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Yan T, Wang Z, Li R, Zhang D, Song Y, Cheng Z. Gyrovirus: current status and challenge. Front Microbiol 2024; 15:1449814. [PMID: 39220040 PMCID: PMC11362077 DOI: 10.3389/fmicb.2024.1449814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024] Open
Abstract
Gyrovirus (GyV) is small, single-stranded circular DNA viruses that has recently been assigned to the family Anelloviridae. In the last decade, many GyVs that have an apparent pan-tropism at the host level were identified by high-throughput sequencing (HTS) technology. As of now, they have achieved global distribution. Several species of GyVs have been demonstrated to be pathogenic to poultry, particularly chicken anemia virus (CAV), causing significant economic losses to the global poultry industry. Although GyVs are highly prevalent in various birds worldwide, their direct involvement in the etiology of specific diseases and the reasons for their ubiquity and host diversity are not fully understood. This review summarizes current knowledge about GyVs, with a major emphasis on their morphofunctional properties, epidemiological characteristics, genetic evolution, pathogenicity, and immunopathogenesis. Additionally, the association between GyVs and various diseases, as well as its potential impact on the poultry industry, have been discussed. Future prevention and control strategies have also been explored. These insights underscore the importance of conducting research to establish a virus culture system, optimize surveillance, and develop vaccines for GyVs.
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Affiliation(s)
| | | | | | | | | | - Ziqiang Cheng
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Tai’an, China
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Mendoza W, Isaza JP, López L, López-Herrera A, Gutiérrez LA. Bovine Leukemia Virus molecular detection and associated factors among dairy herd workers in Antioquia, Colombia. Acta Trop 2024; 256:107253. [PMID: 38782108 DOI: 10.1016/j.actatropica.2024.107253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/18/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024]
Abstract
The Bovine Leukemia Virus (BLV) affects mainly cattle, is transmitted by exposure to contaminated biological fluids, and generates lymphomas in 5 % of infected animals. The zoonotic potential of BLV has been studied, and it is currently unknown if it circulates in human workers on dairy herds in Antioquia. Objective: To determine the frequency of BLV detection, the genotypes of the virus, and the factors associated with its detection in workers for dairy herds in Antioquia, Colombia. Through a cross-sectional study in 51 dairy herds, 164 adults were recruited. A peripheral blood sample was collected from each participant for molecular detection of the BLV env and tax genes, and associated factors were explored through bivariate and multivariate mixed Poisson model analyses. The analysis showed that 82 % (134/164) of the participants were men, with an average age of 40. Using qPCR, the constitutive gene GAPDH was amplified to evaluate the presence of amplification inhibitors in the DNA samples. Using nested PCR, the amplification of the env viral gene was obtained in 13 % (22/164) of the total samples analyzed, while all the samples tested negative for tax. The amplicons of the env gene were sequenced, and the identity compatible with BLV was verified by BLAST analysis (NCBI). Using molecular phylogeny analysis, based on maximum likelihood and haplotype network analysis, it was identified that BLV genotype 1 is present in the evaluated population. 16 % (26/164) of the participants reported having ever had an accident with surgical material during work with cattle; this variable was associated with BLV positivity even after adjusting for other variables (PRa =2.70, 95 % CI= 1.01- 7.21). Considering that other studies have reported the circulation of BLV genotype 1 in cattle from this same region and the present report in humans from dairy herds, the results suggest a possible zoonotic transmission of BLV genotype 1 in Antioquia, reinforcing the need to continue investigating to determine the potential role of this virus as an etiological agent of disease in livestock farmers in the department.
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Affiliation(s)
- Willington Mendoza
- Grupo Biología de Sistemas, Escuela de Ciencias de la Salud, Facultad de Medicina, Universidad Pontificia Bolivariana. Medellín, Colombia
| | - Juan Pablo Isaza
- Grupo Biología de Sistemas, Escuela de Ciencias de la Salud, Facultad de Medicina, Universidad Pontificia Bolivariana. Medellín, Colombia
| | - Lucelly López
- Grupo de Investigación en Salud Pública, Escuela de Ciencias de la Salud, Facultad de Medicina, Universidad Pontificia Bolivariana. Medellín, Colombia
| | - Albeiro López-Herrera
- Grupo de Investigación Biodiversidad y Genética Molecular (BIOGEM), Universidad Nacional de Colombia Sede Medellín, Colombia
| | - Lina A Gutiérrez
- Grupo Biología de Sistemas, Escuela de Ciencias de la Salud, Facultad de Medicina, Universidad Pontificia Bolivariana. Medellín, Colombia.
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Sahnan S, Olivo D, Custer JM, Bandoo RA, Jackson D, Lund MC, McGraw H, Regney M, Aguiar de Souza Penha V, Neil J, Drake D, McGraw K, Varsani A, Kraberger S. Genome analysis of gyroviruses identified in waterfowl in Arizona (USA). Arch Virol 2024; 169:120. [PMID: 38753261 DOI: 10.1007/s00705-024-06049-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/29/2024] [Indexed: 06/13/2024]
Abstract
Gyroviruses are small single-stranded DNA (ssDNA) viruses that are largely associated with birds. Chicken anemia virus is the most extensively studied gyrovirus due to its disease impact on the poultry industry. However, we know much less about gyroviruses infecting other avian species. To investigate gyroviruses infecting waterfowl, we determined six complete genome sequences that fall into three gyrovirus groups, referred to as waterfowl gyrovirus 1 (n = 3), 2 (n = 2), and 3 (n = 1), in organs from hunter-harvested waterfowl from Arizona (USA). The waterfowl gyrovirus 1 variants were identified in multiple organs of a single American wigeon and represent a tentative new species. The waterfowl gyrovirus 2 variants were identified in the livers of two American wigeons and share >70% VP1 nucleotide sequence identity with gyrovirus 9, previously identified in the spleen of a Brazilian Pekin duck (MT318123) and a human fecal sample (KP742975). Waterfowl gyrovirus 3 was identified in a northern pintail spleen sample, and it shares >73% VP1 nucleotide sequence identity with two gyrovirus 13 sequences previously identified in Brazilian Pekin duck spleens (MT318125 and MT318127). These gyroviruses are the first to be identified in waterfowl in North America, as well as in American wigeons and northern pintails.
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Affiliation(s)
- Shawnpreet Sahnan
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA
| | - Diego Olivo
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA
| | - Joy M Custer
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA
| | - Rohan A Bandoo
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA
| | - Danny Jackson
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85719, USA
| | - Michael C Lund
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA
| | - Hannah McGraw
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Melanie Regney
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA
| | - Victor Aguiar de Souza Penha
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Organismal and Evolutionary Research Programme, University of Helsinki, Helsinki, Finland
| | - Julia Neil
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA
| | - Dean Drake
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Kevin McGraw
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Arvind Varsani
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA.
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA.
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287, USA.
- Structural Biology Research Unit, Department of Integrative, Biomedical Sciences, University of Cape Town, Observatory, Cape Town, 7925, South Africa.
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85287, USA.
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Ikechukwu CK, Qin K, Zhang H, Pan J, Zhang W. Novel equid papillomavirus from domestic donkey. Equine Vet J 2024; 56:171-177. [PMID: 37246448 DOI: 10.1111/evj.13957] [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: 10/29/2022] [Accepted: 05/05/2023] [Indexed: 05/30/2023]
Abstract
BACKGROUND Papillomaviruses can be of great medical importance as they infect humans and animals such as Equus species, other livestock and pets. They are responsible for several papillomas and benign tumours in their host. OBJECTIVES To describe a novel equid papillomavirus detected in oral swab samples collected from donkeys (Equus asinus) found on the Northwest plateau of China. STUDY DESIGN Cross-sectional. METHODS Swab samples collected from the oral mucosa of 32 donkeys in the Gansu Province of China, were subjected to viral metagenomic analysis to detect the presence of Papillomavirus. After de novo assembly, a novel papillomavirus genome designated as Equus asinus papillomavirus 3 (EaPV3) was identified in the studied samples. Additional bioinformatic analysis of the assembled genome was done using the Geneious prime software (version 2022.0.2). RESULTS The complete circular genome of EaPV3 is 7430 bp in length with a GC content of 50.8%. The genome was predicted to contain five ORFs coding for three early proteins (E7, E1, and E2) and two late proteins (L1 and L2). Phylogenic analysis of the nucleotide sequences of the concatenated amino acid sequences of the E1E2L1L2 genes revealed that EaPV3 is most closely related to Equus asinus papillomavirus 1 (EaPV1). The genome analysis of EaPV3 revealed similar genome organisation with other equine papillomavirus and the presence of E7 papillomavirus oncoprotein. MAIN LIMITATIONS Since there were no warts in the oral cavity of the donkeys in this study, and no biopsy samples taken, we are unable to conclusively link the novel virus to any clinical condition in the donkeys. CONCLUSIONS The Comparative characterisation of EaPV3 and its closest relatives, as well as phylogenetic analysis demonstrated that it is a novel virus specie that clusters within the Dyochipapilloma PV genus.
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Affiliation(s)
- Chukwudozie Kingsley Ikechukwu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
- Department of Microbiology, University of Nigeria, Nsukka, Nigeria
| | - Kailin Qin
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Han Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Jiamin Pan
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, China
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Vargas-Bermudez DS, Mogollon JD, Franco-Rodriguez C, Jaime J. The Novel Porcine Parvoviruses: Current State of Knowledge and Their Possible Implications in Clinical Syndromes in Pigs. Viruses 2023; 15:2398. [PMID: 38140639 PMCID: PMC10747800 DOI: 10.3390/v15122398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/04/2023] [Accepted: 11/06/2023] [Indexed: 12/24/2023] Open
Abstract
Parvoviruses (PVs) affect various animal species causing different diseases. To date, eight different porcine parvoviruses (PPV1 through PPV8) are recognized in the swine population, all of which are distributed among subfamilies and genera of the Parvoviridae family. PPV1 is the oldest and is recognized as the primary agent of SMEDI, while the rest of the PPVs (PPV2 through PPV8) are called novel PPVs (nPPVs). The pathogenesis of nPPVs is still undefined, and whether these viruses are putative disease agents is unknown. Structurally, the PPVs are very similar; the differences occur mainly at the level of their genomes (ssDNA), where there is variation in the number and location of the coding genes. Additionally, it is considered that the genome of PVs has mutation rates similar to those of ssRNA viruses, that is, in the order of 10-5-10-4 nucleotide/substitution/year. These mutations manifest mainly in the VP protein, constituting the viral capsid, affecting virulence, tropism, and viral antigenicity. For nPPVs, mutation rates have already been established that are similar to those already described; however, within this group of viruses, the highest mutation rate has been reported for PPV7. In addition to the mutations, recombinations are also reported, mainly in PPV2, PPV3, and PPV7; these have been found between strains of domestic pigs and wild boars and in a more significant proportion in VP sequences. Regarding affinity for cell types, nPPVs have been detected with variable prevalence in different types of organs and tissues; this has led to the suggestion that they have a broad tropism, although proportionally more have been found in lung and lymphoid tissue such as spleen, tonsils, and lymph nodes. Regarding their epidemiology, nPPVs are present on all continents (except PPV8, only in Asia), and within pig farms, the highest prevalences detecting viral genomes have been seen in the fattener and finishing groups. The relationship between nPPVs and clinical manifestations has been complicated to establish. However, there is already some evidence that establishes associations. One of them is PPV2 with porcine respiratory disease complex (PRDC), where causality tests (PCR, ISH, and histopathology) lead to proposing the PPV2 virus as a possible agent involved in this syndrome. With the other nPPVs, there is still no clear association with any pathology. These have been detected in different systems (respiratory, reproductive, gastrointestinal, urinary, and nervous), and there is still insufficient evidence to classify them as disease-causing agents. In this regard, nPPVs (except PPV8) have been found to cause porcine reproductive failure (PRF), with the most prevalent being PPV4, PPV6, and PPV7. In the case of PRDC, nPPVs have also been detected, with PPV2 having the highest viral loads in the lungs of affected pigs. Regarding coinfections, nPPVs have been detected in concurrence in healthy and sick pigs, with primary PRDC and PRF viruses such as PCV2, PCV3, and PRRSV. The effect of these coinfections is not apparent; it is unknown whether they favor the replication of the primary agents, the severity of the clinical manifestations, or have no effect. The most significant limitation in the study of nPPVs is that their isolation has been impossible; therefore, there are no studies on their pathogenesis both in vitro and in vivo. For all of the above, it is necessary to propose basic and applied research on nPPVs to establish if they are putative disease agents, establish their effect on coinfections, and measure their impact on swine production.
