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Zhang Y, Talukder S, Bhuiyan MSA, He L, Sarker S. Opportunistic sampling of yellow canary (Crithagra flaviventris) has revealed a high genetic diversity of detected parvoviral sequences. Virology 2024; 595:110081. [PMID: 38599030 DOI: 10.1016/j.virol.2024.110081] [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: 11/03/2023] [Revised: 03/18/2024] [Accepted: 04/03/2024] [Indexed: 04/12/2024]
Abstract
Parvoviruses are known to be significant viral pathogens that infect a wide range of species globally. However, little is known about the parvoviruses circulating in Australian birds, including yellow canaries. Here, we present four parvoviral sequences including three novel parvoviruses detected from 10 yellow canaries (Crithagra flaviventris), named canary chaphamaparvovirus 1 and -2 (CaChPV1 and CaChPV2), canary dependoparvovirus 1 and -2 (CaDePV1 and CaDePV2). The whole genome sequences of CaChPV1, CaChPV2, CaDePV1, and CaDePV2 showed the highest identity with other parvoviruses at 76.4%, 75.9%, 84.0%, and 59.1%, respectively. Phylogenetic analysis demonstrated that CaChPV1 and CaChPV2 were clustered within the genus Chaphamaparvovirus. Meanwhile, CaDePV1 and CaDePV2 fall within the genus Dependoparvovirus and have the closest evolutionary relationship to the bird-associated dependoparvoviruses. Overall, this study enriched our understanding of the genetic diversity among avian parvoviruses within the Parvoviridae family.
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Affiliation(s)
- Yuhao Zhang
- The Key Lab of Animal Disease and Public Health /Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang, 471023, Henan, China
| | - Saranika Talukder
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia
| | - Md Safiul Alam Bhuiyan
- Faculty of Sustainable Agriculture, Livestock Production, Universiti Malaysia Sabah, Sandakan, Sabah, Malaysia
| | - Lei He
- The Key Lab of Animal Disease and Public Health /Luoyang Key Laboratory of Live Carrier Biomaterial and Animal Disease Prevention and Control, Henan University of Science and Technology, Luoyang, 471023, Henan, China.
| | - Subir Sarker
- Biomedical Sciences & Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD 4811, Australia.
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Klukowski N, Eden P, Uddin MJ, Sarker S. Virome of Australia's most endangered parrot in captivity evidenced of harboring hitherto unknown viruses. Microbiol Spectr 2024; 12:e0305223. [PMID: 38047696 PMCID: PMC10783009 DOI: 10.1128/spectrum.03052-23] [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: 08/07/2023] [Accepted: 10/24/2023] [Indexed: 12/05/2023] Open
Abstract
IMPORTANCE The impact of circulating viruses on the critically endangered, orange-bellied parrot (OBP) population can be devastating. The OBP already faces numerous threats to its survival in the wild, including habitat loss, predation, and small population impacts. Conservation of the wild OBP population is heavily reliant on supplementation using OBPs from a managed captive breeding program. These birds may act as a source for introduction of a novel disease agent to the wild population that may affect survival and reproduction. It is, therefore, essential to monitor and assess the health of OBPs and take appropriate measures to prevent and control the spread of viral infections. This requires knowledge of the existing virome to identify novel and emerging viruses and support development of appropriate measures to manage associated risk. By monitoring and protecting these animals from emerging viral diseases, we can help ensure their ongoing survival and preserve the biodiversity of our planet.
