1
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Timm FCB, Campos FS, Janssen L, Dos Santos RN, Paredes-Galarza B, Stone NV, Oliveira MT, Gasparetto R, Müller NFD, Melgarejo ADS, Corrêa ML, Lozano LMV, Salvato RS, Godinho FMDS, Barcellos RB, Teixeira MADS, Riet-Correa G, Cerqueira VD, Bezerra Júnior PS, Franco AC, Roehe PM. The virome of bubaline (Bubalus bubalis) tonsils reveals an unreported bubaline polyomavirus. Braz J Microbiol 2024:10.1007/s42770-024-01449-0. [PMID: 39014291 DOI: 10.1007/s42770-024-01449-0] [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: 12/26/2023] [Accepted: 06/17/2024] [Indexed: 07/18/2024] Open
Abstract
Water buffalo (Bubalus bubalis) farming is increasing in many regions of the world due to the species' ability to thrive in environments where bovine cattle would struggle. Despite water buffaloes being known for their resistance to diseases, there is a lack of data about the diversity of the microbiome of the species. In this study, we examined the virome diversity in palatine tonsils collected from animals from the island of Marajó, northern Pará state, Brazil, which harbors the largest bubaline flock in the country. Tonsil fragments from 60 clinically healthy bubalines were randomly selected from a sample of 293 animals. The samples were purified, extracted, and randomly amplified with phi29 DNA polymerase. After amplification, the products were purified and sequenced. Circular DNA viruses were predominant in the tonsils' virome. Sequences of genome segments representative of members of the genera Alphapolyomavirus (including a previously unreported bubaline polyomavirus genome) and Gemycircularvirus were identified, along with other not yet classified circular virus genomes. As the animals were clinically healthy at the time of sampling, such viruses likely constitute part of the normal tonsillar virome of water buffaloes inhabiting the Ilha do Marajó biome.
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Affiliation(s)
- Francine C B Timm
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Fabrício Souza Campos
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil.
| | - Luis Janssen
- Laboratório de Baculovírus, Instituto de Ciências Biológicas, Universidade de Brasília (UnB), Brasília, Brasil
| | - Raíssa Nunes Dos Santos
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Bruna Paredes-Galarza
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Nicole Vieira Stone
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Martha Trindade Oliveira
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Raíssa Gasparetto
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Nicolas Felipe Drum Müller
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Alanis da Silva Melgarejo
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Miguel Leonetti Corrêa
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Lina Marcela Violet Lozano
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Richard Steiner Salvato
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Centro Estadual de Vigilância em Saúde (CEVS) da Secretaria Estadual da Saúde do Rio Grande do Sul (SESRS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Fernanda Marques de Souza Godinho
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Centro Estadual de Vigilância em Saúde (CEVS) da Secretaria Estadual da Saúde do Rio Grande do Sul (SESRS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Regina Bones Barcellos
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Centro Estadual de Vigilância em Saúde (CEVS) da Secretaria Estadual da Saúde do Rio Grande do Sul (SESRS), Porto Alegre, Rio Grande do Sul, Brasil
| | | | - Gabriela Riet-Correa
- Laboratório de Patologia Animal, Instituto de Medicina Veterinária, Universidade Federal do Pará (UFPA), Castanhal, Pará, Brasil
| | - Valíria Duarte Cerqueira
- Laboratório de Patologia Animal, Instituto de Medicina Veterinária, Universidade Federal do Pará (UFPA), Castanhal, Pará, Brasil
| | - Pedro Soares Bezerra Júnior
- Laboratório de Patologia Animal, Instituto de Medicina Veterinária, Universidade Federal do Pará (UFPA), Castanhal, Pará, Brasil
| | - Ana Cláudia Franco
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil
| | - Paulo Michel Roehe
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brasil.
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2
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Dei Giudici S, Mura L, Bonelli P, Ferretti L, Hawko S, Franzoni G, Angioi PP, Ladu A, Puggioni G, Antuofermo E, Sanna ML, Burrai GP, Oggiano A. First Molecular Characterisation of Porcine Parvovirus 7 (PPV7) in Italy. Viruses 2024; 16:932. [PMID: 38932224 PMCID: PMC11209580 DOI: 10.3390/v16060932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/04/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Porcine parvoviruses (PPVs) are among the most important agents of reproductive failure in swine worldwide. PPVs comprise eight genetically different species ascribed to four genera: Protoparvovirus (PPV1, PPV8), Tetraparvovirus (PPV2-3), Copiparvovirus (PPV4-6), and Chaphamaparvovirus (PPV7). In 2016, PPV7 was firstly detected in the USA and afterwards in Europe, Asia, and South America. Recently, it was also identified in Italy in pig farms with reproductive failure. This study aimed to evaluate the circulation of PPV7 in domestic and wild pigs in Sardinia, Italy. In addition, its coinfection with Porcine Circovirus 2 (PCV2) and 3 (PCV3) was analysed, and PPV7 Italian strains were molecularly characterised. PPV7 was detected in domestic pigs and, for the first time, wild pigs in Italy. The PPV7 viral genome was detected in 20.59% of domestic and wild pig samples. PPV7 detection was significantly lower in domestic pigs, with higher PCV2/PCV3 co-infection rates observed in PPV7-positive than in PPV7-negative domestic pigs. Molecular characterisation of the NS1 gene showed a very high frequency of recombination that could presumably promote virus spreading.
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Affiliation(s)
- Silvia Dei Giudici
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy (A.O.)
| | - Lorena Mura
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy (A.O.)
| | - Piero Bonelli
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy (A.O.)
| | - Luca Ferretti
- Nuffield Department of Medicine, Big Data Institute and Pandemic Sciences Institute, University of Oxford, Oxford OX1 4BH, UK
| | - Salwa Hawko
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Giulia Franzoni
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy (A.O.)
| | - Pier Paolo Angioi
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy (A.O.)
| | - Anna Ladu
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy (A.O.)
| | - Graziella Puggioni
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy (A.O.)
| | | | - Maria Luisa Sanna
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy (A.O.)
| | | | - Annalisa Oggiano
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy (A.O.)