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Affiliation(s)
| | | | | | - Jairo Jaime
- Universidad Nacional de Colombia, Sede Bogotá, Facultad de Medicina Veterinaria y de Zootecnia, Departamento de Salud Animal, Centro de Investigación en Infectología e Inmunología Veterinaria (CI3V), Carrera 30 No. 45-03, Bogotá 111321, CP, Colombia; (D.S.V.-B.); (J.D.M.); (C.F.-R.)
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Afonso CL, Afonso AM. Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples. Vet Sci 2023; 10:690. [PMID: 38133241 PMCID: PMC10747646 DOI: 10.3390/vetsci10120690] [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: 10/13/2023] [Revised: 11/24/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
Direct-targeted next-generation sequencing (tNGS), with its undoubtedly superior diagnostic capacity over real-time PCR (RT-PCR), and direct-non-targeted NGS (ntNGS), with its higher capacity to identify and characterize multiple agents, are both likely to become diagnostic methods of choice in the future. tNGS is a rapid and sensitive method for precise characterization of suspected agents. ntNGS, also known as agnostic diagnosis, does not require a hypothesis and has been used to identify unsuspected infections in clinical samples. Implemented in the form of multiplexed total DNA metagenomics or as total RNA sequencing, the approach produces comprehensive and actionable reports that allow semi-quantitative identification of most of the agents present in respiratory, cloacal, and tissue samples. The diagnostic benefits of the use of direct tNGS and ntNGS are high specificity, compatibility with different types of clinical samples (fresh, frozen, FTA cards, and paraffin-embedded), production of nearly complete infection profiles (viruses, bacteria, fungus, and parasites), production of "semi-quantitative" information, direct agent genotyping, and infectious agent mutational information. The achievements of NGS in terms of diagnosing poultry problems are described here, along with future applications. Multiplexing, development of standard operating procedures, robotics, sequencing kits, automated bioinformatics, cloud computing, and artificial intelligence (AI) are disciplines converging toward the use of this technology for active surveillance in poultry farms. Other advances in human and veterinary NGS sequencing are likely to be adaptable to avian species in the future.
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Amato S, Ramsey J, Ahern TP, Rovnak J, Barlow J, Weaver D, Eyasu L, Singh R, Cintolo-Gonzalez J. Exploring the presence of bovine leukemia virus among breast cancer tumors in a rural state. Breast Cancer Res Treat 2023; 202:325-334. [PMID: 37517027 DOI: 10.1007/s10549-023-07061-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 05/31/2023] [Indexed: 08/01/2023]
Abstract
PURPOSE The bovine leukemia virus (BLV) is a deltaretrovirus that causes malignant lymphoma and lymphosarcomas in cattle globally and has high prevalence among large scale U.S. dairy herds. Associations between presence of BLV DNA in human mammary tissue and human breast cancer incidence have been reported. We sought to estimate the prevalence of BLV DNA in breast cancer tissue samples in a rural state with an active dairy industry. METHODS We purified genomic DNA from 56 fresh-frozen breast cancer tissue samples (51 tumor samples, 5 samples representing adjacent normal breast tissue) banked between 2016 and 2019. Using nested PCR assays, multiple BLV tax sequence primers and primers for the long terminal repeat (LTR) were used to detect BLV DNA in tissue samples and known positive control samples, including the permanently infected fetal lamb kidney cell line (FLK-BLV) and blood from BLV positive cattle. RESULTS The median age of patients from which samples were obtained at the time of treatment was 60 (40-93) and all were female. Ninety percent of patients had invasive ductal carcinoma. The majority were poorly differentiated (60%). On PCR assay, none of the tumor samples tested positive for BLV DNA, despite having consistent signals in positive controls. CONCLUSION We did not find BLV DNA in fresh-frozen breast cancer tumors from patients presenting to a hospital in Vermont. Our findings suggest a low prevalence of BLV in our patient population and a need to reevaluate the association between BLV and human breast cancer.
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Affiliation(s)
- Stas Amato
- Department of General Surgery, University of Vermont Medical Center, Burlington, VT, USA
- Department of Surgery, Larner College of Medicine, University of Vermont, 89 Beaumont Ave., B227, Burlington, VT, 05405, USA
| | - Jon Ramsey
- Department of Biochemistry, University of Vermont, Burlington, VT, USA
| | - Thomas P Ahern
- Department of Surgery, Larner College of Medicine, University of Vermont, 89 Beaumont Ave., B227, Burlington, VT, 05405, USA
| | - Joel Rovnak
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - John Barlow
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, USA
| | - Donald Weaver
- Department of Pathology, University of Vermont Medical Center, Burlington, VT, USA
| | - Lud Eyasu
- Department of Surgery, Larner College of Medicine, University of Vermont, 89 Beaumont Ave., B227, Burlington, VT, 05405, USA
| | - Rohit Singh
- Division of Hematology/Oncology, Department of Medicine, University of Vermont Medical Center, Burlington, VT, USA
| | - Jessica Cintolo-Gonzalez
- Department of General Surgery, University of Vermont Medical Center, Burlington, VT, USA.
- Department of Surgery, Larner College of Medicine, University of Vermont, 89 Beaumont Ave., B227, Burlington, VT, 05405, USA.
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de Quadros DL, Ribeiro VA, Rezende MA, Maté YA, Gomes MA, Secchi K, Strottmann DM, Frandoloso R, Kreutz LC. Oncogenic viral DNA related to human breast cancer found on cattle milk and meat. Comp Immunol Microbiol Infect Dis 2023; 101:102053. [PMID: 37672958 DOI: 10.1016/j.cimid.2023.102053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 08/18/2023] [Accepted: 08/26/2023] [Indexed: 09/08/2023]
Abstract
Bovine leukemia virus (BLV) is a major cause of lymphoma in cattle and has been recently correlated to breast cancer in humans. How and whether BLV might reach humans remains unknown but it could be through cattle-derived milk and meat. Here our aim was to investigate whether BLV DNA could be found in fresh milk and raw meat destined to human consumption and whether anti-BLV antibodies could be detected in human blood at the same geographical region. Milk (n = 36) and meat (n = 54) samples were collected from cows knowingly seropositive or negative to BLV and evaluated by nested PCR targeting BLV tax gene. Human serum samples (n = 900) were tested by ELISA to detect anti-BLV antibodies. BLV DNA was detected in 39 % of the milk samples and in 32 % of meat samples from BLV positive cows. Anti-BLV antibodies were found in 4.1 % of the human serum samples. Our data further supports the hypothesis that BLV might cause a zoonotic infection and indicate that milk and meat from BLV-infected cattle might be considered a potential source of infection to humans.
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Affiliation(s)
- Daniel Lazzari de Quadros
- Universidade de Passo Fundo, Escola de Ciências Agrárias, Inovação e Negócios, Programa de Pós-Graduação em Bioexperimentação, Prédio G3, Campus I, Rodovia BR 285, Km 292, Bairro São José, 99052-900 Passo Fundo, RS, Brazil
| | - Vitoria Agnoletto Ribeiro
- Universidade de Passo Fundo, Escola de Ciências Agrárias, Inovação e Negócios, Programa de Pós-Graduação em Bioexperimentação, Prédio G3, Campus I, Rodovia BR 285, Km 292, Bairro São José, 99052-900 Passo Fundo, RS, Brazil
| | - Mariana Antunes Rezende
- Universidade de Passo Fundo, Escola de Ciências Agrárias, Inovação e Negócios, Programa de Pós-Graduação em Bioexperimentação, Prédio G3, Campus I, Rodovia BR 285, Km 292, Bairro São José, 99052-900 Passo Fundo, RS, Brazil
| | - Yasmin Ampese Maté
- Universidade de Passo Fundo, Escola de Ciências Agrárias, Inovação e Negócios, Programa de Pós-Graduação em Bioexperimentação, Prédio G3, Campus I, Rodovia BR 285, Km 292, Bairro São José, 99052-900 Passo Fundo, RS, Brazil
| | - Márcio Alexandro Gomes
- Universidade de Passo Fundo, Escola de Ciências Agrárias, Inovação e Negócios, Programa de Pós-Graduação em Bioexperimentação, Prédio G3, Campus I, Rodovia BR 285, Km 292, Bairro São José, 99052-900 Passo Fundo, RS, Brazil
| | - Katia Secchi
- Universidade de Passo Fundo, Escola de Ciências Agrárias, Inovação e Negócios, Programa de Pós-Graduação em Bioexperimentação, Prédio G3, Campus I, Rodovia BR 285, Km 292, Bairro São José, 99052-900 Passo Fundo, RS, Brazil
| | - Daisy Maria Strottmann
- Laboratório de Virologia Molecular, Instituto Carlos Chagas (ICC/Fiocruz), Rua Prof. Algacyr Munhoz Mader, 3773, CEP 81350-010 Curitiba, PR, Brazil
| | - Rafael Frandoloso
- Universidade de Passo Fundo, Escola de Ciências Agrárias, Inovação e Negócios, Programa de Pós-Graduação em Bioexperimentação, Prédio G3, Campus I, Rodovia BR 285, Km 292, Bairro São José, 99052-900 Passo Fundo, RS, Brazil
| | - Luiz Carlos Kreutz
- Universidade de Passo Fundo, Escola de Ciências Agrárias, Inovação e Negócios, Programa de Pós-Graduação em Bioexperimentação, Prédio G3, Campus I, Rodovia BR 285, Km 292, Bairro São José, 99052-900 Passo Fundo, RS, Brazil.
