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Van Nguyen T, Kasantikul T, Piewbang C, Techangamsuwan S. Evolutionary dynamics of canine kobuvirus in Vietnam and Thailand reveal the evidence of viral ability to evade host immunity. Sci Rep 2024; 14:12037. [PMID: 38802579 PMCID: PMC11130191 DOI: 10.1038/s41598-024-62833-2] [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: 02/15/2024] [Accepted: 05/21/2024] [Indexed: 05/29/2024] Open
Abstract
Canine kobuvirus (CaKoV) is a pathogen associated with canine gastrointestinal disease (GID). This study examined 327 rectal swabs (RS), including 113 from Vietnam (46 healthy, 67 with GID) and 214 from Thailand (107 healthy and 107 with GID). CaKoV was detected in both countries, with prevalences of 28.3% (33/113) in Vietnam and 7.9% (17/214) in Thailand. Additionally, CaKoV was found in both dogs with diarrhea and healthy dogs. CaKoV was mainly found in puppies under six months of age (30.8%). Co-detection with other canine viruses were also observed. The complete coding sequence (CDS) of nine Vietnamese and four Thai CaKoV strains were characterized. Phylogenetic analysis revealed a close genetic relationship between Vietnamese and Thai CaKoV strains, which were related to the Chinese strains. CDS analysis indicated a distinct lineage for two Vietnamese CaKoV strains. Selective pressure analysis on the viral capsid (VP1) region showed negative selection, with potential positive selection sites on B-cell epitopes. This study, the first of its kind in Vietnam, provides insights into CaKoV prevalence in dogs of different ages and healthy statuses, updates CaKoV occurrence in Thailand, and sheds light on its molecular characteristics and immune evasion strategies.
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Affiliation(s)
- Tin Van Nguyen
- The International Graduate Program of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Faculty of Animal Science and Veterinary Medicine, Nong Lam University, Ho Chi Minh City, Vietnam
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Tanit Kasantikul
- Veterinary Diagnostic Laboratory, Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Chutchai Piewbang
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Somporn Techangamsuwan
- Animal Virome and Diagnostic Development Research Unit, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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Balázs B, Boros Á, Pankovics P, Nagy G, Szekeres S, Urbán P, Reuter G. Detection and complete genome characterization of a genogroup X (GX) sapovirus (family Caliciviridae) from a golden jackal (Canis aureus) in Hungary. Arch Virol 2024; 169:100. [PMID: 38630394 PMCID: PMC11024015 DOI: 10.1007/s00705-024-06034-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/01/2024] [Indexed: 04/19/2024]
Abstract
In this study, a novel genotype of genogroup X (GX) sapovirus (family Caliciviridae) was detected in the small intestinal contents of a golden jackal (Canis aureus) in Hungary and characterised by viral metagenomics and next-generation sequencing techniques. The complete genome of the detected strain, GX/Dömsöd/DOCA-11/2020/HUN (PP105600), is 7,128 nt in length. The ORF1- and ORF2-encoded viral proteins (NSP, VP1, and VP2) have 98%, 95%, and 88% amino acid sequence identity to the corresponding proteins of genogroup GX sapoviruses from domestic pigs, but the nucleic acid sequence identity values for their genes are significantly lower (83%, 77%, and 68%). During an RT-PCR-based epidemiological investigation of additional jackal and swine samples, no other GX strains were detected, but a GXI sapovirus strain, GXI/Tótfalu/WBTF-10/2012/HUN (PP105601), was identified in a faecal sample from a wild boar (Sus scrofa). We report the detection of members of two likely underdiagnosed groups of sapoviruses (GX and GXI) in a golden jackal and, serendipitously, in a wild boar in Europe.
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Affiliation(s)
- Benigna Balázs
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12., Pécs, H-7624, Hungary
| | - Ákos Boros
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12., Pécs, H-7624, Hungary
| | - Péter Pankovics
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12., Pécs, H-7624, Hungary
| | - Gábor Nagy
- Department of Animal Physiology and Health, Hungarian University of Agriculture and Life Science, Kaposvár, Hungary
| | - Sándor Szekeres
- Department of Parasitology and Zoology, University of Veterinary Medicine, Budapest, Hungary
- HUN-REN-UVMB Climate Change: New Blood-Sucking Parasites and Vector-Borne Pathogens Research Group, Budapest, Hungary
| | - Péter Urbán
- Szentágothai Research Centre, Bioinformatics Research Group, Genomics and Bioinformatics Core Facility, University of Pécs, Pécs, Hungary
| | - Gábor Reuter
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti út 12., Pécs, H-7624, Hungary.
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Huang M, Gan J, Xu Z, Guo Y, Chen Z, Gao GF, Liang H, Liu WJ. A black goat-derived novel genotype of Aichi virus C blurs the boundary between caprine and porcine kobuviruses. Virology 2023; 585:215-221. [PMID: 37384968 DOI: 10.1016/j.virol.2023.06.014] [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: 03/27/2023] [Revised: 06/12/2023] [Accepted: 06/21/2023] [Indexed: 07/01/2023]
Abstract
Aichi virus C, a species in the genus Kobuvirus, causes diarrhea diseases in pigs and goats and pose health threat and economic loss for stock farming. A nearly complete genome sequence of caprine kobuvirus GCCDC14 was obtained from an anal swab of a black goat died from diarrhea collected in Hubei, China in 2019. Phylogenetic analyses suggested that GCCDC14 is a novel genotype of Aichi virus C, forming a sister branch to other caprine kobuviruses, with P1 and VP0 genes more closely related to porcine kobuviruses and VP3 in an independent branch. Compared to previous caprine kobuviruses, unique amino acid changes in the poly-l-proline type II helix structure of VP0 and VP1 were found, which may affect the cellular machinery of host and pathogenicity. This study indicates the presence of the kobuvirus with continuously evolving features and emphasizes the surveillance and genetic evolution investigation of kobuviruses for safety of husbandry.
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Affiliation(s)
- Mengkun Huang
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed By the Province and Ministry, Guangxi Medical University, Nanning, 530000, China; NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
| | - Jinxian Gan
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed By the Province and Ministry, Guangxi Medical University, Nanning, 530000, China; NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
| | - Ziqian Xu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China
| | - Yuanyuan Guo
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China; School of Public Health, Shandong University, Jinan, 250012, China
| | - Zhangfu Chen
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China; School of Public Health, Shandong University, Jinan, 250012, China
| | - George F Gao
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed By the Province and Ministry, Guangxi Medical University, Nanning, 530000, China; NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China; School of Public Health, Shandong University, Jinan, 250012, China; CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, 100101, China; Research Unit of Adaptive Evolution and Control of Emerging Viruses (2018RU009), Chinese Academy of Medical Sciences, Beijing, 102206, China.
| | - Hao Liang
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed By the Province and Ministry, Guangxi Medical University, Nanning, 530000, China.
| | - William J Liu
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed By the Province and Ministry, Guangxi Medical University, Nanning, 530000, China; NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, 102206, China; Research Unit of Adaptive Evolution and Control of Emerging Viruses (2018RU009), Chinese Academy of Medical Sciences, Beijing, 102206, China.
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Yan N, Yue H, Liu Q, Wang G, Tang C, Liao M. Isolation and Characteristics of a Novel Aichivirus D from Yak. Microbiol Spectr 2023; 11:e0009923. [PMID: 37097198 PMCID: PMC10269754 DOI: 10.1128/spectrum.00099-23] [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: 01/07/2023] [Accepted: 04/05/2023] [Indexed: 04/26/2023] Open
Abstract
Aichivirus D (AiV-D) is a newly emerging Kobuvirus detected in bovine and sheep, and information is limited regarding its biological significance and prevalence. This study aimed to explore both the prevalence and characteristics of AiV-D in yaks. From May to August 2021, 117 fecal samples were collected from yaks with diarrhea in three provinces of China's Qinghai-Tibet Plateau, 15 of which were selected and pooled for metagenomic analysis. A high abundance of AiV-D sequences was obtained. Of the 117 diarrhea samples, 29 (24.8%) tested AiV-D-positive, including 33.3% (14/42) from Sichuan, 21.1% (8/38) from Qinghai, and 18.9% (7/37) from Tibet, respectively, suggesting a wide geographical distribution of the AiV-D in yaks in the Qinghai-Tibet Plateau. Furthermore, three AiV-D strains were successfully isolated using Vero cells. Significantly, the AiV-D strain could cause diarrhea, intestinal bleeding, and inflammation in yak calves via oral inoculation. The virus was distributed in the ileum, jejunum, duodenum, colon, cecum, and rectum. Based on phylogenetic analysis of the genome and capsid protein P1 (VP0, VP3, and VP1 genes), the yak AiV-D strains likely represent a novel genotype of AiV-D. On the whole, this study identified a novel genotype of AiV-D from yaks, which was successfully isolated, and confirmed that this virus is a diarrhea pathogen in yaks and has a wide geographical distribution in the Qinghai-Tibet Plateau. Our results expand the host range of AiV-D and the pathogen spectrum of yaks and have significant implications for diagnosing and controlling diarrhea in yaks. IMPORTANCE In this study, we identified and successfully isolated a novel genotype of AiV-D from yaks. Animal infection confirmed that this virus can cause diarrhea, intestinal bleeding, and inflammation in yak calves via oral inoculation. The virus was distributed in the ileum, jejunum, cecum, duodenum, colon, and rectum. All of these results have significant implications for diagnosing and controlling diarrhea in yaks. These novel AiV-D strains have a wide geographical distribution in yaks from the Qinghai-Tibet Plateau in China. In addition to expanding the host range of AiV-D and the pathogen spectrum of yaks, these findings can increase knowledge of the prevalence and diversity of AiV-D.
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Affiliation(s)
- Nan Yan
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Hua Yue
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Quan Liu
- School of Life Sciences and Engineering, Foshan University, Foshan, China
| | - Gang Wang
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Guangzhou, China
- Field Observation and Experiment Station on Animal Blight of Guangdong Province, Guangzhou, China
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Cheng Tang
- College of Animal & Veterinary Sciences, Southwest Minzu University, Chengdu, China
| | - Ming Liao
- National and Regional Joint Engineering Laboratory for Medicament of Zoonosis Prevention and Control, Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
- Key Laboratory of Livestock Disease Prevention of Guangdong Province, Guangzhou, China
- Field Observation and Experiment Station on Animal Blight of Guangdong Province, Guangzhou, China
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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Matamoros DJP, Worsfold CS, Campos RC, Acuña HMB, Chacón EC, Sánchez CFJ. Molecular characterization of norovirus and sapovirus detected in animals and humans in Costa Rica: Zoo-anthropozoonotic potential of human norovirus GII.4. Open Vet J 2023; 13:74-89. [PMID: 36777439 PMCID: PMC9897497 DOI: 10.5455/ovj.2023.v13.i1.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/04/2023] [Indexed: 02/05/2023] Open
Abstract
Background Noroviruses (NoV) and sapoviruses (SaV) are major causes of acute viral gastroenteritis in humans worldwide, as well as gastrointestinal infections in animals. However, it has not been determined whether these viruses are zoonotic pathogens. Aim In this study, we investigated the presence of NoV and SaV in stool samples from dogs, pigs, cows, and humans to determine some aspects of the molecular epidemiology and the genetic relationship of several strains present in these species. Methods Polymerase chain reaction and sequencing of NoV and SaV strains present in stool samples from humans and dogs with diarrhea, pigs, and cattle with and without diarrhea were carried out during fragmented periods from 2002 to 2012. Results Of all samples analyzed, 11.6% (123/1,061) of the samples were positive for NoV and 0.88% (9/1,023) were positive for SaV. The phylogenetic analysis confirmed 16 human strains of NoV (HuNoV) belonging to HuNoV G?/GII.P2 (1), GII.4/GII.P4 (5), G?/GII.P4 (9), and GII.6/GII.P6 (1) and allowed us to verify and assign three strains of human SaV to genotypes GI.2 (1) and GII.5 (2). In dogs, eight strains of NoV [HuNoV G?/GII.P4 (4) and canine G?/GVI.P1 (4)] and two strains of canine SaV were determined. In pigs, six strains were assigned to HuNoV G?/GII.P4 and four strains to porcine SaV were assigned to genogroup GIII (2), GVIII (1), and GXI (1). In bovines, five strains were characterized as HuNoV G?/GII.P4. Conclusions This study showed that NoV and SaV prototype strains have been present in humans and dogs in Costa Rica. Additionally, it revealed that the zoonotic potential of SaV is very limited, while the zoonotic implications for HuNoV GII.4 are stronger due to the simultaneous circulation of strains related to HuNoV GII.4 in four species, which suggests a zoo-anthropozoonosis.