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De Maio FA, Winter M, Abate S, Cifuentes S, Iglesias NG, Barrio DA, Bellusci CP. Detection of porcine circovirus 2, porcine parvovirus 1, and torque teno sus virus k2a in wild boars from northeastern Patagonia, Argentina. Arch Virol 2023; 168:208. [PMID: 37462757 DOI: 10.1007/s00705-023-05831-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/06/2023] [Indexed: 07/21/2023]
Abstract
Wild boars can act as a reservoir of pathogenic viruses that affect the pig industry. Here, we assessed the presence of porcine circovirus 2, porcine parvovirus 1, and torque teno sus virus k2a in wild boars in northeastern Patagonia (Argentina). Total DNA was extracted from the tonsils of 27 animals (collected between early 2016 and mid-2019) and used to prepare sample pools, which were subjected to viral detection through two-round PCR assays. Sequencing of the amplification products and phylogenetic analysis confirmed the occurrence of all of the aforementioned infectious agents.
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Affiliation(s)
- Federico Andrés De Maio
- Universidad Nacional de Río Negro, Sede Atlántica, Centro de Investigaciones y Transferencia Río Negro (CONICET-UNRN), Ruta provincial N°1 y Rotonda Cooperación, CP 8500, Viedma, Río Negro, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Marina Winter
- Universidad Nacional de Río Negro, Sede Atlántica, Centro de Investigaciones y Transferencia Río Negro (CONICET-UNRN), Ruta provincial N°1 y Rotonda Cooperación, CP 8500, Viedma, Río Negro, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Sergio Abate
- Universidad Nacional de Río Negro, Sede Atlántica, Centro de Investigaciones y Transferencia Río Negro (CONICET-UNRN), Ruta provincial N°1 y Rotonda Cooperación, CP 8500, Viedma, Río Negro, Argentina
| | - Sabrina Cifuentes
- Universidad Nacional de Río Negro, Sede Atlántica, Centro de Investigaciones y Transferencia Río Negro (CONICET-UNRN), Ruta provincial N°1 y Rotonda Cooperación, CP 8500, Viedma, Río Negro, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Néstor Gabriel Iglesias
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
- Universidad Nacional de Hurlingham (UNAHUR), Buenos Aires, Argentina
| | - Daniel Alejandro Barrio
- Universidad Nacional de Río Negro, Sede Atlántica, Centro de Investigaciones y Transferencia Río Negro (CONICET-UNRN), Ruta provincial N°1 y Rotonda Cooperación, CP 8500, Viedma, Río Negro, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Carolina Paula Bellusci
- Universidad Nacional de Río Negro, Sede Atlántica, Centro de Investigaciones y Transferencia Río Negro (CONICET-UNRN), Ruta provincial N°1 y Rotonda Cooperación, CP 8500, Viedma, Río Negro, Argentina.
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4
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Santiago-Olivares C, Martínez-Alvarado E, Rivera-Toledo E. Persistence of RNA Viruses in the Respiratory Tract: An Overview. Viral Immunol 2023; 36:3-12. [PMID: 36367976 DOI: 10.1089/vim.2022.0135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Respiratory RNA viruses are a major cause of acute lower respiratory tract infections and contribute substantially to hospitalization among infants, elderly, and immunocompromised. Complete viral clearance from acute infections is not always achieved, leading to persistence. Certain chronic respiratory diseases like asthma and chronic obstructive pulmonary disease have been associated with persistent infection by human respiratory syncytial virus and human rhinovirus, but it is still not clear whether RNA viruses really establish long-term infections as it has been recognized for DNA viruses as human bocavirus and adenoviruses. Herein, we summarize evidence of RNA virus persistence in the human respiratory tract, as well as in some animal models, to highlight how long-term infections might be related to development and/or maintenance of chronic respiratory symptoms.
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Affiliation(s)
- Carlos Santiago-Olivares
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Eber Martínez-Alvarado
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Evelyn Rivera-Toledo
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
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5
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Yang S, Zhang D, Ji Z, Zhang Y, Wang Y, Chen X, He Y, Lu X, Li R, Guo Y, Shen Q, Ji L, Wang X, Li Y, Zhang W. Viral Metagenomics Reveals Diverse Viruses in Tissue Samples of Diseased Pigs. Viruses 2022; 14:v14092048. [PMID: 36146854 PMCID: PMC9500892 DOI: 10.3390/v14092048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 11/24/2022] Open
Abstract
The swine industry plays an essential role in agricultural production in China. Diseases, especially viral diseases, affect the development of the pig industry and threaten human health. However, at present, the tissue virome of diseased pigs has rarely been studied. Using the unbiased viral metagenomic approach, we investigated the tissue virome in sick pigs (respiratory symptoms, reproductive disorders, high fever, diarrhea, weight loss, acute death and neurological symptoms) collected from farms of Anhui, Jiangsu and Sichuan Province, China. The eukaryotic viruses identified belonged to the families Anelloviridae, Arteriviridae, Astroviridae, Flaviviridae, Circoviridae and Parvoviridae; prokaryotic virus families including Siphoviridae, Myoviridae and Podoviridae occupied a large proportion in some samples. This study provides valuable information for understanding the tissue virome in sick pigs and for the monitoring, preventing, and treating of viral diseases in pigs.
