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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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2
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Kaszab E, Bali K, Marton S, Ursu K, Farkas SL, Fehér E, Domán M, Martella V, Bányai K. Metagenomic Identification of Novel Eukaryotic Viruses with Small DNA Genomes in Pheasants. Animals (Basel) 2024; 14:237. [PMID: 38254406 PMCID: PMC10812470 DOI: 10.3390/ani14020237] [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: 11/22/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
A panel of intestinal samples collected from common pheasants (Phasianus colchicus) between 2008 and 2017 was used for metagenomic investigation using an unbiased enrichment protocol and different bioinformatic pipelines. The number of sequence reads in the metagenomic analysis ranged from 1,419,265 to 17,507,704 with a viral sequence read rate ranging from 0.01% to 59%. When considering the sequence reads of eukaryotic viruses, RNA and DNA viruses were identified in the samples, including but not limited to coronaviruses, reoviruses, parvoviruses, and CRESS DNA viruses (i.e., circular Rep-encoding single-stranded DNA viruses). Partial or nearly complete genome sequences were reconstructed of at least three different parvoviruses (dependoparvovirus, aveparvovirus and chaphamaparvovirus), as well as gyroviruses and diverse CRESS DNA viruses. Generating information of virus diversity will serve as a basis for developing specific diagnostic tools and for structured epidemiological investigations, useful to assess the impact of these novel viruses on animal health.
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Affiliation(s)
- Eszter Kaszab
- HUN-REN Veterinary Medical Research Institute, 1143 Budapest, Hungary; (E.K.); (K.B.); (S.M.); (E.F.); (M.D.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, 1143 Budapest, Hungary
- One Health Institute, Faculty of Health Sciences, University of Debrecen, 4032 Debrecen, Hungary
| | - Krisztina Bali
- HUN-REN Veterinary Medical Research Institute, 1143 Budapest, Hungary; (E.K.); (K.B.); (S.M.); (E.F.); (M.D.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, 1143 Budapest, Hungary
| | - Szilvia Marton
- HUN-REN Veterinary Medical Research Institute, 1143 Budapest, Hungary; (E.K.); (K.B.); (S.M.); (E.F.); (M.D.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, 1143 Budapest, Hungary
| | - Krisztina Ursu
- Veterinary Diagnostic Directorate, National Food Chain Safety Office, 1143 Budapest, Hungary;
| | - Szilvia L. Farkas
- Department of Obstetrics and Food Animal Medicine Clinic, University of Veterinary Medicine, 1078 Budapest, Hungary;
| | - Enikő Fehér
- HUN-REN Veterinary Medical Research Institute, 1143 Budapest, Hungary; (E.K.); (K.B.); (S.M.); (E.F.); (M.D.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, 1143 Budapest, Hungary
| | - Marianna Domán
- HUN-REN Veterinary Medical Research Institute, 1143 Budapest, Hungary; (E.K.); (K.B.); (S.M.); (E.F.); (M.D.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, 1143 Budapest, Hungary
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari Aldo Moro, 70010 Valenzano, Italy;
| | - Krisztián Bányai
- HUN-REN Veterinary Medical Research Institute, 1143 Budapest, Hungary; (E.K.); (K.B.); (S.M.); (E.F.); (M.D.)
- National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, 1143 Budapest, Hungary
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, 1078 Budapest, Hungary
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3
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Zhao Q, Zhao R, Sun Y, Ji L, Xi Y, Wang X, Shen Q, Ji L, Wang Y, You Z, Yang S, Zhang W. Identification of Multiple Novel Viruses in Fecal Samples of Black-Necked Cranes Using Viral Metagenomic Methods. Viruses 2023; 15:2068. [PMID: 37896845 PMCID: PMC10612090 DOI: 10.3390/v15102068] [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: 09/11/2023] [Revised: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
The black-necked crane is the only species of crane that lives in the high-altitude region of the Tibet Plateau. At present, there is little research on viral diseases of the black-necked crane (Grus nigricollis). In this study, a viral metagenomic approach was employed to investigate the fecal virome of black-necked cranes in Saga County, Shigatse City, Tibet, China. The identified virus families carried by black-necked cranes mainly include Genomoviridae, Parvoviridae, and Picornaviridae. The percentages of sequence reads belonging to these three virus families were 1.6%, 3.1%, and 93.7%, respectively. Among them, one genome was characterized as a novel species in the genus Grusopivirus of the family Picornaviridae, four new parvovirus genomes were obtained and classified into four different novel species within the genus Chaphamaparvovirus of the subfamily Hamaparvovirinae, and four novel genomovirus genomes were also acquired and identified as members of three different species, including Gemykroznavirus haeme1, Gemycircularvirus ptero6, and Gemycircularvirus ptero10. All of these viruses were firstly detected in fecal samples of black-necked cranes. This study provides valuable information for understanding the viral community composition in the digestive tract of black-necked cranes in Tibet, which can be used for monitoring, preventing, and treating potential viral diseases in black-necked cranes.
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Affiliation(s)
- Qifan Zhao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Ran Zhao
- Department of Prevention and Control, Xiamen Animal Disease Prevention and Control Center, Xiamen 361009, China;
| | - Yijie Sun
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Li Ji
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Yuan Xi
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Likai Ji
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Yan Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Zhenqiang You
- School of Public Health, Hangzhou Medical College, Hangzhou 310013, China;
| | - Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang 212013, China; (Q.Z.); (Y.S.); (L.J.); (Y.X.); (X.W.); (Q.S.); (L.J.); (Y.W.)