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Affiliation(s)
- Derling José Pichardo Matamoros
- Postgraduate Program in Agricultural Sciences and Natural Resources (PPCARN), University of Costa Rica (UCR), San Pedro, Costa Rica,Veterinary Virology Diagnostic and Research Unit (UNDIVE), School of Veterinary Medicine, National University, Barreal de Heredia, Costa Rica,Corresponding Author: Derling José Pichardo Matamoros. Postgraduate Program in Agricultural Sciences and Natural Resources (PPCARN), University of Costa Rica (UCR), San Pedro, Costa Rica.
| | | | - Rocío Cortés Campos
- Veterinary Virology Diagnostic and Research Unit (UNDIVE), School of Veterinary Medicine, National University, Barreal de Heredia, Costa Rica,Tropical Diseases Research Program (PIET), School of Veterinary Medicine, National University, Barreal de Heredia, Costa Rica
| | - Hilda María Bolaños Acuña
- National Bacteriological Reference Center of the Costa Rican Institute for Teaching and Research in Health and Nutrition (CNRB-INCIENSA), San Diego, Costa Rica
| | - Elena Campos Chacón
- National Bacteriological Reference Center of the Costa Rican Institute for Teaching and Research in Health and Nutrition (CNRB-INCIENSA), San Diego, Costa Rica
| | - Carlos Francisco Jiménez Sánchez
- Veterinary Virology Diagnostic and Research Unit (UNDIVE), School of Veterinary Medicine, National University, Barreal de Heredia, Costa Rica,Tropical Diseases Research Program (PIET), School of Veterinary Medicine, National University, Barreal de Heredia, Costa Rica
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Bassi C, Guerriero P, Pierantoni M, Callegari E, Sabbioni S. Novel Virus Identification through Metagenomics: A Systematic Review. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122048. [PMID: 36556413 PMCID: PMC9784588 DOI: 10.3390/life12122048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Metagenomic Next Generation Sequencing (mNGS) allows the evaluation of complex microbial communities, avoiding isolation and cultivation of each microbial species, and does not require prior knowledge of the microbial sequences present in the sample. Applications of mNGS include virome characterization, new virus discovery and full-length viral genome reconstruction, either from virus preparations enriched in culture or directly from clinical and environmental specimens. Here, we systematically reviewed studies that describe novel virus identification through mNGS from samples of different origin (plant, animal and environment). Without imposing time limits to the search, 379 publications were identified that met the search parameters. Sample types, geographical origin, enrichment and nucleic acid extraction methods, sequencing platforms, bioinformatic analytical steps and identified viral families were described. The review highlights mNGS as a feasible method for novel virus discovery from samples of different origins, describes which kind of heterogeneous experimental and analytical protocols are currently used and provides useful information such as the different commercial kits used for the purification of nucleic acids and bioinformatics analytical pipelines.
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Affiliation(s)
- Cristian Bassi
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Paola Guerriero
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Marina Pierantoni
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Elisa Callegari
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Silvia Sabbioni
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
- Department of Life Science and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
- Correspondence: ; Tel.: +39-053-245-5319
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Palombieri A, Fruci P, Sarchese V, Robetto S, Orusa R, Arbuatti A, Martella V, Di Martino B, Di Profio F. Detection and Characterization of a Novel Picornavirus in European Badger (Meles meles). Vet Sci 2022; 9:vetsci9110645. [PMID: 36423093 PMCID: PMC9696597 DOI: 10.3390/vetsci9110645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/11/2022] [Accepted: 11/18/2022] [Indexed: 11/22/2022] Open
Abstract
Simple Summary A molecular survey was performed to investigate the gut virome of wild mustelids and sciurids found dead in Northwestern Italy. Using pan-picornavirus primer pair, we discovered a new picornavirus (PV) in the intestinal content of a European badger (Meles meles). The full-length genome of this novel strain was obtained by a sequence-independent single-primer amplification procedure in combination with Oxford Nanopore Technologies sequencing platform. On sequence analysis, the badger PV could be considered the prototype of a new species, proposed as Sakobuvirus B, classified within the still poorly characterized genus Sakobuvirus. The finding of this study poses interesting questions about the genetic diversity of these viruses, suggesting that the PV host range could be wider than expected. Abstract The recent development of unbiased metagenomic next-generation sequencing has provided a richer view of the wild animal virome making it necessary to expand the knowledge about virus diversity in wildlife, as well as to monitor their potential transmission to domestic animals or humans. In the present study, by screening collections of enteric specimens from wild animals, a novel picornavirus was identified in the intestinal content of a badger (Meles meles). By enrichment with a sequence-independent single-primer amplification (SISPA) approach and deep sequencing with Oxford Nanopore Technologies (ONT) platform, the genome sequence of a novel picornavirus strain, Badger/3A-2019/ITA, was reconstructed. On comparison based on the polyprotein sequences, the virus was distantly related (58.7% and 59.7% sequence identity at the nucleotide and amino acid level, respectively) to the feline picornavirus strain FFUP1, identified in 2012 in Portugal and classified into genus Sakobovirus within the species Sakobuvirus A. Upon phylogenetic, pairwise homology, and distance analyses performed on the P1, 2Chel, 3Cpro, and 3Dpol proteins and the complete genomic sequence, the badger picornavirus may be considered a member of a new sakobuvirus species, which we propose as Sakobuvirus B.
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Affiliation(s)
- Andrea Palombieri
- Department of Veterinary Medicine, Università degli Studi di Teramo, 64100 Teramo, Italy
| | - Paola Fruci
- Department of Veterinary Medicine, Università degli Studi di Teramo, 64100 Teramo, Italy
| | - Vittorio Sarchese
- Department of Veterinary Medicine, Università degli Studi di Teramo, 64100 Teramo, Italy
| | - Serena Robetto
- Centro di Referenza Nazionale per le Malattie degli Animali Selvatici (CeRMAS), Istituto Zooprofilattico Sperimentale del Piemonte, della Liguria e della Valle d’Aosta, 11020 Aosta, Italy
| | - Riccardo Orusa
- Centro di Referenza Nazionale per le Malattie degli Animali Selvatici (CeRMAS), Istituto Zooprofilattico Sperimentale del Piemonte, della Liguria e della Valle d’Aosta, 11020 Aosta, Italy
| | - Alessio Arbuatti
- Department of Veterinary Medicine, Università degli Studi di Teramo, 64100 Teramo, Italy
| | - Vito Martella
- Department of Veterinary Medicine, Università Aldo Moro di Bari, 70010 Valenzano, Italy
| | - Barbara Di Martino
- Department of Veterinary Medicine, Università degli Studi di Teramo, 64100 Teramo, Italy
| | - Federica Di Profio
- Department of Veterinary Medicine, Università degli Studi di Teramo, 64100 Teramo, Italy
- Correspondence: ; Tel.: +39-0861-266845
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Schuettenberg A, Piña A, Metrailer M, Peláez-Sánchez RG, Agudelo-Flórez P, Lopez JÁ, Ryle L, Monroy FP, Altin JA, Ladner JT. Highly Multiplexed Serology for Nonhuman Mammals. Microbiol Spectr 2022; 10:e0287322. [PMID: 36125316 PMCID: PMC9602771 DOI: 10.1128/spectrum.02873-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/06/2022] [Indexed: 01/04/2023] Open
Abstract
Emerging infectious diseases represent a serious and ongoing threat to humans. Most emerging viruses are maintained in stable relationships with other species of animals, and their emergence within the human population results from cross-species transmission. Therefore, if we want to be prepared for the next emerging virus, we need to broadly characterize the diversity and ecology of viruses currently infecting other animals (i.e., the animal virosphere). High-throughput metagenomic sequencing has accelerated the pace of virus discovery. However, molecular assays can detect only active infections and only if virus is present within the sampled fluid or tissue at the time of collection. In contrast, serological assays measure long-lived antibody responses to infections, which can be detected within the blood, regardless of the infected tissues. Therefore, serological assays can provide a complementary approach for understanding the circulation of viruses, and while serological assays have historically been limited in scope, recent advancements allow thousands to hundreds of thousands of antigens to be assessed simultaneously using <1 μL of blood (i.e., highly multiplexed serology). The application of highly multiplexed serology for the characterization of the animal virosphere is dependent on the availability of reagents that can be used to capture or label antibodies of interest. Here, we evaluate the utility of commercial immunoglobulin-binding proteins (protein A and protein G) to enable highly multiplexed serology in 25 species of nonhuman mammals, and we describe a competitive fluorescence-linked immunosorbent assay (FLISA) that can be used as an initial screen for choosing the most appropriate capture protein for a given host species. IMPORTANCE Antibodies are generated in response to infections with viruses and other pathogens, and they help protect against future exposures. Mature antibodies are long lived, are highly specific, and can bind to their protein targets with high affinity. Thus, antibodies can also provide information about an individual's history of viral exposures, which has important applications for understanding the epidemiology and etiology of disease. In recent years, there have been large advances in the available methods for broadly characterizing antibody-binding profiles, but thus far, these have been utilized primarily with human samples only. Here, we demonstrate that commercial antibody-binding reagents can facilitate modern antibody assays for a wide variety of mammalian species, and we describe an inexpensive and fast approach for choosing the best reagent for each animal species. By studying antibody-binding profiles in captive and wild animals, we can better understand the distribution and prevalence of viruses that could spill over into humans.
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Affiliation(s)
- Alexa Schuettenberg
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Alejandra Piña
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Morgan Metrailer
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | | | | | - Juan Álvaro Lopez
- Microbiology School, Primary Immunodeficiencies Group, University of Antioquia, Medellín, Colombia
| | - Luke Ryle
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Fernando P. Monroy
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - John A. Altin
- The Translational Genomics Research Institute (TGen), Flagstaff, Arizona, USA
| | - Jason T. Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
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Aftab G, Arfaee F, Akhtardanesh B, Nikbakht Brojeni G. Molecular characterization of canine and feline kobuvirus infections in Iran. VETERINARY RESEARCH FORUM : AN INTERNATIONAL QUARTERLY JOURNAL 2022; 13:447-450. [PMID: 36320293 PMCID: PMC9548235 DOI: 10.30466/vrf.2020.128667.2975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/25/2020] [Indexed: 11/14/2022]
Abstract
Kobuviruses are viral pathogens with broad host range presented in human gastroenteritis cases; but, the pathogenesis of these viruses in companion animals is not well described. In the present study, the presence of canine (CaKVs) and feline kobuviruses (FeKVs) was detected in the 100 fecal samples of diarrhoeic and healthy companion dogs and cats by polymerase chain reaction in Tehran, Iran. The prevalence of infection was estimated as 8.00% and 4.00% in dogs and cats, respectively. All positive samples were belonged to non-diarrhoeic animals except for a feline sample being co-infected with panleukopenia. Sequence analysis showed multiple point mutations in canine and feline Iranian strains and new feline strain was detected in the present study. This is the first detection of CaKVs and FeKVs in Iran; but, the exact role of these enteric viral pathogens and their zoonotic risks are better to be clarified in all endemic regions.
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Affiliation(s)
- Ghazal Aftab
- Department of Clinical Sciences, Faculty of Specialized Veterinary Science, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Farnoosh Arfaee
- Department of Clinical Sciences, Faculty of Specialized Veterinary Science, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Baharak Akhtardanesh
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran; ,Correspondence Baharak Akhtardanesh. DVM, DVSc Department of Clinical Sciences, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran. E-mail:
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10
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Gao Y, He W, Fu J, Li Y, He H, Chen Q. Epidemiological Evidence for Fecal-Oral Transmission of Murine Kobuvirus. Front Public Health 2022; 10:865605. [PMID: 35517645 PMCID: PMC9062591 DOI: 10.3389/fpubh.2022.865605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundMurine Kobuvirus (MuKV) is a novel picornavirus of the genus Kobuvirus, and was first identified in the feces of murine rodents in the USA in 2011. There is limited information on the transmission route of MuKV. Thus, we conducted a study to investigate virus detection rates in fecal, serum, throat, and lung tissue samples from murine rodents.ResultsA total of 413 fecal samples, 385 lung samples, 269 throat swab samples, and 183 serum samples were collected from 413 murine rodents (Rattus norvegicus, Rattus tanezumi, and Rattus rattus) captured in urban Shenzhen. Kobuviruses were detected via RT-PCR. Only fecal samples were positive, with prevalence rates of 34.9% in Rattus norvegicus and 29.4% in Rattus tanezumi. Phylogenetic analysis based on partial 3D and complete VP1 sequence regions indicated that all of the MuKV sequences obtained belonged to Aichivirus A, and were genetically closely related to other MuKVs reported in China, Hungary, and the USA. Twenty-eight full-length MuKV sequences were acquired. Phylogenetic analysis of two sequences randomly selected from the two species (SZ59 and SZ171) indicated that they shared very high nucleotide and amino acid identity with one another (94.0 and 99.3%, respectively), and comparison with human Kobuvirus revealed amino acid identity values of ~80%. Additionally, a sewage-derived sequence shared high similarity with the rat-derived sequences identified in this study, with respective nucleotide and amino acid identity values from 86.5 and 90.7% to 87.2 and 91.1%.ConclusionThe results of the current study provide evidence that murine Kobuvirus is transmitted via the fecal-oral route.