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Affiliation(s)
- Shixing Yang
- School of Medicine, Jiangsu University, Zhenjiang 212013, China
| | - Dianqi Zhang
- School of Medicine, Jiangsu University, Zhenjiang 212013, China
| | - Zexuan Ji
- School of Medicine, Jiangsu University, Zhenjiang 212013, China
| | - Yuyang Zhang
- School of Medicine, Jiangsu University, Zhenjiang 212013, China
| | - Yan Wang
- School of Medicine, Jiangsu University, Zhenjiang 212013, China
| | - Xu Chen
- School of Medicine, Jiangsu University, Zhenjiang 212013, China
| | - Yumin He
- School of Medicine, Jiangsu University, Zhenjiang 212013, China
| | - Xiang Lu
- School of Medicine, Jiangsu University, Zhenjiang 212013, China
| | - Rong Li
- School of Medicine, Jiangsu University, Zhenjiang 212013, China
| | - Yufei Guo
- School of Medicine, Jiangsu University, Zhenjiang 212013, China
| | - Quan Shen
- School of Medicine, Jiangsu University, Zhenjiang 212013, China
| | - Likai Ji
- School of Medicine, Jiangsu University, Zhenjiang 212013, China
| | - Xiaochun Wang
- School of Medicine, Jiangsu University, Zhenjiang 212013, China
| | - Yu Li
- College of Animal Sciences and Techologies, Anhui Agricultural University, Hefei 230036, China
| | - Wen Zhang
- School of Medicine, Jiangsu University, Zhenjiang 212013, China
- Correspondence:
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Wen S, Song Y, Lv X, Meng X, Liu K, Yang J, Diao F, He J, Huo X, Chen Z, Zhai J. Detection and Molecular Characterization of Porcine Parvovirus 7 in Eastern Inner Mongolia Autonomous Region, China. Front Vet Sci 2022; 9:930123. [PMID: 35873677 PMCID: PMC9298536 DOI: 10.3389/fvets.2022.930123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/15/2022] [Indexed: 11/17/2022] Open
Abstract
Porcine parvoviruses (PPV) and porcine circoviruses type 2 (PCV2) are widespread in the pig population. Recently, it was suggested that PPV7 may stimulate PCV2 and PCV3 replication. The present study aimed to make detection and molecular characterization of PPV7 for the first time in eastern Inner Mongolia Autonomous Region, China. Twenty-seven of ninety-four samples (28.72%) and five in eight pig farms were PPV7 positive. Further detection showed that the co-infection rate of PPV7 and PCV2 was 20.21% (19/94), and 9.59% (9/94) for PPV7 and PCV3. In addition, the positive rate of PPV7 in PCV2 positive samples was higher than that in PCV2 negative samples, supporting that PCV2 could act as a co-factor for PPV7 infection. In total, four PPV7 strains were sequenced and designated as NM-14, NM-19, NM-4, and NM-40. The amplified genome sequence of NM-14 and NM-40 were 3,999nt in length, while NM-19 and NM-4 were 3,996nt with a three nucleotides deletion at 3,097–3,099, resulting in an amino acid deletion in the Cap protein. Phylogenetic analysis based on the capsid amino acid (aa) sequences showed that 52 PPV7 strains were divided into two clades, and the four PPV7 strains in this study were all clustered in clade 1. The genome and capsid amino acid sequence of the four PPV7 strains identified in this study shared 80.0–96.9% and 85.9–100% similarity with that of 48 PPV7 reference strains selected in NCBI. Simplot analysis revealed that NM-19 and NM-4 strains were probably produced by recombination of two PPV7 strains from China. The amino acid sequence alignment analysis of capsid revealed that the four PPV7 strains detected in Inner Mongolia had multiple amino acid mutations in the 6 B cell linear epitopes compared with the reference strains, suggesting that the four PPV7 strains may have different characteristics in receptor binding and immunogenicity. In summary, this paper reported the PPV7 infection and molecular characterization in the eastern of Inner Mongolia Autonomous Region for the first time, which is helpful to understand the molecular epidemic characteristics of PPV7.
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Affiliation(s)
- Shubo Wen
- Preventive Veterinary Laboratory, College of Animal Science and Technology, Inner Mongolia Minzu University, Tongliao, China.,Brucellosis Prevention and Treatment Technology Research Center, Inner Mongolia Autonomous Region, Tongliao, China.,Key Laboratory of Zoonose Prevention and Control at Universities of Inner Mongolia Autonomous Region, Tongliao, China
| | - Yang Song
- Preventive Veterinary Laboratory, College of Animal Science and Technology, Inner Mongolia Minzu University, Tongliao, China.,Brucellosis Prevention and Treatment Technology Research Center, Inner Mongolia Autonomous Region, Tongliao, China.,Key Laboratory of Zoonose Prevention and Control at Universities of Inner Mongolia Autonomous Region, Tongliao, China
| | - Xiangyu Lv
- Preventive Veterinary Laboratory, College of Animal Science and Technology, Inner Mongolia Minzu University, Tongliao, China
| | - Xiaogang Meng
- Preventive Veterinary Laboratory, College of Animal Science and Technology, Inner Mongolia Minzu University, Tongliao, China
| | - Kai Liu
- Preventive Veterinary Laboratory, College of Animal Science and Technology, Inner Mongolia Minzu University, Tongliao, China
| | - Jingfeng Yang
- Preventive Veterinary Laboratory, College of Animal Science and Technology, Inner Mongolia Minzu University, Tongliao, China
| | - Fengying Diao
- Preventive Veterinary Laboratory, College of Animal Science and Technology, Inner Mongolia Minzu University, Tongliao, China
| | - Jinfei He
- Preventive Veterinary Laboratory, College of Animal Science and Technology, Inner Mongolia Minzu University, Tongliao, China
| | - Xiaowei Huo
- Preventive Veterinary Laboratory, College of Animal Science and Technology, Inner Mongolia Minzu University, Tongliao, China
| | - Zeliang Chen