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Affiliation(s)
- Natalie Klukowski
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Victoria, Australia
| | - Paul Eden
- Wildlife Conservation and Science, Zoos Victoria, Werribee, Victoria, Australia
| | - Muhammad Jasim Uddin
- School of Veterinary Medicine, Murdoch University, Murdoch, Western Australia, Australia
- Center for Biosecurity and One Health, Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Subir Sarker
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Victoria, Australia
- Biomedical Sciences & Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
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White RT, Taylor W, Klukowski N, Vaughan-Higgins R, Williams E, Petrovski S, Rose JJA, Sarker S. A discovery down under: decoding the draft genome sequence of Pantoea stewartii from Australia's Critically Endangered western ground parrot/kyloring ( Pezoporus flaviventris). Microb Genom 2023; 9:001101. [PMID: 37665208 PMCID: PMC10569725 DOI: 10.1099/mgen.0.001101] [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: 05/25/2023] [Accepted: 08/13/2023] [Indexed: 09/05/2023] Open
Abstract
Pantoea stewartii, a plant pathogen, is primarily transmitted through contaminated seeds and insect vectors, with the corn flea beetle (Chaetocnema pulicaria) being the primary carrier. P. stewartii is a bacterium belonging to the order Enterobacterales and can lead to crop diseases that have a significant economic impact worldwide. Due to its high potential for spread, P. stewartii is classified as a quarantine organism in numerous countries. Despite its impact on agriculture, the limited genome sequences of P. stewartii hamper understanding of its pathogenicity and host specificity, and the development of effective control strategies. In this study, a P. stewartii strain (C10109_Jinnung) was discovered in the faecal matter of the Critically Endangered western ground parrot/kyloring (Pezoporus flaviventris) in Australia, which to our knowledge is the first reported P. stewartii genome from a bird source. Whole-genome sequencing and phylogenomic analysis of strain C10109_Jinnung, obtained from a captive psittacine, provides new insights into the genetic diversity and potential transmission route for the spread of P. stewartii beyond insects and plants, where P. stewartii is typically studied. Our findings provide new insights into the potential transmission route for spread of P. stewartii and expand the known transmission agents beyond insects and plants. Expanding the catalogue of P. stewartii genomes is fundamental to improving understanding of the pathogenicity, evolution and dissemination, and to develop effective control strategies to reduce the substantial economic losses associated with P. stewartii in various crops and the potential impact of endangered animal species.
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Affiliation(s)
- Rhys T. White
- Institute of Environmental Science and Research, Wellington, New Zealand
| | - William Taylor
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Natalie Klukowski
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Victoria, Australia
| | | | - Ernest Williams
- Institute of Environmental Science and Research, Wallaceville, New Zealand
| | - Steve Petrovski
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Victoria, Australia
| | - Jayson J. A. Rose
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Victoria, Australia
| | - Subir Sarker
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Victoria, Australia
- Biomedical Sciences & Molecular Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, Australia
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Sutherland M, Sarker S. Liver virome of a Little Corella (Cacatua sanguinea) reveals coinfection with a novel parvovirus and two beak and feather disease viruses. Aust Vet J 2023; 101:366-372. [PMID: 37497656 DOI: 10.1111/avj.13271] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/07/2023] [Indexed: 07/28/2023]
Abstract
Emerging diseases are acknowledged as a growing threat to wildlife, with the continued identification of pathogenic and potentially pathogenic viruses in avian species resulting from ongoing advances in molecular diagnostic techniques. Parvoviruses under the genus Chaphamaparvovirus (subfamily Hamaparvovirinae) are highly divergent. The detection and characterisation of parvoviruses in psittacine birds is limited. This study reports a novel parvovirus, tentatively named psittaciform chaphamaparvovirus 3 (PsChV-3) under the genus Chaphamaparvovirus, identified in an Australian free-ranging little corella (Cacatua sanguinea). The PsChV-3 genome is 4277 bp in length and encompasses four predicted open-reading frames, including two major genes, a nonstructural replicase gene (NS1), and a structural capsid gene (VP1). The NS1 and VP1 genes showed the closest amino acid identities of 78.8% and 69.7%, respectively, with a recently sequenced psittaciform chaphamaparvovirus 2 from Australian Neophema species grass parrots. In addition, the presence of two complete novel beak and feather disease (BFDV) genomes, 1993 and 1868 nt in length, respectively, were detected from the same bird. Both these BFDV genomes contained two bidirectional ORFs encoding the putative Rep and Cap proteins. Phylogenetic analysis showed that the sequenced novel BFDV genomes clustered in a distinct subclade with other BFDVs isolated from Australian cockatoos. This study contributes to the characterisation chaphamaparvoviruses and BFDV in Australian parrots and supports the need for ongoing monitoring and molecular studies into the avian virome in native Australian psittacine bird species.