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11
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Stamelou E, Giantsis IA, Papageorgiou KV, Petridou E, Davidson I, Polizopοulou ZS, Papa A, Kritas SK. First report of canine Astrovirus and Sapovirus in Greece, hosting both asymptomatic and gastroenteritis symptomatic dogs. Virol J 2022; 19:58. [PMID: 35361253 PMCID: PMC8969266 DOI: 10.1186/s12985-022-01787-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/28/2022] [Indexed: 01/13/2023] Open
Abstract
Background Astrovirus, Norovirus and Sapovirus are widely distributed viruses in humans and animals worldwide. They have frequently been associated with disease, mainly of gastroenteric nature. In dogs, these viruses have been detected both in symptomatic and asymptomatic animals, mainly of young age. Methods In the present epidemiologic study, we investigated the presence of canine Astrovirus (CAstV), canine Norovirus (canine NoV) and canine Sapovirus (Canine SaV) in saliva and stools of 201 domestic dogs originating from throughout Greece, based on two different molecular methods, i.e. conventional and SYBR-Green Real-time RT-PCR. The samples derived from young and adult asymptomatic and symptomatic animals. CAstV was detected in 15/201 (7.5%) and 29/201 (15%) of the examined dogs using conventional RT-PCR and SYBR-Green Real time RT-PCR, respectively. Results The prevalence of the virus was higher at healthy dogs, with a slight discrepancy of the two methods on the aspect of age (67% young dogs with the method of conventional RT-PCR, versus 52% adult positive dogs with the method of SYBR-Green Real-time RT-PCR). Canine SaV was detected in 52/201 (23%) of the dogs (mainly young and asymptomatic), with the method of SYBR-Green Real-time RT-PCR only, while canine NoV was not detected in any sample with either of the two methods applied. Sequencing of the CAstV positive samples resulted in the acquisition of one CAstV sequence. Phylogenetic analysis confirmed the results, clustering the CAstV sequence with homologous canine hosting sequences from other countries. Conclusions CAstV and Canine SaV were proved to circulate in Greek dogs. SYBR-Green Real time RT-PCR showed greater sensitivity in the detection of these viruses. Additionally, we were able to specify the CAstV strain that circulates in Greece, through phylogenetic analysis. To our knowledge, this is the first epidemiological study of CAstV and canine SaV in dogs in Greece, as well as the first time detected in dogs from Greece.
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Affiliation(s)
- Efthymia Stamelou
- School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Ioannis A Giantsis
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100, Florina, Greece.
| | - Konstantinos V Papageorgiou
- School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Evanthia Petridou
- School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Irit Davidson
- Kimron Veterinary Institute, 50250, Bet Dagan, Israel
| | - Zoe S Polizopοulou
- School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Anna Papa
- Laboratory of Microbiology, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Spyridon K Kritas
- School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
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12
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Kaiser FK, van Dyck L, Jo WK, Schreiner T, Pfankuche VM, Wohlsein P, Baumann I, Peters M, Baumgärtner W, Osterhaus ADME, Ludlow M. Detection of Systemic Canine Kobuvirus Infection in Peripheral Tissues and the Central Nervous System of a Fox Infected with Canine Distemper Virus. Microorganisms 2021; 9:microorganisms9122521. [PMID: 34946122 PMCID: PMC8705045 DOI: 10.3390/microorganisms9122521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/17/2021] [Accepted: 12/03/2021] [Indexed: 12/13/2022] Open
Abstract
Canine kobuvirus (CaKV) is a globally distributed pathogen of dogs and is predominantly associated with infection of the gastrointestinal tract. However, an etiological link to enteric disease has not been established since CaKV has been identified in both asymptomatic dogs and animals with diarrheic symptoms. In this study, an extraintestinal CaKV infection was detected by next-generation sequencing in a fox (Vulpes vulpes) in Germany concomitant with a canine distemper virus (canine morbillivirus; CDV) co-infection. Phylogenetic analysis of the complete coding region sequence showed that this strain was most closely related to a CaKV strain detected in a dog in the United Kingdom in 2008. The tissue and cellular tropism of CaKV was characterized by the detection of viral antigens and RNA. CaKV RNA was detected by in situ hybridization in different tissues, including epithelial cells of the stomach and ependymal cells in the brain. The use of a new RT-qPCR assay for CaKV confirmed the systemic distribution of CaKV with viral RNA also detected in the lymph nodes, bladder, trachea, and brain. The detection of a CDV infection in this fox suggests that immunosuppression should be further investigated as a contributing factor to the enhanced extraintestinal spread of CaKV.
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Affiliation(s)
- Franziska K. Kaiser
- Research Center for Infectious Disease and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (F.K.K.); (W.K.J.); (I.B.); (A.D.M.E.O.)
| | - Lydia van Dyck
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (L.v.D.); (T.S.); (V.M.P.); (P.W.); (W.B.)
| | - Wendy K. Jo
- Research Center for Infectious Disease and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (F.K.K.); (W.K.J.); (I.B.); (A.D.M.E.O.)
| | - Tom Schreiner
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (L.v.D.); (T.S.); (V.M.P.); (P.W.); (W.B.)
| | - Vanessa M. Pfankuche
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (L.v.D.); (T.S.); (V.M.P.); (P.W.); (W.B.)
| | - Peter Wohlsein
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (L.v.D.); (T.S.); (V.M.P.); (P.W.); (W.B.)
| | - Ilka Baumann
- Research Center for Infectious Disease and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (F.K.K.); (W.K.J.); (I.B.); (A.D.M.E.O.)
| | - Martin Peters
- Chemisches und Veterinäruntersuchungsamt Westfalen, 59821 Arnsberg, Germany;
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (L.v.D.); (T.S.); (V.M.P.); (P.W.); (W.B.)
| | - Albert D. M. E. Osterhaus
- Research Center for Infectious Disease and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (F.K.K.); (W.K.J.); (I.B.); (A.D.M.E.O.)
| | - Martin Ludlow
- Research Center for Infectious Disease and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (F.K.K.); (W.K.J.); (I.B.); (A.D.M.E.O.)
- Correspondence:
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13
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Suchodolski JS. Analysis of the gut microbiome in dogs and cats. Vet Clin Pathol 2021; 50 Suppl 1:6-17. [PMID: 34514619 PMCID: PMC9292158 DOI: 10.1111/vcp.13031] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/08/2021] [Accepted: 04/20/2021] [Indexed: 12/15/2022]
Abstract
The gut microbiome is an important immune and metabolic organ. Intestinal bacteria produce various metabolites that influence the health of the intestine and other organ systems, including kidney, brain, and heart. Changes in the microbiome in diseased states are termed dysbiosis. The concept of dysbiosis is constantly evolving and includes changes in microbiome diversity and/or structure and functional changes (eg, altered production of bacterial metabolites). Molecular tools are now the standard for microbiome analysis. Sequencing of microbial genes provides information about the bacteria present and their functional potential but lacks standardization and analytical validation of methods and consistency in the reporting of results. This makes it difficult to compare results across studies or for individual clinical patients. The Dysbiosis Index (DI) is a validated quantitative PCR assay for canine fecal samples that measures the abundance of seven important bacterial taxa and summarizes the results as one single number. Reference intervals are established for dogs, and the DI can be used to assess the microbiome in clinical patients over time and in response to therapy (eg, fecal microbiota transplantation). In situ hybridization or immunohistochemistry allows the identification of mucosa‐adherent and intracellular bacteria in animals with intestinal disease, especially granulomatous colitis. Future directions include the measurement of bacterial metabolites in feces or serum as markers for the appropriate function of the microbiome. This article summarizes different approaches to the analysis of gut microbiota and how they might be applicable to research studies and clinical practice in dogs and cats.
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Affiliation(s)
- Jan S Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
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Exploring the Cause of Diarrhoea and Poor Growth in 8-11-Week-Old Pigs from an Australian Pig Herd Using Metagenomic Sequencing. Viruses 2021; 13:v13081608. [PMID: 34452472 PMCID: PMC8402840 DOI: 10.3390/v13081608] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 12/24/2022] Open
Abstract
Diarrhoea and poor growth among growing pigs is responsible for significant economic losses in pig herds globally and can have a wide range of possible aetiologies. Next generation sequencing (NGS) technologies are useful for the detection and characterisation of diverse groups of viruses and bacteria and can thereby provide a better understanding of complex interactions among microorganisms potentially causing clinical disease. Here, we used a metagenomics approach to identify and characterise the possible pathogens in colon and lung samples from pigs with diarrhoea and poor growth in an Australian pig herd. We identified and characterized a wide diversity of porcine viruses including RNA viruses, in particular several picornaviruses—porcine sapelovirus (PSV), enterovirus G (EV-G), and porcine teschovirus (PTV), and a porcine astrovirus (PAstV). Single stranded DNA viruses were also detected and included parvoviruses like porcine bocavirus (PBoV) and porcine parvovirus 2 (PPV2), porcine parvovirus 7 (PPV7), porcine bufa virus (PBuV), and porcine adeno-associated virus (AAV). We also detected single stranded circular DNA viruses such as porcine circovirus type 2 (PCV2) at very low abundance and torque teno sus viruses (TTSuVk2a and TTSuVk2b). Some of the viruses detected here may have had an evolutionary past including recombination events, which may be of importance and potential involvement in clinical disease in the pigs. In addition, our metagenomics data found evidence of the presence of the bacteria Lawsonia intracellularis, Brachyspira spp., and Campylobacter spp. that may, together with these viruses, have contributed to the development of clinical disease and poor growth.
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15
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Shi Y, Tao J, Li B, Shen X, Cheng J, Liu H. The Gut Viral Metagenome Analysis of Domestic Dogs Captures Snapshot of Viral Diversity and Potential Risk of Coronavirus. Front Vet Sci 2021; 8:695088. [PMID: 34307533 PMCID: PMC8292670 DOI: 10.3389/fvets.2021.695088] [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: 04/14/2021] [Accepted: 06/10/2021] [Indexed: 11/13/2022] Open
Abstract
The close relations between dogs (Canis lupus familiaris) and humans lay a foundation for cross species transmissions of viruses. The co-existence of multiplex viruses in the host accelerate viral variations. For effective prediction and prevention of potential epidemic or even pandemic, the metagenomics method was used to investigate the gut virome status of 45 domestic healthy dogs which have extensive contact with human beings. A total of 248.6 GB data (505, 203, 006 valid reads, 150 bp in length) were generated and 325, 339 contigs, which were best matched with viral genes, were assembled from 46, 832, 838 reads. In the aggregate, 9,834 contigs (3.02%) were confirmed for viruses. The top 30 contigs with the most reads abundance were mapped to DNA virus families Circoviridae, Parvoviridae and Herpesviridae; and RNA virus families Astroviridae, Coronaviridae and Picornaviridae, respectively. Numerous sequences were assigned to animal virus families of Astroviridae, Coronaviridae, Circoviridae, etc.; and phage families of Microviridae, Siphoviridae, Ackermannviridae, Podoviridae, Myoviridae and the unclassified phages. Further, several sequences were homologous with the insect and plant viruses, which reflects the diet and habitation of dogs. Significantly, canine coronavirus was uniquely identified in all the samples with high abundance, and the phylogenetic analysis therefore showed close relationship with the human coronavirus strain 229E and NL63, indicating the potential risk of canine coronavirus to infect humans by obtaining the ability of cross-species transmission. This study emphasizes the high detection frequency of virus harbored in the enteric tract of healthy contacted animal, and expands the knowledge of the viral diversity and the spectrum for further disease-association studies, which is meaningful for elucidating the epidemiological and biological role of companion animals in public health.
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Affiliation(s)
- Ying Shi
- Department of Animal Infectious Diseases, Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China.,Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
| | - Jie Tao
- Department of Animal Infectious Diseases, Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China.,Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
| | - Benqiang Li
- Department of Animal Infectious Diseases, Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China.,Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
| | - Xiaohui Shen
- Department of Animal Infectious Diseases, Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jinghua Cheng
- Department of Animal Infectious Diseases, Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China.,Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
| | - Huili Liu
- Department of Animal Infectious Diseases, Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China.,Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
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16
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Di Martino B, Di Profio F, Robetto S, Fruci P, Sarchese V, Palombieri A, Melegari I, Orusa R, Martella V, Marsilio F. Molecular Survey on Kobuviruses in Domestic and Wild Ungulates From Northwestern Italian Alps. Front Vet Sci 2021; 8:679337. [PMID: 34195249 PMCID: PMC8237713 DOI: 10.3389/fvets.2021.679337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/17/2021] [Indexed: 11/13/2022] Open
Abstract
Since the first identification in 1989 in humans, kobuviruses (KoVs) have been identified from a wide range of animal species including carnivores, rodents, birds, ungulates, rabbits, and bats. Several studies have described the identification of genetically related KoVs in the fecal virome of domestic and wild animals suggesting a mutual exchange of viruses. By screening a total of 231 fecal samples from wild and domestic ungulates, KoVs RNA was detected in wild boars (3.2%; 2/63), chamois (4.6%; 2/43), and goats (2.6%; 2/77). On phylogenetic analysis of the partial RdRp sequence, the wild boar strains clustered within the species Aichivirus C whilst the strains identified in domestic and wild ruminants grouped into the species Aichivirus B. The complete VP1 gene was obtained for chamois and goat KoVs. Interestingly, upon phylogenetic analysis the strains grouped together with a KoV of ovine origin within a distinct genetic type (B3) of the species Aichivirus B.
