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      Virus survey in populations of two subspecies of bent-winged bats ( Miniopterus orianae bassanii and oceanensis) in south-eastern Australia reveals a high prevalence of diverse herpesviruses

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          Abstract

          While bats are often viewed as carriers of infectious disease agents, little research has been conducted on the effects these potential pathogens may have on the bat populations themselves. The southern bent-winged bat ( Miniopterus orianae bassanii) is a critically endangered subspecies endemic to south-eastern Australia. Population numbers of this bat have been declining for the past 50 years, but the reasons for this are unclear. As part of a larger study to determine if disease could be a contributing factor to this decline, 351 southern bent-winged bats from four locations were captured, and oral swabs were collected and tested for the presence of potentially pathogenic viruses. Results were compared with those obtained from 116 eastern bent-winged bats ( Miniopterus orianae oceanensis) from three different locations. The eastern bent-winged bat is a related but more common and widespread subspecies whose geographical range overlaps partly with southern bent-winged bats. Herpesviruses were detected in bent-winged bats from all seven locations. At least six novel herpesviruses (five betaherpesviruses and one gammaherpesvirus) were identified. The prevalence of herpesvirus infection was higher in eastern bent-winged bats (44%, 51/116), compared to southern bent-winged bats (27%, 95/351), although this varied across the locations and sampling periods. Adenoviruses and a range of different RNA viruses (lyssaviruses, filoviruses, coronaviruses and henipaviruses) were also tested for but not detected. The detected herpesviruses did not appear to be associated with obvious ill health, and may thus not be playing a role in the population decline of the southern bent-winged bat. The detection of multiple novel herpesviruses at a high prevalence of infection is consistent with our understanding of bats as hosts to a rich diversity of viruses.

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          Most cited references51

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          MRBAYES: Bayesian inference of phylogenetic trees.

          The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
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            Amino acid substitution matrices from protein blocks.

            Methods for alignment of protein sequences typically measure similarity by using a substitution matrix with scores for all possible exchanges of one amino acid with another. The most widely used matrices are based on the Dayhoff model of evolutionary rates. Using a different approach, we have derived substitution matrices from about 2000 blocks of aligned sequence segments characterizing more than 500 groups of related proteins. This led to marked improvements in alignments and in searches using queries from each of the groups.
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              A New Look at the Statistical Model Identification

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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: Writing – original draft
                Role: ConceptualizationRole: InvestigationRole: MethodologyRole: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: InvestigationRole: MethodologyRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: SoftwareRole: Writing – review & editing
                Role: Data curationRole: Formal analysisRole: SoftwareRole: Writing – review & editing
                Role: ConceptualizationRole: Formal analysisRole: MethodologyRole: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                24 May 2018
                2018
                : 13
                : 5
                : e0197625
                Affiliations
                [1 ] Department of Veterinary Biosciences, Melbourne Veterinary School, The Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Werribee, Victoria Australia
                [2 ] The Asia Pacific Centre for Animal Health, The Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
                [3 ] Arthur Rylah Institute for Environmental Research, Department of Environment, Land, Water and Planning, Heidelberg, Victoria, Australia
                [4 ] Victorian Infectious Diseases Reference Laboratory, Doherty Institute, Melbourne, Australia
                University of Reunion Island, RÉUNION
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0002-5602-1973
                http://orcid.org/0000-0003-2407-4496
                Article
                PONE-D-18-03403
                10.1371/journal.pone.0197625
                5967723
                29795610
                86781857-891d-49e7-9962-891965e82f60
                © 2018 Holz et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 31 January 2018
                : 5 May 2018
                Page count
                Figures: 2, Tables: 4, Pages: 17
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100008190, Holsworth Wildlife Research Endowment;
                Award ID: HOLSW2016-R1-F109
                Award Recipient :
                Funded by: Wildlife Disease Association Australasia
                Award Recipient :
                Funded by: Australian Government Threatened Species Discretionary Grants Program
                Award Recipient :
                Funded by: Karst Conservation Fund
                Award Recipient :
                Funded by: David Middleton
                Award Recipient :
                Funded by: Australian Post Graduate Award Scholarship
                Award Recipient :
                Funded by Holsworth Wildlife Research Endowment, HOLSW2016-R1-F109, https://www.ecolsoc.org.au/awards-and-prizes/holsworth-wildlife-research-endowment (PH). Wildlife Disease Association Australasia, http://www.wildlifedisease.org/wda/SECTIONS/Australasian.aspx (PH). Australian Government’s Threatened Species Discretionary Grants Program, Department of Environment, Land, Water and Planning Victoria, http://www.environment.gov.au/biodiversity/threatened/threatened-species-recovery-fund (LL). Karst Conservation Fund, http://www.caves.org.au/conservation/karst-conservation-fund (PH). David Middleton (PH) Australian Postgraduate Award Scholarship, https://studenteforms.app.unimelb.edu.au/apex/f?p=153:2:0:::2:P2_ID:50 (PH). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Vertebrates
                Amniotes
                Mammals
                Bats
                Biology and life sciences
                Organisms
                Viruses
                DNA viruses
                Herpesviruses
                Biology and Life Sciences
                Microbiology
                Medical Microbiology
                Microbial Pathogens
                Viral Pathogens
                Herpesviruses
                Medicine and Health Sciences
                Pathology and Laboratory Medicine
                Pathogens
                Microbial Pathogens
                Viral Pathogens
                Herpesviruses
                Biology and Life Sciences
                Organisms
                Viruses
                Viral Pathogens
                Herpesviruses
                Research and Analysis Methods
                Database and Informatics Methods
                Bioinformatics
                Sequence Analysis
                Sequence Alignment
                Biology and life sciences
                Organisms
                Viruses
                RNA viruses
                Coronaviruses
                Biology and Life Sciences
                Microbiology
                Medical Microbiology
                Microbial Pathogens
                Viral Pathogens
                Coronaviruses
                Medicine and Health Sciences
                Pathology and Laboratory Medicine
                Pathogens
                Microbial Pathogens
                Viral Pathogens
                Coronaviruses
                Biology and Life Sciences
                Organisms
                Viruses
                Viral Pathogens
                Coronaviruses
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Vertebrates
                Amniotes
                Mammals
                Bats
                Fruit Bats
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Polymerase Chain Reaction
                Research and Analysis Methods
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Polymerase Chain Reaction
                Research and Analysis Methods
                Database and Informatics Methods
                Bioinformatics
                Sequence Analysis
                Sequence Motif Analysis
                Research and analysis methods
                Database and informatics methods
                Bioinformatics
                Sequence analysis
                DNA sequence analysis
                Custom metadata
                Due to the endangered status of the bats, exact locations of sampling data cannot be made publicly available. These data are available from the Arthur Rylah Institute ( Research.ARI@ 123456delwp.vic.gov.au ) for researchers who meet the criteria for access to confidential data. All other relevant data are within the paper and its Supporting Information files.

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