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Grimwood RM, Reyes EMR, Cooper J, Welch J, Taylor G, Makan T, Lim L, Dubrulle J, McInnes K, Holmes EC, Geoghegan JL. From islands to infectomes: host-specific viral diversity among birds across remote islands. BMC Ecol Evol 2024; 24:84. [PMID: 38926829 PMCID: PMC11209962 DOI: 10.1186/s12862-024-02277-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 06/23/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Accelerating biodiversity loss necessitates monitoring the potential pathogens of vulnerable species. With a third of New Zealand's avifauna considered at risk of extinction, a greater understanding of the factors that influence microbial transmission in this island ecosystem is needed. We used metatranscriptomics to determine the viruses, as well as other microbial organisms (i.e. the infectomes), of seven bird species, including the once critically endangered black robin (Petroica traversi), on two islands in the remote Chatham Islands archipelago, New Zealand. RESULTS We identified 19 likely novel avian viruses across nine viral families. Black robins harboured viruses from the Flaviviridae, Herpesviridae, and Picornaviridae, while introduced starlings (Sturnus vulgaris) and migratory seabirds (Procellariiformes) carried viruses from six additional viral families. Potential cross-species virus transmission of a novel passerivirus (family: Picornaviridae) between native (black robins and grey-backed storm petrels) and introduced (starlings) birds was also observed. Additionally, we identified bacterial genera, apicomplexan parasites, as well as a novel megrivirus linked to disease outbreaks in other native New Zealand birds. Notably, island effects were outweighed by host taxonomy as a significant driver of viral composition, even among sedentary birds. CONCLUSIONS These findings underscore the value of surveillance of avian populations to identify and minimise escalating threats of disease emergence and spread in these island ecosystems. Importantly, they contribute to our understanding of the potential role of introduced and migratory birds in the transmission of microbes and associated diseases, which could impact vulnerable island-endemic species.
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Affiliation(s)
- Rebecca M Grimwood
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Enzo M R Reyes
- Department of Conservation/Te Papa Atawhai, Nelson, New Zealand
| | - Jamie Cooper
- Department of Conservation/Te Papa Atawhai, Nelson, New Zealand
| | - Jemma Welch
- Department of Conservation/Te Papa Atawhai, Nelson, New Zealand
| | - Graeme Taylor
- Department of Conservation/Te Papa Atawhai, Nelson, New Zealand
| | - Troy Makan
- Department of Conservation/Te Papa Atawhai, Nelson, New Zealand
| | - Lauren Lim
- School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jérémy Dubrulle
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - Kate McInnes
- Department of Conservation/Te Papa Atawhai, Nelson, New Zealand
| | - Edward C Holmes
- School of Medical Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand.
- Institute of Environmental Science and Research, Wellington, 5018, New Zealand.
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2
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Mwakibete L, Greening SS, Kalantar K, Ahyong V, Anis E, Miller EA, Needle DB, Oglesbee M, Thomas WK, Sevigny JL, Gordon LM, Nemeth NM, Ogbunugafor CB, Ayala AJ, Faith SA, Neff N, Detweiler AM, Baillargeon T, Tanguay S, Simpson SD, Murphy LA, Ellis JC, Tato CM, Gagne RB. Metagenomics for Pathogen Detection During a Mass Mortality Event in Songbirds. J Wildl Dis 2024; 60:362-374. [PMID: 38345467 DOI: 10.7589/jwd-d-23-00109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 01/02/2024] [Indexed: 04/06/2024]
Abstract
Mass mortality events in wildlife can be indications of an emerging infectious disease. During the spring and summer of 2021, hundreds of dead passerines were reported across the eastern US. Birds exhibited a range of clinical signs including swollen conjunctiva, ocular discharge, ataxia, and nystagmus. As part of the diagnostic investigation, high-throughput metagenomic next-generation sequencing was performed across three molecular laboratories on samples from affected birds. Many potentially pathogenic microbes were detected, with bacteria forming the largest proportion; however, no singular agent was consistently identified, with many of the detected microbes also found in unaffected (control) birds and thus considered to be subclinical infections. Congruent results across laboratories have helped drive further investigation into alternative causes, including environmental contaminants and nutritional deficiencies. This work highlights the utility of metagenomic approaches in investigations of emerging diseases and provides a framework for future wildlife mortality events.