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Affiliation(s)
- M Sutherland
- The Unusual Pet Vets, 210 Karingal Drive, Frankston, Victoria, 3930, Australia
| | - S Sarker
- Dept. of Microbiology, Anatomy, Physiology, and Pharmacology, School of Agriculture, Biomedicine and Environment, LaTrobe University, Melbourne, Victoria, 3086, Australia
- Biomedical Sciences & Molecular Biology, Australian Institute of Tropical Health and Medicine, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, QLD, 4811, Australia
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Zhai J, Wang Y, Tang B, Zheng S, He S, Zhao W, Chen H, Lin J, Li F, Bao Y, Lancuo Z, Sharshov K, Liu C, Wang W. Comparative analysis of gut DNA viromes in wild and captive Himalayan vultures. Front Microbiol 2023; 14:1120838. [PMID: 37601346 PMCID: PMC10433386 DOI: 10.3389/fmicb.2023.1120838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 07/21/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Himalayan vultures (Gyps hinalayensis) are widely distributed on the Qinghai-Tibetan Plateau and play a crucial role in maintaining the ecological balance by feeding on decayed corpses of wild and domestic animals. Large-scale culture and metagenomics studies have broadened our understanding of viral diversity in animals' gastrointestinal tracts. However, despite the importance of gut viral communities in regulating bacterial diversity and performing symbiotic functions, no gut viral study has been conducted on Himalayan vultures. Furthermore, the impact of captivity on the gut virome of these vultures remains unknown. Methods In this study, metagenomic sequencing methods targeting DNA of virus-like particles enriched from feces were used to characterize the gut DNA viromes of wild and captive Himalayan vultures. Results In total, 22,938 unique viral operational taxonomic units (vOTUs) were identified and assigned to 140 viral genera in 41 viral families. These families included viruses associated with bacteria, animals, plants, insects, and archaea. Phage communities, including Siphoviridae, Microviridae, Myoviridae, Inoviridae, and Herelleviridae, dominated the gut virome of Himalayan vultures. Wild vultures exhibited higher viral richness and diversity compared with those in captivity. The functional capacity of the gut virome was characterized by identifying 93 KEGG pathways, which were significantly enriched in metabolism and genetic information processing. Abundant auxiliary metabolic genes, such as carbohydrate-active enzyme, and antibiotic resistance genes, were also found in the vultures' gut virome. Discussion Our findings reveal the complex and diverse viral community present in the gut virome of Himalayan vultures, which varies between wild, and captive states. The DNA virome dataset establishes a baseline for the vultures' gut virome and will serve as a reference for future virus isolation and cultivation. Understanding the impact of captivity on the gut virome contributes to our knowledge of vultures' response to captivity and aids in optimizing their rehabilitation and implementing protective measures.
