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Sarchese V, Palombieri A, Prandi I, Robetto S, Bertolotti L, Capucchio MT, Orusa R, Mauthe von Degerfeld M, Quaranta G, Vacchetta M, Martella V, Di Martino B, Di Profio F. Molecular Surveillance for Bocaparvoviruses and Bufaviruses in the European Hedgehog ( Erinaceus europaeus). Microorganisms 2024; 12:189. [PMID: 38258015 PMCID: PMC10819369 DOI: 10.3390/microorganisms12010189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/14/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
The presence of bocaparvoviruses (BoVs) and bufaviruses (BuVs) in the European hedgehog (Erinaceus europaeus) was investigated by screening duodenal and liver samples collected from 183 carcasses, delivered to wildlife rescue centers located in northwestern Italy. BoV DNA was detected in 15 animals (8.2%), with prevalences of 7.1% (13/183) and 2.7% (5/183) in intestine and liver samples, respectively. Upon the sequence analyses of the NS1 gene, two highly divergent BoVs (65.5-67.8% nt identities) were identified. Fourteen strains showed the highest identity (98.3-99.4% nt) to the hedgehog BoV strains recently detected in China in Amur hedgehogs (Erinaceus amurensis), whilst four strains were genetically related (98.9-99.4% nt identities) to the porcine BoVs identified in pigs and classified in the species Bocaparvovirus ungulate 4, which included related viruses also found in rats, minks, shrews, and mice. BuV DNA was detected in the duodenal samples of two hedgehogs, with a prevalence rate of 1.1%. The nearly full-length genome of two BuV strains, Hedgehog/331DU-2022/ITA and Hedgehog/1278DU/2019/ITA, was reconstructed. Upon phylogenetic analysis based on the NS and VP aa sequences, the Italian hedgehog BuVs tightly clustered with the BuVs recently identified in the Chinese Amur hedgehogs, within a potential novel candidate species of the genus Protoparvovirus.
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Affiliation(s)
- Vittorio Sarchese
- Department of Veterinary Medicine, Università degli Studi di Teramo, 64100 Teramo, TE, Italy; (V.S.); (A.P.); (B.D.M.)
| | - Andrea Palombieri
- Department of Veterinary Medicine, Università degli Studi di Teramo, 64100 Teramo, TE, Italy; (V.S.); (A.P.); (B.D.M.)
| | - Ilaria Prandi
- Centro Animali Non Convenzionali (C.A.N.C.), Department of Veterinary Sciences, University of Turin, 10095 Grugliasco, TO, Italy; (I.P.); (M.T.C.); (M.M.v.D.); (G.Q.)
| | - 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 Quart, AO, Italy; (S.R.); (R.O.)
| | - Luigi Bertolotti
- Department of Veterinary Sciences, University of Turin, 10095 Grugliasco, TO, Italy;
| | - Maria Teresa Capucchio
- Centro Animali Non Convenzionali (C.A.N.C.), Department of Veterinary Sciences, University of Turin, 10095 Grugliasco, TO, Italy; (I.P.); (M.T.C.); (M.M.v.D.); (G.Q.)
| | - 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 Quart, AO, Italy; (S.R.); (R.O.)
| | - Mitzy Mauthe von Degerfeld
- Centro Animali Non Convenzionali (C.A.N.C.), Department of Veterinary Sciences, University of Turin, 10095 Grugliasco, TO, Italy; (I.P.); (M.T.C.); (M.M.v.D.); (G.Q.)
| | - Giuseppe Quaranta
- Centro Animali Non Convenzionali (C.A.N.C.), Department of Veterinary Sciences, University of Turin, 10095 Grugliasco, TO, Italy; (I.P.); (M.T.C.); (M.M.v.D.); (G.Q.)
| | | | - Vito Martella
- Department of Veterinary Medicine, Università Aldo Moro di Bari, 70010 Valenzano, BA, Italy;
| | - Barbara Di Martino
- Department of Veterinary Medicine, Università degli Studi di Teramo, 64100 Teramo, TE, Italy; (V.S.); (A.P.); (B.D.M.)
| | - Federica Di Profio
- Department of Veterinary Medicine, Università degli Studi di Teramo, 64100 Teramo, TE, Italy; (V.S.); (A.P.); (B.D.M.)
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Hong Y, Ma B, Li J, Shuai J, Zhang X, Xu H, Zhang M. Triplex-Loop-Mediated Isothermal Amplification Combined with a Lateral Flow Immunoassay for the Simultaneous Detection of Three Pathogens of Porcine Viral Diarrhea Syndrome in Swine. Animals (Basel) 2023; 13:1910. [PMID: 37370420 DOI: 10.3390/ani13121910] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/29/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Porcine epidemic diarrhea virus (PEDV), porcine bocavirus (PBoV), and porcine rotavirus (PoRV) are associated with porcine viral diarrhea. In this study, triplex loop-mediated isothermal amplification (LAMP) combined with a lateral flow dipstick (LFD) was established for the simultaneous detection of PEDV, PoRV, and PBoV. The PEDV-gp6, PoRV-vp6, and PBoV-vp1 genes were selected to design LAMP primers. The amplification could be carried out at 64 °C using a miniature metal bath within 30 min. The triplex LAMP-LFD assay exhibited no cross-reactions with other porcine pathogens. The limits of detection (LODs) of PEDV, PoRV, and PBoV were 2.40 × 101 copies/μL, 2.89 × 101 copies/μL, and 2.52 × 101 copies/μL, respectively. The consistency between rt-qPCR and the triplex LAMP-LFD was over 99% in field samples testing. In general, the triplex LAMP-LFD assay was suitable for the rapid and simultaneous detection of the three viruses in the field.
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Affiliation(s)
- Yi Hong
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China
| | - Biao Ma
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China
| | - Jiali Li
- Hangzhou Quickgene Sci-Tech. Co., Ltd., Hangzhou 310018, China
| | - Jiangbing Shuai
- Zhejiang Academy of Science and Technology for Inspection and Quarantine, Hangzhou 310016, China
| | - Xiaofeng Zhang
- Zhejiang Academy of Science and Technology for Inspection and Quarantine, Hangzhou 310016, China
| | - Hanyue Xu
- College of Life Science, China Jiliang University, Hangzhou 310018, China
| | - Mingzhou Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou 310018, China
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3
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Capozza P, Buonavoglia A, Pratelli A, Martella V, Decaro N. Old and Novel Enteric Parvoviruses of Dogs. Pathogens 2023; 12:pathogens12050722. [PMID: 37242392 DOI: 10.3390/pathogens12050722] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Parvovirus infections have been well known for around 100 years in domestic carnivores. However, the use of molecular assays and metagenomic approaches for virus discovery and characterization has led to the detection of novel parvovirus species and/or variants in dogs. Although some evidence suggests that these emerging canine parvoviruses may act as primary causative agents or as synergistic pathogens in the diseases of domestic carnivores, several aspects regarding epidemiology and virus-host interaction remain to be elucidated.
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Affiliation(s)
- Paolo Capozza
- Department of Veterinary Medicine, University of Bari Aldo Moro, 70010 Valenzano, Italy
| | - Alessio Buonavoglia
- Department of Biomedical and Neuromotor Sciences, Dental School, Via Zamboni 33, 40126 Bologna, Italy
| | - Annamaria Pratelli
- Department of Veterinary Medicine, University of Bari Aldo Moro, 70010 Valenzano, Italy
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari Aldo Moro, 70010 Valenzano, Italy
| | - Nicola Decaro
- Department of Veterinary Medicine, University of Bari Aldo Moro, 70010 Valenzano, Italy
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Ochola GO, Li B, Obanda V, Ommeh S, Ochieng H, Yang XL, Onyuok SO, Shi ZL, Agwanda B, Hu B. Discovery of novel DNA viruses in small mammals from Kenya. Virol Sin 2022; 37:491-502. [PMID: 35680114 PMCID: PMC9437603 DOI: 10.1016/j.virs.2022.06.001] [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: 11/18/2021] [Accepted: 05/17/2022] [Indexed: 11/29/2022] Open
Abstract
Emergence and re-emergence of infectious diseases of wildlife origin have led pre-emptive pathogen surveillances in animals to be a public health priority. Rodents and shrews are among the most numerically abundant vertebrate taxa and are known as natural hosts of important zoonotic viruses. Many surveillance programs focused more on RNA viruses. In comparison, much less is known about DNA viruses harbored by these small mammals. To fill this knowledge gap, tissue specimens of 232 animals including 226 rodents, five shrews and one hedgehog were collected from 5 counties in Kenya and tested for the presence of DNA viruses belonging to 7 viral families by PCR. Diverse DNA sequences of adenoviruses, adeno-associated viruses, herpesviruses and polyomaviruses were detected. Phylogenetic analyses revealed that most of these viruses showed distinction from previously described viruses and formed new clusters. Furthermore, this is the first report of the discovery and full-length genome characterization of a polyomavirus in Lemniscomys species. This novel polyomavirus, named LsPyV KY187, has less than 60% amino acid sequence identity to the most related Glis glis polyomavirus 1 and Sciurus carolinensis polyomavirus 1 in both large and small T-antigen proteins and thus can be putatively allocated to a novel species within Betapolyomavirus. Our findings help us better understand the genetic diversity of DNA viruses in rodent and shrew populations in Kenya and provide new insights into the evolution of those DNA viruses in their small mammal reservoirs. It demonstrates the necessity of ongoing pathogen discovery studies targeting rodent-borne viruses in East Africa.
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Affiliation(s)
- Griphin Ochieng Ochola
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China; Mammalogy Section, National Museums of Kenya, Nairobi, 40658-00100, Kenya; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bei Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Vincent Obanda
- Veterinary Services Department, Kenya Wildlife Service, Nairobi, 40241-00100, Kenya
| | - Sheila Ommeh
- Institute of Biotechnology Research, Jomo Kenyatta University of Science and Technology, Nairobi, 62000-00200, Kenya
| | - Harold Ochieng
- Mammalogy Section, National Museums of Kenya, Nairobi, 40658-00100, Kenya
| | - Xing-Lou Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Samson Omondi Onyuok
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; Mammalogy Section, National Museums of Kenya, Nairobi, 40658-00100, Kenya
| | - Zheng-Li Shi
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Bernard Agwanda
- Mammalogy Section, National Museums of Kenya, Nairobi, 40658-00100, Kenya.
| | - Ben Hu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
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He W, Gao Y, Wen Y, Ke X, Ou Z, Fu J, Cheng M, Mo Y, Chen Q. Ungulate bocaparvovirus 4 and rodent bocavirus are different genotypes of the same species of virus. Virol Sin 2022; 37:215-222. [PMID: 35527226 PMCID: PMC9170977 DOI: 10.1016/j.virs.2022.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 02/10/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Wenqiao He
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, 510515, China
| | - Yuhan Gao
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, 510515, China
| | - Yuqi Wen
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, 510515, China
| | - Xuemei Ke
- Xiamen Center for Disease Control and Prevention, Xiamen, 361000, China
| | - Zejin Ou
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, 510515, China
| | - Jiaqi Fu
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, 510515, China
| | - Mingji Cheng
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, 510515, China
| | - Yun Mo
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, 510515, China
| | - Qing Chen
- Department of Epidemiology, School of Public Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, Southern Medical University, Guangzhou, 510515, China.