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Li H, Wang H, Ju H, Lv J, Yang S, Zhang W, Lu H. Comparison of gut viral communities in children under 5 years old and newborns. Virol J 2023; 20:52. [PMID: 36973710 PMCID: PMC10045071 DOI: 10.1186/s12985-023-02013-2] [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: 10/11/2022] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Abstract
OBJECTIVES The gut virome of humans is mainly composed of bacteriophages and their role in shaping the gut microbiome and influencing human health is increasingly recognized. However, little is known about the dynamic changes of the gut virome in children and its role in growth and development. In this study, we collected fecal samples from newborns and children under 5 years old from the same area during the same time period to investigate the gut viral community using viral metagenomic technique. METHODS We used viral metagenomics to compare the gut bacteriophage composition between newborns and children under 5 years of age. We collected fecal samples from 45 newborns who were born at the Affiliated Hospital of Jiangsu University and 45 healthy children who were examined at the same hospital. The two groups were classified as the newborn group and the children group. RESULTS Our sequencing analysis showed that the number of seqeunce reads of the children group were more than that of the newborn group. The results of alpha diversity and beta diversity both indicated that the diversity of the children group was significantly higher than that of the newborn group and the children group is different from the newborn group. The abundance of gut virome in the children group was also higher than that in the newborn group. The analysis of the genetic characteristics of the viruses showed that the phage genome was scattered and clustered with specificity. CONCLUSION Our findings indicate that the gut bacteriophage communities undergo changes over time, presenting diversity and dynamic characteristics. We characterized the composition of gut virome in children and newborns in this region. However, further research is needed to investigate the function of bacteriophages in the ecology of the gastrointestinal tract.
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Affiliation(s)
- Hong Li
- Department of Pediatrics, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212000, P.R. China
- School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Hao Wang
- Department of Clinical Laboratory, Huai'an Hospital, Xuzhou Medical University, Huai'an, Jiangsu, 223002, China
| | - Huimin Ju
- Department of Pediatrics, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212000, P.R. China
| | - Jinquan Lv
- Department of Pediatrics, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212000, P.R. China
| | - Shixing Yang
- School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Wen Zhang
- School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, 212013, China.
| | - Hongyan Lu
- Department of Pediatrics, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212000, P.R. China.
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Shah PT, Bahoussi AN, Cui X, Shabir S, Wu C, Xing L. Genetic diversity, distribution, and evolution of chicken anemia virus: A comparative genomic and phylogenetic analysis. Front Microbiol 2023; 14:1145225. [PMID: 36970671 PMCID: PMC10034120 DOI: 10.3389/fmicb.2023.1145225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 02/20/2023] [Indexed: 03/11/2023] Open
Abstract
Chicken infectious anemia (CIA) is an immunosuppressive poultry disease that causes aplastic anemia, immunosuppression, growth retardation and lymphoid tissue atrophy in young chickens and is responsible for huge economic losses to the poultry industry worldwide. The disease is caused by the chicken anemia virus (CAV), which belongs to the genus Gyrovirus, family Anelloviridae. Herein, we analyzed the full-length genomes of 243 available CAV strains isolated during 1991–2020 and classified them into two major clades, GI and GII, divided into three and four sub-clades, GI a-c, and GII a-d, respectively. Moreover, the phylogeographic analysis revealed that the CAVs spread from Japan to China, China to Egypt and subsequently to other countries, following multiple mutational steps. In addition, we identified eleven recombination events within the coding and non-coding regions of CAV genomes, where the strains isolated in China were the most active and involved in ten of these events. Furthermore, the amino acids variability analysis indicated that the variability coefficient exceeded the estimation limit of 1.00 in VP1, VP2, and VP3 proteins coding regions, demonstrating substantial amino acid drift with the rise of new strains. The current study offers robust insights into the phylogenetic, phylogeographic and genetic diversity characteristics of CAV genomes that may provide valuable data to map the evolutionary history and facilitate preventive measures of CAVs.
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Affiliation(s)
- Pir Tariq Shah
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, Shanxi, China
| | | | - Xiaogang Cui
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, Shanxi, China
| | - Shaista Shabir
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, Shanxi, China
| | - Changxin Wu
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, Shanxi, China
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Shanxi University, Taiyuan, China
- Shanxi Provincial Key Laboratory for Prevention and Treatment of Major Infectious Diseases, Taiyuan, China
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, China
| | - Li Xing
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, Shanxi, China
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Shanxi University, Taiyuan, China
- Shanxi Provincial Key Laboratory for Prevention and Treatment of Major Infectious Diseases, Taiyuan, China
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, China
- *Correspondence: Li Xing,
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11
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Yang M, Yang Q, Bi X, Shi H, Yang J, Cheng X, Yan T, Zhang H, Cheng Z. The Synergy of Chicken Anemia Virus and Gyrovirus Homsa 1 in Chickens. Viruses 2023; 15:v15020515. [PMID: 36851729 PMCID: PMC9964263 DOI: 10.3390/v15020515] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/28/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Chicken anemia virus (CAV) and Gyrovirus homsa 1 (GyH1) are members of the Gyrovirus genus. The two viruses cause similar clinical manifestations in chickens, aplastic anemia and immunosuppression. Our previous investigation displays that CAV and GyH1 often co-infect chickens. However, whether they have synergistic pathogenicity in chickens remains elusive. Here, we established a co-infection model of CAV and GyH1 in specific pathogen-free (SPF) chickens to explore the synergy between CAV and GyH1. We discovered that CAV and GyH1 significantly inhibited weight gain, increased mortality, and hindered erythropoiesis in co-infected chickens. Co-infected chickens exhibited severe immune organ atrophy and lymphocyte exhaustion. The proventriculus and gizzard had severe hemorrhagic necrosis and inflammation. We also discovered that the viral loads and shedding levels were higher and lasted longer in CAV and GyH1 co-infected chickens than in mono-infected chickens. Our results demonstrate that CAV and GyH1 synergistically promote immunosuppression, pathogenicity, and viral replication in co-infected chicken, highlighting the interaction between CAV and GyH1 in the disease process and increasing potential health risk in the poultry breeding industry, and needs further attention.
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12
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Bassi C, Guerriero P, Pierantoni M, Callegari E, Sabbioni S. Novel Virus Identification through Metagenomics: A Systematic Review. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122048. [PMID: 36556413 PMCID: PMC9784588 DOI: 10.3390/life12122048] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
Metagenomic Next Generation Sequencing (mNGS) allows the evaluation of complex microbial communities, avoiding isolation and cultivation of each microbial species, and does not require prior knowledge of the microbial sequences present in the sample. Applications of mNGS include virome characterization, new virus discovery and full-length viral genome reconstruction, either from virus preparations enriched in culture or directly from clinical and environmental specimens. Here, we systematically reviewed studies that describe novel virus identification through mNGS from samples of different origin (plant, animal and environment). Without imposing time limits to the search, 379 publications were identified that met the search parameters. Sample types, geographical origin, enrichment and nucleic acid extraction methods, sequencing platforms, bioinformatic analytical steps and identified viral families were described. The review highlights mNGS as a feasible method for novel virus discovery from samples of different origins, describes which kind of heterogeneous experimental and analytical protocols are currently used and provides useful information such as the different commercial kits used for the purification of nucleic acids and bioinformatics analytical pipelines.
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Affiliation(s)
- Cristian Bassi
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Paola Guerriero
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Marina Pierantoni
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Elisa Callegari
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy
| | - Silvia Sabbioni
- Laboratorio per Le Tecnologie delle Terapie Avanzate (LTTA), University of Ferrara, 44121 Ferrara, Italy
- Department of Life Science and Biotechnology, University of Ferrara, 44121 Ferrara, Italy
- Correspondence: ; Tel.: +39-053-245-5319
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13
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Zhu J, Xiao Q, Wen L, Yin L, Zhang F, Li T, Banma Z, He K, Suolang S. First detection and complete genome analysis of porcine circovirus-like virus P1 and porcine circovirus-2 in yak in China. Vet Med Sci 2022; 8:2553-2561. [PMID: 36049138 PMCID: PMC9677406 DOI: 10.1002/vms3.911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023] Open
Abstract
Porcine circovirus-like virus P1, like porcine circovirus type 2 (PCV2), is a potential pathogen of post-weaning multisystemic wasting syndrome in swine. Yaks are a valuable species and an iconic symbol of the Tibet Plateau which is the highest and largest plateau in the world. In this study, a total of 105 yak diarrheal samples, collected from 13 farms in Linzhi in the Tibet Plateau from January 2019 to December 2021, that were screened for P1 and PCV2 by polymerase chain reaction, 10.48% (n = 11) were positive for P1, 4.76% (n = 5) for PCV2, and 5.71% (n = 6) were positive for coinfection of P1 and PCV2. In addition, the whole genomes of eight P1 strains and eight PCV2 strains were sequenced. Alignment of deduced amino acid sequences of P1 ORF1 and PCV2 ORF2 gene revealed that ON012566 had one unique amino acid mutation at residues 137 (T to P). This mutation has important implication for the study of virus virulence, tissue tropism, and immune response. Phylogenetic analysis shows that the yak-origin P1 strains in this study with cattle-origin P1 reference strains were grouped into one cluster. The yak-origin PCV2 (ON012566) and a buffalo-origin PCV2 (KM116514) reference strain clustered in the same branch in the PCV2b regions. Meanwhile, the remaining PCV2 strains and buffalo-origin PCV2 reference strain (ON012565) clustered in the PCV2d regions. To summarize, to our knowledge, this is the first report on the molecular prevalence and genome characteristics of P1 and PCV2 in yaks in the world and will contribute to further study of the molecular epidemiology, source, and evolution of P1 and PCV2 strains.