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Affiliation(s)
- Jundie Zhai
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - You Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Boyu Tang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Sisi Zheng
- Animal Disease Prevention and Control Center of Qinghai Province, Xining, Qinghai, China
| | - Shunfu He
- Xining Wildlife Park of Qinghai Province, Xining, Qinghai, China
| | - Wenxin Zhao
- Xining Wildlife Park of Qinghai Province, Xining, Qinghai, China
| | - Hanxi Chen
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Jun Lin
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Feng Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Yuzi Bao
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Zhuoma Lancuo
- College of Finance and Economics, Qinghai University, Xining, Qinghai, China
| | - Kirill Sharshov
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
| | - Chuanfa Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wen Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
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White RT, Jelocnik M, Klukowski N, Haque MH, Sarker S. The first genomic insight into Chlamydia psittaci sequence type (ST)24 from a healthy captive psittacine host in Australia demonstrates evolutionary proximity with strains from psittacine, human, and equine hosts. Vet Microbiol 2023; 280:109704. [PMID: 36840991 DOI: 10.1016/j.vetmic.2023.109704] [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: 11/17/2022] [Revised: 02/15/2023] [Accepted: 02/19/2023] [Indexed: 02/24/2023]
Abstract
Chlamydia psittaci is a zoonotic pathogen that infects birds, humans, and other mammals. Notably, recent studies suggested the human-to-human transmission of C. psittaci, and this pathogen also causes equine reproductive loss in Australia. Molecular studies in Australia to date have focused on and described clonal sequence type (ST)24 strains infecting horses, wild psittacine, and humans. In contrast, the genetic identity of C. psittaci strains from captive psittacine hosts is scarce. In 2022, C. psittaci was detected in the faeces of a healthy captive blue-fronted parrot (Amazona aestiva). Genomic DNA was extracted and underwent whole-genome sequencing. Here we report the 1,160,701 bp circular chromosome of C. psittaci strain BF_amazon_parrot13 and the 7,553 bp circular plasmid pCpsBF_amazon_parrot13. Initial in silico multi-locus sequence typing and ompA genotyping revealed that BF_amazon_parrot13 belongs to the clonal ST24 lineage and has an ompA genotype A. Further context involved the genomes of 31 published ST24 strains, utilising a single-nucleotide variant (SNV) based clustering approach. Despite temporal, host, and biogeographical separation, a core-genome SNV-based phylogeny revealed that BF_amazon_parrot13 clustered in a distinct subcluster with seven C. psittaci strains from equines in Australia (maximum pairwise distance of 13 SNVs). BF_amazon_parrot13 represents the first complete C. psittaci ST24 genome from a captive psittacine in Australia. Furthermore, by using whole-genome sequencing to coordinate surveillance, we can also learn more about the possible health risks and routes of chlamydia transmission among people, livestock, wild animals, and domesticated animals.
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Affiliation(s)
- Rhys T White
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, Queensland 4557, Australia; The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Infectious Disease Research Centre, Brisbane, Queensland 4072, Australia; The University of Queensland, Australian Centre for Ecogenomics, Brisbane, Queensland 4072, Australia.
| | - Martina Jelocnik
- University of the Sunshine Coast, Centre for Bioinnovation, Sippy Downs, Sunshine Coast, Queensland 4557, Australia.
| | - Natalie Klukowski
- La Trobe University, School of Agriculture, Biomedicine and Environment, Department of Microbiology, Anatomy, Physiology and Pharmacology, Melbourne, Victoria 3086, Australia.
| | - Md Hakimul Haque
- Rajshahi University, Faculty of Veterinary and Animal Sciences, Department of Veterinary and Animal Sciences, Rajshahi 6205, Bangladesh.
| | - Subir Sarker
- La Trobe University, School of Agriculture, Biomedicine and Environment, Department of Microbiology, Anatomy, Physiology and Pharmacology, Melbourne, Victoria 3086, Australia.
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Sarker S, Raidal SR. A Novel Pathogenic Avipoxvirus Infecting Vulnerable Cook's Petrel ( Pterodroma cookii) in Australia Demonstrates a High Genomic and Evolutionary Proximity with South African Avipoxviruses. Microbiol Spectr 2023; 11:e0461022. [PMID: 36749064 PMCID: PMC10100368 DOI: 10.1128/spectrum.04610-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/06/2023] [Indexed: 02/08/2023] Open
Abstract
Avipoxviruses are assumed to be restricted to avian hosts and are considered to be important viral pathogens that may impact the conservation of many vulnerable or endangered birds. Recent reports of avipoxvirus-like viruses from reptiles suggest that cross-species transmission may be possible within birds and other species. Most of the avipoxviruses in wild and sea birds remain uncharacterized, and their genetic variability is unclear. Here, cutaneous pox lesions were used to recover a novel, full-length Cook's petrelpox virus (CPPV) genome from a vulnerable Cook's petrel (Pterodroma cookii), and this was followed by the detection of immature virions using transmission electron microscopy (TEM). The CPPV genome was 314,065 bp in length and contained 357 predicted open-reading frames (ORFs). While 323 of the ORFs of the CPPV genome had the greatest similarity with the gene products of other avipoxviruses, a further 34 ORFs were novel. Subsequent phylogenetic analyses showed that the CPPV was most closely related to other avipoxviruses that were isolated mostly from South African bird species and demonstrated the highest sequence similarity with a recently isolated flamingopox virus (88.9%) in South Africa. Considering the sequence similarity observed between CPPV and other avipoxviruses, TEM evidence of poxvirus particles, and phylogenetic position, this study concluded that CPPV is a distinct candidate of avipoxviruses. IMPORTANCE Emerging viral disease is a significant concern with potential consequences for human, animal, and environmental health. Over the past several decades, multiple novel viruses have been found in wildlife species, including birds, and they can pose a threat to vulnerable and endangered species. Cook's petrel is currently listed as vulnerable. The threats to the species vary, but are, to a large degree, due to anthropogenic impacts, such as climate change, habitat loss, pollution, and other disturbances by humans. Knowledge of viral pathogens, including poxvirus of Cook's petrel is currently virtually nonexistent.