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6
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Capai L, Piorkowski G, Maestrini O, Casabianca F, Masse S, de Lamballerie X, Charrel RN, Falchi A. Detection of porcine enteric viruses (Kobuvirus, Mamastrovirus and Sapelovirus) in domestic pigs in Corsica, France. PLoS One 2022; 17:e0260161. [PMID: 35030164 PMCID: PMC8759673 DOI: 10.1371/journal.pone.0260161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 11/03/2021] [Indexed: 11/19/2022] Open
Abstract
Many enteric viruses are found in pig farms around the world and can cause death of animals or important production losses for breeders. Among the wide spectrum of enteric viral species, porcine Sapelovirus (PSV), porcine Kobuvirus (PKoV) and porcine Astrovirus (PAstV) are frequently found in pig feces. In this study we investigated sixteen pig farms in Corsica, France, to evaluate the circulation of three enteric viruses (PKoV, PAstV-1 and PSV). In addition to the three viruses studied by RT-qPCR (908 pig feces samples), 26 stool samples were tested using the Next Generation Sequencing method (NGS). Our results showed viral RNA detection rates (i) of 62.0% [58.7-65.1] (n = 563/908) for PSV, (ii) of 44.8% [41.5-48.1] (n = 407/908) for PKoV and (iii) of 8.6% [6.8-10.6] (n = 78/908) for PAstV-1. Significant differences were observed for all three viruses according to age (P-value = 2.4e-13 for PAstV-1; 2.4e-12 for PKoV and 0.005 for PSV). The type of breeding was significantly associated with RNA detection only for PAstV-1 (P-value = 9.6e-6). Among the 26 samples tested with NGS method, consensus sequences corresponding to 10 different species of virus were detected. This study provides first insight on the presence of three common porcine enteric viruses in France. We also showed that they are frequently encountered in pigs born and bred in Corsica, which demonstrates endemic local circulation.
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Affiliation(s)
- Lisandru Capai
- UR 7310, Laboratoire de Virologie, Université de Corse, Corte, France
| | - Géraldine Piorkowski
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Oscar Maestrini
- Laboratoire de Recherche sur le Développement de l’Elevage (LRDE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Corte, France
| | - François Casabianca
- Laboratoire de Recherche sur le Développement de l’Elevage (LRDE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Corte, France
| | - Shirley Masse
- UR 7310, Laboratoire de Virologie, Université de Corse, Corte, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Rémi N. Charrel
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Alessandra Falchi
- UR 7310, Laboratoire de Virologie, Université de Corse, Corte, France
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Jager MC, Tomlinson JE, Lopez-Astacio RA, Parrish CR, Van de Walle GR. Small but mighty: old and new parvoviruses of veterinary significance. Virol J 2021; 18:210. [PMID: 34689822 PMCID: PMC8542416 DOI: 10.1186/s12985-021-01677-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/08/2021] [Indexed: 12/14/2022] Open
Abstract
In line with the Latin expression "sed parva forti" meaning "small but mighty," the family Parvoviridae contains many of the smallest known viruses, some of which result in fatal or debilitating infections. In recent years, advances in metagenomic viral discovery techniques have dramatically increased the identification of novel parvoviruses in both diseased and healthy individuals. While some of these discoveries have solved etiologic mysteries of well-described diseases in animals, many of the newly discovered parvoviruses appear to cause mild or no disease, or disease associations remain to be established. With the increased use of animal parvoviruses as vectors for gene therapy and oncolytic treatments in humans, it becomes all the more important to understand the diversity, pathogenic potential, and evolution of this diverse family of viruses. In this review, we discuss parvoviruses infecting vertebrate animals, with a special focus on pathogens of veterinary significance and viruses discovered within the last four years.
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Affiliation(s)
- Mason C Jager
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Joy E Tomlinson
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Robert A Lopez-Astacio
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Colin R Parrish
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Gerlinde R Van de Walle
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
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8
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Emerging Parvoviruses in Domestic Cats. Viruses 2021; 13:v13061077. [PMID: 34200079 PMCID: PMC8229815 DOI: 10.3390/v13061077] [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: 05/17/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 11/16/2022] Open
Abstract
Parvovirus infections in cats have been well known for around 100 years. Recently, the use of molecular assays and metagenomic approaches for virus discovery and characterization has led to the detection of novel parvovirus lineages and/or species infecting the feline host. However, the involvement of emerging parvoviruses in the onset of gastroenteritis or other feline diseases is still uncertain.
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9
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Aryal M, Liu G. Porcine Bocavirus: A 10-Year History since Its Discovery. Virol Sin 2021; 36:1261-1272. [PMID: 33909219 PMCID: PMC8080206 DOI: 10.1007/s12250-021-00365-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 12/11/2020] [Indexed: 12/14/2022] Open
Abstract
Porcine bocavirus (PBoV) is a single-stranded DNA virus, belongs to the genus Bocaparvovirus of family Parvoviridae. It was discovered along with porcine circovirus 2 (PCV 2) and torque tenovirus (TTV) in the lymph nodes of pigs suffering from postweaning multisystemic wasting syndrome (PMWS) in Sweden in 2009. PBoV has been reported throughout the world, mostly in weaning piglets, and has a broad range of tissue tropism. Since PBoV is prevalent in healthy as well as clinically infected pigs and is mostly associated with coinfection with other viruses, the pathogenic nature of PBoV is still unclear. Currently, there are no cell lines available for the study of PBoV, and animal model experiments have not been described. This review summarizes the current state of knowledge about PBoV, including the epidemiology, evolution analysis, detection methods, pathogenesis and public health concerns.
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Affiliation(s)
- Manita Aryal
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Guangliang Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China.
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10
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Paim WP, Maggioli MF, Weber MN, Rezabek G, Narayanan S, Ramachandran A, Canal CW, Bauermann FV. Virome characterization in serum of healthy show pigs raised in Oklahoma demonstrated great diversity of ssDNA viruses. Virology 2021; 556:87-95. [PMID: 33550118 DOI: 10.1016/j.virol.2021.01.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 02/08/2023]
Abstract
In the United States, show pigs are raised to compete in agricultural events. These animals are usually raised in small herds with extensive human, domestic, and wild animal contact. Therefore, pathogen monitoring in this animal category is critical for improved disease surveillance and preparedness. This study characterized the virome of healthy show pigs using high-throughput sequencing using pooled serum samples from 2018 or 2019 (200 samples each pool). Results demonstrated the presence of DNA viral families (Parvoviridae, Circoviridae, and Herpesviridae) and RNA families (Arteriviridae, Flaviviridae, and Retroviridae). Twenty-three viral species were identified, including the first detection of porcine bufavirus in the US. Moreover, important swine pathogens identified included porcine reproductive and respiratory syndrome virus, atypical porcine pestivirus, and porcine circovirus (PCV). Additionally, complete coding genomes of 17 viruses from the Parvoviridae, Anelloviridae, and Circoviridae families were retrieved and included the first near full-length genomes of US Ungulate bocaparvovirus 3 species.
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Affiliation(s)
- Willian P Paim
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University (OSU), Stillwater, OK, 74078, USA; Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Mayara F Maggioli
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University (OSU), Stillwater, OK, 74078, USA
| | - Matheus N Weber
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Grant Rezabek
- Serology diagnostic Section, Oklahoma Animal Disease Diagnostic Laboratory (OADDL), College of Veterinary Medicine, Oklahoma State University (OSU), Stillwater, OK, 74078, USA
| | - Sai Narayanan
- Molecular diagnostic Section, Oklahoma Animal Disease Diagnostic Laboratory (OADDL), College of Veterinary Medicine, Oklahoma State University (OSU), Stillwater, OK, 74078, USA
| | - Akhilesh Ramachandran
- Molecular diagnostic Section, Oklahoma Animal Disease Diagnostic Laboratory (OADDL), College of Veterinary Medicine, Oklahoma State University (OSU), Stillwater, OK, 74078, USA
| | - Cláudio W Canal
- Laboratório de Virologia, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Fernando V Bauermann
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University (OSU), Stillwater, OK, 74078, USA.
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11
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Li C, Shan T, Chen Z, Zhou J, Li H, Tong G, Liu G. Isolation and complete genome analysis of a novel duck picornavirus in China. Vet Microbiol 2020; 253:108950. [PMID: 33341468 DOI: 10.1016/j.vetmic.2020.108950] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 12/02/2020] [Indexed: 01/13/2023]
Abstract
A novel duck picornavirus, designated as duck/AH15/CHN/2015, was isolated and identified from Cherry Valley ducks with short beak and dwarfism syndrome in 2015 in Anhui province of China. Duck/AH15/CHN/2015 has the highest degree of amino acid sequence identity (approximately 43 %) with duck hepatitis A viruses (DHAV) Complete genome analysis revealed that duck/AH15/CHN/2015 possesses a typical picornavirus-like genomic organization, 5' UTR-L-P1 (VP0-VP3-VP1)-P2 (2A1-2A2- 2B-2C)-P3 (3A-3B-3C-3D)-3'UTR-poly (A). The 5'UTR contains a potential type IV internal ribosome entry site, while a conserved "barbell"-like structure is found at the 3'UTR, which is similar to DHAV. Compared to the closest related DHAVs, two unrelated 2A proteins were predicted in duck/AH15/CHN/2015, while three unrelated 2A proteins were presented in DHAVs. Based on the amino acid identity comparison and phylogenetic analysis of P1, 2C, and 3CD (3C and 3D), duck/AH15/CHN/2015 was closely related to but distinct from DHAVs, and it was proposed to be a member of a novel species in the genus Avihepatovirus of the family Picornaviridae.
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Affiliation(s)
- Chuanfeng Li
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, China
| | - Tongling Shan
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, China
| | - Zongyan Chen
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, China
| | - Jiewen Zhou
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, China
| | - Hang Li
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, China
| | - Guangzhi Tong
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, China.
| | - Guangqing Liu
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Shanghai, 200241, China.