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Affiliation(s)
- Jiaping Zhu
- Institute of Veterinary MedicineJiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and TechnologyMinistry of Agriculture and Rural AffairsNanjingChina
- College of Animal ScienceTibet Agricultural and Animal Husbandry University, Provincial Key Laboratory of Tibet Plateau Animal Epidemic Disease ResearchLinZhiChina
| | - Qi Xiao
- Institute of Veterinary MedicineJiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and TechnologyMinistry of Agriculture and Rural AffairsNanjingChina
- Jiangsu Co‐innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesYangzhou UniversityYangzhouChina
- Jiangsu Key Laboratory for Food Quality and Safety—State Key Laboratory Cultivation Base of Ministry of Science and TechnologyNanjingChina
| | - Libin Wen
- Institute of Veterinary MedicineJiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and TechnologyMinistry of Agriculture and Rural AffairsNanjingChina
- Jiangsu Co‐innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesYangzhou UniversityYangzhouChina
- Jiangsu Key Laboratory for Food Quality and Safety—State Key Laboratory Cultivation Base of Ministry of Science and TechnologyNanjingChina
| | - Lihong Yin
- Institute of Veterinary MedicineJiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and TechnologyMinistry of Agriculture and Rural AffairsNanjingChina
- College of Animal ScienceTibet Agricultural and Animal Husbandry University, Provincial Key Laboratory of Tibet Plateau Animal Epidemic Disease ResearchLinZhiChina
| | - Fengxi Zhang
- Institute of Veterinary MedicineJiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and TechnologyMinistry of Agriculture and Rural AffairsNanjingChina
- College of Animal ScienceTibet Agricultural and Animal Husbandry University, Provincial Key Laboratory of Tibet Plateau Animal Epidemic Disease ResearchLinZhiChina
| | - Tianjiao Li
- College of Animal ScienceTibet Agricultural and Animal Husbandry University, Provincial Key Laboratory of Tibet Plateau Animal Epidemic Disease ResearchLinZhiChina
| | - Zelang Banma
- College of Animal ScienceTibet Agricultural and Animal Husbandry University, Provincial Key Laboratory of Tibet Plateau Animal Epidemic Disease ResearchLinZhiChina
| | - Kongwang He
- Institute of Veterinary MedicineJiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and TechnologyMinistry of Agriculture and Rural AffairsNanjingChina
- Jiangsu Co‐innovation Center for Prevention and Control of Important Animal Infectious Diseases and ZoonosesYangzhou UniversityYangzhouChina
- Jiangsu Key Laboratory for Food Quality and Safety—State Key Laboratory Cultivation Base of Ministry of Science and TechnologyNanjingChina
| | - Sizhu Suolang
- College of Animal ScienceTibet Agricultural and Animal Husbandry University, Provincial Key Laboratory of Tibet Plateau Animal Epidemic Disease ResearchLinZhiChina
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Bovine Polyomavirus-1 (Epsilonpolyomavirus bovis): An Emerging Fetal Pathogen of Cattle That Causes Renal Lesions Resembling Polyomavirus-Associated Nephropathy of Humans. Viruses 2022; 14:v14092042. [PMID: 36146848 PMCID: PMC9502773 DOI: 10.3390/v14092042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/17/2022] Open
Abstract
Bovine polyomavirus-1 (BoPyV-1, Epsilonpolyomavirus bovis) is widespread in cattle and has been detected in commercialized beef at supermarkets in the USA and Germany. BoPyV-1 has been questioned as a probable zoonotic agent with documented increase in seropositivity in people exposed to cattle. However, to date, BoPyV-1 has not been causally associated with pathology or disease in any animal species, including humans. Here we describe and illustrate pathological findings in an aborted bovine fetus naturally infected with BoPyV-1, providing evidence of its pathogenicity and probable abortigenic potential. Our results indicate that: (i) BoPyV-1 can cause severe kidney lesions in cattle, including tubulointerstitial nephritis with cytopathic changes and necrosis in tubular epithelial cells, tubular and interstitial inflammation, and interstitial fibroplasia; (ii) lesions are at least partly attributable to active viral replication in renal tubular epithelial cells, which have abundant intranuclear viral inclusions; (iii) BoPyV-1 large T (LT) antigen, resulting from early viral gene expression, can be detected in infected renal tubular epithelial cells using a monoclonal antibody raised against Simian Virus-40 polyomavirus LT antigen; and (iv) there is productive BoPyV-1 replication and virion assembly in the nuclei of renal tubular epithelial cells, as demonstrated by the ultrastructural observation of abundant arrays of viral particles with typical polyomavirus morphology. Altogether, these lesions resemble the “cytopathic-inflammatory pathology pattern” proposed in the pathogenesis of Human polyomavirus-1-associated nephropathy in immunocompromised people and kidney allograft recipients. Additionally, we sequenced the complete genome of the BoPyV-1 infecting the fetus, which represents the first whole genome of a BoPyV-1 from the Southern Hemisphere. Lastly, the BoPyV-1 strain infecting this fetus was isolated, causing a cytopathic effect in Madin–Darby bovine kidney cells. We conclude that BoPyV-1 is pathogenic to the bovine fetus under natural circumstances. Further insights into the epidemiology, biology, clinical relevance, and zoonotic potential of BoPyV-1 are needed.
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15
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Liu Y, Lv Q, Li Y, Yu Z, Huang H, Lan T, Wang W, Cao L, Shi Y, Sun W, Zheng M. Cross-species transmission potential of chicken anemia virus and avian gyrovirus 2. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 99:105249. [PMID: 35183752 DOI: 10.1016/j.meegid.2022.105249] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/18/2021] [Accepted: 02/14/2022] [Indexed: 11/20/2022]
Abstract
The Gyrovirus genus consists of nonenveloped, icosahedral viruses with small circular single-stranded DNA genomes. Gyroviruses have been detected in diverse hosts, including humans, chickens, rodents, and cats. Two Gyroviruses were detected in canine serum samples using PCR in this study. The results indicated that four serum samples were positive for CAV (0.28%, 2/700) or AGV2 (0.28%, 2/700). Additionally, recombination analysis showed that AGV2 and CAV might have originated from the recombination of viruses similar to those detected in chickens and humans. We detected a total of 14 mutations in CAV VP1 amino acid sequences and identified new mutations at positions 31, 388, 390, 399, and 421 for the first time. The identification of T390C, C912T, T1230C, and T1297C mutations in AGV2 VP1, R93C mutations in AGV2 VP2, and R58C mutations AGV2 VP3 indicated that the differences might be related to a transboundary movement among hosts, which requires further elucidation. To the best of our knowledge, this study is the first report of an AGV2-infected dog in China, suggesting that the cross-species transmission of viruses with circular single-stranded DNA genomes is a public health concern.
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Affiliation(s)
- Yumeng Liu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Qiao Lv
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Yuying Li
- Institute of Virology, Wenzhou University, Wenzhou 325035, China
| | - Ziping Yu
- Institute of Virology, Wenzhou University, Wenzhou 325035, China
| | - Haixin Huang
- Institute of Virology, Wenzhou University, Wenzhou 325035, China
| | - Tian Lan
- Institute of Virology, Wenzhou University, Wenzhou 325035, China
| | - Wei Wang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; Institute of Virology, Wenzhou University, Wenzhou 325035, China
| | - Liang Cao
- College of Laboratory, Jilin Medical University, Jilin 132013, China
| | - Yaokai Shi
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Wenchao Sun
- Institute of Virology, Wenzhou University, Wenzhou 325035, China.
| | - Min Zheng
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; Guangxi Centre for Animal Disease Control and Prevention, Nanning 530001, China.
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16
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Billington C, Kingsbury JM, Rivas L. Metagenomics Approaches for Improving Food Safety: A Review. J Food Prot 2022; 85:448-464. [PMID: 34706052 DOI: 10.4315/jfp-21-301] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/21/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Advancements in next-generation sequencing technology have dramatically reduced the cost and increased the ease of microbial whole genome sequencing. This approach is revolutionizing the identification and analysis of foodborne microbial pathogens, facilitating expedited detection and mitigation of foodborne outbreaks, improving public health outcomes, and limiting costly recalls. However, next-generation sequencing is still anchored in the traditional laboratory practice of the selection and culture of a single isolate. Metagenomic-based approaches, including metabarcoding and shotgun and long-read metagenomics, are part of the next disruptive revolution in food safety diagnostics and offer the potential to directly identify entire microbial communities in a single food, ingredient, or environmental sample. In this review, metagenomic-based approaches are introduced and placed within the context of conventional detection and diagnostic techniques, and essential considerations for undertaking metagenomic assays and data analysis are described. Recent applications of the use of metagenomics for food safety are discussed alongside current limitations and knowledge gaps and new opportunities arising from the use of this technology. HIGHLIGHTS
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Affiliation(s)
- Craig Billington
- Institute of Environmental Science and Research, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand
| | - Joanne M Kingsbury
- Institute of Environmental Science and Research, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand
| | - Lucia Rivas
- Institute of Environmental Science and Research, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand
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Righi F, Arnaboldi S, Filipello V, Ianiro G, Di Bartolo I, Calò S, Bellini S, Trogu T, Lelli D, Bianchi A, Bonardi S, Pavoni E, Bertasi B, Lavazza A. Torque Teno Sus Virus (TTSuV) Prevalence in Wild Fauna of Northern Italy. Microorganisms 2022; 10:microorganisms10020242. [PMID: 35208696 PMCID: PMC8875128 DOI: 10.3390/microorganisms10020242] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 11/24/2022] Open
Abstract
Torque teno sus virus (TTSuV) is a non-enveloped circular ssDNA virus which frequently infects swine and has been associated with hepatic, respiratory, and autoimmune disorders. TTSuV’s pathogenic role is still uncertain, and clear data in the literature on virus reservoirs are lacking. The aims of this study were to investigate the presence of potentially zoonotic TTSuV in wild animals in Northern Italy and to evaluate their role as reservoirs. Liver samples were collected between 2016 and 2020 during four hunting seasons from wild boars (Sus scrofa), red deer (Cervus elaphus), roe deer (Capreolus capreolus), and chamois (Rupicapra rupicapra). Samples originated from areas in Northern Italy characterized by different traits, i.e., mountains and flatland with, respectively low and high farm density and anthropization. Viral identification was carried out by end-point PCR with specific primers for TTSuV1a and TTSuVk2a species. TTSuV prevalence in wild boars was higher in the mountains than in the flatland (prevalence of 6.2% and 2.3%, respectively). In wild ruminants only TTSuVk2a was detected (with a prevalence of 9.4%). Our findings shed light on the occurrence and distribution of TTSuV in some wild animal species, investigating their possible role as reservoirs.
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Affiliation(s)
- Francesco Righi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy; (F.R.); (V.F.); (S.C.); (S.B.); (T.T.); (D.L.); (E.P.); (B.B.); (A.L.)
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 20133 Milan, Italy
| | - Sara Arnaboldi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy; (F.R.); (V.F.); (S.C.); (S.B.); (T.T.); (D.L.); (E.P.); (B.B.); (A.L.)
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 20133 Milan, Italy
- Correspondence: ; Tel.: +39-030-229-0781
| | - Virginia Filipello
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy; (F.R.); (V.F.); (S.C.); (S.B.); (T.T.); (D.L.); (E.P.); (B.B.); (A.L.)
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 20133 Milan, Italy
| | - Giovanni Ianiro
- Emerging Zoonoses Unit, Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (G.I.); (I.D.B.)
| | - Ilaria Di Bartolo
- Emerging Zoonoses Unit, Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (G.I.); (I.D.B.)
| | - Stefania Calò
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy; (F.R.); (V.F.); (S.C.); (S.B.); (T.T.); (D.L.); (E.P.); (B.B.); (A.L.)
| | - Silvia Bellini
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy; (F.R.); (V.F.); (S.C.); (S.B.); (T.T.); (D.L.); (E.P.); (B.B.); (A.L.)
| | - Tiziana Trogu
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy; (F.R.); (V.F.); (S.C.); (S.B.); (T.T.); (D.L.); (E.P.); (B.B.); (A.L.)
| | - Davide Lelli
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy; (F.R.); (V.F.); (S.C.); (S.B.); (T.T.); (D.L.); (E.P.); (B.B.); (A.L.)
| | - Alessandro Bianchi
- Istituto Zooprofilattico della Lombardia e dell’Emilia Romagna (IZSLER), 23100 Sondrio, Italy;
| | - Silvia Bonardi
- Veterinary Science Department, Università degli Studi di Parma, 43100 Parma, Italy;
| | - Enrico Pavoni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy; (F.R.); (V.F.); (S.C.); (S.B.); (T.T.); (D.L.); (E.P.); (B.B.); (A.L.)
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 20133 Milan, Italy
| | - Barbara Bertasi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy; (F.R.); (V.F.); (S.C.); (S.B.); (T.T.); (D.L.); (E.P.); (B.B.); (A.L.)