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Affiliation(s)
- Subir Sarker
- Department of Microbiology, Anatomy, Physiology and Pharmacology, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, Victoria, Australia
| | - Shane R. Raidal
- School of Agricultural, Environmental and Veterinary Sciences, Faculty of Science and Health, Charles Sturt University, Wagga, New South Wales, Australia
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A screening of wild bird samples enhances our knowledge about the biodiversity of avian adenoviruses. Vet Res Commun 2023; 47:297-303. [PMID: 35661294 PMCID: PMC9873698 DOI: 10.1007/s11259-022-09931-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 04/25/2022] [Indexed: 01/28/2023]
Abstract
Wild birds are threatened by anthropic effects on a global scale, and their adenoviruses might contribute to their endangerment. Thus, it is important to reveal the real biodiversity of avian adenoviruses, as, unfortunately, this research topic is far from being prioritized. The turkey hemorrhagic enteritis is an economically important disease causing high mortalities, and its causative siadenoviral agent is only distantly related to other avian siadenoviruses in phylogenetic analyses. Both to enhance our knowledge about the biodiversity of wild bird adenoviruses and to possibly trace back the origin of the turkey hemorrhagic enteritis virus, numerous Hungarian wild bird samples were screened for adenoviruses using PCR, and the detected strains were typed molecularly. The screening revealed numerous new adenovirus types, several of which represent novel adenovirus species as well, in the genera Atadenovirus, Aviadenovirus and Siadenovirus.
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Characterization of a Novel Complete-Genome Sequence of a Galliform Chaphamaparvovirus from a Free-Range Laying Chicken Clinically Diagnosed with Spotty Liver Disease. Microbiol Resour Announc 2022; 11:e0101722. [PMID: 36301112 PMCID: PMC9670884 DOI: 10.1128/mra.01017-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This study reports a novel complete genome of galliform chaphamaparvovirus 4, which was detected in the bile of a free-range laying chicken diagnosed with spotty liver disease. The genome was 4,367 bp in length, enclosed by two identical inverted terminal repeats. The detection of this novel chaphamaparvovirus represents a notable concern for the poultry industry in Australia.
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Unravelling Bile Viromes of Free-Range Laying Chickens Clinically Diagnosed with Spotty Liver Disease: Emergence of Many Novel Chaphamaparvoviruses into Multiple Lineages. Viruses 2022; 14:v14112543. [PMID: 36423151 PMCID: PMC9695665 DOI: 10.3390/v14112543] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022] Open
Abstract
Spotty liver disease (SLD) causes substantial egg production losses and chicken mortality; therefore, it is a disease that concerns Australian egg farmers. Over the last few decades, much research has been conducted to determine the etiologic agents of SLD and to develop potential therapeutics; however, SLD still remains a major issue for the chicken industries globally and remained without the elucidation of potentially multiple pathogens involved. To help fill this gap, this study was aimed at understanding the viral diversity of bile samples from which the SLD-causing bacterium, Campylobacter hepaticus, has been isolated and characterised. The collected samples were processed and sequenced using high-throughput next-generation sequencing. Remarkably, this study found 15 galliform chaphamaparvoviruses (GaChPVs), of which 14 are novel under the genus Chaphamaparvovirus. Among them, nine were complete genomes that showed between 41.7% and 78.3% genome-wide pairwise similarities to one another. Subsequent phylogenetic analysis using the NS1 gene exhibited a multiple incursion of chaphamaparvovirus lineages, including a novel lineage of unknown ancestral history in free-range laying chickens in Australia. This is the first evidence of circulating many parvoviruses in chickens in Australia, which has increased our knowledge of the pathogen diversity that may have an association with SLD in chickens.