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12
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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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13
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Co-infection with porcine bocavirus and porcine circovirus 2 affects inflammatory cytokine production and tight junctions of IPEC-J2 cells. Virus Genes 2018; 54:684-693. [DOI: 10.1007/s11262-018-1596-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 08/10/2018] [Indexed: 12/16/2022]
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14
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A TaqMan-based real-time PCR assay for the detection of Ungulate bocaparvovirus 2. J Virol Methods 2018; 261:17-21. [PMID: 30076874 DOI: 10.1016/j.jviromet.2018.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/25/2018] [Accepted: 07/25/2018] [Indexed: 01/14/2023]
Abstract
Ungulate bocaparvoviruses (UBoV) 2-5 are recently discovered porcine bocaparvoviruses belonging to the family Parvoviridae, and are considered to be a potentially major cause of swine diseases. In order to detect local UBoV2 epidemics in China, we developed a TaqMan-based real-time PCR (qPCR) assay targeting the UBoV2 VP1 gene and compared the results of qPCR with conventional PCR (cPCR). The qPCR reproducibly detected a recombinant DNA plasmid containing the VP1 gene over a range of eight orders of magnitude, from 9.97 × 10-1-106 copies/μL, with a lower limit of detection of 9.97 copies/μL, compared with approximately 9.97 × 102 copies/μL for cPCR. The qPCR assay showed no cross-reactivity with other UBoVs or other porcine viruses. This qPCR assay detected UBoV2 in 18.1% (84/463) of pig samples collected from Chinese swine herds, with the highest infection rate of 35.3% (53/150) in loose stools. UBoV2 was not detected in liver samples. The TaqMan-based qPCR assay established in this study was highly sensitive and specific for the diagnosis and quantification of UBoV2. The results of this study will further our understanding of the etiology, epidemiology, and pathogenesis of UBoV2 infection.
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15
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Zhang C, Song F, Xiu L, Liu Y, Yang J, Yao L, Peng J. Identification and characterization of a novel rodent bocavirus from different rodent species in China. Emerg Microbes Infect 2018; 7:48. [PMID: 29593218 PMCID: PMC5874251 DOI: 10.1038/s41426-018-0052-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 02/05/2018] [Accepted: 02/11/2018] [Indexed: 01/20/2023]
Abstract
Members in the genus Bocaparvovirus are closely related to human health and have a wide host range. The diverse hosts raise the possibility of crossing species barrier, which is a feature of emerging viruses. Among the mammalian hosts, rodents are generally acknowledged to be important reservoirs of emerging viruses. Here, rodent samples collected from six provinces and autonomous regions of China (Liaoning, Inner Mongolia, Tibet, Xinjiang, Guangxi and Yunnan) were used to investigate the prevalence and distribution of bocaparvoviruses. By using next-generation sequencing first, a partial non-structural protein 1 (NS1) gene belonging to a possible novel bocaparvovirus was discovered. Following this, PCR-based screening of NS1 gene was conducted in 485 rodent samples, with 106 positive results found in seven rodent species (Rattus norvegicus, Mus musculus, Apodemus agrarius, Cricetulus barabensis, Rattus flavipectus, Rattus rattus and Rhombomys opimus). Finally, six nearly full-length genomes and three complete CDS were obtained and the newly identified bocaparvovirus was tentatively named rodent bocavirus (RoBoV). RoBoV has three ORFs: NS1, NP1, and VP, which are characteristics of bocaparvoviruses. Phylogenetic analyses revealed that porcine bocavirus isolate PBoV-KU14, a member of Ungulate bocaparvovirus 4, was the most related virus to RoBoV, with 92.1-92.9% amino acid identities in NS1 protein. Alignments of RoBoV-related sequences showed RoBoV isolates could be classified into two clades, demonstrating an inter-host genetic diversity. The results indicate a potential interspecies transmission of RoBoV between rodents and swine and expand our knowledge on bocaparvoviruses in rodent populations.
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Affiliation(s)
- Chi Zhang
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China
| | - Fenglin Song
- Liaoning Entry-Exit Inspection and Quarantine Bureau, Shenyang, 116001, China
| | - Leshan Xiu
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China
| | - Yang Liu
- Jilin Entry-Exit Inspection and Quarantine Bureau, Changchun, 130062, China
| | - Jian Yang
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China
| | - Lisi Yao
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, China.
| | - Junping Peng
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100176, China.
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16
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Liu C, Liu F, Li Z, Qu L, Liu D. First report of feline bocavirus associated with severe enteritis of cat in Northeast China, 2015. J Vet Med Sci 2018; 80:731-735. [PMID: 29459503 PMCID: PMC5938208 DOI: 10.1292/jvms.17-0444] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Feline bocavirus (FBoV) is a newly identified bocavirus of cats in the family
Parvoviridae. A novel FBoV HRB2015-LDF was first identified from the cat
with severe enteritis in Northeast China, with an overall positive rate of 2.78% (1/36).
Phylogenetic and homologous analysis of the complete genome showed that FBoV HRB2015-LDF
was clustered into the FBoV branch and closely related to other FBoVs, with 68.7–97.5%
identities. And the genes of VP1, NPA and NS1 shared 70.7–97.6, 72.4–98.6 and 67.2–98.0%
nucleotide identities with other FBoVs, respectively. The results suggested that the FBoVs
could be divided into two distinct lineages, and the difference of nucleotide identities
was >20–30% between the lineages.
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Affiliation(s)
- Chunguo Liu
- 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
| | - Zhigang Li
- Wendengying Veterinary Station, Weihai, Shandong 264413, China
| | - Liandong Qu
- State Key Lab of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China
| | - Dafei Liu
- State Key Lab of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, Heilongjiang 150069, China.,College of Wildlife Resources, Northeast Forestry University, Harbin, Heilongjiang 150040, China
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17
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First molecular detection of porcine bocavirus in Malaysia. Trop Anim Health Prod 2017; 50:733-739. [PMID: 29243138 DOI: 10.1007/s11250-017-1489-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 12/05/2017] [Indexed: 01/19/2023]
Abstract
Several strains of porcine bocaviruses have been reported worldwide since their first detection in Sweden in 2009. Subsequently, the virus has been reported to be associated with gastrointestinal and respiratory signs in weaner and grower pigs. Although Malaysia is host to a self-sufficient swine livestock industry, there is no study that describes porcine bocavirus in the country. This report is the first to describe porcine bocavirus (PBoV) in Malaysian swine herds. PBoV was identified in various tissues from sick and runt pigs using the conventional PCR method with primers targeting conserved regions encoding for the nonstructural protein (NS1) gene. Out of 103 samples tested from 17 pigs, 32 samples from 15 pigs were positive for porcine bocavirus. In addition, a higher detection rate was identified from mesenteric lymph nodes (52.9%), followed by tonsil (37.0%), and lungs (33.3%). Pairwise comparison and phylogenetic analyses based on a 658-bp fragment of NS1 gene revealed that the Malaysian PBoV strains are highly similar to PBoV3 isolated in Minnesota, USA. The presence of porcine bocavirus in Malaysia and their phylogenetic bond was marked for the first time by this study. Further studies will establish the molecular epidemiology of PBoV in Malaysia and clarify pathogenicity of the local isolates.
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18
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Lau SKP, Ahmed SS, Tsoi HW, Yeung HC, Li KSM, Fan RYY, Zhao PSH, Lau CCC, Lam CSF, Choi KKF, Chan BCH, Cai JP, Wong SSY, Chen H, Zhang HL, Zhang L, Wang M, Woo PCY, Yuen KY. Bats host diverse parvoviruses as possible origin of mammalian dependoparvoviruses and source for bat-swine interspecies transmission. J Gen Virol 2017; 98:3046-3059. [PMID: 29106348 DOI: 10.1099/jgv.0.000969] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Compared to the enormous species diversity of bats, relatively few parvoviruses have been reported. We detected diverse and potentially novel parvoviruses from bats in Hong Kong and mainland China. Parvoviruses belonging to Amdoparvovirus, Bocaparvovirus and Dependoparvovirus were detected in alimentary, liver and spleen samples from 16 different chiropteran species of five families by PCR. Phylogenetic analysis of partial helicase sequences showed that they potentially belonged to 25 bocaparvovirus, three dependoparvovirus and one amdoparvovirus species. Nearly complete genome sequencing confirmed the existence of at least four novel bat bocaparvovirus species (Rp-BtBoV1 and Rp-BtBoV2 from Rhinolophus pusillus, Rs-BtBoV2 from Rhinolophus sinicus and Rol-BtBoV1 from Rousettus leschenaultii) and two novel bat dependoparvovirus species (Rp-BtAAV1 from Rhinolophus pusillus and Rs-BtAAV1 from Rhinolophus sinicus). Rs-BtBoV2 was closely related to Ungulate bocaparvovirus 5 with 93, 72.1 and 78.7 % amino acid identities in the NS1, NP1 and VP1/VP2 genes, respectively. The detection of bat bocaparvoviruses, including Rs-BtBoV2, closely related to porcine bocaparvoviruses, suggests recent interspecies transmission of bocaparvoviruses between bats and swine. Moreover, Rp-BtAAV1 and Rs-BtAAV1 were most closely related to human AAV1 with 48.7 and 57.5 % amino acid identities in the rep gene. The phylogenetic relationship between BtAAVs and other mammalian AAVs suggests bats as the ancestral origin of mammalian AAVs. Furthermore, parvoviruses of the same species were detected from multiple bat species or families, supporting the ability of bat parvoviruses to cross species barriers. The results extend our knowledge on the diversity of bat parvoviruses and the role of bats in parvovirus evolution and emergence in humans and animals.
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Affiliation(s)
- Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Syed Shakeel Ahmed
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Hoi-Wah Tsoi
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Hazel C Yeung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Kenneth S M Li
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Rachel Y Y Fan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Pyrear S H Zhao
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Candy C C Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Carol S F Lam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Kelvin K F Choi
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Ben C H Chan
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Jian-Piao Cai
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Samson S Y Wong
- Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Honglin Chen
- State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Hai-Lin Zhang
- Yunnan Institute of Endemic Disease Control and Prevention, Dali, Yunnan, PR China.,Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Dali, Yunnan, PR China
| | - Libiao Zhang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangzhou, Guangdong Province, PR China.,Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangzhou, Guangdong Province, PR China.,Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong Province, PR China
| | - Ming Wang
- Guangzhou Centre for Disease Control, Guangzhou, Guangdong Province, PR China
| | - Patrick C Y Woo
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
| | - Kwok-Yung Yuen
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,State Key Laboratory of Emerging Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR.,Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR
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19
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Bovo S, Mazzoni G, Ribani A, Utzeri VJ, Bertolini F, Schiavo G, Fontanesi L. A viral metagenomic approach on a non-metagenomic experiment: Mining next generation sequencing datasets from pig DNA identified several porcine parvoviruses for a retrospective evaluation of viral infections. PLoS One 2017; 12:e0179462. [PMID: 28662150 PMCID: PMC5491021 DOI: 10.1371/journal.pone.0179462] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/29/2017] [Indexed: 12/14/2022] Open
Abstract
Shot-gun next generation sequencing (NGS) on whole DNA extracted from specimens collected from mammals often produces reads that are not mapped (i.e. unmapped reads) on the host reference genome and that are usually discarded as by-products of the experiments. In this study, we mined Ion Torrent reads obtained by sequencing DNA isolated from archived blood samples collected from 100 performance tested Italian Large White pigs. Two reduced representation libraries were prepared from two DNA pools constructed each from 50 equimolar DNA samples. Bioinformatic analyses were carried out to mine unmapped reads on the reference pig genome that were obtained from the two NGS datasets. In silico analyses included read mapping and sequence assembly approaches for a viral metagenomic analysis using the NCBI Viral Genome Resource. Our approach identified sequences matching several viruses of the Parvoviridae family: porcine parvovirus 2 (PPV2), PPV4, PPV5 and PPV6 and porcine bocavirus 1-H18 isolate (PBoV1-H18). The presence of these viruses was confirmed by PCR and Sanger sequencing of individual DNA samples. PPV2, PPV4, PPV5, PPV6 and PBoV1-H18 were all identified in samples collected in 1998-2007, 1998-2000, 1997-2000, 1998-2004 and 2003, respectively. For most of these viruses (PPV4, PPV5, PPV6 and PBoV1-H18) previous studies reported their first occurrence much later (from 5 to more than 10 years) than our identification period and in different geographic areas. Our study provided a retrospective evaluation of apparently asymptomatic parvovirus infected pigs providing information that could be important to define occurrence and prevalence of different parvoviruses in South Europe. This study demonstrated the potential of mining NGS datasets non-originally derived by metagenomics experiments for viral metagenomics analyses in a livestock species.