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Affiliation(s)
| | - Sabrina S Greening
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | | | - Vida Ahyong
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
| | - Eman Anis
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
- Department of Pathobiology, PADLS New Bolton Center, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | - Erica A Miller
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | - David B Needle
- New Hampshire Veterinary Diagnostic Lab, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Michael Oglesbee
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - W Kelley Thomas
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Joseph L Sevigny
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Lawrence M Gordon
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Nicole M Nemeth
- Southeastern Cooperative Wildlife Disease Study and Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, Georgia 30602, USA
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Georgia 30602, USA
| | - C Brandon Ogbunugafor
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Andrea J Ayala
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Seth A Faith
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Norma Neff
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
| | | | - Tessa Baillargeon
- New Hampshire Veterinary Diagnostic Lab, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Stacy Tanguay
- New Hampshire Veterinary Diagnostic Lab, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Stephen D Simpson
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire 03824, USA
| | - Lisa A Murphy
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
- Department of Pathobiology, PADLS New Bolton Center, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | - Julie C Ellis
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
| | - Cristina M Tato
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
| | - Roderick B Gagne
- Department of Pathobiology, Wildlife Futures Program, University of Pennsylvania School of Veterinary Medicine, New Bolton Center, Kennett Square, Pennsylvania 19348, USA
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3
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Wierenga JR, Grimwood RM, Taylor HS, Hunter S, Argilla LS, Webster T, Lim L, French R, Schultz H, Jorge F, Bostina M, Burga L, Swindells-Wallace P, Holmes EC, McInnes K, Morgan KJ, Geoghegan JL. Total infectome investigation of diphtheritic stomatitis in yellow-eyed penguins (Megadyptes antipodes) reveals a novel and abundant megrivirus. Vet Microbiol 2023; 286:109895. [PMID: 37890432 DOI: 10.1016/j.vetmic.2023.109895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/15/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023]
Abstract
First identified in 2002, diphtheritic stomatitis (DS) is a devastating disease affecting yellow-eyed penguins (Megadyptes antipodes, or hoiho in te reo Māori). The disease is associated with oral lesions in chicks and has caused significant morbidity and mortality. DS is widespread among yellow-eyed penguin chicks on mainland New Zealand yet appears to be absent from the subantarctic population. Corynebacterium spp. have previously been suspected as causative agents yet, due to inconsistent cultures and inconclusive pathogenicity, their role in DS is unclear. Herein, we used a metatranscriptomic approach to identify potential causative agents of DS by revealing the presence and abundance of all viruses, bacteria, fungi and protozoa - together, the infectome. Oral and cloacal swab samples were collected from presymptomatic, symptomatic and recovered chicks along with a control group of healthy adults. Two novel viruses from the Picornaviridae were identified, one of which - yellow-eyed penguin megrivirus - was highly abundant in chicks irrespective of health status but not detected in healthy adults. Tissue from biopsied oral lesions also tested positive for the novel megrivirus upon PCR. We found no overall clustering among bacteria, protozoa and fungi communities at the genus level across samples, although Paraclostridium bifermentans was significantly more abundant in oral microbiota of symptomatic chicks compared to other groups. The detection of a novel and highly abundant megrivirus has sparked a new line of inquiry to investigate its potential association with DS.
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Affiliation(s)
- Janelle R Wierenga
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand; Wildbase, School of Veterinary Science, Massey University, New Zealand
| | - Rebecca M Grimwood
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Harry S Taylor
- Biodiversity Group, Department of Conservation/Te Papa Atawhai, New Zealand; Diagnostic and Surveillance Services, Biosecurity New Zealand, Ministry for Primary Industries, New Zealand
| | - Stuart Hunter
- Wildbase, School of Veterinary Science, Massey University, New Zealand
| | - Lisa S Argilla
- Wildlife Hospital, Dunedin, Otago Polytechnic School of Veterinary Nursing, New Zealand
| | | | - Lauren Lim
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Rebecca French
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Hendrik Schultz
- Biodiversity Group, Department of Conservation/Te Papa Atawhai, New Zealand
| | - Fátima Jorge
- Otago Micro and Nano Imaging, University of Otago, Dunedin, New Zealand
| | - Mihnea Bostina
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Laura Burga
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | | | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Australia
| | - Kate McInnes
- Biodiversity Group, Department of Conservation/Te Papa Atawhai, New Zealand
| | - Kerri J Morgan
- Wildbase, School of Veterinary Science, Massey University, New Zealand
| | - Jemma L Geoghegan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand; Institute of Environmental Science and Research, Wellington, New Zealand.