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Molecular characterisation of a novel pathogenic avipoxvirus from an Australian little crow (Corvus bennetti) directly from the clinical sample. Sci Rep 2022; 12:15053. [PMID: 36064742 PMCID: PMC9445014 DOI: 10.1038/s41598-022-19480-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/30/2022] [Indexed: 11/29/2022] Open
Abstract
Avipoxviruses are thought to be restricted to avian hosts and considered significant pathogens that may impact the conservation of many birds. However, reports of avipoxvirus-like viruses from reptiles suggest that cross-species transmission, within birds and other species, may be possible. The vast majority of avipoxviruses in wild birds remain uncharacterised and their genetic variability is unclear. Here, cutaneous pox lesions were used to recover a novel full-length crowpox virus genome from an Australian little crow (Corvus bennetti), followed by the detection of immature and intracellular mature virions using electron microscopy. The CRPV genome was 328,768 bp in length and contained 403 predicted open-reading frames. While 356 of the ORFs of CRPV genome had the greatest similarity with other avipoxviruses gene products, a further 47 ORFs were novel. Subsequent phylogenetic analyses showed that the CRPV was most closely related to other avipoxviruses isolated from passerine and marine bird species and demonstrated the highest sequence similarity with an albatrosspox virus (84.4%). Considering the sequence similarity observed between CRPV and other avipoxviruses and phylogenetic position, this study concluded that the CRPV to be a distinct available candidate of avipoxviruses.
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Gellért Á, Benkő M, Harrach B, Peters M, Kaján GL. The genome and phylogenetic analyses of tit siadenoviruses reveal both a novel avian host and viral species. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 103:105326. [PMID: 35779784 DOI: 10.1016/j.meegid.2022.105326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 06/10/2022] [Accepted: 06/26/2022] [Indexed: 06/15/2023]
Abstract
In both a Eurasian blue tit (Cyanistes caeruleus) and a great tit (Parus major), found dead in North Rhine-Westphalia, Germany, intranuclear inclusion bodies were observed in the kidneys during the histologic examination. Siadenoviruses were detected in both samples, and the nucleotide sequence of the partial DNA polymerase, obtained from the blue tit, was almost identical with that of great tit adenovirus type 1, reported from Hungary previously. The sequence, derived from the German great tit sample was more similar to great tit adenovirus 2, yet divergent enough to forecast the possible establishment of a novel viral type and species. Therefore, the complete genome was subjected to next generation sequencing. The annotation revealed a typical siadenoviral genome layout, and phylogenetic analyses proved the distinctness of the novel virus type: great tit adenovirus 3. We propose the establishment of a new species (Siadenovirus carbocapituli) within the genus Siadenovirus to contain great tit adenovirus types 2 and 3. As both of the newly-detected viruses originated from histologically confirmed cases, and several siadenoviruses have been associated with avian nephritis earlier, we assume that the renal pathology might have been also of adenoviral origin. Additionally, we performed structural studies on two virus-coded proteins. The viral sialidase and the fiber knob were modeled using the AlphaFold2 program. According to the results of the sialic acid docking studies, the fiber trimer of the new great tit adenovirus 3 binds this acid with good affinity. As sialic acid is expressed in the kidney, it can be hypothesized that it is used during the receptor binding and entry of the virus. Strong binding of sialic acid was also predictable for the viral sialidase albeit its enzymatic activity remains disputable since, within its catalytic site, an asparagine residue was revealed instead of the conserved aspartic acid.