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Affiliation(s)
- Samuele Bovo
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Bologna, Italy
- Department of Biological, Geological, and Environmental Sciences (BiGeA), Biocomputing Group, University of Bologna, Bologna, Italy
| | - Gianluca Mazzoni
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Bologna, Italy
- Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anisa Ribani
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Bologna, Italy
| | - Valerio Joe Utzeri
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Bologna, Italy
| | - Francesca Bertolini
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Bologna, Italy
- Department of Animal Science, Iowa State University, Iowa, United States of America
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Bologna, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences (DISTAL), Division of Animal Sciences, University of Bologna, Bologna, Italy
- * E-mail:
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20
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First Complete Genome Sequences of Porcine Bocavirus Strains from East Africa. GENOME ANNOUNCEMENTS 2017; 5:5/14/e00093-17. [PMID: 28385838 PMCID: PMC5383886 DOI: 10.1128/genomea.00093-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the first complete genome sequences of two strains of porcine bocavirus (JOA_011 and JOA_015) detected in Uganda and Kenya, respectively. These data will help in understanding the molecular and evolutionary characteristics of the porcine bocaviruses in this region and the development of appropriate diagnostic and control tools.
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21
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Ungulate copiparvovirus 2 in healthy and postweaning multisystemic wasting syndrome-affected pigs. Trop Anim Health Prod 2017; 49:945-949. [DOI: 10.1007/s11250-017-1279-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 03/15/2017] [Indexed: 10/19/2022]
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22
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Lau SKP, Yeung HC, Li KSM, Lam CSF, Cai JP, Yuen MC, Wang M, Zheng BJ, Woo PCY, Yuen KY. Identification and genomic characterization of a novel rat bocavirus from brown rats in China. INFECTION GENETICS AND EVOLUTION 2016; 47:68-76. [PMID: 27871815 DOI: 10.1016/j.meegid.2016.11.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/15/2016] [Accepted: 11/14/2016] [Indexed: 01/19/2023]
Abstract
Despite recent discoveries of novel animal bocaparvoviruses, current understandings on the diversity and evolution of bocaparvoviruses are still limited. We report the identification and genome characterization of a novel bocaparvovirus, rat bocaparvovirus (RBoV), in brown rats (Rattus norvegicus) in China. RBoV was detected in 11.5%, 2.4%, 16.2% and 0.3% of alimentary, respiratory, spleen and kidney samples respectively, of 636 brown rats by PCR, but not in samples of other rodent species, suggesting that brown rats are the primary reservoir of RBoV. Six RBoV genomes sequenced from three brown rats revealed the presence of three ORFs, characteristic of bocaparvoviruses. Phylogenetic analysis showed that RBoV was distantly related to other bocaparvoviruses, forming a distinct cluster within the genus, with ≤55.5% nucleotide identities to the genome of ungulate bocaparvovirus 3, supporting its classification as a novel bocaparvovirus species. RBoV possessed a putative second exon encoding the C-terminal region of NS1 and conserved RNA splicing signals, similar to human bocaparvoviruses and canine bocaparvovirus. In contrast to human, feline and canine bocaparvoviruses which demonstrates inter/intra-host viral diversity, partial VP1/VP2 sequences of 49 RBoV strains demonstrated little inter-host genetic diversity, suggesting a single genetic group. Although the pathogenicity of RBoV remains to be determined, its presence in different host tissues suggests wide tissue tropism. RBoV represents the first bocaparvovirus in rodents with genome sequenced, which extends our knowledge on the host range of bocaparvoviruses. Further studies are required to better understand the epidemiology, genetic diversity and pathogenicity of bocaparvoviruses in different rodent populations.
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Affiliation(s)
- Susanna K P Lau
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China; Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Hazel C Yeung
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Kenneth S M Li
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Carol S F Lam
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Jian-Piao Cai
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Ming-Chi Yuen
- Food and Environmental Hygiene Department, The Government of the Hong Kong Special Administrative Region, Hong Kong, China
| | - Ming Wang
- Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Bo-Jian Zheng
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China; Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China; Department of Microbiology, The University of Hong Kong, Hong Kong, China.
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China; Department of Microbiology, The University of Hong Kong, Hong Kong, China.
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23
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Lau SKP, Ahmed SS, Yeung HC, Li KSM, Fan RYY, Cheng TYC, Cai JP, Wang M, Zheng BJ, Wong SSY, Woo PCY, Yuen KY. Identification and interspecies transmission of a novel bocaparvovirus among different bat species in China. J Gen Virol 2016; 97:3345-3358. [PMID: 27902362 DOI: 10.1099/jgv.0.000645] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We report the discovery of a novel bocaparvovirus, bat bocaparvovirus (BtBoV), in one spleen, four respiratory and 61 alimentary samples from bats of six different species belonging to three families, Hipposideridae, Rhinolophidae and Vespertilionidae. BtBoV showed a higher detection rate in alimentary samples of Rhinolophus sinicus (5.7 %) than those of other bat species (0.43-1.59 %), supporting R. sinicus as the primary reservoir and virus spillover to accidental bat species. BtBoV peaked during the lactating season of R. sinicus, and it was more frequently detected among female than male adult bats (P<0.05), and among lactating than non-lactating female bats (P<0.0001). Positive BtBoV detection was associated with lower body weight in lactating bats (P<0.05). Ten nearly complete BtBoV genomes from three bat species revealed a unique large ORF1 spanning NS1 and NP1 in eight genomes and conserved splicing signals leading to multiple proteins, as well as a unique substitution in the conserved replication initiator motif within NS1. BtBoV was phylogenetically distantly related to known bocaparvoviruses with ≤57.3 % genome identities, supporting BtBoV as a novel species. Ms-BtBoV from Miniopterus schreibersii and Hp-BtBoV from Hipposideros pomona demonstrated 97.2-99.9 % genome identities with Rs-BtBoVs from R. sinicus, supporting infection of different bat species by a single BtBoV species. Rs-BtBoV_str15 represents the first bat parvovirus genome with non-coding regions sequenced, which suggested the presence of head-to-tail genomic concatamers or episomal forms of the genome. This study represents the first to describe interspecies transmission in BoVs. The high detection rates in lactating female and juvenile bats suggest possible vertical transmission of BtBoV.
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Affiliation(s)
- Susanna K P Lau
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, PR China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Syed Shakeel Ahmed
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Hazel C Yeung
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Kenneth S M Li
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Rachel Y Y Fan
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Toni Y C Cheng
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Jian-Piao Cai
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Ming Wang
- Guangzhou Center for Disease Control and Prevention, Guangzhou, PR China
| | - Bo-Jian Zheng
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, PR China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, PR China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR China.,Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China
| | - Samson S Y Wong
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, PR China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, PR China
| | - Patrick C Y Woo
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, PR China.,Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, PR China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR China
| | - Kwok-Yung Yuen
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, PR China.,Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, PR China.,Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, PR China.,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, PR China
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24
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Zheng X, Liu G, Opriessnig T, Wang Z, Yang Z, Jiang Y. Development and validation of a multiplex conventional PCR assay for simultaneous detection and grouping of porcine bocaviruses. J Virol Methods 2016; 236:164-169. [PMID: 27448821 DOI: 10.1016/j.jviromet.2016.06.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/22/2016] [Accepted: 06/22/2016] [Indexed: 12/13/2022]
Abstract
Porcine bocavirus (PBoV), a newly described porcine parvovirus, has received attention because it can be commonly identified in clinically affected pigs including pigs with post-weaning multisystemic wasting syndrome (PWMS) and pigs with diarrhea. In recent years, novel PBoVs have been identified and were classified into three genogroups, but the ability to detect and classify these novel PBoVs is not comprehensive to date. In this study, a multiplex conventional PCR assay for simultaneous detection and grouping of PBoVs was developed by screening combinations of mixed primer pairs followed by optimization of the PCR conditions. This method exclusively amplifies targeted fragments of 531bp from the VP1 gene of PBoV G1, 291bp from the NP1 gene of PBoV G2, and 384bp from the NP1/VP1 gene of PBoV G3. The assay has a detection limit of 1.0×10(3)copies/μL for PBoV G1 4.5×10(3) for PBoV G2 and 3.8×10(3) for PBoV G3 based on testing mixed purified plasmid constructs containing the specific viral target fragments. The performance of the multiplex PCR assay was comparable to that of the single PCRs which used the same primer pairs. Using the newly established multiplex PCR assay, 227 field samples including faeces, serum and tissue samples from pigs were investigated. All three PBoV genogroups were detected in the clinical samples with a detection rate of 1.3%, 2.6% and 12.3%, respectively for PBoV G1, G2 and G3. Additionally, coinfections with two or more PBoV were detected in 1.7% of the samples investigated. These results indicate the multiplex PCR assay is specific, sensitive and rapid, and can be used for the detection and differentiation of single and multiple infections of the three PBoV genogroups in pigs.
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Affiliation(s)
- Xiaowen Zheng
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Gaopeng Liu
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Tanja Opriessnig
- The Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK; Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Zining Wang
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Zongqi Yang
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yonghou Jiang
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China.