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4
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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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5
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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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Novel Chaphamaparvovirus in Insectivorous Molossus molossus Bats, from the Brazilian Amazon Region. Viruses 2023; 15:v15030606. [PMID: 36992315 PMCID: PMC10054343 DOI: 10.3390/v15030606] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/17/2023] [Accepted: 02/18/2023] [Indexed: 02/25/2023] Open
Abstract
Chaphamaparvovirus (CHPV) is a recently characterized genus of the Parvoviridae family whose members can infect different hosts, including bats, which constitute the second most diverse order of mammals and are described worldwide as important transmitters of zoonotic diseases. In this study, we identified a new CHPV in bat samples from the municipality of Santarém (Pará state, North Brazil). A total of 18 Molossus molossus bats were analyzed using viral metagenomics. In five animals, we identified CHPVs. These CHPV sequences presented the genome with a size ranging from 3797 to 4284 bp. Phylogenetic analysis-based nucleotide and amino acid sequences of the VP1 and NS1 regions showed that all CHPV sequences are monophyletic. They are also closely related to CHPV sequences previously identified in bats in southern and southeast Brazil. According to the International Committee on Taxonomy of Viruses (ICTV) classification criteria for this species (the CHPV NS1 gene region must have 85% identity to be classified in the same species), our sequences are likely a new specie within the genus Chaphamaparvovirus, since they have less than 80% identity with other CHPV described earlier in bats. We also make some phylogenetic considerations about the interaction between CHPV and their host. We suggest a high level of specificity of CPHV and its hosts. Thus, the findings contribute to improving information about the viral diversity of parvoviruses and show the importance of better investigating bats, considering that they harbor a variety of viruses that may favor zoonotic events.
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7
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Hao X, Li Y, Chen B, Wang H, Wang X, Xiao X, Zhou P, Li S. Detection of FeChPV in a cat shelter outbreak of upper respiratory tract disease in China. Front Microbiol 2022; 13:1064747. [PMID: 36569076 PMCID: PMC9773189 DOI: 10.3389/fmicb.2022.1064747] [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: 10/08/2022] [Accepted: 11/14/2022] [Indexed: 12/14/2022] Open
Abstract
Feline parvovirus often causes a fatal infectious disease and has a serious impact on domestic cats and wild felines. Feline chaphamaparvovirus (FeChPV) is a novel type of feline parvovirus that has been successively identified in Canada, Italy, and Turkey. The prevalence and pathogenicity of FeChPV in other regions is still unknown. In this study, we recorded the detection of FeChPV in a cat shelter in China. A high prevalence (81.08%, 30/37) of FeChPV was detected in cats with symptoms of upper respiratory tract disease (URTD) in this cat shelter. Multiple pathogen testing indicated high coinfection rates of 80% (24/30) with other common viruses in FeChPV-positive cats. Analyses of the necropsy and histopathological findings revealed severe lymphadenitis, encephalitis, and viral DNA in several tissues (including brain) of the deceased cat. Finally, we obtained nearly full-length genomes of four strains with 98.4%~98.6% homology with previously reported genomes. Notably, VP1 proteins showed seven unique amino acid mutations, while NS1 proteins carried eight mutations. In the evolutionary tree based on VP1 and NS1, the sequences clustered in a large branch with Italian and Canadian FeChPV strains. Given the possible association of FeChPV with URTD, further studies are necessary to evaluate the pathogenicity and epidemiological characteristics of this novel feline pathogen.
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Affiliation(s)
- Xiangqi Hao
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China,Guangdong Provincial Pet Engineering Technology Research Center, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yanchao Li
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China,Guangdong Provincial Pet Engineering Technology Research Center, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Bo Chen
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China,Guangdong Provincial Pet Engineering Technology Research Center, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Hanhong Wang
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China,Guangdong Provincial Pet Engineering Technology Research Center, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xinrui Wang
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China,Guangdong Provincial Pet Engineering Technology Research Center, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xiangyu Xiao
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China,Guangdong Provincial Pet Engineering Technology Research Center, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Pei Zhou
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China,Guangdong Provincial Pet Engineering Technology Research Center, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China,*Correspondence: Pei Zhou,
| | - Shoujun Li
- Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China,Guangdong Provincial Pet Engineering Technology Research Center, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China,Shoujun Li,
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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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9
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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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10
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Kubacki J, Qi W, Fraefel C. Differential Viral Genome Diversity of Healthy and RSS-Affected Broiler Flocks. Microorganisms 2022; 10:microorganisms10061092. [PMID: 35744610 PMCID: PMC9231120 DOI: 10.3390/microorganisms10061092] [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: 04/29/2022] [Revised: 05/18/2022] [Accepted: 05/23/2022] [Indexed: 01/17/2023] Open
Abstract
The intestinal virus community contributes to health and disease. Runting and stunting syndrome (RSS) is associated with enteric viruses and leads to economic losses in the poultry industry. However, many viruses that potentially cause this syndrome have also been identified in healthy animals. To determine the difference in the virome of healthy and diseased broilers, samples from 11 healthy and 17 affected broiler flocks were collected at two time points and analyzed by Next-Generation Sequencing. Virus genomes of Parvoviridae, Astroviridae, Picornaviridae, Caliciviridae, Reoviridae, Adenoviridae, Coronaviridae, and Smacoviridae were identified at various days of poultry production. De novo sequence analysis revealed 288 full or partial avian virus genomes, of which 97 belonged to the novel genus Chaphamaparvovirus. This study expands the knowledge of the diversity of enteric viruses in healthy and RSS-affected broiler flocks and questions the association of some viruses with the diseases.
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Affiliation(s)
- Jakub Kubacki
- Institute of Virology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland;
- Correspondence:
| | - Weihong Qi
- Functional Genomics Center Zurich, 8057 Zurich, Switzerland;
| | - Cornel Fraefel
- Institute of Virology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland;
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11
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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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