- Preventive Veterinary Laboratory, College of Animal Science and Technology, Inner Mongolia Minzu University, Tongliao, China.,Brucellosis Prevention and Treatment Technology Research Center, Inner Mongolia Autonomous Region, Tongliao, China.,Key Laboratory of Zoonose Prevention and Control at Universities of Inner Mongolia Autonomous Region, Tongliao, China
| | - Jingbo Zhai
- Preventive Veterinary Laboratory, College of Animal Science and Technology, Inner Mongolia Minzu University, Tongliao, China.,Brucellosis Prevention and Treatment Technology Research Center, Inner Mongolia Autonomous Region, Tongliao, China.,Key Laboratory of Zoonose Prevention and Control at Universities of Inner Mongolia Autonomous Region, Tongliao, China
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7
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László Z, Pankovics P, Reuter G, Cságola A, Bodó K, Gáspár G, Albert M, Bíró H, Boros Á. Development and Large-Scale Testing of a Novel One-Step Triplex RT-qPCR Assay for Simultaneous Detection of “Neurotropic” Porcine Sapeloviruses, Teschoviruses (Picornaviridae) and Type 3 Porcine Astroviruses (Astroviridae) in Various Samples including Nasal Swabs. Viruses 2022; 14:v14030513. [PMID: 35336920 PMCID: PMC8952109 DOI: 10.3390/v14030513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 11/16/2022] Open
Abstract
Porcine sapeloviruses, teschoviruses of family Picornaviridae and type 3 porcine astroviruses of family Astroviridae are (re-)emerging enteric pathogens that could be associated with severe, disseminated infections in swine, affecting multiple organs including the central nervous system (CNS). Furthermore, small-scale pioneer studies indicate the presence of these viruses in porcine nasal samples to various extents. The laboratory diagnostics are predominantly based on the detection of the viral RNA from faecal and tissue samples using different nucleic-acid-based techniques such as RT-qPCR. In this study, a novel highly sensitive one-step triplex RT-qPCR assay was introduced which can detect all known types of neurotropic sapelo-, tescho- and type 3 astroviruses in multiple types of samples of swine. The assay was evaluated using in vitro synthesized RNA standards and a total of 142 archived RNA samples including known sapelo-, tescho- and type 3 astrovirus positive and negative CNS, enteric and nasal specimens. The results of a large-scale epidemiological investigation of these viruses on n = 473 nasal swab samples from n = 28 industrial-type swine farms in Hungary indicate that all three neurotropic viruses, especially type 3 astroviruses, are widespread and endemically present on most of the investigated farms.
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Affiliation(s)
- Zoltán László
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, 7624 Pécs, Hungary; (Z.L.); (P.P.); (G.R.); (G.G.)
| | - Péter Pankovics
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, 7624 Pécs, Hungary; (Z.L.); (P.P.); (G.R.); (G.G.)
| | - Gábor Reuter
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, 7624 Pécs, Hungary; (Z.L.); (P.P.); (G.R.); (G.G.)
| | - Attila Cságola
- Ceva Phylaxia Ltd., 1107 Budapest, Hungary; (A.C.); (M.A.)
| | - Kornélia Bodó
- Department of Immunology and Biotechnology, Clinical Center, Medical School, University of Pécs, Szigeti u, 12, 7643 Pécs, Hungary;
| | - Gábor Gáspár
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, 7624 Pécs, Hungary; (Z.L.); (P.P.); (G.R.); (G.G.)
| | - Mihály Albert
- Ceva Phylaxia Ltd., 1107 Budapest, Hungary; (A.C.); (M.A.)
| | | | - Ákos Boros
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, 7624 Pécs, Hungary; (Z.L.); (P.P.); (G.R.); (G.G.)
- Correspondence: ; Tel.: +36-72-536-251
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The first report of porcine parvovirus 7 (PPV7) in Colombia demonstrates the presence of variants associated with modifications at the level of the VP2-capsid protein. PLoS One 2021; 16:e0258311. [PMID: 34914702 PMCID: PMC8675767 DOI: 10.1371/journal.pone.0258311] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 09/23/2021] [Indexed: 12/15/2022] Open
Abstract
There are a wide variety of porcine parvoviruses (PPVs) referred to as PPV1 to PPV7. The latter was discovered in 2016 and later reported in some countries in America, Asia, and Europe. PPV7 as a pathogenic agent or coinfection with other pathogens causing disease has not yet been determined. In the present study, we report the identification of PPV7 for the first time in Colombia, where it was found retrospectively since 2015 in 40% of the provinces that make up the country (13/32), and the virus was ratified for 2018 in 4/5 provinces evaluated. Additionally, partial sequencing (nucleotides 380 to 4000) was performed of four Colombian strains completely covering the VP2 and NS1 viral genes. A sequence identity greater than 99% was found when comparing them with reference strains from the USA and China. In three of the four Colombian strains, an insertion of 15 nucleotides (five amino acids) was found in the PPV7-VP2 capsid protein (540–5554 nt; 180–184 aa). Based on this insertion, the VP2 phylogenetic analysis exhibited two well-differentiated evolutionarily related groups. To evaluate the impact of this insertion on the structure of the PPV7-VP2 capsid protein, the secondary structure of two different Colombian strains was predicted, and it was determined that the insertion is located in the coil region and not involved in significant changes in the structure of the protein. The 3D structure of the PPV7-VP2 capsid protein was determined by threading and homology modeling, and it was shown that the insertion did not imply a change in the shape of the protein. Additionally, it was determined that the insertion is not involved in suppressing a potential B cell epitope, although the increase in length of the epitope could affect the interaction with molecules that allow a specific immune response.