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25
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Zheng X, Liu G, Opriessnig T, Wang Z, Yang Z, Jiang Y. Rapid detection and grouping of porcine bocaviruses by an EvaGreen(®) based multiplex real-time PCR assay using melting curve analysis. Mol Cell Probes 2016; 30:195-204. [PMID: 27180269 DOI: 10.1016/j.mcp.2016.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 05/08/2016] [Accepted: 05/10/2016] [Indexed: 01/20/2023]
Abstract
Several novel porcine bocaviruses (PBoVs) have been identified in pigs in recent years and association of these viruses with respiratory signs or diarrhea has been suggested. In this study, an EvaGreen(®)-based multiplex real-time PCR (EG-mPCR) with melting curve analysis was developed for simultaneous detection and grouping of novel PBoVs into the same genogroups G1, G2 and G3. Each target produced a specific amplicon with a melting peak of 81.3 ± 0.34 °C for PBoV G1, 78.2 ± 0.37 °C for PBoV G2, and 85.0 ± 0.29 °C for PBoV G3. Non-specific reactions were not observed when other pig viruses were used to assess the EG-mPCR assay. The sensitivity of the EG-mPCR assay using purified plasmid constructs containing the specific viral target fragments was 100 copies for PBoV G1, 50 for PBoV G2 and 100 for PBoV G3. The assay is able to detect and distinguish three PBoV groups with intra-assay and inter-assay variations ranging from 0.13 to 1.59%. The newly established EG-mPCR assay was validated with 227 field samples from pigs. PBoV G1, G2 and G3 was detected in 15.0%, 25.1% and 41.9% of the investigated samples and coinfections of two or three PBoV groups were also detected in 25.1% of the cases, indicating that all PBoV groups are prevalent in Chinese pigs. The agreement of the EG-mPCR assay with an EvaGreen-based singleplex real-time PCR (EG-sPCR) assay was 99.1%. This EG-mPCR will serve as a rapid, sensitive, reliable and cost effective alternative for routine surveillance testing of multiple PBoVs in pigs and will enhance our understanding of the epidemiological features and possible also pathogenetic changes associated with these viruses in pigs.
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Affiliation(s)
- Xiaowen Zheng
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Gaopeng Liu
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Tanja Opriessnig
- The Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK; Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Zining Wang
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Zongqi Yang
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yonghou Jiang
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China.
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26
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Saekhow P, Ikeda H. Prevalence and genomic characterization of porcine parvoviruses detected in Chiangmai area of Thailand in 2011. Microbiol Immunol 2015; 59:82-8. [PMID: 25431024 DOI: 10.1111/1348-0421.12218] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Revised: 11/17/2014] [Accepted: 11/24/2014] [Indexed: 12/23/2022]
Abstract
Porcine parvovirus (PPV) causes reproductive failure in sows and has spread worldwide. Several new types of porcine parvoviruses have recently been identified in pig herds. The prevalence of five porcine parvoviruses in the Chiangmai area of Thailand was studied. The prevalence in 80 pigs was 53% for PPV (PPV-Kr or -NADL2 being the new abbreviations), 83% for PPV2 (CnP-PARV4), 73% for PPV3 (P-PARV4), 44% for PPV4 (PPV4), and 18% for PBo-likeV (PBoV7). Over 60% of the pigs carried more than three of the five porcine parvoviruses and occurrence together of the two pairs of viral genes, PPV1/PPV3 and PPV2/PBo-likeV were observed. Phylogenetic analyses for PPV2 and PPV3 indicated the existence of only two major clades of PPV2 and one major clade of PPV3.
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Affiliation(s)
- Prayuth Saekhow
- Laboratory of Veterinary Hygiene, Graduate School of Veterinary Medicine and Life Science, Nippon Veterinary and Life Science University, 1-7-1, Kyonan-cho, Musashino-shi, Tokyo, 180-8602, Japan; Department of Veterinary Biosciences and Public Health, Faculty of Veterinary Medicine, Chiang Mai University, Mae Hia, Muang, Chiang Mai, 50100, Thailand
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27
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Saekhow P, Kishizuka S, Sano N, Mitsui H, Akasaki H, Mawatari T, Ikeda H. Coincidental detection of genomes of porcine parvoviruses and porcine circovirus type 2 infecting pigs in Japan. J Vet Med Sci 2015; 77:1581-6. [PMID: 26166811 PMCID: PMC4710713 DOI: 10.1292/jvms.15-0167] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The infection status of 15 viruses in 120 pigs aged about 6 months was investigated based
on tonsil specimens collected from a slaughterhouse. Only 5 species of porcine
parvoviruses and porcine circovirus type 2 (PCV2) were detected at high frequencies; 67%
for porcine parvovirus (PPV) (PPV-Kr or -NADL2 as the new abbreviation), 58% for PPV2
(CnP-PARV4), 39% for PPV3 (P-PARV4), 33% for PPV4 (PPV4), 55% for PBo-likeV (PBoV7) and
80% for PCV2. A phylogenetic analysis of PPV3 suggested that Japanese PPV3s showed a
slight variation, and possibly, there were farms harboring homogeneous or heterogeneous
PPV3s. Statistical analyses indicated that the detection of PCV2 was significantly
coincidental with each detection of PPV, PPV2 and PPV3, and PPV and PPV4 were also
coincidentally detected. The concurrent infection with PCV2 and porcine parvoviruses in
the subclinically infected pigs may resemble the infection status of pigs with the
clinical manifestations of porcine circovirus associated disease which occurs in 3–5
months old pigs and is thought to be primarily caused by the PCV2 infection.
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Affiliation(s)
- Prayuth Saekhow
- Laboratory of Veterinary Hygiene, Graduate School of Veterinary Medicine and Life Science, Nippon Veterinary and Life Science University, Musashino, Tokyo 180-8602, Japan
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28
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Gunn L, Collins PJ, Fanning S, McKillen J, Morgan J, Staines A, O'Shea H. Detection and characterisation of novel bocavirus (genus Bocaparvovirus) and gastroenteritis viruses from asymptomatic pigs in Ireland. Infect Ecol Epidemiol 2015; 5:27270. [PMID: 26065833 PMCID: PMC4462827 DOI: 10.3402/iee.v5.27270] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 05/10/2015] [Accepted: 05/11/2015] [Indexed: 12/13/2022] Open
Abstract
Background Livestock animals have been the assumed source of several human epidemics in recent years, for example, influenza H1N1, rotavirus G8/G9, and MERS-CoV. Surveillance of novel viruses in animals is essential to evaluate the risk to human and animal health and to determine any economic impact, for example, failure to thrive. There is a paucity of data regarding detection and characterisation of gastroenteritis viruses, particularly novel viruses, in porcines in Ireland. Recently, a number of small novel porcine DNA viruses have emerged globally, for example, torque teno sus virus, porcine bocavirus, and parvoviruses 2 & 4, and little is known about the biology and potential pathogenicity of these viruses. Bocaparvovirus is a genetically distinct group of viruses which has been recently detected in humans and animals. Methods In this study, the presence of gastroenteritis viruses (rotavirus A, porcine circovirus, adenovirus, and porcine bocavirus) was investigated in a selection of archived faecal samples from asymptomatic piglets from a commercial farm in Ireland. A total of 104 specimens were pooled and screened using conventional molecular techniques (PCR and RT-PCR), a subset of specimens (n=44) were then examined individually. Viral diversity was then investigated using statistical and phylogenetic techniques. Results Initial screening showed a high prevalence of PBoV in this farm, with the formation of three distinct groups in phylogenetic analysis. Other viruses were also investigated in this study with the first report of PCV, PAdV and lineage I G5 RVA in Ireland. Some specimens contained >1 virus, with statistical analysis indicating a strong correlation for mixed infections of PBoV and PAdV on this farm. Conclusion Investigating the diversity of circulating enteric viruses on Irish porcine farms is important to improve the prophylactic tools available and to facilitate the early detection of changes in circulating viruses.
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Affiliation(s)
- Lynda Gunn
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
| | | | - Séamus Fanning
- School of Public Health, Physio & Pop Sc, Science Centre - South, Dublin 4, Ireland
| | - John McKillen
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, United Kingdom
| | - John Morgan
- School of Microbiology, University College Cork, Cork, Ireland
| | - Anthony Staines
- School of Nursing, Dublin City University, Dublin 9, Ireland
| | - Helen O'Shea
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland;
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29
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Porcine bocavirus: achievements in the past five years. Viruses 2014; 6:4946-60. [PMID: 25514206 PMCID: PMC4276938 DOI: 10.3390/v6124946] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 12/01/2014] [Accepted: 12/02/2014] [Indexed: 01/05/2023] Open
Abstract
Porcine bocavirus is a recently discovered virus that infects pigs and is classified within the Bocavirus genus (family Parvoviridae, subfamily Parvovirinae). The viral genome constitutes linear single-stranded DNA and has three open reading frames that encode four proteins: NS1, NP1, VP1, and VP2. There have been more than seven genotypes discovered to date. These genotypes have been classified into three groups based on VP1 sequence. Porcine bocavirus is much more prevalent in piglets that are co-infected with other pathogens than in healthy piglets. The virus can be detected using PCR, loop-mediated isothermal amplification, cell cultures, indirect immunofluorescence, and other molecular virology techniques. Porcine bocavirus has been detected in various samples, including stool, serum, lymph nodes, and tonsils. Because this virus was discovered only five years ago, there are still many unanswered questions that require further research. This review summarizes the current state of knowledge and primary research achievements regarding porcine bocavirus.
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30
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Dumarest M, Muth E, Cheval J, Gratigny M, Hébert C, Gagnieur L, Eloit M. Viral diversity in swine intestinal mucus used for the manufacture of heparin as analyzed by high-throughput sequencing. Biologicals 2014; 43:31-6. [PMID: 25466699 PMCID: PMC7172073 DOI: 10.1016/j.biologicals.2014.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 09/18/2014] [Accepted: 10/23/2014] [Indexed: 12/17/2022] Open
Abstract
Heparin is one of the main pharmaceutical products manufactured from raw animal material. In order to describe the viral burden associated with this raw material, we performed high-throughput sequencing (HTS) on mucus samples destined for heparin manufacturing, which were collected from European pigs. We identified Circoviridae and Parvoviridae members as the most prevalent contaminating viruses, together with viruses from the Picornaviridae, Astroviridae, Reoviridae, Caliciviridae, Adenoviridae, Birnaviridae, and Anelloviridae families. Putative new viral species were also identified. The load of several known or novel small non-enveloped viruses, which are particularly difficult to inactivate or eliminate during heparin processing, was quantified by qPCR. Analysis of the combined HTS and specific qPCR results will influence the refining and validation of inactivation procedures, as well as aiding in risk analysis of viral heparin contamination.