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4
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Shan T, Yang S, Wang H, Wang H, Zhang J, Gong G, Xiao Y, Yang J, Wang X, Lu J, Zhao M, Yang Z, Lu X, Dai Z, He Y, Chen X, Zhou R, Yao Y, Kong N, Zeng J, Ullah K, Wang X, Shen Q, Deng X, Zhang J, Delwart E, Tong G, Zhang W. Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses. MICROBIOME 2022; 10:60. [PMID: 35413940 PMCID: PMC9001828 DOI: 10.1186/s40168-022-01246-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 02/16/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Wild birds may harbor and transmit viruses that are potentially pathogenic to humans, domestic animals, and other wildlife. RESULTS Using the viral metagenomic approach, we investigated the virome of cloacal swab specimens collected from 3182 birds (the majority of them wild species) consisting of > 87 different species in 10 different orders within the Aves classes. The virus diversity in wild birds was higher than that in breeding birds. We acquired 707 viral genomes from 18 defined families and 4 unclassified virus groups, with 265 virus genomes sharing < 60% protein sequence identities with their best matches in GenBank comprising new virus families, genera, or species. RNA viruses containing the conserved RdRp domain with no phylogenetic affinity to currently defined virus families existed in different bird species. Genomes of the astrovirus, picornavirus, coronavirus, calicivirus, parvovirus, circovirus, retrovirus, and adenovirus families which include known avian pathogens were fully characterized. Putative cross-species transmissions were observed with viruses in wild birds showing > 95% amino acid sequence identity to previously reported viruses in domestic poultry. Genomic recombination was observed for some genomes showing discordant phylogenies based on structural and non-structural regions. Mapping the next-generation sequencing (NGS) data respectively against the 707 genomes revealed that these viruses showed distribution pattern differences among birds with different habitats (breeding or wild), orders, and sampling sites but no significant differences between birds with different behavioral features (migratory and resident). CONCLUSIONS The existence of a highly diverse virome highlights the challenges in elucidating the evolution, etiology, and ecology of viruses in wild birds. Video Abstract.
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Affiliation(s)
- Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Shixing Yang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Haoning Wang
- School of Geography and Tourism, Harbin University, Harbin, 150886, Heilongjiang, China
- Key Laboratory of Wildlife diseases and Biosecurity Management of Heilongjiang Province, Harbin, 150886, Heilongjiang, China
| | - Hao Wang
- Department of Clinical Laboratory, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, 223002, Jiangsu, China
| | - Ju Zhang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Ga Gong
- Animal Science College, Tibet Agriculture and Animal Husbandry University, Nyingchi, 860000, Tibet, China
| | - Yuqing Xiao
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Jie Yang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Xiaolong Wang
- Wildlife and Protected Area College/Center of Conservation Medicine and Ecological Safety Northeast Forestry University, Harbin, 150006, Heilongjiang, China
| | - Juan Lu
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Min Zhao
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Zijun Yang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Xiang Lu
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Ziyuan Dai
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Yumin He
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Xu Chen
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Rui Zhou
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Yuxin Yao
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Ning Kong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China
| | - Jian Zeng
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Kalim Ullah
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Xiaochun Wang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Quan Shen
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA, 94118, USA
| | - Jianmin Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, 94118, USA
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94118, USA
| | - Guangzhi Tong
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Disease and Zoonose, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
| | - Wen Zhang
- School of Medicine, Jiangsu University, Zhenjiang, 212003, Jiangsu, China.
- International Center for Genomics Research, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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5
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Chang WS, Rose K, Holmes EC. Meta-transcriptomic analysis of the virome and microbiome of the invasive Indian myna ( Acridotheres tristis) in Australia. One Health 2021; 13:100360. [PMID: 34917744 PMCID: PMC8666354 DOI: 10.1016/j.onehlt.2021.100360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/03/2021] [Accepted: 12/05/2021] [Indexed: 11/03/2022] Open
Abstract
Invasive species exert a serious impact on native fauna and flora and have become the target of eradication and management efforts worldwide. Invasive avian species can also be important pathogen reservoirs, although their viromes and microbiomes have rarely been studied. As one of the top 100 invasive pest species globally, the expansion of Indian mynas (Acridotheres tristis) into peri-urban and rural environments, in conjunction with increasing free-ranging avian agricultural practices, may increase the risk of microbial pathogens jumping species boundaries. Herein, we used a meta-transcriptomic approach to explore the microbes present in brain, liver and large intestine of 16 invasive Indian myna birds in Sydney, Australia. From this, we discovered seven novel viruses from the families Adenoviridae, Caliciviridae, Flaviviridae, Parvoviridae and Picornaviridae. Interestingly, each of the novel viruses identified shared less than 80% genomic similarity with their closest relatives from other avian species, indicative of a lack of detectable virus transmission between invasive mynas to native or domestic species. Of note, we also identified two coccidian protozoa, Isospora superbusi and Isospora greineri, from the liver and gut tissues of mynas. Overall, these data demonstrate that invasive mynas can harbor a diversity of viruses and other microorganisms such that ongoing pathogen surveillance in this species is warranted.