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Affiliation(s)
- Barbara Di Martino
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Federica Di Profio
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Serena Robetto
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Centro di Referenza Nazionale per le Malattie degli Animali Selvatici (CeRMAS), Aosta, Italy
| | - Paola Fruci
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Vittorio Sarchese
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Andrea Palombieri
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Irene Melegari
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
| | - Riccardo Orusa
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Centro di Referenza Nazionale per le Malattie degli Animali Selvatici (CeRMAS), Aosta, Italy
| | - Vito Martella
- Department of Veterinary Medicine, Università Aldo Moro di Bari, Valenzano, Italy
| | - Fulvio Marsilio
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Teramo, Italy
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Genomic characterization and phylogenetic analysis of a new canine picornavirus variant in the mainland of China. Virus Res 2021; 296:198351. [PMID: 33639222 DOI: 10.1016/j.virusres.2021.198351] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/10/2021] [Accepted: 02/19/2021] [Indexed: 11/21/2022]
Abstract
A new canine picornavirus (CanPV) variant, designated as dog/SH1901/CHN/2019, was detected in a pool of various canine fecal samples in the mainland of China using a viral metagenomic analysis, and its nearly complete genome sequence was determined and analyzed. Sequence analyses revealed that it had a standard picornavirus genome organization, a type I internal ribosome entry site (IRES) in the 5'UTR. However, dog/SH1901/CHN/2019 has generated a serial of unique aa mutations and 7aa insertion when compared with the closely related CanPVs. Phylogenetic analysis and pairwise sequence comparisons based on the P1, 2C, 3C, and 3D protein sequences showed that dog/SH1901/ CHN/2019 was closely related to CanPV strains 244 F, 325 F and 6D, which clustered into an independent evolutionary clade and distantly related to CanPV strain A128thr of the genus Mischivirus, which indicated the unclassified CanPV strains may belong to a novel species or genus in the family Picornaviridae. This study extends our knowledge on the evolution and genetic diversity of CanPVs.
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Duplex SYBR Green I-based real-time PCR assay for the rapid detection of canine kobuvirus and canine astrovirus. J Virol Methods 2021; 290:114066. [PMID: 33453300 DOI: 10.1016/j.jviromet.2021.114066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 01/11/2021] [Accepted: 01/11/2021] [Indexed: 11/21/2022]
Abstract
A duplex SYBR Green I-based real-time PCR assay was established for the simultaneous detection of canine kobuvirus (CaKoV) and canine astrovirus (CaAstV). This assay can easily distinguish the two viruses according to their different melting temperatures (Tm) of 80 °C for CaKoV and 86.5 °C for CaAstV; other canine enteroviruses used as controls showed no specific melting peaks. The detection limit of this assay was determined to be 101 copies/μL for both viruses. This method exhibited high repeatability and reproducibility, with a coefficient of variation less than 1.5 %. A total of 48 fecal samples were collected for clinical testing by real-time PCR and confirmed by sequencing. Real-time PCR assay showed a 10.4 % CaKoV-positive rate and a 4.2 % CaAstV-positive rate, and the positive rate of co-infection of the two viruses was 2.1 %, which was consistent with the sequencing results. This assay has many advantages over conventional PCR: it is rapid, sensitive, specific, and reliable for detecting these two viruses in one sample, and it can be used as a tool to detect CaKoV and CaAstV infection or co-infection in clinical settings.
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Weber M, Mosena A, da Silva M, Canova R, de Lorenzo C, Olegário J, Budaszewski R, Baumbach L, Soares J, Sonne L, Varela A, Mayer F, de Oliveira L, Canal C. Virome of crab-eating (Cerdocyon thous) and pampas foxes (Lycalopex gymnocercus) from southern Brazil and Uruguay. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104421. [PMID: 32580027 PMCID: PMC7306396 DOI: 10.1016/j.meegid.2020.104421] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 01/16/2023]
Abstract
Crab-eating (Cerdocyon thous) and Pampas foxes (Lycalopex gymnocercus) are wild canids distributed in South America. Domestic dogs (Canis lupus familiaris) and wild canids may share viral pathogens, including rabies virus (RABV), canine distemper virus (CDV), and canine parvovirus 2 (CPV-2). To characterize the virome of these wild canid species, the present work evaluated the spleen and mesenteric lymph node virome of 17 crab-eating and five Pampas foxes using high-throughput sequencing (HTS). Organ samples were pooled and sequenced using an Illumina MiSeq platform. Additional PCR analyses were performed to identify the frequencies and host origin for each virus detected by HTS. Sequences more closely related to the Paramyxoviridae, Parvoviridae and Anelloviridae families were detected, as well as circular Rep-encoding single-stranded (CRESS) DNA viruses. CDV was found only in crab-eating foxes, whereas CPV-2 was found in both canid species; both viruses were closely related to sequences reported in domestic dogs from southern Brazil. Moreover, the present work reported the detection of canine bocavirus (CBoV) strains that were genetically divergent from CBoV-1 and 2 lineages. Finally, we also characterized CRESS DNA viruses and anelloviruses with marked diversity. The results of this study contribute to the body of knowledge regarding wild canid viruses that can potentially be shared with domestic canids or other species.
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Affiliation(s)
- M.N. Weber
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil,Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - A.C.S. Mosena
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - M.S. da Silva
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - R. Canova
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - C. de Lorenzo
- Setor de Patologia Veterinária, Faculdade de Veterinária, UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - J.C. Olegário
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - R.F. Budaszewski
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - L.F. Baumbach
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - J.F. Soares
- Laboratório Protozoologia e Riquettsioses Vetoriais, Faculdade de Veterinária, UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - L. Sonne
- Setor de Patologia Veterinária, Faculdade de Veterinária, UFRGS, Porto Alegre, Rio Grande do Sul, Brazil
| | - A.P.M. Varela
- Laboratório de Biologia Molecular, Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Secretaria da Agricultura, Pecuária eDesenvolvimento Rural do Rio Grande do Sul (SEAPDR-RS), Eldorado do Sul, Rio Grande do Sul, Brazil
| | - F.Q. Mayer
- Laboratório de Biologia Molecular, Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Secretaria da Agricultura, Pecuária eDesenvolvimento Rural do Rio Grande do Sul (SEAPDR-RS), Eldorado do Sul, Rio Grande do Sul, Brazil
| | - L.G.S. de Oliveira
- Plataforma de Salud Animal, Instituto Nacional de Investigación Agropecuaria (INIA) Tacuarembó, Tacuarembó, Uruguay
| | - C.W. Canal
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil,Corresponding author at: Av Bento Gonçalves 9090, Laboratório de Virologia, Faculdade de Veterinária, UFRGS, CEP 91540-000 Porto Alegre, Rio Grande do Sul, Brazil
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20
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Identification and full-genome sequencing of canine kobuvirus in canine fecal samples collected from Anhui Province, eastern China. Arch Virol 2020; 165:2495-2501. [PMID: 32776176 PMCID: PMC7415332 DOI: 10.1007/s00705-020-04773-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 07/09/2020] [Indexed: 11/29/2022]
Abstract
Canine kobuvirus (CaKoV), a newly described virus, is the causative agent of gastroenteritis in dogs. In this study, 57 fecal samples from dogs with diarrhea in Anhui Province, eastern China, were collected. Among these, five samples were identified to be infected with CaKoV, by polymerase chain reaction targeting the CaKoV 3D gene. The five CaKoV strains were subjected to phylogenetic analysis. The sequences of VP1 from the five CaKoV strains were 93.6%–96.1% identical to each other and 91.75%–97.95% identical to other reported CaKoV VP1 sequences. In addition, the complete genome of one strain was successfully amplified and sequenced. The genome consisted of 8223 nucleotides and shared 94.6%–97.0% nucleotide and 93.1%–94.0% amino acid sequence identity with other CaKoV isolates. Phylogenetic analysis revealed that the CaKoV strain from Anhui Province was similar to other Chinese strains, and it was more closely related to feline and mouse kobuviruses than to sheep and bovine kobuviruses. Interestingly, all of the CaKoV-positive samples were coinfected with canine parvovirus. The finding of CaKoV infection in dogs with diarrhea and coinfection with canine parvovirus are a cause for concern and highlight the need for management and preventive measures.
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21
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Wang Z, Jiang Y, Liu X, Lin W, Feng Q, Xin T, Guo X, Hou S, Zhu H, Jia H. Epidemiological and phylogenetic analysis of canine kobuviruses in Tangshan, China. Arch Virol 2020; 165:2317-2322. [PMID: 32643035 PMCID: PMC7341465 DOI: 10.1007/s00705-020-04727-y] [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: 02/15/2020] [Accepted: 06/04/2020] [Indexed: 12/05/2022]
Abstract
Canine kobuviruses (CaKoV) have been found in healthy and diarrheic dogs as well as asymptomatic wild carnivores in various countries. In order to investigate the prevalence and evolution of CaKoV in Tangshan, China, 82 dog fecal samples from pet hospitals in Tangshan were subjected to RT-PCR targeting a segment of the 3D gene of CaKoV. Using this method, we identified CaKoV in 14 samples (17.07%, 14/82). Of the CaKoV-positive samples, 78.57% (11/14) and 50% (7/14) were positive for canine parvovirus and canine coronavirus, respectively. The nucleotide sequences of the 14 strains 96.6%–100% identical to each other and 77.6%–99.2% identical to representative sequences from the NCBI GenBank database. We also amplified the 14 VP1 gene sequences and found that they were 93.3%–99.6% identical to each other and 73.3%–97.8% identical to representative sequences from the NCBI GenBank database. Phylogenetic analysis revealed that the 14 CaKoV strains from Tangshan are closely related to those identified in China and Thailand and display less similarity to those found in Africa, the United States, and Europe. Our data suggest that CaKoV circulated in young pet dogs in Tangshan and displays a high co-infection rate with CCoV and CPV. However, the relationship between the three viruses and their roles in the host requires further investigation.
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Affiliation(s)
- Zhaoyang Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Yajun Jiang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Xueting Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Weidong Lin
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Qianqian Feng
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Ting Xin
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Xiaoyu Guo
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Shaohua Hou
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Hongfei Zhu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Hong Jia
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China.
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22
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Wang R, Zhang W, Ye R, Pan Z, Li G, Su S. One-step multiplex TaqMan probe-based method for real-time PCR detection of four canine diarrhea viruses. Mol Cell Probes 2020; 53:101618. [PMID: 32534013 PMCID: PMC7286240 DOI: 10.1016/j.mcp.2020.101618] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 05/26/2020] [Accepted: 06/04/2020] [Indexed: 02/02/2023]
Abstract
Viral canine diarrhea has high morbidity and mortality and is prevalent worldwide, resulting in severe economic and spiritual losses to pet owners. However, diarrhea pathogens have similar clinical symptoms and are difficult to diagnose clinically. Thus, fast and accurate diagnostic methods are of great significance for prevention and accurate treatment. In this study, we developed a one-step multiplex TaqMan probe-based real-time PCR for the differential diagnosis of four viruses causing canine diarrhea including, CPV (Canine Parvovirus), CCoV (Canine Coronavirus), CAstV (Canine Astrovirus), and CaKoV (Canine Kobuviruses). The limit of detection was up to 102 copies/μL and performed well with high sensitivity and specificity. This assay was optimized and used to identify possible antagonistic relationships between viruses. From this, artificial pre-experiments were performed for mixed infections, and a total of 82 canine diarrhea field samples were collected from different animal hospitals in Zhejiang, China to assess the method. The virus prevalence was significantly higher than what previously reported based on RT-PCR (Reverse Transcription-Polymerase Chain Reaction). Taken together, these results suggest that the method can be used as a preferred tool for monitoring laboratory epidemics, timely prevention, and effective monitoring of disease progression.
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Affiliation(s)
- Ruyi Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Wenyan Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Rui Ye
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Zhongzhou Pan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Gairu Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Shuo Su
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.