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Affiliation(s)
- Marine Dumarest
- Institut Pasteur, Laboratory of Pathogen Discovery, Department of Virology, 28 rue du Docteur Roux, F-75724 Paris, France
| | - Erika Muth
- PathoQuest, Bâtiment François Jacob, 25 rue du Dr Roux, 75015 Paris, France
| | - Justine Cheval
- PathoQuest, Bâtiment François Jacob, 25 rue du Dr Roux, 75015 Paris, France
| | - Marlène Gratigny
- PathoQuest, Bâtiment François Jacob, 25 rue du Dr Roux, 75015 Paris, France
| | - Charles Hébert
- PathoQuest, Bâtiment François Jacob, 25 rue du Dr Roux, 75015 Paris, France
| | - Léa Gagnieur
- Institut Pasteur, Laboratory of Pathogen Discovery, Department of Virology, 28 rue du Docteur Roux, F-75724 Paris, France
| | - Marc Eloit
- Institut Pasteur, Laboratory of Pathogen Discovery, Department of Virology, 28 rue du Docteur Roux, F-75724 Paris, France; PathoQuest, Bâtiment François Jacob, 25 rue du Dr Roux, 75015 Paris, France; Ecole Nationale Vétérinaire d'Alfort, UMR 1161 Virologie ENVA, INRA, ANSES, 7 Avenue Général de Gaulle, F-94704 Maisons Alfort, France.
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Evolutionary, epidemiological, demographical, and geographical dissection of porcine bocavirus in China and America. Virus Res 2014; 195:13-24. [PMID: 25289962 DOI: 10.1016/j.virusres.2014.09.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 09/24/2014] [Accepted: 09/25/2014] [Indexed: 12/26/2022]
Abstract
Porcine bocavirus was first discovered in Swedish pigs with post-weaning multisystemic wasting syndrome (PMWS) in 2009. Many efforts have been implemented to investigate the porcine bocavirus, but it remains enigmatic. In the current study, we utilized data from both China and the USA. The China-derived data included 403 pig samples collected from five provinces, 122 gene sequences from the GenBank database, and 637 old porcine bocavirus (PBoV) cases. The USA-derived data comprised 181 pig samples from 18 states, 39 new gene sequences, and 85 new emerging cases. First, we executed a comprehensive analysis of the disease's prevalence, phylogenetics, evolutionary distances, mutation network, geographical distribution, occurrence frequency, and phylogeographical estimation in both China and the USA. The results showed that the positive rates of PBoV (42.0%, 76/181) in American samples were significantly higher than those (11.4%, 46/403) in the Chinese samples. All PBoV cases from these countries can be divided into six groups: PBoV1 (group 1), PBoV2 (group 2), PBoV3C (group 3), PBoV5 (group 4), PBoV3/4 (group 5), and PBoV6V7V (group 6). PBoV1 and PBoV2 were epidemic strains from 2006 to 2011 in China, whereas the PBoV3 subtypes were epidemic from 2010 to 2012 in China and the USA. At present, PBoV3C (group 3), PBoV5 (group 4), and PBoV3/4 (group 5) are epidemic viruses and co-exist in China and the USA. The geographical distribution of PBoV mainly lies in the east and south coastal areas of China and the central states of the USA. Jiangsu Province and the state of Minnesota were the centers of high occurrence frequency of PBoV with six outbreaks. The old PBoV cases involved 14 provinces and regions of China and North Carolina in the USA, whereas the new emerging cases involved five provinces in China and 13 states in the USA, of which two provinces and 12 states reported for the first time that piglets were infected by PBoV. Hong Kong, Hebei, and Jiangsu Provinces and the states of Minnesota and North Carolina were possibly geographical origins of PBoV in China and America, respectively. These data can help us systematically understand porcine bocavirus in China and America and find effective strategies for its treatment.
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32
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Zhang W, Li L, Deng X, Kapusinszky B, Delwart E. What is for dinner? Viral metagenomics of US store bought beef, pork, and chicken. Virology 2014; 468-470:303-310. [PMID: 25217712 PMCID: PMC4252299 DOI: 10.1016/j.virol.2014.08.025] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 08/14/2014] [Accepted: 08/22/2014] [Indexed: 12/16/2022]
Abstract
We describe here the metagenomics-derived viral sequences detected in beef, pork, and chicken purchased from stores in San Francisco. In beef we detected four previously reported viruses (two parvoviruses belonging to different genera, an anellovirus, and one circovirus-like virus) and one novel bovine polyomavirus species (BPyV2-SF) whose closest relatives infect primates. Detection of porcine hokovirus in beef indicated that this parvovirus can infect both ungulate species. In pork we detected four known parvoviruses from three genera, an anellovirus, and pig circovirus 2. Chicken meat contained numerous gyrovirus sequences including those of chicken anemia virus and of a novel gyrovirus species (GyV7-SF). Our results provide an initial characterization of some of the viruses commonly found in US store-bought meats which included a diverse group of parvoviruses and viral families with small circular DNA genomes. Whether any of these viruses can infect humans will require testing human sera for specific antibodies. Eukaryotic viral genomes in store-bought beef, pork, and chicken are identified. A novel bovine polyomavirus genome, closest to a group of viruses from primates, is sequenced. Porcine hokovirus is detected in beef samples. A small circovirus-like circular DNA genome in beef is genetically characterized. Several species of gyrovirus including a novel species are detected in chicken meat.
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Affiliation(s)
- Wen Zhang
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Microbiology, School of Medicine, Jiangsu University, Jiangsu, Zhenjiang 212013, China; Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118, USA
| | - Linlin Li
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118, USA
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118, USA
| | - Beatrix Kapusinszky
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA 94118, USA; Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118, USA.
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Bodewes R, Lapp S, Hahn K, Habierski A, Förster C, König M, Wohlsein P, Osterhaus ADME, Baumgärtner W. Novel canine bocavirus strain associated with severe enteritis in a dog litter. Vet Microbiol 2014; 174:1-8. [PMID: 25263495 PMCID: PMC7117162 DOI: 10.1016/j.vetmic.2014.08.025] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/29/2014] [Accepted: 08/26/2014] [Indexed: 12/13/2022]
Abstract
An outbreak of fatal enteritis occurred in a dog litter. Major known causes of enteritis of young dogs were excluded. A novel canine bocavirus 2 strain was detected by random PCR and NGS. CaBoV-2 was detected in the intestinal tract and lymphoid tissue by ISH. No additional cases were identified by a small retrospective analysis.
Bocaviruses are small non-enveloped viruses with a linear ssDNA genome, that belong to the genus Bocaparvovirus of the subfamiliy Parvovirinae. Bocavirus infections are associated with a wide spectrum of disease in humans and various mammalian species. Here we describe a fatal enteritis associated with infection with a novel strain of canine bocavirus 2 (CaBoV-2), that occurred in a litter of German wirehaired pointers. Necropsy performed on three puppies revealed an enteritis reminiscent of canine parvovirus associated enteritis, accompanied with signs of lymphocytolytic disease in bone marrow, spleen, lymph nodes and thymus. While other major causes of enteritis of young dogs, including canine parvovirus, were excluded, by random PCR in combination with next-generation sequencing, a novel CaBoV-2 strain was detected. Phylogenetic analysis of the genome of this novel canine bocavirus strain indicated that this virus was indeed most closely related to group 2 canine bocaviruses. Infection with canine bocavirus was confirmed by in situ hybridization, which revealed the presence of CaBoV-2 nucleic acid in the intestinal tract and lymphoid tissues of the dogs. In a small-scale retrospective analysis concerning the role of CaBoV-2 no additional cases were identified. The findings of this study provide novel insights into the pathogenicity of canine bocaviruses.
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Affiliation(s)
- Rogier Bodewes
- Department of Viroscience, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands.
| | - Stefanie Lapp
- Department of Pathology, University of Veterinary Medicine Hannover, Bünteweg 17, D-30559 Hannover, Germany
| | - Kerstin Hahn
- Department of Pathology, University of Veterinary Medicine Hannover, Bünteweg 17, D-30559 Hannover, Germany
| | - André Habierski
- Department of Pathology, University of Veterinary Medicine Hannover, Bünteweg 17, D-30559 Hannover, Germany
| | - Christine Förster
- Institute of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University, Schubertstraße 81, 35392 Gießen, Germany
| | - Matthias König
- Institute of Virology, Faculty of Veterinary Medicine, Justus-Liebig-University, Schubertstraße 81, 35392 Gießen, Germany
| | - Peter Wohlsein
- Department of Pathology, University of Veterinary Medicine Hannover, Bünteweg 17, D-30559 Hannover, Germany
| | - Albert D M E Osterhaus
- Department of Viroscience, Erasmus MC, Dr. Molewaterplein 50, 3015GE Rotterdam, The Netherlands; Department of Pathology, University of Veterinary Medicine Hannover, Bünteweg 17, D-30559 Hannover, Germany; Viroclinics Biosciences B.V., Marconistraat 16, 3029 AK Rotterdam, The Netherlands
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Bünteweg 17, D-30559 Hannover, Germany
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Zhang W, Li L, Deng X, Kapusinszky B, Pesavento PA, Delwart E. Faecal virome of cats in an animal shelter. J Gen Virol 2014; 95:2553-2564. [PMID: 25078300 DOI: 10.1099/vir.0.069674-0] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We describe the metagenomics-derived feline enteric virome in the faeces of 25 cats from a single shelter in California. More than 90 % of the recognizable viral reads were related to mammalian viruses and the rest to bacterial viruses. Eight viral families were detected: Astroviridae, Coronaviridae, Parvoviridae, Circoviridae, Herpesviridae, Anelloviridae, Caliciviridae and Picobirnaviridae. Six previously known viruses were also identified: feline coronavirus type 1, felid herpes 1, feline calicivirus, feline norovirus, feline panleukopenia virus and picobirnavirus. Novel species of astroviruses and bocaviruses, and the first genome of a cyclovirus in a feline were characterized. The RNA-dependent RNA polymerase region from four highly divergent partial viral genomes in the order Picornavirales were sequenced. The detection of such a diverse collection of viruses shed within a single shelter suggested that such animals experience robust viral exposures. This study increases our understanding of the viral diversity in cats, facilitating future evaluation of their pathogenic and zoonotic potentials.
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Affiliation(s)
- Wen Zhang
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118, USA.,Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China.,Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118, USA
| | - Linlin Li
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118, USA.,Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118, USA
| | - Xutao Deng
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118, USA.,Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118, USA
| | - Beatrix Kapusinszky
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118, USA.,Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118, USA
| | - Patricia A Pesavento
- Department of Pathology, Microbiology, and Immunology, University of California Davis, Davis, CA 95616, USA
| | - Eric Delwart
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118, USA.,Blood Systems Research Institute, Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 94118, USA
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Zhang B, Tang C, Yue H, Ren Y, Song Z. Viral metagenomics analysis demonstrates the diversity of viral flora in piglet diarrhoeic faeces in China. J Gen Virol 2014; 95:1603-1611. [DOI: 10.1099/vir.0.063743-0] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
To investigate the diversity of viral flora, we used metagenomics to study the viral communities in a pooled faecal sample of 27 diarrhoeic piglets from intensive commercial farms in China. The 15 distinct mammalian viruses identified in the pooled diarrhoeic sample were, in order of abundance of nucleic acid sequence, Porcine epidemic diarrhea virus (PEDV), sapovirus, porcine bocavirus-4 (PBoV-4), sapelovirus, torovirus, coronavirus, PBoV-2, stool-associated single-stranded DNA virus (poSCV), astrovirus (AstV), kobuvirus, posavirus-1, porcine enterovirus-9 (PEV-9), porcine circovirus-like (po-circo-like) virus, picobirnavirus (PBV) and Torque teno sus virus 2 (TTSuV-2). The prevalence rate of each virus was verified from diarrhoeic and healthy piglets by PCR assay. A mean of 5.5 different viruses were shed in diarrhoeic piglets, and one piglet was in fact co-infected with 11 different viruses. By contrast, healthy piglets shed a mean of 3.2 different viruses. Compared with samples from healthy piglets, the co-infection of PEDV and PBoV had a high prevalence rate in diarrhoea samples, suggesting a correlation with the appearance of diarrhoea in piglets. Furthermore, we report here for the first time the presence of several recently described viruses in China, and the identification of novel genotypes. Therefore, our investigation results provide an unbiased survey of viral communities and prevalence in faecal samples of piglets.