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Affiliation(s)
- Wei-Shan Chang
- School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Karrie Rose
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Australian Registry of Wildlife Health, Taronga Conservation Society Australia, Mosman, NSW 2088, Australia
| | - Edward C Holmes
- School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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POECIVIRUS IS PRESENT IN INDIVIDUALS WITH BEAK DEFORMITIES IN SEVEN SPECIES OF NORTH AMERICAN BIRDS. J Wildl Dis 2021; 57:273-281. [PMID: 33822149 DOI: 10.7589/jwd-d-20-00017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 08/08/2020] [Indexed: 11/20/2022]
Abstract
Avian keratin disorder (AKD), a disease of unknown etiology characterized by debilitating beak overgrowth, has increasingly affected wild bird populations since the 1990s. A novel picornavirus, poecivirus, is closely correlated with disease status in Black-capped Chickadees (Poecile atricapillus) in Alaska, US. However, our knowledge of the relationship between poecivirus and beak deformities in other species and other geographic areas remains limited. The growing geographic scope and number of species affected by AKD-like beak deformities require a better understanding of the causative agent to evaluate the population-level impacts of this epizootic. Here, we tested eight individuals from six avian species with AKD-consistent deformities for the presence of poecivirus: Mew Gull (Larus canus), Hairy Woodpecker (Picoides villosus), Black-billed Magpie (Pica hudsonia), American Crow (Corvus brachyrhynchos), Red-breasted Nuthatch (Sitta canadensis), and Blackpoll Warbler (Setophaga striata). The birds were sampled in Alaska and Maine (1999-2016). We used targeted PCR followed by Sanger sequencing to test for the presence of poecivirus in each specimen and to obtain viral genome sequence from virus-positive host individuals. We detected poecivirus in all individuals tested, but not in negative controls (water and tissue samples). Furthermore, we used unbiased metagenomic sequencing to test for the presence of other pathogens in six of these specimens (Hairy Woodpecker, two American Crows, two Red-breasted Nuthatches, Blackpoll Warbler). This analysis yielded additional viral sequences from several specimens, including the complete coding region of poecivirus from one Red-breasted Nuthatch, which we confirmed via targeted PCR followed by Sanger sequencing. This study demonstrates that poecivirus is present in individuals with AKD-consistent deformities from six avian species other than Black-capped Chickadee. While further investigation will be required to explore whether there exists a causal link between this virus and AKD, this study demonstrates that poecivirus is not geographically restricted to Alaska, but rather occurs elsewhere in North America.
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Fried WA, Soltero-Rivera M, Ramesh A, Lommer MJ, Arzi B, DeRisi JL, Horst JA. Use of unbiased metagenomic and transcriptomic analyses to investigate the association between feline calicivirus and feline chronic gingivostomatitis in domestic cats. Am J Vet Res 2021; 82:381-394. [PMID: 33904799 DOI: 10.2460/ajvr.82.5.381] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To identify associations between microbes and host genes in cats with feline chronic gingivostomatitis (FCGS), a debilitating inflammatory oral mucosal disease with no known cause, compared with healthy cats and cats with periodontitis (control cats). ANIMALS 19 control cats and 23 cats with FCGS. PROCEDURES At least 1 caudal oral mucosal swab specimen was obtained from each cat. Each specimen underwent unbiased metatranscriptomic next-generation RNA sequencing (mNGS). Filtered mNGS reads were aligned to all known genetic sequences from all organisms and to the cat transcriptome. The relative abundances of microbial and host gene read alignments were compared between FCGS-affected cats and control cats and between FCGS-affected cats that did and did not clinically respond to primary treatment. Assembled feline calicivirus (FCV) genomes were compared with reverse transcription PCR (RT-PCR) primers commonly used to identify FCV. RESULTS The only microbe strongly associated with FCGS was FCV, which was detected in 21 of 23 FCGS-affected cats but no control cats. Problematic base pair mismatches were identified between the assembled FCV genomes and RT-PCR primers. Puma feline foamy virus was detected in 9 of 13 FCGS-affected cats that were refractory to treatment and 5 healthy cats but was not detected in FCGS-affected cats that responded to tooth extractions. The most differentially expressed genes in FCGS-affected cats were those associated with antiviral activity. CONCLUSIONS AND CLINICAL RELEVANCE Results suggested that FCGS pathogenesis has a viral component. Many FCV strains may yield false-negative results on RT-PCR-based assays. Coinfection of FCGS-affected cats with FCV and puma feline foamy virus may adversely affect response to treatment.