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9
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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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10
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Shi Y, Tao J, Li B, Shen X, Cheng J, Liu H. The Gut Viral Metagenome Analysis of Domestic Dogs Captures Snapshot of Viral Diversity and Potential Risk of Coronavirus. Front Vet Sci 2021; 8:695088. [PMID: 34307533 PMCID: PMC8292670 DOI: 10.3389/fvets.2021.695088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/10/2021] [Indexed: 11/13/2022] Open
Abstract
The close relations between dogs (Canis lupus familiaris) and humans lay a foundation for cross species transmissions of viruses. The co-existence of multiplex viruses in the host accelerate viral variations. For effective prediction and prevention of potential epidemic or even pandemic, the metagenomics method was used to investigate the gut virome status of 45 domestic healthy dogs which have extensive contact with human beings. A total of 248.6 GB data (505, 203, 006 valid reads, 150 bp in length) were generated and 325, 339 contigs, which were best matched with viral genes, were assembled from 46, 832, 838 reads. In the aggregate, 9,834 contigs (3.02%) were confirmed for viruses. The top 30 contigs with the most reads abundance were mapped to DNA virus families Circoviridae, Parvoviridae and Herpesviridae; and RNA virus families Astroviridae, Coronaviridae and Picornaviridae, respectively. Numerous sequences were assigned to animal virus families of Astroviridae, Coronaviridae, Circoviridae, etc.; and phage families of Microviridae, Siphoviridae, Ackermannviridae, Podoviridae, Myoviridae and the unclassified phages. Further, several sequences were homologous with the insect and plant viruses, which reflects the diet and habitation of dogs. Significantly, canine coronavirus was uniquely identified in all the samples with high abundance, and the phylogenetic analysis therefore showed close relationship with the human coronavirus strain 229E and NL63, indicating the potential risk of canine coronavirus to infect humans by obtaining the ability of cross-species transmission. This study emphasizes the high detection frequency of virus harbored in the enteric tract of healthy contacted animal, and expands the knowledge of the viral diversity and the spectrum for further disease-association studies, which is meaningful for elucidating the epidemiological and biological role of companion animals in public health.
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Affiliation(s)
- Ying Shi
- Department of Animal Infectious Diseases, Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China.,Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
| | - Jie Tao
- Department of Animal Infectious Diseases, Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China.,Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
| | - Benqiang Li
- Department of Animal Infectious Diseases, Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China.,Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
| | - Xiaohui Shen
- Department of Animal Infectious Diseases, Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jinghua Cheng
- Department of Animal Infectious Diseases, Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China.,Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
| | - Huili Liu
- Department of Animal Infectious Diseases, Institute of Animal Husbandry and Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China.,Shanghai Key Laboratory of Agricultural Genetic Breeding, Shanghai, China.,Shanghai Engineering Research Center of Pig Breeding, Shanghai, China
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11
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Molecular detection of Porcine cytomegalovirus (PCMV) in wild boars from Northeastern Patagonia, Argentina. Rev Argent Microbiol 2021; 53:325-332. [PMID: 33593665 DOI: 10.1016/j.ram.2020.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 09/26/2020] [Accepted: 12/18/2020] [Indexed: 11/21/2022] Open
Abstract
Porcine cytomegalovirus (PCMV) is a recognized pathogen of domestic swine that is widely distributed around the world. PCMV is the etiological agent of inclusion body rhinitis and has also been associated with other diseases that cause substantial losses in swine production. Wild boar populations can act as reservoirs of numerous infectious agents that affect pig livestock, including PCMV. The aim of this work was to assess the circulation of this virus in free-living wild boars that inhabit Northeastern Patagonia (Buenos Aires and Río Negro Provinces), Argentina. Nested-PCR assays were conducted to evaluate the presence of PCMV in samples of tonsil tissue collected from 62 wild boar individuals. It was found that the overall rate of infection was about 56%, with significant higher values (almost 90%) in the age group corresponding to piglets (animals less than 6 months old). In addition, a seasonal variation was observed in the PCMV detection rate, with an increase during the transition from summer to autumn. In conclusion, this study confirmed that wild boars are major carriers and dispersal agents of PCMV in Northeastern Patagonia, which raises the necessity to evaluate the extent to which this virus affects local livestock production.
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12
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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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13
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Pirolo M, Espinosa-Gongora C, Bogaert D, Guardabassi L. The porcine respiratory microbiome: recent insights and future challenges. Anim Microbiome 2021; 3:9. [PMID: 33499988 PMCID: PMC7934557 DOI: 10.1186/s42523-020-00070-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/16/2020] [Indexed: 01/07/2023] Open
Abstract
Understanding the structure of the respiratory microbiome and its complex interactions with opportunistic pathogenic bacteria has become a topic of great scientific and economic interest in livestock production, given the severe consequences of respiratory disease on animal health and welfare. The present review focuses on the microbial structures of the porcine upper and lower airways, and the factors that influence microbiome development and onset of respiratory disease. Following a literature search on PubMed and Scopus, 21 articles were selected based on defined exclusion criteria (20 studies performed by 16S rRNA gene sequencing and one by shotgun metagenomics). Analysis of the selected literature indicated that the microbial structure of the upper respiratory tract undergoes a remarkable evolution after birth and tends to stabilise around weaning. Antimicrobial treatment, gaseous ammonia concentration, diet and floor type are amongst the recognized environmental factors influencing microbiome structure. The predominant phyla of the upper respiratory tract are Proteobacteria and Firmicutes with significant differences at the genus level between the nasal and the oropharyngeal cavity. Only five studies investigated the lower respiratory tract and their results diverged in relation to the relative abundance of these two phyla and even more in the composition of the lung microbiome at the genus level, likely because of methodological differences. Reduced diversity and imbalanced microbial composition are associated with an increased risk of respiratory disease. However, most studies presented methodological pitfalls concerning specimen collection, sequencing target and depth, and lack of quality control. Standardization of sampling and sequencing procedures would contribute to a better understanding of the structure of the microbiota inhabiting the lower respiratory tract and its relationship with pig health and disease.
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Affiliation(s)
- Mattia Pirolo
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.,Department of Science, Roma Tre University, Rome, Italy
| | - Carmen Espinosa-Gongora
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Debby Bogaert
- Center for Inflammation Research, University of Edinburgh, Edinburgh, UK
| | - Luca Guardabassi
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark. .,Department of Pathobiology & Population Sciences, Royal Veterinary College, United Kingdom, Hawkhead Lane, North Mymms, Hatfield, Herts, AL9 7TA, UK.