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Affiliation(s)
- Bin Zhang
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu 610041, PR China
| | - Cheng Tang
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu 610041, PR China
| | - Hua Yue
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu 610041, PR China
| | - Yupeng Ren
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu 610041, PR China
| | - Zhigang Song
- College of Life Science and Technology, Southwest University for Nationalities, Chengdu 610041, PR China
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36
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Wang X, Bai A, Zhang J, Kong M, Cui Y, Ma X, Ai X, Tang Q, Cui S. A new nanoPCR molecular assay for detection of porcine bocavirus. J Virol Methods 2014; 202:106-11. [PMID: 24642242 DOI: 10.1016/j.jviromet.2014.02.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 02/24/2014] [Accepted: 02/27/2014] [Indexed: 01/23/2023]
Abstract
Nanoparticle-assisted polymerase chain reaction (nanoPCR) is a novel method for the rapid amplification of DNA and has been used for the detection of virus. For detection of porcine bocavirus (PBoV), a sensitive and specific nanoPCR assay was developed with a pair of primers that were designed based on NS1 gene sequences available in GenBank. Under the optimized conditions of the PBoV nanoPCR assay, the nanoPCR assay was 100-fold more sensitive than a conventional PCR assay. The lower detection limit of the nanoPCR assay was about 6.70×10(1) copies. The nanoPCR assay amplified the specific 482-bp fragment of the PBoV NS1 recombinant plasmid but did not produce any product with genomic DNA or cDNA of porcine parvovirus, porcine circovirus type II, porcine reproductive and respiratory syndrome virus, pseudorabies virus, classic swine fever virus, Encephalomyocarditis virus, Porcine Teschovirus or African swine fever virus plasmid. Of 65 clinical samples collected from diseased pigs, 73.8% and 86.2% were determined to be PBoV positive by PBoV conventional PCR and PBoV nanoPCR assay, respectively. Of 36 clinical samples from healthy pigs, 27.8% and 44.4% were PBoV positive by PBoV conventional PCR and PBoV nanoPCR assay, respectively. The nanoPCR assay will be useful for diagnosing PBoV and for studying its epidemiology and pathology.
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Affiliation(s)
- Xiaoling Wang
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, China
| | - Aiquan Bai
- Foshan University, Foshan, Guandong, China.
| | - Jing Zhang
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, China
| | - Miaomiao Kong
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, China
| | - Yuchao Cui
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, China
| | - Xingjie Ma
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, China
| | - Xia Ai
- College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, China
| | - Qinghai Tang
- Nanyang Normal University, 1638 Wolong Road, Nanyang 473061, China.
| | - Shangjin Cui
- Division of Swine Infectious Diseases, State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, China.
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37
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Detection and genetic analysis of porcine bocavirus in different swine herds in North Central China. ScientificWorldJournal 2014; 2014:947084. [PMID: 24701194 PMCID: PMC3950361 DOI: 10.1155/2014/947084] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 01/12/2014] [Indexed: 02/07/2023] Open
Abstract
Porcine Bocavirus (PBoV) has been reported to be associated with postweaning multisystemic wasting syndrome and pneumonia in pigs. In this study, a survey was conducted to evaluate the prevalence of PBoV in slaughter pigs, sick pigs, asymptomatic pigs and classical swine fever virus (CSFV) eradication plan herds in five provinces of China (Henan, Liaoning, Shandong, Hebei and Tianjin) by means of PCR targeting NS1 gene of PBoV. Among the total of 403 tissue samples, 11.41% were positive for PBoV. The positive rates of spleen (20.75%) and inguinal lymph node (27.18%) are higher than those of other organs. PCR products of twenty PBoV positive samples from slaughter pigs were sequenced for phylogenetic analysis. The result revealed that PBoV could be divided into 6 groups (PBoV-a~PBoV-f). All PBoV sequenced in this study belong to PBoV-a-PBoV-d with 90.1% to 99% nucleotide identities. Our results exhibited significant genetic diversity of PBoV and suggested a complex prevalence of PBoV in Chinese swine herds. Whether this diversity of PBoV has a significance to pig production or even public health remains to be further studied.
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38
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Jiang YH, Xiao CT, Yin SH, Gerber PF, Halbur PG, Opriessnig T. High prevalence and genetic diversity of porcine bocaviruses in pigs in the USA, and identification of multiple novel porcine bocaviruses. J Gen Virol 2014; 95:453-465. [DOI: 10.1099/vir.0.057042-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Viruses in the genus Bocavirus are associated with respiratory and enteric disease in dogs and cattle. In addition, novel porcine bocaviruses (PBoVs) have been identified in domestic and wild pigs in recent years, but are of unknown relevance to date. The objectives of this study were to determine the prevalence ra
tes and genetic diversity of PBoVs in pigs in the USA. Using newly established multiplex real-time PCR assays, 385 lung, lymph node, serum and faecal samples from pigs with various disease conditions were investigated. A high PBoV prevalence rate ranging from 21.3 to 50.8 % was identified in the investigated samples and often two or more PBoV species were detected in the same sample. Cloning and sequencing analysis of the partial non-structural protein NS1 and the capsid proteins VP1 and VP2 of DNA samples positive for PBoV groups 1 (n = 6), 2 (n = 16) and 3 (n = 42), including subgroups 3A, 3B or 3C, revealed a high genetic diversity especially for the PBoV G3 VP2 gene, whereas the PBoV group 1 VP1 gene displayed a low nucleotide polymorphism. Using primer walking, 18 partial or nearly complete genomes of PBoVs were obtained and six of the 18 nearly complete genomes represented novel PBoV species. Recombination analysis using partial NS1, VP1 and VP2 genes and the nearly complete genomes indicated possible recombination events within and between PBoVs. Further studies will be required to reveal the possible pathogenic role of these diverse PBoVs.
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Affiliation(s)
- Yong-Hou Jiang
- College of Life Science, Zhejiang Sci-Tech University, Hangzhou, PR China
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Chao-Ting Xiao
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Shuang-Hui Yin
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Priscilla F. Gerber
- Laboratório de Pesquisa em Virologia Animal, Departamento de Medicina Veterinária Preventiva, Universidade Federal de Minas Gerais, Minas Gerais, Brazil
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Patrick G. Halbur
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Tanja Opriessnig
- The Roslin Institute and The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
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39
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Wang E, Liu W, Yang B, Liu J, Ma X, Lan X. Complete sequence and phylogenetic analysis of a porcine bocavirus strain swBoV CH437. Virus Genes 2014; 48:387-90. [PMID: 24469465 DOI: 10.1007/s11262-013-1032-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 12/31/2013] [Indexed: 12/25/2022]
Abstract
Porcine bocavirus (PBoV), a member of genus Bocavirus, family Parvoviridae, was first identified in 2009 in Swedish swine herds suffering from postweaning multisystemic wasting syndrome. Up to date, the different species of PBoVs have been reported in different countries. Especially, the virus isolated in China was complicated. In this study, we detected a novel PBoV strain swBoV CH437 from clinical samples collected in Gansu Province, Northwest China. The complete genome of swBoV CH437 was 5,275 nucleotides (nt) in length and contains three ORFs: ORF1 encodes NS1 (2,004 nt, 667 aa), ORF3 encodes NP1 (681 nt, 226 aa), and ORF2 encodes VP1 (2,049 nt, 682 aa) and VP2 (1,641 nt, 546 aa). Sequence analysis demonstrated that the NS1 gene shared 24.2-88.6 % nucleotide sequence identity, the NP1 shared 21.3-89.9 %, less than 95 % nucleotide sequence identity with other PBoV strains. Therefore, we propose that swBoV CH437 should be classified as a novel PBoV species.
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Affiliation(s)
- Enli Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Grazing Animal Diseases, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
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40
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Wu R, Wen Y, Huang X, Wen X, Yan Q, Huang Y, Ma X, Cao S. First complete genomic characterization of a porcine parvovirus 5 isolate from China. Arch Virol 2013; 159:1533-6. [PMID: 24327097 DOI: 10.1007/s00705-013-1948-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 11/06/2013] [Indexed: 12/30/2022]
Abstract
To investigate porcine parvovirus 5 (PPV5) infections in swine herds in China, clinical specimens of piglet lungs were examined for the presence of PPV5 using a polymerase chain reaction method. A strain of PPV5 was detected, and its genome was sequenced and analyzed. In the sequence alignment and phylogenetic analysis, the Chinese PPV5 strain clustered into a distinct clade with the reference PPV5 strains. These results provide direct evidence that PPV5 is present in pigs in China. Extensive epidemiological studies are warranted to determine the geographic distribution of PPV5 in China.
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Affiliation(s)
- Rui Wu
- College of Veterinary Medicine, Sichuan Agricultural University, 46 Xinkang Road, Yucheng District, Ya'an, 625000, Sichuan, China
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41
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Bodewes R, van der Giessen J, Haagmans BL, Osterhaus ADME, Smits SL. Identification of multiple novel viruses, including a parvovirus and a hepevirus, in feces of red foxes. J Virol 2013; 87:7758-64. [PMID: 23616657 PMCID: PMC3700315 DOI: 10.1128/jvi.00568-13] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 04/12/2013] [Indexed: 02/07/2023] Open
Abstract
Red foxes (Vulpes vulpes) are the most widespread members of the order of Carnivora. Since they often live in (peri)urban areas, they are a potential reservoir of viruses that transmit from wildlife to humans or domestic animals. Here we evaluated the fecal viral microbiome of 13 red foxes by random PCR in combination with next-generation sequencing. Various novel viruses, including a parvovirus, bocavirus, adeno-associated virus, hepevirus, astroviruses, and picobirnaviruses, were identified.
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Affiliation(s)
- Rogier Bodewes
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands.