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8
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Metatranscriptomic Analysis of Virus Diversity in Urban Wild Birds with Paretic Disease. J Virol 2020; 94:JVI.00606-20. [PMID: 32581107 PMCID: PMC7459558 DOI: 10.1128/jvi.00606-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/16/2020] [Indexed: 02/08/2023] Open
Abstract
Wildlife naturally harbor a diverse array of infectious microorganisms and can be a source of novel diseases in domestic animals and human populations. Using unbiased RNA sequencing, we identified highly diverse viruses in native birds from Australian urban environments presenting with paresis. This research included the clinical investigation and description of poorly understood recurring syndromes of unknown etiology: clenched claw syndrome and black and white bird disease. As well as identifying a range of potentially disease-causing viral pathogens, this study describes methods that can effectively and efficiently characterize emergent disease syndromes in free-ranging wildlife and promotes further surveillance for specific pathogens of potential conservation and zoonotic concern. Wild birds are major natural reservoirs and potential dispersers of a variety of infectious diseases. As such, it is important to determine the diversity of viruses they carry and use this information to help understand the potential risks of spillover to humans, domestic animals, and other wildlife. We investigated the potential viral causes of paresis in long-standing, but undiagnosed, disease syndromes in wild Australian birds. RNA from diseased birds was extracted and pooled based on tissue type, host species, and clinical manifestation for metagenomic sequencing. Using a bulk and unbiased metatranscriptomic approach, combined with clinical investigation and histopathology, we identified a number of novel viruses from the families Astroviridae, Adenoviridae, Picornaviridae, Polyomaviridae, Paramyxoviridae, Parvoviridae, and Circoviridae in common urban wild birds, including Australian magpies, magpie larks, pied currawongs, Australian ravens, and rainbow lorikeets. In each case, the presence of the virus was confirmed by reverse transcription (RT)-PCR. These data revealed a number of candidate viral pathogens that may contribute to coronary, skeletal muscle, vascular, and neuropathology in birds of the Corvidae and Artamidae families and neuropathology in members of the Psittaculidae. The existence of such a diverse virome in urban avian species highlights the importance and challenges in elucidating the etiology and ecology of wildlife pathogens in urban environments. This information will be increasingly important for managing disease risks and conducting surveillance for potential viral threats to wildlife, livestock, and human health. IMPORTANCE Wildlife naturally harbor a diverse array of infectious microorganisms and can be a source of novel diseases in domestic animals and human populations. Using unbiased RNA sequencing, we identified highly diverse viruses in native birds from Australian urban environments presenting with paresis. This research included the clinical investigation and description of poorly understood recurring syndromes of unknown etiology: clenched claw syndrome and black and white bird disease. As well as identifying a range of potentially disease-causing viral pathogens, this study describes methods that can effectively and efficiently characterize emergent disease syndromes in free-ranging wildlife and promotes further surveillance for specific pathogens of potential conservation and zoonotic concern.
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9
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Plumage and bill abnormalities in albatross chicks on Marion Island. Polar Biol 2019. [DOI: 10.1007/s00300-019-02528-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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10
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Van Hemert C, Meixell BW, Smith MM, Handel CM. Prevalence and diversity of avian blood parasites in a resident northern passerine. Parasit Vectors 2019; 12:292. [PMID: 31182151 PMCID: PMC6558893 DOI: 10.1186/s13071-019-3545-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 05/30/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Climate-related changes are expected to influence the prevalence and distribution of vector-borne haemosporidian parasites at northern latitudes, although baseline information about resident birds is still lacking. In this study, we investigated prevalence and genetic diversity of Plasmodium, Haemoproteus, and Leucocytozoon parasites infecting the northwestern crow (Corvus caurinus), a non-migratory passerine with unique life-history characteristics. This species occupies both intertidal and forested habitats and is subject to high prevalence of avian keratin disorder (AKD), a disease that causes gross beak deformities. Investigation of avian blood parasites in northwestern crows at sites broadly distributed across coastal Alaska provided an opportunity to evaluate specific host factors related to parasite infection status and assess geographical patterns of prevalence. RESULTS We used molecular methods to screen for haemosporidian parasites in northwestern crows and estimated genus-specific parasite prevalence with occupancy modeling that accounts for imperfect detection of parasite infection. We observed considerable geographical and annual variation in prevalence of Plasmodium, Haemoproteus, and Leucocytozoon, but these patterns were not correlated with indices of local climatic conditions. Our models also did not provide support for relationships between the probability of parasite infection and body condition or the occurrence of co-infections with other parasite genera or clinical signs of AKD. In our phylogenetic analyses, we identified multiple lineages of each parasite genus, with Leucocytozoon showing greater diversity than Plasmodium or Haemoproteus. CONCLUSIONS Results from this study expand our knowledge about the prevalence and diversity of avian blood parasites in northern resident birds as well as corvids worldwide. We detected all three genera of avian haemosporidians in northwestern crows in Alaska, although only Leucocytozoon occurred at all sites in both years. Given the strong geographical and annual variation in parasite prevalence and apparent lack of correlation with climatic variables, it appears that there are other key factors responsible for driving transmission dynamics in this region. Thus, caution is warranted when using standard climatic or geographical attributes in a predictive framework. Our phylogenetic results demonstrate lower host specificity for some lineages of Leucocytozoon than is typically reported and provide insights about genetic diversity of local haemosporidian parasites in Alaska.