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 20133 Milan, Italy
| | - Antonio Lavazza
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy; (F.R.); (V.F.); (S.C.); (S.B.); (T.T.); (D.L.); (E.P.); (B.B.); (A.L.)
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Canuti M, Rodrigues B, Bouchard É, Whitney HG, Lang AS, Dufour SC, Verhoeven JT. Distinct epidemiological profiles of porcine circovirus 3 and fox circovirus in Canadian foxes (Vulpes spp.). CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100161. [DOI: 10.1016/j.crmicr.2022.100161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
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19
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Identification and Characterization of Circular Single-Stranded DNA Genomes in Sheep and Goat Milk. Viruses 2021; 13:v13112176. [PMID: 34834982 PMCID: PMC8621823 DOI: 10.3390/v13112176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 12/21/2022] Open
Abstract
In recent years, a variety of circular replicase-encoding single-stranded (CRESS) DNA viruses and unclassified virus-like DNA elements have been discovered in a broad range of animal species and environmental samples. Key questions to be answered concern their presence in the human diet and their potential impact on disease emergence. Especially DNA elements termed bovine meat and milk factors (BMMF) are suspected to act as co-factors in the development of colon and breast cancer. To expand our knowledge on the occurrence of these potential pathogens in human nutrition, a total of 73 sheep and 40 goat milk samples were assayed by combining rolling circle amplification (RCA), PCR and Sanger sequencing. The present study further includes retail milk from the aforementioned species. We recovered 15 single stranded (ss) circular genomes. Of those, nine belong to the family Genomoviridae and six are members of the unclassified group of BMMF. Thus, dairy sheep and goats add to dispersal of CRESS viruses and circular ssDNA elements, which enter the food chain via milk. The presence of these entities is therefore more widespread in Bovidae than initially assumed and seems to be part of the common human nutrition.
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20
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Li G, Zhou D, Zhao M, Liu Q, Hao X, Yan T, Yuan S, Zhang S, Cheng Z. Kinetic analysis of pathogenicity and tissue tropism of gyrovirus 3 in experimentally infected chickens. Vet Res 2021; 52:120. [PMID: 34526128 PMCID: PMC8442313 DOI: 10.1186/s13567-021-00990-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/09/2021] [Indexed: 12/03/2022] Open
Abstract
Gyrovirus 3 (GyV3), the third novel emerging species of the genus Gyrovirus of the Anelloviridae family, has been described in multiple hosts. Epidemiologically, there are suggestions that GyV3 is associated with diarrhea/proventriculitis, however, no direct causal evidence exists between GyV3 infection and specific clinical diseases. Herein, we infected special pathogen-free (SPF) chickens with GyV3, and then assessed the pathogenicity and tissue tropism. The results revealed that GyV3 induced persistent infection characterized by diarrhea, aplastic anemia, immunosuppression, and persistent systemic lymphocytic inflammation. Clinically, the infected chickens presented ruffled feathers, diarrhea, anemia, and weight loss. Aplastic anemia was characterized by progressive depletion of hematopoietic cells in the bone marrow, immunosuppression was associated with atrophy of the thymus, spleen, and bursa of Fabricious, progressive lymphocytic inflammations were characterized by proventriculitis, adrenalitis, pancreatitis, hepatitis, nephritis, and bronchitis. Viral loads of GyV3 in tissues exhibited “M”, “N”, “W” or “V” type dynamic changes. The highest level of viral loads was reported in bone marrow at 7dpi, followed by the adrenal gland at 2 dpi, the sciatic nerve at 7 dpi, and bile at 35 dpi. The bone marrow and kidney demonstrate the strongest immunostaining of GyV3-VP1 antigen and were suggested as the target tissues of GyV3. Collectively, GyV3 is an immunosuppressive pathogenic virus that targets the bone marrow and kidney in chickens. Exploring the pathogenicity and tissue tropism of GyV3 will guide the basic understanding of the biology of GyV3 and its pathogenesis in chickens.
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Affiliation(s)
- Gen Li
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China.,College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Defang Zhou
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Manda Zhao
- Department of Animal Science and Technology, Vocational-Technical School of Husbandry and Veterinary Medicine, Weifang, China
| | - Qing Liu
- Service Center of Jinan Zoo, Jinan, China
| | - Xiaojing Hao
- Qindao Husbandry and Veterinary Institute, Qingdao, China
| | - Tianxing Yan
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Shiyu Yuan
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Shicheng Zhang
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China
| | - Ziqiang Cheng
- College of Veterinary Medicine, Shandong Agricultural University, Tai'an, 271018, China.
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21
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NGS Techniques Reveal a High Diversity of RNA Viral Pathogens and Papillomaviruses in Fresh Produce and Irrigation Water. Foods 2021; 10:foods10081820. [PMID: 34441597 PMCID: PMC8394881 DOI: 10.3390/foods10081820] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/22/2021] [Accepted: 07/31/2021] [Indexed: 02/07/2023] Open
Abstract
Fresh fruits and vegetables are susceptible to microbial contamination at every stage of the food production chain, and as a potential source of pathogens, irrigation water quality is a critical factor. Next-generation sequencing (NGS) techniques have been flourishing and expanding to a wide variety of fields. However, their application in food safety remains insufficiently explored, and their sensitivity requires improvement. In this study, quantitative polymerase chain reaction (qPCR) assays showed low but frequent contamination of common circulating viral pathogens, which were found in 46.9% of samples of fresh produce: 6/12 lettuce samples, 4/12 strawberries samples, and 5/8 parsley samples. Furthermore, the application of two different NGS approaches, target enrichment sequencing (TES) for detecting viruses that infect vertebrates and amplicon deep sequencing (ADS), revealed a high diversity of viral pathogens, especially Norovirus (NoV) and Human Papillomavirus (HPV), in fresh produce and irrigation water. All NoV and HPV types found in fresh fruit and vegetable samples were also detected in irrigation water sources, indicating that these viruses are common circulating pathogens in the population and that irrigation water may be the most probable source of viral pathogens in food samples.
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22
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Yuan S, Yan T, Huang L, Hao X, Zhao M, Zhang S, Zhou D, Cheng Z. Cross-species pathogenicity of gyrovirus 3 in experimentally infected chickens and mice. Vet Microbiol 2021; 261:109191. [PMID: 34385005 DOI: 10.1016/j.vetmic.2021.109191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/01/2021] [Indexed: 11/26/2022]
Abstract
Gyrovirus 3 (GyV3) has been identified in humans and other hosts, suggesting its cross-species pathogenicity, which poses an increased public health risk. In the current study, we established chicken and mouse models of GyV3 infection. We found that GyV3 induced persistent infections, characterized by viremia, aplastic anemia, immunosuppression, and systematic lymphocytic inflammation, in both species. Kinetic viral loads and antigen expression demonstrated rapid viral replication and broad tissue tropism of GyV3 in both models. The highest viral loads and the strongest antigen immunostaining were present in bone marrow and cerebrum in both chickens and mice, indicating that these are target tissues for GyV3. Genetic diversity analysis of VP1 in infected chickens and mice showed that GyV3 adapts to new hosts via rapid evolution of the hypervariable region of the gene encoding the structural protein VP1. Overall, our results indicate that GyV3 is a cross-species pathogenic virus; therefore, more attention needs to be paid to high levels of GyV3-induced neurotropism and aplastic anemia as a public health risk.
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Affiliation(s)
- Shiyu Yuan
- College of Veterinary Medicine, Shandong Agricultural University, Tai`an, 271018, China
| | - Tianxing Yan
- College of Veterinary Medicine, Shandong Agricultural University, Tai`an, 271018, China
| | - Libo Huang
- College of Veterinary Medicine, Shandong Agricultural University, Tai`an, 271018, China
| | - Xiaojing Hao
- Qingdao Husbandry and Veterinary Institute, Qingdao, 266000, China
| | - Manda Zhao
- Department of Animal Science and Technology, Vocational-technical School of Husbandry and Veterinary Medicine, Weifang, 261061, China
| | - Shicheng Zhang
- College of Veterinary Medicine, Shandong Agricultural University, Tai`an, 271018, China
| | - Defang Zhou
- College of Veterinary Medicine, Shandong Agricultural University, Tai`an, 271018, China
| | - Ziqiang Cheng
- College of Veterinary Medicine, Shandong Agricultural University, Tai`an, 271018, China.
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23
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Taxonomic updates for the genus Gyrovirus (family Anelloviridae): recognition of several new members and establishment of species demarcation criteria. Arch Virol 2021; 166:2937-2942. [PMID: 34347169 DOI: 10.1007/s00705-021-05194-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The genus Gyrovirus was assigned to the family Anelloviridae in 2017 with only one recognized species, Chicken anemia virus. Over the last decade, many diverse viruses related to chicken anemia virus have been identified but not classified. Here, we provide a framework for the classification of new species in the genus Gyrovirus and communicate the establishment of nine new species. We adopted the 'Genus + freeform epithet' binomial system for the naming of these species.
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24
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Hui A, Altan E, Slovis N, Fletcher C, Deng X, Delwart E. Circovirus in Blood of a Febrile Horse with Hepatitis. Viruses 2021; 13:v13050944. [PMID: 34065502 PMCID: PMC8161410 DOI: 10.3390/v13050944] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 12/12/2022] Open
Abstract
Circoviruses infect vertebrates where they can result in a wide range of disease signs or in asymptomatic infections. Using viral metagenomics we analyzed a pool of five sera from four healthy and one sick horse. Sequences from parvovirus-H, equus anellovirus, and distantly related to mammalian circoviruses were recognized. PCR identified the circovirus reads as originating from a pregnant mare with fever and hepatitis. That horse's serum was also positive by real time PCR for equine parvovirus H and negative for the flavivirus equine hepacivirus. The complete circular genome of equine circovirus 1 strain Charaf (EqCV1-Charaf) was completed using PCR and Sanger sequencing. EqCV1 replicase showed 73-74% identity to those of their closest relatives, pig circoviruses 1/2, and elk circovirus. The closest capsid proteins were from the same ungulate circoviruses with 62-63% identity. The overall nucleotide identity of 72% to its closest relative indicates that EqCV1 is a new species in the Circovirus genus, the first reported in genus Equus. Whether EqCV1 alone or in co-infections can result in disease and its prevalence in different equine populations will require further studies now facilitated using EqCV1's genome sequence.
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Affiliation(s)
- Alvin Hui
- Vitalant Research Institute, San Francisco, CA 94118, USA; (A.H.); (E.A.); (X.D.)
| | - Eda Altan
- Vitalant Research Institute, San Francisco, CA 94118, USA; (A.H.); (E.A.); (X.D.)
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA
| | - Nathan Slovis
- Hagyard Equine Medical Institute, 4250 Iron Works Pike, Lexington, KY 40361, USA; (N.S.); (C.F.)
| | - Caitlin Fletcher
- Hagyard Equine Medical Institute, 4250 Iron Works Pike, Lexington, KY 40361, USA; (N.S.); (C.F.)
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA 94118, USA; (A.H.); (E.A.); (X.D.)
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA 94118, USA; (A.H.); (E.A.); (X.D.)
- Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA
- Correspondence:
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25
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Viral Metagenomic Analysis Reveals a Human Rhinovirus from Hospitalized Neonates. Microbiol Resour Announc 2021; 10:10/15/e00106-21. [PMID: 33858922 PMCID: PMC8050964 DOI: 10.1128/mra.00106-21] [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: 11/22/2022] Open
Abstract
Here, the coding-complete genome of a human rhinovirus (HRV) belonging to the HRV-A clade was determined from a pool containing nine nasopharyngeal secretion specimens from hospitalized neonates. PCR screening indicated that this HRV variant was present in a cohort of 45 hospitalized neonates, with a positivity rate of 11.1% (5/45 patients). Here, the coding-complete genome of a human rhinovirus (HRV) belonging to the HRV-A clade was determined from a pool containing nine nasopharyngeal secretion specimens from hospitalized neonates. PCR screening indicated that this HRV variant was present in a cohort of 45 hospitalized neonates, with a positivity rate of 11.1% (5/45 patients).
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26
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Cibulski S, Alves de Lima D, Fernandes Dos Santos H, Teixeira TF, Tochetto C, Mayer FQ, Roehe PM. A plate of viruses: Viral metagenomics of supermarket chicken, pork and beef from Brazil. Virology 2021; 552:1-9. [PMID: 33032031 PMCID: PMC7521440 DOI: 10.1016/j.virol.2020.09.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/12/2020] [Accepted: 09/13/2020] [Indexed: 02/08/2023]
Abstract
A viral metagenomics study was conducted in beef, pork, and chicken sold in supermarkets from Southern Brazil. From chicken, six distinct gyroviruses (GyV) were detected, including GyV3 and GyV6, which for the first time were detected in samples from avian species, plus a novel smacovirus species and two highly divergent circular Rep-encoding ssDNA (CRESS-DNA) viruses. From pork, genomes of numerous anelloviruses, porcine parvovirus 5 (PPV5) and 6 (PPV6), two new genomoviruses and two new CRESS-DNA viruses were found. Finally, two new CRESS-DNA genomes were recovered from beef. Although none of these viruses have history of transmission to humans, the findings reported here reveal that such agents are inevitably consumed in diets that include these types of meat.
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Affiliation(s)
- Samuel Cibulski
- Centro de Biotecnologia - CBiotec, Laboratório de Biotecnologia Celular e Molecular, Universidade Federal da Paraíba - UFPB, João Pessoa, Paraíba, Brazil.
| | - Diane Alves de Lima
- Departamento de Microbiologia Imunologia e Parasitologia, Laboratório de Virologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil; Centro Universitário da Serra Gaúcha - FSG, Caxias do Sul, Grande do Sul, Brazil
| | - Helton Fernandes Dos Santos
- Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria - UFSM, Santa Maria, Rio Grande do Sul, Brazil
| | - Thais Fumaco Teixeira
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria de Agricultura, Pecuária e Desenvolvimento Rural, Eldorado do Sul, RS, Brazil
| | - Caroline Tochetto
- Departamento de Microbiologia Imunologia e Parasitologia, Laboratório de Virologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Fabiana Quoos Mayer
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria de Agricultura, Pecuária e Desenvolvimento Rural, Eldorado do Sul, RS, Brazil
| | - Paulo Michel Roehe
- Departamento de Microbiologia Imunologia e Parasitologia, Laboratório de Virologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
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27
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Xiao Y, Wang H, Feng L, Pan J, Chen Z, Wang H, Yang S, Shen Q, Wang X, Shan T, Zhang W. Fecal, oral, blood and skin virome of laboratory rabbits. Arch Virol 2020; 165:2847-2856. [PMID: 33034764 PMCID: PMC7546134 DOI: 10.1007/s00705-020-04808-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 08/11/2020] [Indexed: 12/24/2022]
Abstract
Here, we investigated the fecal, oral, blood, and skin virome of 10 laboratory rabbits using a viral metagenomic method. In the oral samples, we detected a novel polyomavirus (RabPyV), and phylogenetic analysis based on the large T antigen, VP1 and VP2 regions indicated that the novel strain might have undergone a recombination event. Recombination analysis based on related genomes confirmed that RabPyV is a multiple recombinant between rodent-like and avian-like polyomaviruses. In fecal samples, three partial or complete genome sequences of viruses belonging to the families Picobirnaviridae, Parvoviridae, Microviridae and Coronaviridae were characterized, and phylogenetic trees were constructed based on the predicted amino acid sequences of viral proteins. This study increases the amount of genetic information on viruses present in laboratory rabbits.
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Affiliation(s)
- Yuqing Xiao
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Hao Wang
- Department of Clinical Laboratory, Huai'an Hospital, Xuzhou Medical University, Huai'an, 223002, Jiangsu, China
| | - Lei Feng
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jiamin Pan
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Zeyu Chen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Huiling Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Shixing Yang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Quan Shen
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Xiaochun Wang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Tongling Shan
- Department of Swine Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
| | - Wen Zhang
- Department of Microbiology, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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28
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Bovine Polyomavirus 2 is a Probable Cause of Non-Suppurative Encephalitis in Cattle. Pathogens 2020; 9:pathogens9080620. [PMID: 32751201 PMCID: PMC7459705 DOI: 10.3390/pathogens9080620] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/26/2020] [Accepted: 07/27/2020] [Indexed: 12/22/2022] Open
Abstract
Tissues from two cows with neurological signs that were admitted to the Vetsuisse Faculty under suspicion of rabies and bovine spongiform encephalopathy (BSE), respectively, were further analyzed for this case report. After histopathological examination and exclusion of BSE and rabies, the animals were diagnosed with etiologically unresolved disseminated non-suppurative encephalitis. Using next-generation sequencing, we detected the full genome of bovine polyomavirus 2 (BoPyV2) in brain samples from both animals. This virus has been identified in beef samples in three independent studies conducted in the United States and Germany, but has not been linked to any disease. Analysis of the two new BoPyV2 genome sequences revealed close phylogenetic relationships to one another and to BoPyV2 isolates detected in beef samples. In situ hybridization demonstrated the presence of viral nucleic acid in all investigated brain areas and in areas with signs of inflammation in both animals. Thus, we provide the first evidence that BoPyV2 is a probable cause of non-suppurative encephalitis in cattle, and encourage further molecular and serological testing to elucidate the disease's epidemiology, as well as experimental transmission studies to prove causality between the infection and disease.
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29
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Loiko MR, Varela APM, Tochetto C, Lopes BC, Scheffer CM, Morel AP, Vidaletti MR, Lima DA, Cerva C, Mayer FQ, Roehe PM. Novel Gyrovirus genomes recovered from free-living pigeons in Southern Brazil. Virology 2020; 548:132-135. [PMID: 32838934 DOI: 10.1016/j.virol.2020.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/17/2020] [Accepted: 07/02/2020] [Indexed: 01/15/2023]
Abstract
Wild birds carry a number of infectious agents, some of which may have pathogenic potential for the host and others species, including humans. Domestic pigeons (Columba livia) are important targets of study since these increasingly cohabit urban spaces, being possible spillover sources of pathogens to humans. In the present study, two genomes (PiGyV_Tq/RS/Br and PiGyV_RG/RS/Br), representative of Gyrovirus genus, family Anelloviridae, were detected in sera of free-living pigeons collected in Southern Brazil. The genomes exhibit less than 50% identity to previously described members of Gyrovirus genus, suggesting that they constitute a new viral species circulating in pigeons, to which the name "pigeon gyrovirus (PiGyV)" is proposed. The current study characterizes these two PiGyV genomes which, to date, are the first gyrovirus species identified in domestic pigeons.
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Affiliation(s)
- M R Loiko
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, UFRGS, Av. Sarmento Leite 500, Sala 208, CEP 90050-170, Porto Alegre, RS, Brazil; Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual de Agricultura, Pecuária e Desenvolvimento Rural, CEP 92990-000, Eldorado do Sul, RS, Brazil; Feevale - Universidade Feevale, RS-239, 2755, CEP 93525-075, Novo Hamburgo, RS, Brazil
| | - A P M Varela
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, UFRGS, Av. Sarmento Leite 500, Sala 208, CEP 90050-170, Porto Alegre, RS, Brazil; Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual de Agricultura, Pecuária e Desenvolvimento Rural, CEP 92990-000, Eldorado do Sul, RS, Brazil
| | - C Tochetto
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, UFRGS, Av. Sarmento Leite 500, Sala 208, CEP 90050-170, Porto Alegre, RS, Brazil; Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual de Agricultura, Pecuária e Desenvolvimento Rural, CEP 92990-000, Eldorado do Sul, RS, Brazil
| | - B C Lopes
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual de Agricultura, Pecuária e Desenvolvimento Rural, CEP 92990-000, Eldorado do Sul, RS, Brazil
| | - C M Scheffer
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, UFRGS, Av. Sarmento Leite 500, Sala 208, CEP 90050-170, Porto Alegre, RS, Brazil; Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual de Agricultura, Pecuária e Desenvolvimento Rural, CEP 92990-000, Eldorado do Sul, RS, Brazil
| | - A P Morel
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual de Agricultura, Pecuária e Desenvolvimento Rural, CEP 92990-000, Eldorado do Sul, RS, Brazil; Falcoaria e Consultoria Ambiental - HAYABUSA, São Francisco de Paula, RS, Brazil
| | - M R Vidaletti
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual de Agricultura, Pecuária e Desenvolvimento Rural, CEP 92990-000, Eldorado do Sul, RS, Brazil
| | - D A Lima
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, UFRGS, Av. Sarmento Leite 500, Sala 208, CEP 90050-170, Porto Alegre, RS, Brazil; Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual de Agricultura, Pecuária e Desenvolvimento Rural, CEP 92990-000, Eldorado do Sul, RS, Brazil
| | - C Cerva
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual de Agricultura, Pecuária e Desenvolvimento Rural, CEP 92990-000, Eldorado do Sul, RS, Brazil
| | - F Q Mayer
- Centro de Pesquisa em Saúde Animal, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria Estadual de Agricultura, Pecuária e Desenvolvimento Rural, CEP 92990-000, Eldorado do Sul, RS, Brazil.
| | - P M Roehe
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, UFRGS, Av. Sarmento Leite 500, Sala 208, CEP 90050-170, Porto Alegre, RS, Brazil
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30
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Cibulski S, Weber MN, de Sales Lima FE, Lima DAD, Fernandes Dos Santos H, Teixeira TF, Varela APM, Tochetto C, Mayer FQ, Roehe PM. Viral metagenomics in Brazilian Pekin ducks identifies two gyrovirus, including a new species, and the potentially pathogenic duck circovirus. Virology 2020; 548:101-108. [PMID: 32838930 DOI: 10.1016/j.virol.2020.05.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/24/2020] [Accepted: 05/24/2020] [Indexed: 01/01/2023]
Abstract
Viral metagenomics coupled to high-throughput sequencing has provided a powerful tool for large-scale detection of known and unknown viruses associated to distinct hosts and environments. Using this approach, known and novel viruses have been characterized from sylvatic and commercial avian hosts, increasing our understanding of the viral diversity in these species. In the present work we applied an exploratory viral metagenomics on organs (spleen, liver and bursa of Fabricious) of Pekin ducks from Southern Brazil. The virome contained sequences related to a known duck pathogen (duck circovirus) and a number of other circular ssDNA viruses. Additionally, we detected avian gyrovirus 9 (to date detected only in human feces) and one new avian gyrovirus species, to which is proposed the name avian gyrovirus 13 (GyV13). This study is expected to contribute to the knowledge of the viral diversity in Pekin ducks.