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14
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Bach MJ, Donin DG, Fernandes SR, Martins GB, Alberton GC. Rational use of antibiotics for treatment of urinary infection in sows. CIÊNCIA ANIMAL BRASILEIRA 2021. [DOI: 10.1590/1809-6891v22e-68919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Abstract The endemic character of urinary infections (UI) in sows makes collective antimicrobial therapies via feed a routine. This, however, generates sub-doses unable to heal and contribute to the selection of antibiotic-resistant bacteria. The use of individual therapy is the most appropriate procedure to be performed on animals with UI. With this study, we aimed to evaluate the occurrence of UI in sows housed in the western region of Paraná and the efficacy and cost-benefit of individual treatment. A total of 353 females were selected from five different herds, submitted to urine collection in the final third of pregnancy by spontaneous urination method. The samples were analyzed physically and chemically with the use of reagent strips, and the presence of nitrite was a determinant for positivity for UI. The animals with UI had urine submitted to a bacteriological evaluation, were treated with parenteral medication (marbofloxacin - single dose - 8 mg/kg), and submitted to a new urine collection 24h and 48h after the first. UI was observed in 4.53% of the females evaluated (16/353). Escherichia coli and Streptococcus sp. were the most frequently isolated agents. Seven days after the use of marbofloxacin 87.5% (14/16) of the animals were negative for UI, which demonstrates the efficacy of UI parenteral control. The diagnosis associated with individual therapy at the expense of collective medication was highly cost-effective, made it possible to drastically reduce the number of medicated animals, and was efficient in controlling UI. Thus, it is concluded that it is possible to make rational use of antibiotics by treating only sows that are proven to be positive for UI. This reduces the number of unnecessarily medicated animals and reduces the cost due to the use of antimicrobials only in sick animals.
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15
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Complete Coding Sequence of a Pasivirus Found in Swedish Pigs. Microbiol Resour Announc 2020; 9:9/39/e00747-20. [PMID: 32972933 PMCID: PMC7516144 DOI: 10.1128/mra.00747-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report the complete coding sequence of a pasivirus found in the tonsil of a conventionally reared pig from a herd with respiratory disease in Sweden. The genome displays 75% to 87% and 81% to 94% nucleotide and amino acid sequence identity, respectively, to genomes of pasiviruses from other parts of the world. Here, we report the complete coding sequence of a pasivirus found in the tonsil of a conventionally reared pig from a herd with respiratory disease in Sweden. The genome displays 75% to 87% and 81% to 94% nucleotide and amino acid sequence identity, respectively, to genomes of pasiviruses from other parts of the world.
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16
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Porcine Parvovirus 7: Evolutionary Dynamics and Identification of Epitopes toward Vaccine Design. Vaccines (Basel) 2020; 8:vaccines8030359. [PMID: 32635618 PMCID: PMC7565409 DOI: 10.3390/vaccines8030359] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/01/2020] [Accepted: 07/01/2020] [Indexed: 12/21/2022] Open
Abstract
Porcine parvovirus 7 (PPV7) belonging to the genus Chapparvovirus in the family Parvoviridae, has been identified in the USA, Sweden, Poland, China, South Korea and Brazil. Our objective was to determine the phylogeny, estimate the time of origin and evolutionary dynamics of PPV7, and use computer-based immune-informatics to assess potential epitopes of its Cap, the main antigenic viral protein, for vaccines or serology. Regarding evolutionary dynamics, PPV7 had 2 major clades, both of which possibly had a common ancestor in 2004. Furthermore, PPV7 strains from China were the most likely ancestral strains. The nucleotide substitution rates of NS1 and Cap genes were 8.01 × 10−4 and 2.19 × 10−3 per site per year, respectively, which were higher than those reported for PPV1-4. The antigenic profiles of PPV7 Cap were revealed and there were indications that PPV7 used antigenic shift to escape from the host’s immune surveillance. Linear B cell epitopes and CD8 T cell epitopes of Cap with good antigenic potential were identified in silico; these conserved B cell epitopes may be candidates for the PPV7 vaccine or for the development of serological diagnostic methods.
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17
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Webb B, Rakibuzzaman A, Ramamoorthy S. Torque teno viruses in health and disease. Virus Res 2020; 285:198013. [PMID: 32404273 DOI: 10.1016/j.virusres.2020.198013] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 12/19/2022]
Abstract
Torque teno viruses (TTVs) are small, ubiquitous, viruses with a highly diverse, single-stranded, negative sense DNA genome and wide host range. They are detected at high rates in both healthy and diseased individuals and are considered a significant part of the mammalian virome. Similar to human TTVs, swine TTVs (TTSuVs) are epidemiologically linked to several coinfections including porcine circovirus types 2 and 3 and the porcine reproductive and respiratory disease syndrome virus. Experimental infection of gnotobiotic pigs with TTSuVs resulted in lesions in multiple organs and exacerbation of coinfections, making TTSuVs the only members of the Anelloviridae family with experimental evidence for pathogenicity. However, due to the lack of reliable cell culture and animal models, mechanistic studies on viral immunity and pathogenesis are limited. The objective of this review is to summarize the current status of knowledge regarding the biology, detection, pathogenesis and public health significance of TTSuVs, while identifying gaps in knowledge which limit the field.
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Affiliation(s)
- Brett Webb
- Veterinary Diagnostic Laboratory, North Dakota State University, Fargo, ND, United States
| | - Agm Rakibuzzaman
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, United States
| | - Sheela Ramamoorthy
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, United States.