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Turan T, Işıdan H. Molecular characterization of canine astrovirus, vesivirus and circovirus, isolated from diarrheic dogs in Turkey. IRANIAN JOURNAL OF VETERINARY RESEARCH 2020; 21:172-179. [PMID: 33178294 PMCID: PMC7608039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 03/02/2020] [Accepted: 06/24/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Canine astrovirus (CAstV) has been considered the primary cause of gastroenteritis in young animals worldwide, while canine vesivirus (CVeV) and canine circovirus (CCiV) are occasionally reported. AIMS This study aimed to investigate the existence and molecular characteristics for these three viruses in Turkey. Methods: Faecal samples from 150 shelter dogs with gastrointestinal problems (127 adults and 23 puppies) were collected and examined by reverse transcription-polymerase chain reaction (RT-PCR) analysis based on the partial sequence of RdRp gene (ORF1b) for CAstV, ORF2 gene of CVeV and capsid protein (Cap) and replication associated protein (Rep) gene of CCiV. Randomly selected positive samples were submitted to sequencing and molecular analyses were conducted based on partial sequences. RESULTS It was found that 66% (99/150) of diarrhoeic dogs were positive for CAstV, 3.33% (5/150) for CVeV, and 6% (9/150) for CCiV. Four sub-genotypes for CAstV and two sub-genotypes for CVeV were suggested according to molecular analyses. The phylogenetic relationship of CCiV with other strains obtained from various areas was further demonstrated. CONCLUSION This study emphasizes the importance of emerging viruses for canids, classification of them and their proportional contribution in gastroenteritis cases. We concluded that astrovirus infection must be considered as the major cause of diarrhea in dogs; However, the prevalences of vesivirus and circovirus were relatively low in cases makes them less important in Turkey.
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Affiliation(s)
| | - H. Işıdan
- Virology Department, Faculty of Veterinary Medicine, Sivas Cumhuriyet University, 58140, Sivas, Turkey
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24
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Kaszab E, Doszpoly A, Lanave G, Verma A, Bányai K, Malik YS, Marton S. Metagenomics revealing new virus species in farm and pet animals and aquaculture. GENOMICS AND BIOTECHNOLOGICAL ADVANCES IN VETERINARY, POULTRY, AND FISHERIES 2020. [PMCID: PMC7149329 DOI: 10.1016/b978-0-12-816352-8.00002-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Viral metagenomics is slowly taking over the traditional and widely used molecular techniques for the investigation of pathogenic viruses responsible for illness and inflicting great economic burden on the farm animal industry. Owing to the continued improvements in sequencing technologies and the dramatic reduction of per base costs of sequencing the use of next generation sequencing have been key factors in this progress. Discoveries linked to viral metagenomics are expected to be beneficial to the field of veterinary medicine starting from the development of better diagnostic assays to the design of new subunit vaccines with minimal investments. With these achievements the research has taken a giant leap even toward the better healthcare of animals and, as a result, the animal sector could be growing at an unprecedented pace.
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25
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Zeghbib S, Herczeg R, Kemenesi G, Zana B, Kurucz K, Urbán P, Madai M, Földes F, Papp H, Somogyi B, Jakab F. Genetic characterization of a novel picornavirus in Algerian bats: co-evolution analysis of bat-related picornaviruses. Sci Rep 2019; 9:15706. [PMID: 31673141 PMCID: PMC6823487 DOI: 10.1038/s41598-019-52209-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/15/2019] [Indexed: 12/13/2022] Open
Abstract
Bats are reservoirs of numerous zoonotic viruses. The Picornaviridae family comprises important pathogens which may infect both humans and animals. In this study, a bat-related picornavirus was detected from Algerian Minioptreus schreibersii bats for the first time in the country. Molecular analyses revealed the new virus originates to the Mischivirus genus. In the operational use of the acquired sequence and all available data regarding bat picornaviruses, we performed a co-evolutionary analysis of mischiviruses and their hosts, to authentically reveal evolutionary patterns within this genus. Based on this analysis, we enlarged the dataset, and examined the co-evolutionary history of all bat-related picornaviruses including their hosts, to effectively compile all possible species jumping events during their evolution. Furthermore, we explored the phylogeny association with geographical location, host-genus and host-species in both data sets.
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Affiliation(s)
- Safia Zeghbib
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Róbert Herczeg
- Bioinformatics Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Gábor Kemenesi
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Brigitta Zana
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Kornélia Kurucz
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Péter Urbán
- Bioinformatics Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Mónika Madai
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Fanni Földes
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Henrietta Papp
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Balázs Somogyi
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Ferenc Jakab
- Virological Research Group, BSL-4 Laboratory, Szentágothai Research Centre, University of Pécs, Pécs, Hungary.
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary.
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Di Martino B, Di Profio F, Melegari I, Marsilio F. Feline Virome-A Review of Novel Enteric Viruses Detected in Cats. Viruses 2019; 11:v11100908. [PMID: 31575055 PMCID: PMC6832874 DOI: 10.3390/v11100908] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/28/2019] [Accepted: 09/28/2019] [Indexed: 12/13/2022] Open
Abstract
Recent advances in the diagnostic and metagenomic investigations of the feline enteric environment have allowed the identification of several novel viruses that have been associated with gastroenteritis in cats. In the last few years, noroviruses, kobuviruses, and novel parvoviruses have been repetitively detected in diarrheic cats as alone or in mixed infections with other pathogens, raising a number of questions, with particular regards to their pathogenic attitude and clinical impact. In the present article, the current available literature on novel potential feline enteric viruses is reviewed, providing a meaningful update on the etiology, epidemiologic, pathogenetic, clinical, and diagnostic aspects of the infections caused by these pathogens.
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Affiliation(s)
- Barbara Di Martino
- Laboratory of Infectious Diseases, Faculty of Veterinary Medicine, University of Teramo, 64100 Teramo, Italy.
| | - Federica Di Profio
- Laboratory of Infectious Diseases, Faculty of Veterinary Medicine, University of Teramo, 64100 Teramo, Italy.
| | - Irene Melegari
- Laboratory of Infectious Diseases, Faculty of Veterinary Medicine, University of Teramo, 64100 Teramo, Italy.
| | - Fulvio Marsilio
- Laboratory of Infectious Diseases, Faculty of Veterinary Medicine, University of Teramo, 64100 Teramo, Italy.
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27
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Katsuta R, Sunaga F, Oi T, Doan YH, Tsuzuku S, Suzuki Y, Sano K, Katayama Y, Omatsu T, Oba M, Furuya T, Ouchi Y, Shirai J, Mizutani T, Oka T, Nagai M. First identification of Sapoviruses in wild boar. Virus Res 2019; 271:197680. [PMID: 31398366 DOI: 10.1016/j.virusres.2019.197680] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/01/2019] [Accepted: 08/01/2019] [Indexed: 01/14/2023]
Abstract
Sapoviruses (SaVs) are enteric viruses that have been detected in human and animals previously; however, SaVs have not been identified in wild boar yet. Using a metagenomics approach, we identified SaVs in fecal samples of free-living wild boars in Japan for the first time. Six of the 48 specimens identified belonged to one genogroup (G)III, one GV and four GVI SaV sequence reads. We successfully determined complete genome of GV and GVI SaV strains using the long reverse transcription PCR strategy and the 5' rapid amplification of cDNA end method. Phylogenetic tree analysis and pairwise distance calculation revealed that GV SaV detected from wild boar was related to recently assigned GV.5 strains from pig, while GVI SaV was assigned to a new genotype within GVI. Moreover, wild boar may act as a reservoir for transmission of SaVs to the pig population (and vice versa) because GIII, GV, and GVI SaVs were all detected in pigs previously.
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Affiliation(s)
- Risako Katsuta
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa 252-5201, Japan
| | - Fujiko Sunaga
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa 252-5201, Japan
| | - Toru Oi
- Faculty of Bioresources and Environmental Science, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
| | - Yen Hai Doan
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo 208-0011, Japan
| | - Satoko Tsuzuku
- Kenpoku Livestock Hygiene Service Center, Mito, Ibaraki 310-0002, Japan
| | - Yoshihisa Suzuki
- Mie Chuo Livestock Hygiene Service Center, Tsu, Mie 514-0061, Japan
| | - Kaori Sano
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan; Department of Pathology, National Institute of Infectious Diseases, Shinjuku, Tokyo 162-0052, Japan
| | - Yukie Katayama
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Tsutomu Omatsu
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Mami Oba
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Tetsuya Furuya
- Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Yoshinao Ouchi
- Kenpoku Livestock Hygiene Service Center, Mito, Ibaraki 310-0002, Japan
| | - Junsuke Shirai
- Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Tetsuya Mizutani
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Tomoichiro Oka
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo 208-0011, Japan.
| | - Makoto Nagai
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa 252-5201, Japan; Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.
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28
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Charoenkul K, Janetanakit T, Chaiyawong S, Bunpapong N, Boonyapisitsopa S, Tangwangvivat R, Amonsin A. First detection and genetic characterization of canine Kobuvirus in domestic dogs in Thailand. BMC Vet Res 2019; 15:254. [PMID: 31324182 PMCID: PMC6642606 DOI: 10.1186/s12917-019-1994-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/04/2019] [Indexed: 11/30/2022] Open
Abstract
Background Canine Kobuvirus (CaKoV) has been detected both in healthy and diarrheic dogs and in asymptomatic wild carnivores. In this study, we conducted a survey of CaKoV at small animal hospitals in Bangkok and vicinity of Thailand during September 2016 to September 2018. Results Three hundred and seven rectal swab samples were collected from healthy dogs (n = 55) and dogs with gastroenteritis symptoms (n = 252). Of 307 swab samples tested by using one-step RT-PCR specific to 3D gene, we found CaKoV positivity at 17.59% (54/307). CaKoVs could be detected in both sick (19.44%) and healthy (9.09%) animals. In relation to age group, CaKoV could be frequently detected in younger dogs (25.45%). Our result showed no seasonal pattern of CaKoV infection in domestic dogs. In this study, we characterized CaKoVs by whole genome sequencing (n = 4) or 3D and VP1 gene sequencing (n = 8). Genetic and phylogenetic analyses showed that whole genomes of Thai CaKoVs were closely related to Chinese CaKoVs with highest 99.5% amino acid identity suggesting possible origin of CaKoVs in Thailand. Conclusions In conclusion, this study was the first to report the detection and genetic characteristics of CaKoVs in domestic dogs in Thailand. CaKoVs could be detected in both sick and healthy dogs. The virus is frequently detected in younger dogs. Thai CaKoVs were genetically closely related and grouped with Chinese CaKoVs. Our result raises the concerns to vet practitioners that diarrhea in dogs due to canine Kobuvirus infection should not be ignored. Electronic supplementary material The online version of this article (10.1186/s12917-019-1994-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kamonpan Charoenkul
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Taveesak Janetanakit
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Supassama Chaiyawong
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Napawan Bunpapong
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Veterinary Diagnostic Laboratory, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Supanat Boonyapisitsopa
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Ratanaporn Tangwangvivat
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Alongkorn Amonsin
- Center of Excellence for Emerging and Re-emerging Infectious Diseases in Animals, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand. .,Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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29
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Melegari I, Di Profio F, Palombieri A, Sarchese V, Diakoudi G, Robetto S, Orusa R, Marsilio F, Bányai K, Martella V, Di Martino B. Molecular detection of canine bufaviruses in wild canids. Arch Virol 2019; 164:2315-2320. [PMID: 31168750 PMCID: PMC7086671 DOI: 10.1007/s00705-019-04304-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 05/03/2019] [Indexed: 11/27/2022]
Abstract
Novel protoparvoviruses genetically related to human and non-human primate bufaviruses (BuVs) have been detected recently in respiratory and enteric specimens collected from dogs and cats. In this study, by molecular screening of archival collections of faecal samples from wolves and foxes, we detected BuVs with a rate of 17.1% (7/41) and 10.5% (9/86), respectively. Sequence analysis of a portion of the ORF2 gene region of nine positive samples showed that the viruses in these samples were closely related to BuVs (97.5–99.0% nucleotide sequence identity) found in domestic carnivores.
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Affiliation(s)
- Irene Melegari
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Piazza Aldo Moro, 45, 64100, Teramo, Italy
| | - Federica Di Profio
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Piazza Aldo Moro, 45, 64100, Teramo, Italy
| | - Andrea Palombieri
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Piazza Aldo Moro, 45, 64100, Teramo, Italy
| | - Vittorio Sarchese
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Piazza Aldo Moro, 45, 64100, Teramo, Italy
| | - Georgia Diakoudi
- Faculty of Veterinary Medicine, Università Aldo Moro di Bari, Valenzano, Italy
| | - Serena Robetto
- Istituto Zooprofilattico Sperimentale del Piemonte, della Liguria e della Valle d'Aosta, Torino, Italy
| | - Riccardo Orusa
- Istituto Zooprofilattico Sperimentale del Piemonte, della Liguria e della Valle d'Aosta, Torino, Italy
| | - Fulvio Marsilio
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Piazza Aldo Moro, 45, 64100, Teramo, Italy
| | - Kristián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Vito Martella
- Faculty of Veterinary Medicine, Università Aldo Moro di Bari, Valenzano, Italy
| | - Barbara Di Martino
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Piazza Aldo Moro, 45, 64100, Teramo, Italy.