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42
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Detection of novel porcine bocaviruses in fecal samples of asymptomatic pigs in Cameroon. INFECTION GENETICS AND EVOLUTION 2013; 17:277-82. [DOI: 10.1016/j.meegid.2013.03.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 02/21/2013] [Accepted: 03/01/2013] [Indexed: 12/17/2022]
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43
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Xiao CT, Giménez-Lirola LG, Jiang YH, Halbur PG, Opriessnig T. Characterization of a novel porcine parvovirus tentatively designated PPV5. PLoS One 2013; 8:e65312. [PMID: 23762339 PMCID: PMC3676418 DOI: 10.1371/journal.pone.0065312] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 04/25/2013] [Indexed: 12/28/2022] Open
Abstract
A new porcine parvovirus (PPV), provisionally designated as PPV5, was identified in U.S. pigs. Cloning and sequencing from a circular or head-to-tail concatemeric array revealed that the PPV5 possesses the typical genomic organization of parvoviruses with two major predicted open reading frames (ORF1 and ORF2), and is most closely related to PPV4 with overall genomic identities of 64.1–67.3%. The amino acid identities between PPV5 and PPV4 were 84.6%–85.1% for ORF1 and 54.0%–54.3% for ORF2. Unlike PPV4, but similar to bovine parvovirus 2 (BPV2), PPV5 lacks the additional ORF3 and has a much longer ORF2. Moreover, the amino acid sequences of ORF1 and ORF2 of BPV2 showed higher homologies to PPV5 than to PPV4. The conserved motifs of the Ca2+ binding loop (YXGXG) and the catalytic center (HDXXY) of phospholipase A2 (PLA2) were identified in VP1 (ORF2) of PPV5, as well as in BPV2, but were not present in PPV4. Phylogenetic analyses revealed that PPV5, PPV4 and BPV2 form a separate clade different from the genera Parvovirus and Bocavirus. Further epidemiologic investigations of PPV4 and PPV5 in U.S. pigs of different ages indicated a slightly higher prevalence for PPV5 (6.6%; 32/483) compared to PPV4 (4.1%; 20/483), with detection of concurrent PPV4 and PPV5 in 15.6% (7/45) of lungs of infected pigs. Evidence for potential vertical transmission or association with reproductive failure was minimal for both PPV4 and PPV5. The high similarity to PPV4 and the lack of ORF3 may suggest PPV5 is an intermediate of PPV4 during the evolution of parvoviruses in pigs.
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Affiliation(s)
- Chao-Ting Xiao
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Luis G. Giménez-Lirola
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Yong-Hou Jiang
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Patrick G. Halbur
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Tanja Opriessnig
- Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
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44
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Molecular evolutionary genetic analysis of emerging parvoviruses identified in pigs. INFECTION GENETICS AND EVOLUTION 2013; 16:369-76. [DOI: 10.1016/j.meegid.2013.03.017] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 03/07/2013] [Accepted: 03/12/2013] [Indexed: 12/18/2022]
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45
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McMenamy MJ, McKillen J, McNair I, Duffy C, Blomström AL, Charreyre C, Welsh M, Allan G. Detection of a porcine boca-like virus in combination with porcine circovirus type 2 genotypes and Torque teno sus virus in pigs from postweaning multisystemic wasting syndrome (PMWS)-affected and non-PMWS-affected farms in archival samples from Great Britain. Vet Microbiol 2013; 164:293-8. [PMID: 23578709 DOI: 10.1016/j.vetmic.2013.03.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 10/25/2012] [Accepted: 03/01/2013] [Indexed: 01/14/2023]
Abstract
In this study we detail the detection and genetic analysis of a novel porcine boca-like virus (PBo-likeV) in archival sera and tissue samples from pigs from farms in Great Britain. We also investigate the distribution of porcine circovirus type 2 (PCV2) genotypes and Torque teno sus virus (TTSuV) genogroups 1 and 2 in combination with this novel PBo-likeV. PBo-likeV was detected in over 70% of all tissues investigated. Over 24% of all tissues recovered from PMWS-affected animals had all viruses present and 25% of tissues recovered from non-PMWS-affected pigs were positive for all 4 viruses.
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Affiliation(s)
- Michael J McMenamy
- Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, Northern Ireland BT4 3SD, United Kingdom.
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46
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Li L, Pesavento PA, Leutenegger CM, Estrada M, Coffey LL, Naccache SN, Samayoa E, Chiu C, Qiu J, Wang C, Deng X, Delwart E. A novel bocavirus in canine liver. Virol J 2013; 10:54. [PMID: 23402347 PMCID: PMC3577433 DOI: 10.1186/1743-422x-10-54] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 01/31/2013] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Bocaviruses are classified as a genus within the Parvoviridae family of single-stranded DNA viruses and are pathogenic in some mammalian species. Two species have been previously reported in dogs, minute virus of canines (MVC), associated with neonatal diseases and fertility disorders; and Canine bocavirus (CBoV), associated with respiratory disease. FINDINGS In this study using deep sequencing of enriched viral particles from the liver of a dog with severe hemorrhagic gastroenteritis, necrotizing vasculitis, granulomatous lymphadenitis and anuric renal failure, we identified and characterized a novel bocavirus we named Canine bocavirus 3 (CnBoV3). The three major ORFs of CnBoV3 (NS1, NP1 and VP1) shared less than 60% aa identity with those of other bocaviruses qualifying it as a novel species based on ICTV criteria. Inverse PCR showed the presence of concatemerized or circular forms of the genome in liver. CONCLUSIONS We genetically characterized a bocavirus in a dog liver that is highly distinct from prior canine bocaviruses found in respiratory and fecal samples. Its role in this animal's complex disease remains to be determined.
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Affiliation(s)
- Linlin Li
- Blood Systems Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Patricia A Pesavento
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | | | | | - Lark L Coffey
- Blood Systems Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Samia N Naccache
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, CA, USA
| | - Erik Samayoa
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, CA, USA
| | - Charles Chiu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, CA, USA
| | - Jianming Qiu
- Department of Microbiology, University of Kansas, KS, USA
| | - Chunlin Wang
- Stanford Genome Technology Center, Stanford, CA, USA
| | - Xutao Deng
- Blood Systems Research Institute, San Francisco, CA, USA
| | - Eric Delwart
- Blood Systems Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
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47
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Abstract
Astroviruses have been widely described in mammalian and avian species. Here, we report a complete genome sequence of a novel porcine astrovirus (PoAstV) isolated from a porcine fecal sample in China. The genome consists of 6,611 nucleotides, excluding the 3' poly(A) tail, and has two open reading frames (ORFs). ORF1 maps between nucleotide positions 19 and 4211 and encodes a 1,396-amino-acid (aa) polyprotein precursor consisting of nonstructural protein and putative RNA-dependent RNA polymerase, and ORF2 maps between nucleotide positions 4202 and 6531 and encodes a 775-aa polyprotein which is a capsid precursor protein. The genome sequence of the virus was distinct enough from those of the known PoAstVs to be considered a novel sequence. Phylogenetic analysis based on the predicted amino acid sequence of the complete capsid region showed that this strain may be a novel porcine astrovirus.
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48
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Genetic characterisation of a porcine bocavirus detected in domestic pigs in Uganda. Virus Genes 2012; 47:370-3. [PMID: 23225112 PMCID: PMC3907790 DOI: 10.1007/s11262-012-0855-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 11/21/2012] [Indexed: 12/20/2022]
Abstract
Porcine bocaviruses (PoBoVs) are small linear ssDNA viruses belonging to the genus bocavirus in the family Parvoviridae. The genome encodes four proteins—the non-structural protein 1 (NS1), the NP1 protein (unknown function) and the two structural proteins VP1 and VP2. In recent years, a number of different highly divergent PoBoV species have been discovered. PoBoVs have been shown to be present in pig populations in Europe, Asia and in the United States of America. In this study, we present the first data of the presence of PoBoV in Africa, specifically in Uganda. A PCR targeting a PoBoV species that have previously been detected in both Sweden and China was used to screen 95 serum samples from domestic pigs in Uganda. Two pigs were found to be positive for this specific PoBoV and the complete coding region was amplified from one of these samples. The amino acid sequence comparison of all these proteins showed a high identity (98–99 %) to the published Chinese sequences (strains: H18 and SX) belonging to the same PoBoV species. The same was true for the Swedish sequences from the same species. To the other PoBoV species the divergence was higher and only a 28–43 % protein sequence identity was seen comparing the different proteins.
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Virome analysis for identification of novel mammalian viruses in bat species from Chinese provinces. J Virol 2012; 86:10999-1012. [PMID: 22855479 DOI: 10.1128/jvi.01394-12] [Citation(s) in RCA: 218] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bats are natural hosts for a large variety of zoonotic viruses. This study aimed to describe the range of bat viromes, including viruses from mammals, insects, fungi, plants, and phages, in 11 insectivorous bat species (216 bats in total) common in six provinces of China. To analyze viromes, we used sequence-independent PCR amplification and next-generation sequencing technology (Solexa Genome Analyzer II; Illumina). The viromes were identified by sequence similarity comparisons to known viruses. The mammalian viruses included those of the Adenoviridae, Herpesviridae, Papillomaviridae, Retroviridae, Circoviridae, Rhabdoviridae, Astroviridae, Flaviridae, Coronaviridae, Picornaviridae, and Parvovirinae; insect viruses included those of the Baculoviridae, Iflaviridae, Dicistroviridae, Tetraviridae, and Densovirinae; fungal viruses included those of the Chrysoviridae, Hypoviridae, Partitiviridae, and Totiviridae; and phages included those of the Caudovirales, Inoviridae, and Microviridae and unclassified phages. In addition to the viruses and phages associated with the insects, plants, and bacterial flora related to the diet and habitation of bats, we identified the complete or partial genome sequences of 13 novel mammalian viruses. These included herpesviruses, papillomaviruses, a circovirus, a bocavirus, picornaviruses, a pestivirus, and a foamy virus. Pairwise alignments and phylogenetic analyses indicated that these novel viruses showed little genetic similarity with previously reported viruses. This study also revealed a high prevalence and diversity of bat astroviruses and coronaviruses in some provinces. These findings have expanded our understanding of the viromes of bats in China and hinted at the presence of a large variety of unknown mammalian viruses in many common bat species of mainland China.
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Abstract
Using a high-throughput DNA sequencing method, one DNA sequence (contig01006), suspected to belong to a novel porcine bocavirus (PBoV), was found with a high rate of detection (19.6 %) in fecal samples from healthy piglets. Moreover, a novel PBoV (tentatively named PBoV3C) with a nearly complete genome sequence (5235 bp) was identified. PBoV3C exhibits typical genome characteristics of bocaviruses and shows the highest genomic sequence identity (78 % to 81 %) to PBoV3A/B (PBoV3/4-UK) and PBoV3D/E (PBoV3/4-HK), respectively. Phylogenetic and recombination analysis indicated high diversity, prevalence and complexity among the PBoVs. The phospholipase A2 (PLA2) site of VP1 and the secondary structure of VP2 of PBoV3C were also analyzed. Additionally, we propose a uniform method of PBoV nomenclature based on the VP1 gene.
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