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Affiliation(s)
- Caroline Van Hemert
- U.S. Geological Survey, Alaska Science Center, 4210 University Dr., Anchorage, AK 99508 USA
| | - Brandt W. Meixell
- U.S. Geological Survey, Alaska Science Center, 4210 University Dr., Anchorage, AK 99508 USA
| | - Matthew M. Smith
- U.S. Geological Survey, Alaska Science Center, 4210 University Dr., Anchorage, AK 99508 USA
| | - Colleen M. Handel
- U.S. Geological Survey, Alaska Science Center, 4210 University Dr., Anchorage, AK 99508 USA
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11
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METAGENOMIC NEXT-GENERATION SEQUENCING REVEALS MIAMIENSIS AVIDUS (CILIOPHORA: SCUTICOCILIATIDA) IN THE 2017 EPIZOOTIC OF LEOPARD SHARKS ( TRIAKIS SEMIFASCIATA) IN SAN FRANCISCO BAY, CALIFORNIA, USA. J Wildl Dis 2018; 55:375-386. [PMID: 30289337 DOI: 10.7589/2018-04-097] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
During March to August of 2017, hundreds of leopard sharks ( Triakis semifasciata) stranded and died on the shores of San Francisco Bay, California, US. Similar mass stranding events occurred in 1967 and 2011, but analysis of those epizootics was incomplete, and no etiology was confirmed. Our investigation of the 2017 epizootic revealed severe meningoencephalitis in stranded sharks, raising suspicion for infection. We pursued a strategy for unbiased pathogen detection using metagenomic next-generation sequencing followed by orthogonal validation and further screening. We showed that the ciliated protozoan pathogen, Miamiensis avidus, was present in the central nervous system of leopard ( n=12) and other shark species ( n=2) that stranded in San Francisco Bay but was absent in leopard sharks caught elsewhere. This ciliated protozoan has been implicated in devastating outbreaks in teleost marine fish but not in wild elasmobranchs. Our results highlight the benefits of adopting unbiased metagenomic sequencing in the study of wildlife health and disease.
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12
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Zylberberg M, Van Hemert C, Handel CM, DeRisi JL. Avian keratin disorder of Alaska black-capped chickadees is associated with Poecivirus infection. Virol J 2018; 15:100. [PMID: 29903045 PMCID: PMC6003155 DOI: 10.1186/s12985-018-1008-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 05/28/2018] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Avian keratin disorder (AKD) is an epizootic of debilitating beak deformities, first documented in black-capped chickadees (Poecile atricapillus) in Alaska during the late 1990s. Similar deformities have now been recorded in dozens of species of birds across multiple continents. Despite this, the etiology of AKD has remained elusive, making it difficult to assess the impacts of this disease on wild populations. We previously identified an association between infection with a novel picornavirus, Poecivirus, and AKD in a small cohort of black-capped chickadees. METHODS To test if the association between Poecivirus and AKD holds in a larger study population, we used targeted PCR followed by Sanger sequencing to screen 124 symptomatic and asymptomatic black-capped chickadees for Poecivirus infection. We further compared the efficacy of multiple non-terminal field sampling methods (buccal swabs, cloacal swabs, fecal samples, and blood samples) for Poecivirus screening. Finally, we used both in situ hybridization and a strand-specific expression assay to localize Poecivirus to beak tissue of AKD-positive individuals and to determine if virus is actively replicating in beak tissue. RESULTS Poecivirus was detected in 28/28 (100%) individuals with AKD, but only 9/96 (9.4%) asymptomatic individuals with apparently normal beaks (p < 0.0001). We found that cloacal swabs are the most sensitive of these sample types for detecting Poecivirus in birds with AKD, but that buccal swabs should be combined with cloacal swabs in evaluating the infection status of asymptomatic birds. Finally, we used both in situ hybridization and a strand-specific expression assay to localize Poecivirus to beak tissue of AKD-positive individuals and to provide evidence of active viral replication. CONCLUSION The data presented here show a strong, statistically significant relationship between Poecivirus infection and AKD, and provide evidence that Poecivirus is indeed an avian virus, infecting and actively replicating in beak tissue of AKD-affected BCCH. Taken together, these data corroborate and extend the evidence for a potential causal association between Poecivirus and AKD in the black-capped chickadee. Poecivirus continues to warrant further investigation as a candidate agent of AKD.