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Miyabe FM, Ribeiro J, Alfieri AF, Alfieri AA. Detection of canine kobuvirus RNA in diarrheic fecal samples of dogs with parvoviruses. Braz J Microbiol 2019; 50:871-874. [PMID: 31140097 PMCID: PMC6863268 DOI: 10.1007/s42770-019-00095-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/20/2019] [Indexed: 12/11/2022] Open
Abstract
Canine kobuvirus (CaKV) is a member of the Picornaviridae family and the Kobuvirus genus. CaKV was first described in fecal samples from diarrheic dogs in the USA in 2011, with subsequent reports in the UK, Italy, South Korea, China, Tanzania, and Japan. CaKV is frequently identified in feces of animals with or without clinical signs of gastroenteritis. The present study investigated the presence of CaKV in fecal samples from 53 diarrheic dogs from Londrina, southern Brazil. Using a RT-PCR assay, CaKV RNA was identified in three dogs, resulting in an overall occurrence rate of 5.7%. In addition, coinfection with canine parvovirus subtype 2b was detected in all CaKV-positive diarrheic fecal samples. Using a phylogenetic analysis based on the VP1 gene sequence, the Brazilian CaKV field strains were found to be very similar to a previously identified CaKV strain from Brazil that was found in the tissue of a puppy and were also found to be clustered with other CaKV strains detected worldwide and other kobuvirus strains identified in mouse, feline, and human hosts.
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Affiliation(s)
- Flavia Megumi Miyabe
- Laboratory of Animal Virology, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid - Campus Universitário, PO Box 10011, Londrina, PR, 86057-970, Brazil.,Multi-User Animal Health Laboratory, Molecular Biology Unit, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid - Campus Universitário, PO Box 10011, Londrina, PR, 86057-970, Brazil
| | - Juliane Ribeiro
- Laboratory of Animal Virology, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid - Campus Universitário, PO Box 10011, Londrina, PR, 86057-970, Brazil.,Multi-User Animal Health Laboratory, Molecular Biology Unit, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid - Campus Universitário, PO Box 10011, Londrina, PR, 86057-970, Brazil
| | - Alice Fernandes Alfieri
- Laboratory of Animal Virology, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid - Campus Universitário, PO Box 10011, Londrina, PR, 86057-970, Brazil.,Multi-User Animal Health Laboratory, Molecular Biology Unit, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid - Campus Universitário, PO Box 10011, Londrina, PR, 86057-970, Brazil
| | - Amauri Alcindo Alfieri
- Laboratory of Animal Virology, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid - Campus Universitário, PO Box 10011, Londrina, PR, 86057-970, Brazil. .,Multi-User Animal Health Laboratory, Molecular Biology Unit, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid - Campus Universitário, PO Box 10011, Londrina, PR, 86057-970, Brazil.
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31
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Bhatta TR, Chamings A, Vibin J, Alexandersen S. Detection and characterisation of canine astrovirus, canine parvovirus and canine papillomavirus in puppies using next generation sequencing. Sci Rep 2019; 9:4602. [PMID: 30872719 PMCID: PMC6418273 DOI: 10.1038/s41598-019-41045-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/27/2019] [Indexed: 12/22/2022] Open
Abstract
Gastroenteritis in young animals is a clinical presentation with many infectious and non- infectious aetiologies. We used next generation sequencing (NGS) to investigate the possible infectious causes of gastroenteritis in puppies from a dog kennel in Victoria, Australia. The near complete genome of a canine astrovirus was obtained from pooled faecal samples, and was found to be 94.7% identical with a canine astrovirus detected in the United Kingdom in 2012. The phylogenetic analysis of the capsid gene found similarities to those of canine astroviruses identified in Italy in 2005 and in UK and Hungary in 2012, but distant from that of a canine astrovirus previously identified in Australia in 2012. Thus, different serotypes of canine astrovirus are likely circulating in Australia. The close relationship to European astroviruses also suggested that there had been recent movements of ancestor canine astroviruses between Australia and Europe. NGS also detected other infections in the puppies including several canine papillomaviruses and a canine parvovirus (vaccine strain) as well as a very low level of campylobacter. Canine astrovirus was the probable cause of diarrhoea in these puppies, with the possible involvement of campylobacter bacteria. NGS was effective as a non-targeted method to determine the likely infectious cause of gastroenteritis.
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Affiliation(s)
- Tarka Raj Bhatta
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, 3220, Australia.,Deakin University, School of Medicine, Geelong, VIC, 3220, Australia
| | - Anthony Chamings
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, 3220, Australia.,Deakin University, School of Medicine, Geelong, VIC, 3220, Australia
| | - Jessy Vibin
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, 3220, Australia.,Deakin University, School of Medicine, Geelong, VIC, 3220, Australia
| | - Soren Alexandersen
- Geelong Centre for Emerging Infectious Diseases, Geelong, VIC, 3220, Australia. .,Deakin University, School of Medicine, Geelong, VIC, 3220, Australia. .,Barwon Health, University Hospital Geelong, Geelong, VIC, 3220, Australia.
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32
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Salamunova S, Jackova A, Mandelik R, Novotny J, Vlasakova M, Vilcek S. Molecular detection of enteric viruses and the genetic characterization of porcine astroviruses and sapoviruses in domestic pigs from Slovakian farms. BMC Vet Res 2018; 14:313. [PMID: 30340595 PMCID: PMC6194665 DOI: 10.1186/s12917-018-1640-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 10/02/2018] [Indexed: 11/11/2022] Open
Abstract
Background Surveillance and characterization of pig enteric viruses such as transmissible gastroenteritis virus (TGEV), porcine epidemic diarrhea virus (PEDV), rotavirus, astrovirus (PAstV), sapovirus (PSaV), kobuvirus and other agents is essential to evaluate the risks to animal health and determination of economic impacts on pig farming. This study reports the detection and genetic characterization of PAstV, PSaV in healthy and diarrheic domestic pigs and PEDV and TGEV in diarrheic pigs of different age groups. Results The presence of PAstV and PSaV was studied in 411 rectal swabs collected from healthy (n = 251) and diarrheic (n = 160) pigs of different age categories: suckling (n = 143), weaned (n = 147) and fattening (n = 121) animals on farms in Slovakia. The presence of TGEV and PEDV was investigated in the diarrheic pigs (n = 160). A high presence of PAstV infections was detected in both healthy (94.4%) and diarrheic (91.3%) pigs. PSaV was detected less often, but also equally in clinically healthy (8.4%) and diarrheic (10%) pigs. Neither TGEV nor PEDV was detected in any diarrheic sample. The phylogenetic analysis of a part of the RdRp region revealed the presence of all five lineages of PAstV in Slovakia (PAstV-1 – PAstV-5), with the most frequent lineages being PAstV-2 and PAstV-4. Analysis of partial capsid genome sequences of the PSaVs indicated that virus strains belonged to genogroup GIII. Most of the PSaV sequences from Slovakia clustered with sequences originating from neighbouring countries. Conclusions Due to no significant difference between healthy and diarrheic pigs testing of the presence of PAstV and PSaV provides no diagnostic value. Genetic diversity of PAstV was very high as all five lineages were identified in pig farms in Slovakia. PSaV strains were genetically related to the strains circulating in Central European region.
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Affiliation(s)
- Slavomira Salamunova
- University of Veterinary Medicine and Pharmacy, Komenskeho 73, 040 00, Kosice, Slovakia
| | - Anna Jackova
- University of Veterinary Medicine and Pharmacy, Komenskeho 73, 040 00, Kosice, Slovakia
| | - Rene Mandelik
- University of Veterinary Medicine and Pharmacy, Komenskeho 73, 040 00, Kosice, Slovakia
| | - Jaroslav Novotny
- University of Veterinary Medicine and Pharmacy, Komenskeho 73, 040 00, Kosice, Slovakia
| | - Michaela Vlasakova
- University of Veterinary Medicine and Pharmacy, Komenskeho 73, 040 00, Kosice, Slovakia
| | - Stefan Vilcek
- University of Veterinary Medicine and Pharmacy, Komenskeho 73, 040 00, Kosice, Slovakia.
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33
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Characterization of dog serum virome from Northeastern Brazil. Virology 2018; 525:192-199. [PMID: 30292963 DOI: 10.1016/j.virol.2018.09.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/26/2018] [Accepted: 09/26/2018] [Indexed: 11/24/2022]
Abstract
Domestic dogs share habitats with human, a fact that makes them a potential source of zoonotic viruses. Moreover, knowledge regarding possible bloodborne pathogens is important due to the increasing application of blood transfusion in dogs. In the present study, we evaluated the serum virome of 520 dogs using throughput sequencing (HTS). The serum samples were pooled and sequenced using an Illumina MiSeq platform. Our unbiased method identified prevalent canine pathogens as canine protoparvovirus 1 (canine parvovirus 2), undersearched agents as canine bocaparvovirus 1 (minute virus of canines) and canine circovirus, circular viruses closely related to viruses recently found in human samples, and new parvovirus and anelloviruses. The dog virome described in the present work furthers the knowledge concerning the viral population in domestic animals. The present data includes information regarding viral agents that are potentially transmitted through blood transfusion among dogs.
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Seroprevalence of sapovirus in dogs using baculovirus-expressed virus-like particles. Virus Res 2018; 251:1-5. [PMID: 29698676 DOI: 10.1016/j.virusres.2018.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/17/2018] [Accepted: 04/20/2018] [Indexed: 11/23/2022]
Abstract
Caliciviruses of the Sapovirus genus have been recently detected in dogs. Canine sapoviruses (SaVs) have been identified in the stools of young or juvenile animals with gastro-enteric disease at low prevalence (2.0-2.2%), but whether they may have a role as enteric pathogens and to which extent dogs are exposed to SaVs remains unclear. Here, we report the expression in a baculovirus system of virus like-particles (VLPs) of a canine SaV strain, the prototype virus Bari/4076/2007/ITA. The recombinant antigen was used to develop an enzyme-linked immunosorbent assay (ELISA). By screening an age-stratified collection of serum samples from 516 dogs in Italy, IgG antibodies specific for the canine SaV VLPs were detected in 40.3% (208/516) of the sera. Also, as observed for SaV infection in humans, we observed a positive association between seropositivity and age, with the highest prevalence rates in dogs older than 4 years of age.
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35
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Moreno PS, Wagner J, Kirkwood CD, Gilkerson JR, Mansfield CS. Characterization of the fecal virome in dogs with chronic enteropathy. Vet Microbiol 2018; 221:38-43. [PMID: 29981706 DOI: 10.1016/j.vetmic.2018.05.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/18/2018] [Accepted: 05/29/2018] [Indexed: 01/21/2023]
Abstract
The fecal virome has been investigated in humans and various animal species using next generation sequencing. However, limited information is available about the fecal virome of dogs with chronic enteropathy (CE). We aimed to characterize the canine fecal virome of dogs with CE and compare it with the virome of previously analyzed healthy dogs.A total of 16 adult dogs; 8 healthy dogs (data from a parallel study) and 8 dogs with CE had fecal samples assessed by viral shotgun sequencing. Fecal samples were subjected to enrichment of viral nucleic acids prior to sequencing and metagenomic analyses. Characterization of the complete genome of a canine kobuvirus was performed by Sanger sequencing. An additional 21 healthy dogs and 14 dogs with CE were further analyzed for the prevalence of canine kobuvirus.Three fecal samples from dogs with CE contained in total 3 eukaryotic viral families. In contrast, 4/8 fecal samples previously identified from healthy dogs, contained 5 eukaryotic viral families with 2 families exclusive to this group. Bacteriophages were identified in all fecal samples from CE and healthy dogs. Canine kobuvirus was identified in one dog with CE, by shotgun sequencing, and the complete genome was then characterized. This kobuvirus was classified within canine kobuvirus group, being similar to strains from Korea and China. The larger prevalence study did not detect additional samples positive for canine kobuvirus. The fecal virome of dogs with CE differs in number and type of viral families from healthy dogs. The first Australian canine kobuvirus sequence was identified and characterized from a dog with CE.