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Affiliation(s)
- Samuel Cibulski
- Centro de Biotecnologia - CBiotec, Laboratório de Biotecnologia Celular e Molecular, Universidade Federal da Paraíba - UFPB, João Pessoa, Paraíba, Brazil.
| | - Matheus Nunes Weber
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil
| | - Francisco Esmaile de Sales Lima
- Departamento de Microbiologia Imunologia e Parasitologia, Laboratório de Virologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Diane Alves de Lima
- Departamento de Microbiologia Imunologia e Parasitologia, Laboratório de Virologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Helton Fernandes Dos Santos
- Departamento de Microbiologia Imunologia e Parasitologia, Laboratório de Virologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil; Departamento de Medicina Veterinária Preventiva, Universidade Federal de Santa Maria - UFSM, Santa Maria, Rio Grande do Sul, Brazil
| | - Thais Fumaco Teixeira
- Departamento de Microbiologia Imunologia e Parasitologia, Laboratório de Virologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Ana Paula Muterle Varela
- Departamento de Microbiologia Imunologia e Parasitologia, Laboratório de Virologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Caroline Tochetto
- Departamento de Microbiologia Imunologia e Parasitologia, Laboratório de Virologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
| | - Fabiana Quoos Mayer
- Laboratório de Biologia Molecular, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Eldorado do Sul, RS, Brazil
| | - Paulo Michel Roehe
- Departamento de Microbiologia Imunologia e Parasitologia, Laboratório de Virologia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Porto Alegre, Rio Grande do Sul, Brazil
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Desdouits M, de Graaf M, Strubbia S, Oude Munnink BB, Kroneman A, Le Guyader FS, Koopmans MPG. Novel opportunities for NGS-based one health surveillance of foodborne viruses. ONE HEALTH OUTLOOK 2020; 2:14. [PMID: 33829135 PMCID: PMC7993515 DOI: 10.1186/s42522-020-00015-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/01/2020] [Indexed: 05/15/2023]
Abstract
Foodborne viral infections rank among the top 5 causes of disease, with noroviruses and hepatitis A causing the greatest burden globally. Contamination of foods by infected food handlers or through environmental pollution are the main sources of foodborne illness, with a lesser role for consumption of products from infected animals. Viral partial genomic sequencing has been used for more than two decades to track foodborne outbreaks and whole genome or metagenomics next-generation-sequencing (NGS) are new additions to the toolbox of food microbiology laboratories. We discuss developments in the field of targeted and metagenomic NGS, with an emphasis on application in food virology, the challenges and possible solutions towards future routine application.
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Affiliation(s)
- Marion Desdouits
- IFREMER, Laboratoire de Microbiologie, LSEM/SG2M, Nantes, France
| | - Miranda de Graaf
- Viroscience Department, Erasmus Medical Centre, Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Sofia Strubbia
- IFREMER, Laboratoire de Microbiologie, LSEM/SG2M, Nantes, France
| | - Bas B. Oude Munnink
- Viroscience Department, Erasmus Medical Centre, Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Annelies Kroneman
- Centre for Infectious Disease Control, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | | | - Marion P. G. Koopmans
- Viroscience Department, Erasmus Medical Centre, Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
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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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Parainfluenza Virus 5 Infection in Neurological Disease and Encephalitis of Cattle. Int J Mol Sci 2020; 21:ijms21020498. [PMID: 31941046 PMCID: PMC7013525 DOI: 10.3390/ijms21020498] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/10/2020] [Accepted: 01/11/2020] [Indexed: 12/22/2022] Open
Abstract
The etiology of viral encephalitis in cattle often remains unresolved, posing a potential risk for animal and human health. In metagenomics studies of cattle with bovine non-suppurative encephalitis, parainfluenza virus 5 (PIV5) was identified in three brain samples. Interestingly, in two of these animals, bovine herpesvirus 6 and bovine astrovirus CH13 were additionally found. We investigated the role of PIV5 in bovine non-suppurative encephalitis and further characterized the three cases. With traditional sequencing methods, we completed the three PIV5 genomes, which were compared to one another. However, in comparison to already described PIV5 strains, unique features were revealed, like an 81 nucleotide longer open reading frame encoding the small hydrophobic (SH) protein. With in situ techniques, we demonstrated PIV5 antigen and RNA in one animal and found a broad cell tropism of PIV5 in the brain. Comparative quantitative analyses revealed a high viral load of PIV5 in the in situ positive animal and therefore, we propose that PIV5 was probably the cause of the disease. With this study, we clearly show that PIV5 is capable of naturally infecting different brain cell types in cattle in vivo and therefore it is a probable cause of encephalitis and neurological disease in cattle.
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Kaszab E, Doszpoly A, Lanave G, Verma A, Bányai K, Malik YS, Marton S. Metagenomics revealing new virus species in farm and pet animals and aquaculture. GENOMICS AND BIOTECHNOLOGICAL ADVANCES IN VETERINARY, POULTRY, AND FISHERIES 2020. [PMCID: PMC7149329 DOI: 10.1016/b978-0-12-816352-8.00002-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Viral metagenomics is slowly taking over the traditional and widely used molecular techniques for the investigation of pathogenic viruses responsible for illness and inflicting great economic burden on the farm animal industry. Owing to the continued improvements in sequencing technologies and the dramatic reduction of per base costs of sequencing the use of next generation sequencing have been key factors in this progress. Discoveries linked to viral metagenomics are expected to be beneficial to the field of veterinary medicine starting from the development of better diagnostic assays to the design of new subunit vaccines with minimal investments. With these achievements the research has taken a giant leap even toward the better healthcare of animals and, as a result, the animal sector could be growing at an unprecedented pace.
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Zhai SL, Lu SS, Wei WK, Lv DH, Wen XH, Zhai Q, Chen QL, Sun YW, Xi Y. Reservoirs of Porcine Circoviruses: A Mini Review. Front Vet Sci 2019; 6:319. [PMID: 31616677 PMCID: PMC6763682 DOI: 10.3389/fvets.2019.00319] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 09/05/2019] [Indexed: 01/01/2023] Open
Abstract
Porcine circovirus (PCV) is one of the smallest known DNA viruses in mammals. At present, PCVs are divided into three species, PCV1, PCV2, and PCV3. PCV1 and PCV2 were found in the 1970s and the 1990s, respectively, whereas PCV3 was discovered recently in 2016. PCV1 does not cause diseases in pigs. However, PCV3, similar to PCV2, is reported to be associated with several swine diseases, including porcine dermatitis and nephropathy syndrome (PDNS) and reproductive failure. PCVs are very common in domestic pigs as well as wild boars. However, PCVs have been occasionally isolated from non-porcine animals, including ruminants (such as cattle, goats, wild chamois, and roe deers), rodents (such as NMRI mice, BALB/c mice, Black C57 mice, ICR mice, Mus musculus, and Rattus rattus), canines (such as dogs, minks, foxes, and raccoon dogs), insects (such as flies, mosquitoes, and ticks), and shellfish. Moreover, PCVs are frequently reported in biological products, including human vaccines, animal vaccines, porcine-derived commercial pepsin products, and many cell lines. PCVs are also abundant in the environment, including water samples and air samples. Interestingly, PCV1 and/or PCV2 antibody or antigen has also been detected in sera, stool samples and respiratory swab samples of human, revealing zoonotic potential of PCVs. Thus, PCVs inhabit many types of reservoirs. In this review, we summarize the reservoirs of PCVs, and this information would be helpful in understanding the natural circulating status and possible cross-species transmission of PCVs.
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Affiliation(s)
- Shao-Lun Zhai
- Key Laboratory of Animal Disease Prevention of Guangdong Province, Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Shou-Sheng Lu
- Guangdong Center for Animal Disease Prevention and Control, Guangzhou, China
| | - Wen-Kang Wei
- Key Laboratory of Animal Disease Prevention of Guangdong Province, Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Dian-Hong Lv
- Key Laboratory of Animal Disease Prevention of Guangdong Province, Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Xiao-Hui Wen
- Key Laboratory of Animal Disease Prevention of Guangdong Province, Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Qi Zhai
- Key Laboratory of Animal Disease Prevention of Guangdong Province, Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Qin-Ling Chen
- Key Laboratory of Animal Disease Prevention of Guangdong Province, Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Yan-Wei Sun
- Guangdong Center for Animal Disease Prevention and Control, Guangzhou, China
| | - Yun Xi
- Department of Clinical Laboratory, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
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Genomic Characterization of Diverse Gyroviruses Identified in the Feces of Domestic Cats. Sci Rep 2019; 9:13303. [PMID: 31527770 PMCID: PMC6746754 DOI: 10.1038/s41598-019-49955-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 09/03/2019] [Indexed: 12/22/2022] Open
Abstract
Gyroviruses (GyVs) are small, single-stranded, circular DNA viruses in the genus Gyrovirus, which consists of the chicken anemia virus (CAV) prototype and nine other viral species. These different GyV species have been reported in chickens, humans, mice, and companion animals. To date, CAV has been identified in the feces of domestic cats, while the circulation of other GyV species in cats is currently unknown. In the present study, 197 fecal samples were collected from pet cats in northeast China, and samples were screened for different GyV species by PCR. Twelve GyV strains were identified from the feces of pet cats. These included 4 positive for CAV, 3 for HGyV/AGV2, 3 for GyV3 and 2 positive for GyV6. The complete genome sequences of the 12 cat-sourced GyV strains showed 93.9-99.7% nucleotide identities to the homologous reference GyV strains. Phylogenetic analyses based on the complete genomes, VP1, VP2 and VP3 genes showed the identical classification of GyV species with previous reports. Moreover, one and four unique amino acid substitutions were identified in the VP1 protein of the cat-sourced HGyV/AGV2 and GyV6 strains, respectively, and one substitution was also observed in the VP2 protein of one GyV6 strain identified in this study. In conclusion, our investigation demonstrates that the diverse GyV species were circulating in domestic cats, and provides the first molecular evidence for the circulation of HGyV/AGV2, GyV3 and GyV6 in domestic cats. These cat-origin GyVs possessed considerable genetic diversity. This study also raises the possibility that domestic cats, as reservoirs for gyroviruses, may inadvertently disseminate viruses to other species, e.g., humans and chickens.