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Affiliation(s)
- Maxine Zylberberg
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, 94158 USA
| | | | - Colleen M. Handel
- U. S. Geological Survey, Alaska Science Center, Anchorage, AK 99508 USA
| | - Joseph L. DeRisi
- Department of Pathology, University of California, San Francisco, California, 94143 USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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13
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Bai H, Sun Y, Liu N, Liu Y, Xue F, Li Y, Xu S, Ni A, Ye J, Chen Y, Chen J. Genome-wide detection of CNVs associated with beak deformity in chickens using high-density 600K SNP arrays. Anim Genet 2018; 49:226-236. [PMID: 29642269 DOI: 10.1111/age.12652] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2018] [Indexed: 11/30/2022]
Abstract
Beak deformity (crossed beaks) is found in several indigenous chicken breeds including Beijing-You studied here. Birds with deformed beaks have reduced feed intake and poor production performance. Recently, copy number variation (CNV) has been examined in many species and is recognized as a source of genetic variation, especially for disease phenotypes. In this study, to unravel the genetic mechanisms underlying beak deformity, we performed genome-wide CNV detection using Affymetrix chicken high-density 600K data on 48 deformed-beak and 48 normal birds using penncnv. As a result, two and eight CNV regions (CNVRs) covering 0.32 and 2.45 Mb respectively on autosomes were identified in deformed-beak and normal birds respectively. Further RT-qPCR studies validated nine of the 10 CNVRs. The ratios of six CNVRs were significantly different between deformed-beak and normal birds (P < 0.01). Within these six regions, three and 21 known genes were identified in deformed-beak and normal birds respectively. Bioinformatics analysis showed that these genes were enriched in six GO terms and one KEGG pathway. Five candidate genes in the CNVRs were further validated using RT-qPCR. The expression of LRIG2 (leucine rich repeats and immunoglobulin like domains 2) was lower in birds with deformed beaks (P < 0.01). Therefore, the LRIG2 gene could be considered a key factor in view of its known functions and its potential roles in beak deformity. Overall, our results will be helpful for future investigations of the genomic structural variations underlying beak deformity in chickens.
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Affiliation(s)
- H Bai
- Key Laboratory of Animal Genetics Breeding and Reproduction (Poultry), Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Y Sun
- Key Laboratory of Animal Genetics Breeding and Reproduction (Poultry), Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - N Liu
- Key Laboratory of Animal Genetics Breeding and Reproduction (Poultry), Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Y Liu
- Key Laboratory of Animal Genetics Breeding and Reproduction (Poultry), Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - F Xue
- Key Laboratory of Animal Genetics Breeding and Reproduction (Poultry), Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Y Li
- Key Laboratory of Animal Genetics Breeding and Reproduction (Poultry), Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - S Xu
- Key Laboratory of Animal Genetics Breeding and Reproduction (Poultry), Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - A Ni
- Key Laboratory of Animal Genetics Breeding and Reproduction (Poultry), Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - J Ye
- Key Laboratory of Animal Genetics Breeding and Reproduction (Poultry), Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Y Chen
- Beijing General Station of Animal Husbandry Service, Beijing, 102200, China
| | - J Chen
- Key Laboratory of Animal Genetics Breeding and Reproduction (Poultry), Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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14
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Bodewes R. Novel viruses in birds: Flying through the roof or is a cage needed? Vet J 2018; 233:55-62. [PMID: 29486880 DOI: 10.1016/j.tvjl.2017.12.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 09/28/2017] [Accepted: 12/28/2017] [Indexed: 01/17/2023]
Abstract
Emerging viral diseases continue to have a major global impact on human beings and animals. To be able to take adequate measures in case of an outbreak of an emerging disease, rapid detection of the causative agent is a crucial first step. In this review, various aspects of virus discovery are discussed, with a special focus on recently discovered viruses in birds. Novel viruses with a potential major impact have been discovered in domestic and wild bird species in recent years using various virus discovery methods. Only a few studies report the detection of novel viruses in endangered bird species, although increased knowledge about viruses circulating in these species is important. Additional studies focusing on the exact role of a novel virus in disease and on the impact of a novel virus on bird populations are often lacking. Intensive collaboration between different disciplines is needed to obtain useful information about the role of these novel viruses.