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Affiliation(s)
- Ákos Gellért
- Veterinary Medical Research Institute, Eötvös Loránd Research Network, 1581 Budapest, P.O. box 18, Hungary
| | - Mária Benkő
- Veterinary Medical Research Institute, Eötvös Loránd Research Network, 1581 Budapest, P.O. box 18, Hungary
| | - Balázs Harrach
- Veterinary Medical Research Institute, Eötvös Loránd Research Network, 1581 Budapest, P.O. box 18, Hungary
| | - Martin Peters
- Chemical and Veterinary Investigation Office Westphalia, Zur Taubeneiche 10-12, 59821 Arnsberg, Germany
| | - Győző L Kaján
- Veterinary Medical Research Institute, Eötvös Loránd Research Network, 1581 Budapest, P.O. box 18, Hungary.
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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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Characterization of a Near-Complete Genome Sequence of a Chaphamaparvovirus from an Australian Boobook Owl (Ninox boobook). Microbiol Resour Announc 2022; 11:e0024922. [PMID: 35438543 PMCID: PMC9119055 DOI: 10.1128/mra.00249-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study reports a complete genome sequence of a variant of psittacine chaphamaparvovirus 2 detected in kidney tissue from an Australian boobook (Ninox boobook), compiled using next-generation sequencing. The genome was 4,312 bp long, encoding four open reading frames. The detection of this variant in boobook represents a significant host-switching event.
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Special Issue: Emerging Wildlife Viral Diseases. Viruses 2022; 14:v14040807. [PMID: 35458537 PMCID: PMC9026112 DOI: 10.3390/v14040807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 04/10/2022] [Indexed: 12/10/2022] Open
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Genome Sequence of a Beak and Feather Disease Virus from an Unusual Novel Host, Australian Boobook Owl (Ninox boobook). Microbiol Resour Announc 2022; 11:e0017222. [PMID: 35319253 PMCID: PMC9022591 DOI: 10.1128/mra.00172-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The beak and feather disease virus (BFDV) is a pathogen of psittacine birds. BFDVs infecting nonpsittacine birds remain largely uncharacterized. We report the genome of a BFDV from a boobook owl (Ninox boobook), a nonpsittacine bird. The genome consisted of 1,993 bp containing two major bidirectionally transcribed open reading frames.
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Molecular and Phylogenetic Characterisation of a Highly Divergent Novel Parvovirus (Psittaciform Chaphamaparvovirus 2) in Australian Neophema Parrots. Pathogens 2021; 10:pathogens10121559. [PMID: 34959514 PMCID: PMC8706300 DOI: 10.3390/pathogens10121559] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/23/2021] [Accepted: 11/29/2021] [Indexed: 11/23/2022] Open
Abstract
Parvoviruses under the genus Chaphamaparvovirus (subfamily Hamaparvovirinae) are highly divergent and have recently been identified in many animals. However, the detection and characterisation of parvoviruses in psittacine birds are limited. Therefore, this study reports a novel parvovirus, tentatively named psittaciform chaphamaparvovirus 2 (PsChPV-2) under the genus Chaphamaparvovirus, which was identified in Australian Neophema birds. The PsChPV-2 genome is 4371 bp in length and encompasses four predicted open-reading frames, including two major genes, a nonstructural replicase gene (NS1), and a structural capsid gene (VP1). The NS1 and VP1 genes showed the closest amino acid identities of 56.2% and 47.7%, respectively, with a recently sequenced psittaciform chaphamaparvovirus 1 from a rainbow lorikeet (Trichoglossus moluccanus). Subsequent phylogenetic analyses exhibited that the novel PsChPV-2 is most closely related to other chaphamaparvoviruses of avian origin and has the greatest sequence identity with PsChPV-1 (60.6%). Further systematic investigation is warranted to explore the diversity with many avian-associated parvoviruses likely to be discovered.
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