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Affiliation(s)
- Paloma S Moreno
- Enteric Viruses Group, Murdoch Children's Research Institute, VIC, Australia; Translational Research and Animal Clinical Trial Study (TRACTS) group, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, VIC, Australia.
| | - Josef Wagner
- Enteric Viruses Group, Murdoch Children's Research Institute, VIC, Australia; Department of Pediatrics, The University of Melbourne, VIC, Australia
| | - Carl D Kirkwood
- Department of Pediatrics, The University of Melbourne, VIC, Australia
| | - James R Gilkerson
- Centre for Equine Infectious Diseases, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, VIC, Australia
| | - Caroline S Mansfield
- Translational Research and Animal Clinical Trial Study (TRACTS) group, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, VIC, Australia
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Terio V, Bottaro M, Di Pinto A, Fusco G, Barresi T, Tantillo G, Martella V. Occurrence of Aichi virus in retail shellfish in Italy. Food Microbiol 2018; 74:120-124. [PMID: 29706327 DOI: 10.1016/j.fm.2018.02.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 02/05/2018] [Accepted: 02/15/2018] [Indexed: 11/25/2022]
Abstract
AiV-1 is considered an emerging human enteric pathogens and foodborne transmission has been documented as an important source of exposure for humans, chiefly in relation to non-safe, risky food habits. We surveyed the presence of AiV-1 in retail shellfish, including oysters and mussles, identifying the virus in 3/170 (1.8%) of the analysed samples. The AiV-1 positive samples were of different geographic origin. Upon sequence analysis of a portion of the 3CD junction region, two AiV strains identified from harvesting areas in Northern Italy were characterised as genotype B and displayed 99-100% identity at the nucleotide level to other AiV-1 strains detected in sewages in Central Italy in 2012, suggesting that such strains are stably circulating in Italian ecosystems. Interestingly, a strain identified from mussles harvested in Southern Italy could not be characterised firmly, as inferred in the Bayesian analysis and by sequence comparison, indicating that different AiV strains are also circulating in Italy. Viral contamination in retail shellfish challenges the microbiological guidelines for food control and requires the development and optimization of additional diagnostic and prevention strategies.
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Affiliation(s)
- Valentina Terio
- Department of Veterinary Medicine (DiMeV), University of Bari, Provincial Road to Casamassima km 3, 70010, Valenzano (Ba), Italy.
| | - Marilisa Bottaro
- Department of Veterinary Medicine (DiMeV), University of Bari, Provincial Road to Casamassima km 3, 70010, Valenzano (Ba), Italy
| | - Angela Di Pinto
- Department of Veterinary Medicine (DiMeV), University of Bari, Provincial Road to Casamassima km 3, 70010, Valenzano (Ba), Italy
| | - Giovanna Fusco
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Division of Caserta, Via Jervolino n. 19, 81029, Caserta, Italy
| | - Teodosio Barresi
- Department of Veterinary Medicine (DiMeV), University of Bari, Provincial Road to Casamassima km 3, 70010, Valenzano (Ba), Italy
| | - Giuseppina Tantillo
- Department of Veterinary Medicine (DiMeV), University of Bari, Provincial Road to Casamassima km 3, 70010, Valenzano (Ba), Italy
| | - Vito Martella
- Department of Veterinary Medicine (DiMeV), University of Bari, Provincial Road to Casamassima km 3, 70010, Valenzano (Ba), Italy
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Caddy SL. New viruses associated with canine gastroenteritis. Vet J 2018; 232:57-64. [PMID: 29428093 PMCID: PMC7110870 DOI: 10.1016/j.tvjl.2017.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 11/28/2017] [Accepted: 12/09/2017] [Indexed: 01/10/2023]
Abstract
A number of novel viruses have been associated with canine gastroenteritis in recent years, from viral families as diverse as Caliciviridae and Picornaviridae to Parvoviridae and Circoviridae. The ability of many of these viruses to cause disease is uncertain, but epidemiological studies are continually adding to our knowledge of these potential pathogens. This review presents a summary of the latest research and current understanding of novel viruses associated with canine gastroenteritis.
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Affiliation(s)
- S L Caddy
- Magdalene College, University of Cambridge, Cambridge, UK; Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
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38
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Liu D, Liu F, Guo D, Hu X, Li Z, Li Z, Ma J, Liu C. One-step triplex PCR/RT-PCR to detect canine distemper virus, canine parvovirus and canine kobuvirus. J Vet Med Sci 2018; 81:1040-1042. [PMID: 29367517 PMCID: PMC6656820 DOI: 10.1292/jvms.17-0442] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
To rapidly distinguish Canine distemper virus (CDV), canine parvovirus (CPV), and canine kobuvirus (CaKoV) in practice, a one-step multiplex PCR/RT-PCR assay was developed, with detection
limits of 102.1 TCID50 for CDV, 101.9 TCID50 for CPV and 103 copies for CaKoV. This method did not amplify nonspecific DNA or RNA from
other canine viruses. Therefore, the assay provides a sensitive tool for the rapid clinical detection and epidemiological surveillance of CDV, CPV and CaKoV in dogs.
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Affiliation(s)
- Dafei Liu
- College of Wildlife Resources, Northeast Forestry University, Harbin, Heilongjiang 150040, China.,State Key Lab of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Fei Liu
- Shanghai Hile Bio-Pharmaceutical Co., Ltd., Shanghai, 201403, China
| | - Dongchun Guo
- State Key Lab of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Xiaoliang Hu
- State Key Lab of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Zhijie Li
- State Key Lab of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Zhigang Li
- Wendengying Veterinary Station, Weihai, Shandong 264413, China
| | - Jianzhang Ma
- College of Wildlife Resources, Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Chunguo Liu
- State Key Lab of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
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Greninger AL. A decade of RNA virus metagenomics is (not) enough. Virus Res 2018; 244:218-229. [PMID: 29055712 PMCID: PMC7114529 DOI: 10.1016/j.virusres.2017.10.014] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 10/14/2017] [Accepted: 10/17/2017] [Indexed: 12/16/2022]
Abstract
It is hard to overemphasize the role that metagenomics has had on our recent understanding of RNA virus diversity. Metagenomics in the 21st century has brought with it an explosion in the number of RNA virus species, genera, and families far exceeding that following the discovery of the microscope in the 18th century for eukaryotic life or culture media in the 19th century for bacteriology or the 20th century for virology. When the definition of success in organism discovery is measured by sequence diversity and evolutionary distance, RNA viruses win. This review explores the history of RNA virus metagenomics, reasons for the successes so far in RNA virus metagenomics, and methodological concerns. In addition, the review briefly covers clinical metagenomics and environmental metagenomics and highlights some of the critical accomplishments that have defined the fast pace of RNA virus discoveries in recent years. Slightly more than a decade in, the field is exhausted from its discoveries but knows that there is yet even more out there to be found.
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Affiliation(s)
- Alexander L Greninger
- Virology Division, Department of Laboratory Medicine, University of Washington, Seattle, WA, United States; Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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40
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Abstract
Next-generation sequencing has opened avenues to studying complex populations such as the bacteriome (all bacteria), mycobiome (all fungi), and virome (all viruses in a given sample). Viromes are less often investigated as compared to bacteriomes. The reasons are mostly methodological: because no common pan-viral sequence signature exists, metagenomic sequencing remains the only option. This brings about the need of laborious virus enrichment, multiple signal amplification steps with virtually no possibility of interim quality control, and complicated bioinformatic analysis of the ensuing sequence data. Nevertheless, over the past decade virome sequencing has been enormously successful in identifying new agents in human and animal diseases, and in characterizing viruses in various ecological niches. Recently, virome sequencing has been also employed in studies of non-infectious diseases, which has brought about new challenges of sensitivity, costs, and reproducibility in testing of large sets of samples. Here, we present a detailed protocol that has been utilized in virome studies where hundreds of samples had to be reliably tested in order to assess the association of the stool virome with susceptibility to type 1 diabetes, a non-infectious autoimmune disease.
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Affiliation(s)
- Lenka Kramná
- Department of Pediatrics, Second Faculty of Medicine, Charles University, Prague, Czech Republic
- Department of Medical Microbiology, Second Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ondřej Cinek
- Department of Pediatrics, Second Faculty of Medicine, Charles University, Prague, Czech Republic.
- Department of Medical Microbiology, Second Faculty of Medicine, Charles University, Prague, Czech Republic.
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Yang B, Yang B, Shan X, Li B, Ma X, Yin X, Zhang Y, Liu Y, Lan X. Short communication: Immune responses in sows induced by porcine sapovirus virus-like particles reduce viral shedding in suckled piglets. Res Vet Sci 2017; 117:196-199. [PMID: 29294432 DOI: 10.1016/j.rvsc.2017.12.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 12/14/2017] [Accepted: 12/26/2017] [Indexed: 11/16/2022]
Abstract
Porcine sapovirus (PoSaV) is a potential threat to public health owing to its capacity for reassortment with human sapovirus strains. However, there is still no vaccine available for the prevention and control of this infectious disease. In this study, we developed PoSaV virus-like particles (VLPs) using a baculovirus expression system. Immunization with PoSaV VLPs induced high titers of serum antibody specific for VP1 in sows. The results of our challenge study demonstrated that maternally-derived antibodies (MDA) induced by VLP immunization dramatically reduced viral shedding of PoSaV in the feces of next generation piglets. Therefore, the results of this study indicate that the immune responses of sows elicited by PoSaV VLPs can inhibit in vivo viral replication in their offspring and represent a promising strategy for developing vaccines against PoSaV.
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Affiliation(s)
- Bo Yang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China; College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Bin Yang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.
| | - Xingna Shan
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Baoyu Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China
| | - Xiaojun Ma
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiangping Yin
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.
| | - Yun Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.
| | - Yongsheng Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.
| | - Xi Lan
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, China.
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42
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Gomez DE, Weese JS. Viral enteritis in calves. THE CANADIAN VETERINARY JOURNAL = LA REVUE VETERINAIRE CANADIENNE 2017; 58:1267-1274. [PMID: 29203935 PMCID: PMC5680732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A complex community of bacteria, viruses, fungi, protists, and other microorganisms inhabit the gastrointestinal tract of calves and play important roles in gut health and disease. The viral component of the microbiome (the virome) is receiving increasing attention for its role in neonatal calf diarrhea (NCD). Rotavirus and coronavirus have for a long time been associated with NCD and commercial vaccines have been produced against these agents. Recently, several other viruses which may play a role in diarrhea have been discovered in calf fecal samples, mostly by sequence-based methods. These viruses include torovirus, norovirus, nebovirus, astrovirus, kobuvirus, and enterovirus. Most studies have involved epidemiologic investigations seeking to show association with diarrhea for each virus alone or in combination with potential pathogens. However, determining the contribution of these viruses to calf diarrhea has been challenging and much uncertainty remains concerning their roles as primary pathogens, co-infection agents, or commensals.
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Affiliation(s)
- Diego E. Gomez
- Address all correspondence to Dr. Diego E. Gomez; e-mail:
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43
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Prevalence and genomic characteristics of canine kobuvirus in southwest China. Arch Virol 2017; 163:459-466. [DOI: 10.1007/s00705-017-3648-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 10/02/2017] [Indexed: 10/18/2022]
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Melegari I, Sarchese V, Di Profio F, Robetto S, Carella E, Bermudez Sanchez S, Orusa R, Martella V, Marsilio F, Di Martino B. First molecular identification of kobuviruses in wolves (Canis lupus) in Italy. Arch Virol 2017; 163:509-513. [PMID: 29101539 PMCID: PMC7086812 DOI: 10.1007/s00705-017-3637-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/20/2017] [Indexed: 11/28/2022]
Abstract
Canine kobuviruses (CaKoVs) were first identified in diarrhoeic and asymptomatic dogs in 2011 in the USA. Subsequent studies have demonstrated a worldwide distribution of these viruses, but it is not clear if CaKoVs play a role as enteric pathogens of dogs. More recently, CaKoV RNA has been detected in wild carnivores, including red fox, golden jackal, side-striped jackal and spotted hyena. In this study, we addressed the hypothesis that wolves are susceptible to CaKoV infections. A total of 185 wolf stool samples were collected from necropsied animals and from transects in the Liguria, Piemonte and Valle D'Aosta regions of Italy, and CaKoV RNA was identified in two of these specimens. Both samples were obtained from necropsied wolves, with a prevalence rate of 4.9% (2/41). Sequence analysis of the full-length VP1 region showed that these strains displayed the highest nucleotide (nt) sequence identity (86.3-98.5%) to canine strains identified in the UK and Africa, and to kobuviruses that were previously detected in other African wild carnivores. This suggests that genetically related CaKoV strains circulate in domestic and wild carnivores, with interspecies transmission being not uncommon among carnivores of different ecosystems.