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Affiliation(s)
- R Bodewes
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
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15
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Abstract
Picornaviruses are small, nonenveloped, icosahedral RNA viruses with positive-strand polarity. Although the vast majority of picornavirus infections remain asymptomatic, many picornaviruses are important human and animal pathogens and cause diseases that affect the central nervous system, the respiratory and gastrointestinal tracts, heart, liver, pancreas, skin and eye. A stunning increase in the number of newly identified picornaviruses in the past decade has shown that picornaviruses are globally distributed and infect vertebrates of all classes. Moreover, picornaviruses exhibit a surprising diversity of both genome sequences and genome layouts, sometimes challenging the definition of taxonomic relevant criteria. At present, 35 genera comprising 80 species and more than 500 types are acknowledged. Fifteen species within five new and three existing genera have been proposed in 2017, but more than 50 picornaviruses still remain unassigned.
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Affiliation(s)
- Roland Zell
- Division of Experimental Virology, Institute for Medical Microbiology, Jena University Hospital, Friedrich Schiller University, Hans-Knöll-Str. 2, 07745, Jena, Germany.
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16
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Boros Á, Pankovics P, Mátics R, Adonyi Á, Bolba N, Phan TG, Delwart E, Reuter G. Genome characterization of a novel megrivirus-related avian picornavirus from a carnivorous wild bird, western marsh harrier (Circus aeruginosus). Arch Virol 2017; 162:2781-2789. [PMID: 28500443 DOI: 10.1007/s00705-017-3403-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/04/2017] [Indexed: 11/29/2022]
Abstract
In this study, the complete genome of a novel picornavirus called harrier picornavirus 1 (HaPV-1) strain harrier/MR-01/HUN/2014 (KY488458) was sequenced and analysed from a cloacal sample of a threatened, carnivorous wild bird, western marsh harrier (Circus aeruginosus). HaPV-1 was detectable from 2 of the 3 samples from harriers. HaPV-1 is phylogenetically related to megriviruses (genus Megrivirus) from domestic chicken, turkey and duck, showing a similar genome organization pattern; it also has an avian picornavirus-like "Unit A" motif in the 3' UTR. Unlike the type-IV internal ribosomal entry site (IRES) of megriviruses, HaPV-1 is predicted to contain a type-II-like IRES, suggesting modular exchange of IRES elements between picornavirus genomes.
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Affiliation(s)
- Ákos Boros
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary.,Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12, Pécs, 7624, Hungary
| | - Péter Pankovics
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary.,Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12, Pécs, 7624, Hungary
| | - Róbert Mátics
- Hungarian Nature Research Society (HuNaReS), Ajka, Hungary.,Department of Pathophysiology, University of Pécs Medical Center, Pécs, Hungary
| | - Ádám Adonyi
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary
| | - Nóra Bolba
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary.,Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12, Pécs, 7624, Hungary
| | - Tung Gia Phan
- Blood Systems Research Institute, San Francisco, CA, USA.,University of California, San Francisco, CA, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA.,University of California, San Francisco, CA, USA
| | - Gábor Reuter
- Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary. .,Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12, Pécs, 7624, Hungary.
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17
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Speer B, Powers LV. Anatomy and Disorders of the Beak and Oral Cavity of Birds. Vet Clin North Am Exot Anim Pract 2016; 19:707-36. [PMID: 27497203 DOI: 10.1016/j.cvex.2016.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cranial kinesis of the avian beak is complex; particularly in birds with prokinetic beak movement, such as psittacine birds. A number of diseases can result in damage to the bony and soft tissue structures of the beak and can lead to secondary pathology, such as beak deviation, abnormal rhamphothecal growth and wear, and opportunistic infections. A solid understanding of species-specific anatomic variations is essential before attempting rhamphothecal restoration or surgical repair. Many diseases of the oral cavity can appear similar on initial clinical evaluation and therefore warrant appropriate diagnostic testing.
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Affiliation(s)
- Brian Speer
- The Medical Center for Birds, 3805 Main Street, Oakley, CA 94561, USA.
| | - Lauren Virginia Powers
- Avian and Exotic Pet Service, Carolina Veterinary Specialists, 12117 Statesville Road, Huntersville, NC 28078, USA
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