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18
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Damian D, Maghembe R, Damas M, Wensman JJ, Berg M. Application of Viral Metagenomics for Study of Emerging and Reemerging Tick-Borne Viruses. Vector Borne Zoonotic Dis 2020; 20:557-565. [PMID: 32267808 DOI: 10.1089/vbz.2019.2579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ticks are important vectors for different tick-borne viruses, some of which cause diseases and death in humans, livestock, and wild animals. Tick-borne encephalitis virus, Crimean-Congo hemorrhagic fever virus, Kyasanur forest disease virus, severe fever with thrombocytopenia syndrome virus, Heartland virus, African swine fever virus, Nairobi sheep disease virus, and Louping ill virus are just a few examples of important tick-borne viruses. The majority of tick-borne viruses have RNA genomes that routinely undergo rapid genetic modifications such as point mutations during their replication. These genomic changes can influence the spread of viruses to new habitats and hosts and lead to the emergence of novel viruses that can pose a threat to public health. Therefore, investigation of the viruses circulating in ticks is important to understand their diversity, host and vector range, and evolutionary history, as well as to predict new emerging pathogens. The choice of detection method is important, as most methods detect only those viruses that have been previously well described. On the other hand, viral metagenomics is a useful tool to simultaneously identify all the viruses present in a sample, including novel variants of already known viruses or completely new viruses. This review describes tick-borne viruses, their historical background of emergence, and their reemergence in nature, and the use of viral metagenomics for viral discovery and studies of viral evolution.
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Affiliation(s)
- Donath Damian
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Reuben Maghembe
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Modester Damas
- Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Jonas Johansson Wensman
- Section of Ruminant Medicine, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mikael Berg
- Section of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
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19
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Garcia-Camacho LA, Vargas-Ruiz A, Marin-Flamand E, Ramírez-Álvarez H, Brown C. A retrospective study of DNA prevalence of porcine parvoviruses in Mexico and its relationship with porcine circovirus associated disease. Microbiol Immunol 2020; 64:366-376. [PMID: 32096557 DOI: 10.1111/1348-0421.12782] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 02/17/2020] [Accepted: 02/20/2020] [Indexed: 02/05/2023]
Abstract
Worldwide, many emerging porcine parvoviruses (PPVs) have been linked to porcine circovirus-2 (PCV2) associated disease (PCVAD), which includes post-weaning multi-systemic wasting syndrome (PMWS), PCV2-related reproductive failure (PCV2-RF), as well as other syndromes. To determine the DNA prevalence of PPVs and their relationship with PMWS and PCV2-RF in Mexico, 170 formalin-fixed paraffin-embedded tissues were selected from archival collections to detect PPVs using a nested polymerase chain reaction. The tissues were composed of 50 PMWS cases, 20 age-matched tissues from healthy pigs, 56 PCV2-related reproductive failure (PCV2+ -RF) cases, and 44 PCV2- -RF cases. Overall, PPV2 and PPV6 were the most prevalent species (90.0% and 74.7%, respectively). In 8-11 week old pigs, the highest prevalence was for PPV6 and PPV3. Concerning reproductive failure, the PCV2-affected farms had a significantly higher prevalence for PPV6 (61.6%) and PPV5 (36.4%) than the PCV2-unaffected farms (35.0% and 5.0%, respectively). The concurrent infection rate was high, being significant for PPV2/PPV4 and PPV1/PPV5 within the PMWS cases and for PPV6/PPV5 among the PCV2+ -RF tissues. PPV5 showed a significant relationship with PMWS, whereas PPV5 and PPV6 were significant for PCVAD. The prevalence and coinfection rate of PPVs in Mexico were markedly higher than that described in other countries, denoting that PPV5 and PPV6 might have a potential role in PCVAD in Mexico. It is concluded that it is likely that the density population of pigs in Mexico is contributing to high PPV inter-species and PCV2 coinfections which might lead to a different pathogenic outcome.
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Affiliation(s)
- Lucia Angélica Garcia-Camacho
- Department of Biological Sciences, College of Superior Studies Cuautitlan, The National Autonomous University of Mexico, Cuautitlan Izcalli, Mexico
| | - Alejandro Vargas-Ruiz
- Department of Biological Sciences, College of Superior Studies Cuautitlan, The National Autonomous University of Mexico, Cuautitlan Izcalli, Mexico
| | - Ernesto Marin-Flamand
- Department of Biological Sciences, College of Superior Studies Cuautitlan, The National Autonomous University of Mexico, Cuautitlan Izcalli, Mexico
| | - Hugo Ramírez-Álvarez
- Department of Biological Sciences, College of Superior Studies Cuautitlan, The National Autonomous University of Mexico, Cuautitlan Izcalli, Mexico
| | - Corrie Brown
- Department of Pathology, College of Veterinary Medicine, The University of Georgia, Athens, Georgia
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20
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Da Silva MS, Budaszewski RF, Weber MN, Cibulski SP, Paim WP, Mósena ACS, Canova R, Varela APM, Mayer FQ, Pereira CW, Canal CW. Liver virome of healthy pigs reveals diverse small ssDNA viral genomes. INFECTION GENETICS AND EVOLUTION 2020; 81:104203. [PMID: 32035977 DOI: 10.1016/j.meegid.2020.104203] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/08/2020] [Accepted: 01/20/2020] [Indexed: 02/07/2023]
Abstract
Brazil is a major exporter of pork meat worldwide. Swine liver is a common ingredient in food consumed by humans, thus emphasizing the importance of evaluating the presence of associated pathogens in swine liver. To obtain knowledge, this study aimed to provide insights into the viral communities of livers collected from slaughtered pigs from southern Brazil. The 46 livers were processed and submitted for high-throughput sequencing (HTS). The sequences were most closely related to Anelloviridae, Circoviridae and Parvoviridae families. The present work also describes the first Brazilian PCV1 and the first PPV6 and PPV7 from South America. Virus frequencies revelead 63% of samples positive for TTSuV1, 71% for TTSuVk2, 10.8% for PCV, 13% for PPV and 6% for PBov. This report addresses the diversity of the liver virome of healthy pigs and expands the number of viruses detected, further characterizing their genomes to assist future studies.
