the kidney tissue of a deceased Weddell seal from the Ross Sea, Antarctica. The circular genome (5186 nt) has typical features of polyomaviruses with a small and larger T-antigen open reading frames (ORFs) and three ORFs encoding VP1, VP2 and VP3 capsid proteins. The genome of the Weddell seal polyomavirus (WsPyV) shares 85.4% genome-wide pairwise identity with a polyomavirus identified in a California sea lion. To our knowledge WsPyV is the first viral genome identified in Antarctic pinnipeds and the third polyomavirus to be identified from an Antarctic animal, the other two being from Adélie penguin (Pygoscelis adeliae) and a sharp-spined notothen (Trematomus pennellii), both sampled in the Ross sea. The GenBank accession number: KX533457.
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Affiliation(s)
- Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85287-5001, USA.
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand.
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, 7001, South Africa.
| | - Greg Frankfurter
- Wildlife Health Center, School of Veterinary Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Daisy Stainton
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Maketalena F Male
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
| | - Simona Kraberger
- School of Biological Sciences, University of Canterbury, Christchurch, 8140, New Zealand
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Jennifer M Burns
- Department of Biological Sciences, University of Alaska Anchorage, 3211 Providence Drive, Anchorage, AK, 99508, USA.
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