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Affiliation(s)
- Irene Melegari
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Piazza Aldo Moro, 45, 64100, Teramo, Italy
| | - Vittorio Sarchese
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Piazza Aldo Moro, 45, 64100, Teramo, Italy
| | - Federica Di Profio
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Piazza Aldo Moro, 45, 64100, Teramo, Italy
| | - Serena Robetto
- Centro di Referenza Nazionale per le Malattie degli Animali Selvatici (CeRMAS), Istituto Zooprofilattico Sperimentale del Piemonte, della Liguria e della Valle d'Aosta, Aosta, Italy
| | - Emanuele Carella
- Centro di Referenza Nazionale per le Malattie degli Animali Selvatici (CeRMAS), Istituto Zooprofilattico Sperimentale del Piemonte, della Liguria e della Valle d'Aosta, Aosta, Italy
| | - Sandra Bermudez Sanchez
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Piazza Aldo Moro, 45, 64100, Teramo, Italy
| | - Riccardo Orusa
- Centro di Referenza Nazionale per le Malattie degli Animali Selvatici (CeRMAS), Istituto Zooprofilattico Sperimentale del Piemonte, della Liguria e della Valle d'Aosta, Aosta, Italy
| | - Vito Martella
- Department of Veterinary Medicine, Università Aldo Moro di Bari, Valenzano, Bari, Italy
| | - Fulvio Marsilio
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Piazza Aldo Moro, 45, 64100, Teramo, Italy
| | - Barbara Di Martino
- Faculty of Veterinary Medicine, Università degli Studi di Teramo, Piazza Aldo Moro, 45, 64100, Teramo, Italy.
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Barry AF, Durães-Carvalho R, Oliveira-Filho EF, Alfieri AA, Van der Poel WHM. High-resolution phylogeny providing insights towards the epidemiology, zoonotic aspects and taxonomy of sapoviruses. INFECTION GENETICS AND EVOLUTION 2017; 56:8-13. [PMID: 28951203 DOI: 10.1016/j.meegid.2017.09.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 10/18/2022]
Abstract
The evolution, epidemiology and zoonotic aspects of Sapoviruses (SaV) are still not well explored. In this study, we applied high-resolution phylogeny to investigate the epidemiological and zoonotic origins as well as taxonomic classification of animal and human SaV. Bayesian framework analyses showed an increase in porcine SaV (PoSaV) population dynamics and genetic diversity between 1975 and 1982, resulting in a SaV gene flow and generation of new strains among porcine and human populations. Our results also show the contribution of different animal populations involved in SaV epidemiology and highlight zoonotic aspects, as exemplified by the crucial role that swine, dogs, mink and humans play in SaV spread. Additionally, phylogenetic analysis suggests that bats may play key role in SaV epidemiology. According to our hypothesis, these animals may act as reservoirs or intermediate host species, contributing to viral spread in zoonotic and other epidemiological scenarios and facilitating the generation of new SaV genogroups and genotypes through recombination events. Data from large-scale phylogeny partition based on patristic distance, did not show a correlation between transmission clusters on generation of SaV genogroups, nevertheless we present both important findings about SaV taxonomy and important considerations useful for further taxonomical studies.
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Affiliation(s)
- A F Barry
- Laboratory of Animal Virology, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Campus Universitário, PO Box 6001, 86051-990 Londrina, Paraná, Brazil
| | - R Durães-Carvalho
- Department of Virology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation (FIOCRUZ), Av. Professor Moraes Rego s/n, Cidade Universitária, Recife, PE 50740-465, Brazil.
| | - E F Oliveira-Filho
- Department of Virology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation (FIOCRUZ), Av. Professor Moraes Rego s/n, Cidade Universitária, Recife, PE 50740-465, Brazil
| | - A A Alfieri
- Laboratory of Animal Virology, Department of Preventive Veterinary Medicine, Universidade Estadual de Londrina, Campus Universitário, PO Box 6001, 86051-990 Londrina, Paraná, Brazil
| | - W H M Van der Poel
- Wageningen Bioveterinary Research, Wageningen University and Research, Department of Virology, P.O. Box 65, 8200 AB Lelystad, Edelhertweg 15, 8219 PH Lelystad, The Netherlands
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Case-Control Comparison of Enteric Viromes in Captive Rhesus Macaques with Acute or Idiopathic Chronic Diarrhea. J Virol 2017; 91:JVI.00952-17. [PMID: 28659484 DOI: 10.1128/jvi.00952-17] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 06/13/2017] [Indexed: 12/12/2022] Open
Abstract
Diarrhea is the major cause of non-research-associated morbidity and mortality affecting the supply of rhesus macaques and, potentially, their responses to experimental treatments. Idiopathic chronic diarrhea (ICD) in rhesus macaques also resembles ulcerative colitis, one form of human inflammatory bowel disease. To test for viral etiologies, we characterized and compared the fecal viromes from 32 healthy animals, 31 animals with acute diarrhea, and 29 animals with ICD. The overall fractions of eukaryotic viral reads were 0.063% for the healthy group, 0.131% for the acute-diarrhea group, and 0.297% for the chronic-diarrhea group. Eukaryotic viruses belonging to 6 viral families, as well as numerous circular Rep-encoding single-stranded DNA (CRESS DNA) viral genomes, were identified. The most commonly detected sequences were from picornaviruses, making up 59 to 88% of all viral reads, followed by 9 to 17% for CRESS DNA virus sequences. The remaining 5 virus families, Adenoviridae, Astroviridae, Anelloviridae, Picobirnaviridae, and Parvoviridae, collectively made up 1 to 3% of the viral reads, except for parvoviruses, which made up 23% of the viral reads in the healthy group. Detected members of the families Picornaviridae and Parvoviridae were highly diverse, consisting of multiple genera, species, and genotypes. Coinfections with members of up to six viral families were detected. Complete and partial viral genomes were assembled and used to measure the number of matching short sequence reads in feces from the 92 animals in the two clinical and the healthy control groups. Several enterovirus genotypes and CRESS DNA genomes were associated with ICD relative to healthy animals. Conversely, higher read numbers from different parvoviruses were associated with healthy animals. Our study reveals a high level of enteric coinfections with diverse viruses in a captive rhesus macaque colony and identifies several viruses positively or negatively associated with ICD.
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First complete genome sequences of genogroup V, genotype 3 porcine sapoviruses: common 5'-terminal genomic feature of sapoviruses. Virus Genes 2017. [PMID: 28643180 DOI: 10.1007/s11262-017-1481-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Sapoviruses (SaVs) are enteric viruses and have been detected in various mammals. They are divided into multiple genogroups and genotypes based on the entire major capsid protein (VP1) encoding region sequences. In this study, we determined the first complete genome sequences of two genogroup V, genotype 3 (GV.3) SaV strains detected from swine fecal samples, in combination with Illumina MiSeq sequencing of the libraries prepared from viral RNA and PCR products. The lengths of the viral genome (7494 nucleotides [nt] excluding polyA tail) and short 5'-untranslated region (14 nt) as well as two predicted open reading frames are similar to those of other SaVs. The amino acid differences between the two porcine SaVs are most frequent in the central region of the VP1-encoding region. A stem-loop structure which was predicted in the first 41 nt of the 5'-terminal region of GV.3 SaVs and the other available complete genome sequences of SaVs may have a critical role in viral genome replication. Our study provides complete genome sequences of rarely reported GV.3 SaV strains and highlights the common 5'-terminal genomic feature of SaVs detected from different mammalian species.
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Moreno PS, Wagner J, Mansfield CS, Stevens M, Gilkerson JR, Kirkwood CD. Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics. PLoS One 2017; 12:e0178433. [PMID: 28570584 PMCID: PMC5453527 DOI: 10.1371/journal.pone.0178433] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 05/12/2017] [Indexed: 01/01/2023] Open
Abstract
The virome has been increasingly investigated in numerous animal species and in different sites of the body, facilitating the identification and discovery of a variety of viruses. In spite of this, the faecal virome of healthy dogs has not been investigated. In this study we describe the faecal virome of healthy dogs and dogs with acute diarrhoea in Australia, using a shotgun metagenomic approach. Viral sequences from a range of different virus families, including both RNA and DNA families, and known pathogens implicated in enteric disease were documented. Twelve viral families were identified, of which four were bacteriophages. Eight eukaryotic viral families were detected: Astroviridae, Coronaviridae, Reoviridae, Picornaviridae, Caliciviridae, Parvoviridae, Adenoviridae and Papillomaviridae. Families Astroviridae, Picornaviridae and Caliciviridae were found only in dogs with acute diarrhoea, with Astroviridae being the most common family identified in this group. Due to its prevalence, characterisation the complete genome of a canine astrovirus was performed. These studies indicate that metagenomic analyses are useful for the investigation of viral populations in the faeces of dogs. Further studies to elucidate the epidemiological and biological relevance of these findings are warranted.
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Affiliation(s)
- Paloma S. Moreno
- Enteric Viruses Group, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
- Translational Research and Animal Clinical Trial Study (TRACTS) group, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- * E-mail:
| | - Josef Wagner
- Enteric Viruses Group, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Caroline S. Mansfield
- Translational Research and Animal Clinical Trial Study (TRACTS) group, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Matthew Stevens
- Australian Genome Research Facility, Melbourne, Victoria, Australia
| | - James R. Gilkerson
- Centre for Equine Infectious Diseases, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Carl D. Kirkwood
- Enteric Viruses Group, Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
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A molecular survey for selected viral enteropathogens revealed a limited role of Canine circovirus in the development of canine acute gastroenteritis. Vet Microbiol 2017; 204:54-58. [PMID: 28532806 PMCID: PMC7131434 DOI: 10.1016/j.vetmic.2017.04.007] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/10/2017] [Accepted: 04/10/2017] [Indexed: 11/24/2022]
Abstract
A molecular survey for selected viral enteropathogens was conducted in dogs with and without acute gastroenteritis. Canine parvovirus and coronavirus were strongly associated with occurrence of enteric disease. Canine circovirus infections correlated with acute gastroenteritis only when associated with other enteric viruses.
Canine circovirus (CanineCV) is a canine virus, whose pathogenetic role is still uncertain. Based on recent data suggesting its role as entheropathogen, a case-control study was conducted between 2013 and 2016 to investigate the association of CanineCV with gastroenteritis in dogs, alone or in combination with other viral pathogens, including canine parvovirus (CPV), canine coronavirus (CCoV) and canine distemper virus (CDV). A total of 219 dogs suffering from acute gastroenteritis disorders and 67 controls randomly recruited among healthy dogs or patients presenting without enteric signs were screened by a panel of real-time (RT-)PCR assays for CanineCV, CPV, CCoV and CDV. A high prevalence of viral infections was detected in dogs with gastroenteritis (77.16%), with CPV representing the most frequently detected enteropathogen, followed by CanineCV and CCoV. While CPV and CCoV infections displayed a strong association with occurrence of acute gastroenteritis (p < 0.00001), detection of CanineCV in control dogs (28.35%) occurred with prevalence comparable to that of clinical cases (32.42%), so that its correlation with gastrointestinal disease was not statistically supported (p = 0.530988). Different from the clinical cases, where co-infections were frequently observed, all positive samples from the control group contained single infections. Noteworthy, a significant association was calculated between co-infections with CanineCV and occurrence of acute gastroenteritis (p < 0.00001). This study supports the role of CanineCV as a co-pathogen in the development of gastrointestinal disease, mainly acting in synergism with other enteric viruses.
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Bergallo M, Galliano I, Montanari P, Brusin MR, Finotti S, Paderi G, Gabiano C. Development of a quantitative real-time PCR assay for sapovirus in children under 5-years-old in Regina Margherita Hospital of Turin, Italy. Can J Microbiol 2017; 63:296-302. [DOI: 10.1139/cjm-2016-0482] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Gastroenteritis is a common disease in children. It is characterized by diarrhea, vomiting, abdominal pain, and fever. Sapovirus (SaV) is a causative agent of acute gastroenteritis, but it causes milder illness than do rotavirus and norovirus. There is high variability in the analytical performance of quantitative PCR-based assays among clinical laboratories. This study developed a reverse transcription real-time PCR method to detect SaV in fecal specimens collected from children under 5-years-old with acute gastroenteritis. Of 137 episodes of acute gastroenteritis, 15 (10.9%) were associated with SaV genomic detection, with a median viral load of 6.6(log10) ± 7.1(log10) genomes/mg fecal specimens. There was a significant difference in detection rate between males and females (9.48% (13/15) vs. 1.46% (2/15), p = 0.0232). Among the 15 SaV-positive cases, 6 were also positive for rotavirus. Viral RNA recovery rate ranged from 46% to 77% in the manual RNAzol protocol and from 31% to 90% in the automated Maxwell protocol. We also studied whether human genomic DNA influences the sensitivity of the assay: its presence caused a decrease in PCR sensitivity. The development of a laboratory-designed real-time PCR TaqMan assay for quantitative detection of SaV and the optimization and standardization of this assay, using stools of children with acute gastroenteritis, are described.
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Affiliation(s)
- Massimiliano Bergallo
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy
| | - Ilaria Galliano
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy
| | - Paola Montanari
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy
| | - Martina Rosa Brusin
- Struttura Complessa, Pediatric University Regina Margherita Hospital, Piazza Polonia 94, 1016 Turin, Italy
| | - Serena Finotti
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy
| | - Giulia Paderi
- Department of Public Health and Pediatric Sciences, University of Turin, Medical School, 10136 Turin, Italy
| | - Clara Gabiano
- Struttura Complessa, Pediatric University Regina Margherita Hospital, Piazza Polonia 94, 1016 Turin, Italy
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