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Affiliation(s)
- M S Da Silva
- Laboratório de Virologia Veterinária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Brazil
| | - R F Budaszewski
- Laboratório de Virologia Veterinária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Brazil
| | - M N Weber
- Laboratório de Virologia Veterinária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Brazil
| | - S P Cibulski
- Departamento de Biotecnologia, Universidade Federal da Paraíba (UFPB), João Pessoa, Paraíba, Brazil
| | - W P Paim
- Laboratório de Virologia Veterinária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Brazil
| | - A C S Mósena
- Laboratório de Virologia Veterinária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Brazil
| | - R Canova
- Laboratório de Virologia Veterinária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Brazil
| | - A P M Varela
- Laboratório de Biologia Molecular, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Fundação Estadual de Pesquisa Agropecuária, Eldorado do Sul, Rio Grande do Sul, Brazil
| | - F Q Mayer
- Laboratório de Biologia Molecular, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Fundação Estadual de Pesquisa Agropecuária, Eldorado do Sul, Rio Grande do Sul, Brazil
| | - C W Pereira
- Secretaria de Agricultura, Pecuária e Desenvolvimento Rural do Estado do Rio Grande do Sul, Brazil
| | - C W Canal
- Laboratório de Virologia Veterinária, Faculdade de Veterinária, Universidade Federal do Rio Grande do Sul, Brazil.
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21
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Virus Metagenomics in Farm Animals: A Systematic Review. Viruses 2020; 12:v12010107. [PMID: 31963174 PMCID: PMC7019290 DOI: 10.3390/v12010107] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 02/07/2023] Open
Abstract
A majority of emerging infectious diseases are of zoonotic origin. Metagenomic Next-Generation Sequencing (mNGS) has been employed to identify uncommon and novel infectious etiologies and characterize virus diversity in human, animal, and environmental samples. Here, we systematically reviewed studies that performed viral mNGS in common livestock (cattle, small ruminants, poultry, and pigs). We identified 2481 records and 120 records were ultimately included after a first and second screening. Pigs were the most frequently studied livestock and the virus diversity found in samples from poultry was the highest. Known animal viruses, zoonotic viruses, and novel viruses were reported in available literature, demonstrating the capacity of mNGS to identify both known and novel viruses. However, the coverage of metagenomic studies was patchy, with few data on the virome of small ruminants and respiratory virome of studied livestock. Essential metadata such as age of livestock and farm types were rarely mentioned in available literature, and only 10.8% of the datasets were publicly available. Developing a deeper understanding of livestock virome is crucial for detection of potential zoonotic and animal pathogens and One Health preparedness. Metagenomic studies can provide this background but only when combined with essential metadata and following the “FAIR” (Findable, Accessible, Interoperable, and Reusable) data principles.
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22
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Viral Metagenomics Revealed Sendai Virus and Coronavirus Infection of Malayan Pangolins ( Manis javanica). Viruses 2019; 11:v11110979. [PMID: 31652964 PMCID: PMC6893680 DOI: 10.3390/v11110979] [Citation(s) in RCA: 232] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/21/2019] [Accepted: 10/21/2019] [Indexed: 12/14/2022] Open
Abstract
Pangolins are endangered animals in urgent need of protection. Identifying and cataloguing the viruses carried by pangolins is a logical approach to evaluate the range of potential pathogens and help with conservation. This study provides insight into viral communities of Malayan Pangolins (Manis javanica) as well as the molecular epidemiology of dominant pathogenic viruses between Malayan Pangolin and other hosts. A total of 62,508 de novo assembled contigs were constructed, and a BLAST search revealed 3600 ones (≥300 nt) were related to viral sequences, of which 68 contigs had a high level of sequence similarity to known viruses, while dominant viruses were the Sendai virus and Coronavirus. This is the first report on the viral diversity of pangolins, expanding our understanding of the virome in endangered species, and providing insight into the overall diversity of viruses that may be capable of directly or indirectly crossing over into other mammals.
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23
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Wang Y, Yang KK, Wang J, Wang XP, Zhao L, Sun P, Li YD. Detection and molecular characterization of novel porcine parvovirus 7 in Anhui province from Central-Eastern China. INFECTION GENETICS AND EVOLUTION 2019; 71:31-35. [PMID: 30876889 DOI: 10.1016/j.meegid.2019.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 03/09/2019] [Accepted: 03/09/2019] [Indexed: 12/27/2022]
Abstract
Porcine parvovirus 7 (PPV7), a new serotype of the porcine parvovirus, was discovered in swine of the USA in 2016. Recently, PPV7 was detected in Anhui province, China. Twenty-four of the 120 lung samples were PPV7-positive. Three PPV7 strains were sequenced and named PPV7/China/AHbz, PPV7/China/AHhf, and PPV7/China/AHmas, respectively. The complete genome and NS1 gene nucleotides of the three PPV7 strains showed 80.0%-98.4% and 94.4%-98.7% sequence identity, respectively, to the other PPV7 strains obtained from NCBI. The three PPV7 strains from Anhui share a common origin with a PPV7 GX49 strain isolated in Guangxi. These results help to understand the molecular epidemiology of PPV7.
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Affiliation(s)
- Yong Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui Province, China
| | - Kan-Kan Yang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui Province, China
| | - Jing Wang
- Animal husbandry base teaching and research section, College of Animal Science and Technology, Hebei North University, Zhangjiakou 075131, Hebei Province, China
| | - Xiao-Peng Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui Province, China
| | - Liang Zhao
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui Province, China
| | - Pei Sun
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui Province, China.
| | - Yong-Dong Li
- Municipal Key Laboratory of Virology, Ningbo Municipal Center for Disease Control and Prevention, Ningbo, 315010, Zhejiang Province, China.
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