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Franzo G, Grassi L, Tucciarone CM, Drigo M, Martini M, Pasotto D, Mondin A, Menandro ML. A wild circulation: High presence of Porcine circovirus 3 in different mammalian wild hosts and ticks. Transbound Emerg Dis 2019; 66:1548-1557. [PMID: 30901142 DOI: 10.1111/tbed.13180] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/14/2019] [Indexed: 12/01/2022]
Abstract
Porcine circovirus 3 (PCV-3) has emerged as a potential threat for swine industry, being consistently reported in the presence of several clinical signs all around the world. Recently, its presence in wild boar has been demonstrated at high prevalence. This evidence is surprising since the lower density of wild populations might not be expected to sustain such efficient viral transmission. Porcine circoviruses were proven to exhibit a certain plasticity in the host tropism and were detected in unrelated species, like mice, dogs and ruminants. However, if this scenario applies also to wild animals remains to be established. Therefore, this study aimed to investigate the presence of PCV-3 in wild ungulates other than wild boar and in related hematophagous ectoparasites. One hundred and nine animals were sampled from different hilly and mountain areas of Friuli Venezia Giulia, including 9 chamois (Rupicapra rupicapra), 17 red deer (Cervus elaphus), 4 mouflons (Ovis musimon), 50 roe deer (Capreolus capreolus) and 29 wild boars (Sus scrofa). Additionally, host-matched ectoparasites were collected when present. Porcine circovirus 3 was diagnosed using molecular techniques and sequencing. This study results confirmed the high PCV-3 occurrence in wild boar and reported for the first time its presence, at low prevalence, in chamois and roe deer. Moreover, two ticks (Ixodes ricinus), one of which non-engorged, collected from PCV-3 negative roe deer, tested PCV-3 positive. The genetic characterization of some of the strains collected from non-swine hosts allowed to prove that, albeit clearly part of PCV-3 species, they were genetically unique, demonstrating the absence of among-samples contamination and thus confirming the actual presence of PCV-3 genome in these new hosts. Therefore, this study highlights an unexpected broad PCV-3 distribution and circulation in the wild, rising further questions on porcine circoviruses infectious cycle, epidemiology and origin, which will deserve additional investigations.
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Affiliation(s)
- Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Legnaro, Italy
| | - Laura Grassi
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Legnaro, Italy
| | - Claudia Maria Tucciarone
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Legnaro, Italy
| | - Michele Drigo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Legnaro, Italy
| | - Marco Martini
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Legnaro, Italy
| | - Daniela Pasotto
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Legnaro, Italy
| | - Alessandra Mondin
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Legnaro, Italy
| | - Maria Luisa Menandro
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, Legnaro, Italy
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Altan E, Kubiski SV, Boros Á, Reuter G, Sadeghi M, Deng X, Creighton EK, Crim MJ, Delwart E. A Highly Divergent Picornavirus Infecting the Gut Epithelia of Zebrafish ( Danio rerio) in Research Institutions Worldwide. Zebrafish 2019; 16:291-299. [PMID: 30939077 DOI: 10.1089/zeb.2018.1710] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Zebrafish have been extensively used as a model system for research in vertebrate development and pathogen-host interactions. We describe the complete genome of a novel picornavirus identified during a viral metagenomics analysis of zebrafish gut tissue. The closest relatives of this virus showed identity of <20% in their P1 capsids and <36% in their RdRp qualifying zebrafish picornavirus-1 (ZfPV-1) as member of a novel genus with a proposed name of Cyprivirus. Reverse transcription (RT)-PCR testing of zebrafish from North America, Europe, and Asia showed ZfPV-1 to be globally distributed, being detected in 23 of 41 (56%) institutions tested. In situ hybridization of whole zebrafish showed viral RNA was restricted to a subset of enterocytes and cells in the subjacent lamina propria of the intestine and the intestinal mucosa. This naturally occurring and apparently asymptomatic infection (in wild-type zebrafish lineage AB) provides a natural infection system to study picornavirus-host interactions in an advanced vertebrate model organism. Whether ZfPV-1 infection affects any immunological, developmental, or other biological processes in wild-type or mutant zebrafish lineages remains to be determined.
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Affiliation(s)
- Eda Altan
- 1 Vitalant Research Institute, San Francisco, California.,2 Department of Laboratory Medicine, University of California, San Francisco, California
| | - Steven V Kubiski
- 3 Institute for Conservation Research, San Diego Zoo Global, San Diego, California
| | - Ákos Boros
- 4 Regional Laboratory of Virology, National Reference Laboratory of Gastroenteric Viruses, ÁNTSZ Regional Institute of State Public Health Service, Pécs, Hungary.,5 Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Gábor Reuter
- 5 Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Mohammadreza Sadeghi
- 1 Vitalant Research Institute, San Francisco, California.,6 Department of Virology, University of Helsinki, Helsinki, Finland
| | - Xutao Deng
- 1 Vitalant Research Institute, San Francisco, California.,2 Department of Laboratory Medicine, University of California, San Francisco, California
| | | | | | - Eric Delwart
- 1 Vitalant Research Institute, San Francisco, California.,2 Department of Laboratory Medicine, University of California, San Francisco, California
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40
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Viral metagenomics reveals significant viruses in the genital tract of apparently healthy dairy cows. Arch Virol 2019; 164:1059-1067. [PMID: 30783771 DOI: 10.1007/s00705-019-04158-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 01/03/2019] [Indexed: 01/03/2023]
Abstract
The virome in genital tract secretion samples collected from 80 dairy cattle in Shanghai, China, was characterized. Viruses detected included members of the families Papillomaviridae, Polyomaviridae, Hepeviridae, Parvoviridae, Astroviridae, Picornaviridae, and Picobirnaviridae. A member of a new species within the genus Dyoxipapillomavirus and six circular Rep-encoding single-stranded DNA (ssDNA) (CRESS-DNA) viral genomes were fully sequenced and phylogenetically analyzed. The prevalence of bovine polyomaviruses 1 and 2 was measured by PCR to be 10% (8/80) and 6.25% (5/80), respectively. PCR screening also indicated that the novel papillomavirus ujs-21015 and bovine herpesvirus 6 were present in three and two out of the 80 samples, respectively.
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Sukmak M, Thanantong N, Poolperm P, Boonsoongnern A, Ratanavanichrojn N, Jirawattanapong P, Woonwong Y, Soda N, Kaminsonsakul T, Phuttapatimok S, Wajjwalku W. The retrospective identification and molecular epidemiology of porcine circovirus type 3 (
PCV
3) in swine in Thailand from 2006 to 2017. Transbound Emerg Dis 2018; 66:611-616. [DOI: 10.1111/tbed.13057] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/18/2018] [Accepted: 10/25/2018] [Indexed: 01/11/2023]
Affiliation(s)
- Manakorn Sukmak
- Department of Farm Resources and Production Medicine Faculty of Veterinary Medicine Kasetsart University Nakhon Pathom Thailand
| | - Narut Thanantong
- Department of Farm Resources and Production Medicine Faculty of Veterinary Medicine Kasetsart University Nakhon Pathom Thailand
| | - Pariwat Poolperm
- Department of Farm Resources and Production Medicine Faculty of Veterinary Medicine Kasetsart University Nakhon Pathom Thailand
| | - Alongkot Boonsoongnern
- Department of Farm Resources and Production Medicine Faculty of Veterinary Medicine Kasetsart University Nakhon Pathom Thailand
| | - Nattavut Ratanavanichrojn
- Department of Farm Resources and Production Medicine Faculty of Veterinary Medicine Kasetsart University Nakhon Pathom Thailand
| | - Pichai Jirawattanapong
- Department of Farm Resources and Production Medicine Faculty of Veterinary Medicine Kasetsart University Nakhon Pathom Thailand
| | - Yonlayong Woonwong
- Department of Farm Resources and Production Medicine Faculty of Veterinary Medicine Kasetsart University Nakhon Pathom Thailand
| | - Nantana Soda
- Faculty of Veterinary Medicine Kamphaeng Saen Veterinary Diagnostic Center (KVDC) Kasetsart University Nakhon Pathom Thailand
| | - Tanyanant Kaminsonsakul
- Faculty of Veterinary Medicine Kamphaeng Saen Veterinary Diagnostic Center (KVDC) Kasetsart University Nakhon Pathom Thailand
| | - Sahathat Phuttapatimok
- Faculty of Veterinary Medicine Kamphaeng Saen Veterinary Diagnostic Center (KVDC) Kasetsart University Nakhon Pathom Thailand
| | - Worawidh Wajjwalku
- Department of Farm Resources and Production Medicine Faculty of Veterinary Medicine Kasetsart University Nakhon Pathom Thailand
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Ye X, Berg M, Fossum C, Wallgren P, Blomström AL. Detection and genetic characterisation of porcine circovirus 3 from pigs in Sweden. Virus Genes 2018; 54:466-469. [PMID: 29564688 PMCID: PMC5951868 DOI: 10.1007/s11262-018-1553-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 03/10/2018] [Indexed: 01/27/2023]
Abstract
Porcine circovirus 3 (PCV3) is a newly detected circovirus belonging to the family Circoviridae with a circular ssDNA genome of 2000 bp that encodes two proteins-the replicase protein and the capsid protein. PCV3 was discovered for the first time in the US in 2016. After this initial discovery, PCV3 was detected in other parts of the world such as in China, South Korea, Italy and Poland. In this study, 49 tissue samples from Swedish pig herds were screened for PCV3 using PCR and 10 samples were positive and one was uncertain. The entire PCV3 genome and a mini PCV-like virus (MPCLV) were obtained from one of these samples. These two viruses showed a high sequence identity to PCV3 viruses from other countries as well as to MPCLV from the US. However, the sequence identity to PCV1 and 2 was only 31-48% on amino acid level. This is the first detection and complete genetic characterisation of PCV3 in Swedish pigs. It is also interesting to note that one of the positive samples was collected in 1993, showing that PCV3 has been present for a long time.
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Affiliation(s)
- Xingyu Ye
- Guangyuan Center for Animal Disease Control and Prevention, Guangyuan, 628017, China
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07, Uppsala, Sweden
| | - Mikael Berg
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07, Uppsala, Sweden
| | - Caroline Fossum
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07, Uppsala, Sweden
| | - Per Wallgren
- National veterinary institute (SVA), 751 89, Uppsala, Sweden
| | - Anne-Lie Blomström
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Box 7028, 750 07, Uppsala, Sweden.
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43
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Fegan N, Jenson I. The role of meat in foodborne disease: Is there a coming revolution in risk assessment and management? Meat Sci 2018; 144:22-29. [PMID: 29716760 DOI: 10.1016/j.meatsci.2018.04.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/17/2018] [Accepted: 04/18/2018] [Indexed: 12/12/2022]
Abstract
Meat has featured prominently as a source of foodborne disease and a public health concern. For about the past 20 years the risk management paradigm has dominated international thinking about food safety. Control through the supply chain is supported by risk management concepts, as the public health risk at the point of consumption becomes the accepted outcome based measure. Foodborne pathogens can be detected at several points in the supply chain and determining the source of where these pathogens arise and how they behave throughout meat production and processing are important parts of risk based approaches. Recent improvements in molecular and genetic based technologies and data analysis for investigating source attribution and pathogen behaviour have enabled greater insights into how foodborne outbreaks occur and where controls can be implemented. These new approaches will improve our understanding of the role of meat in foodborne disease and are expected to have a significant impact on our understanding in the coming years.
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Affiliation(s)
- Narelle Fegan
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, 671 Sneydes Rd, Werribee, VIC 3030, Australia.
| | - Ian Jenson
- Meat and Livestock Australia, Level 1, 40 Mount Street, North Sydney, NSW 2060, Australia
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Abstract
PURPOSE OF REVIEW The purpose of this review is to provide an update on recent literature and findings concerning selected foodborne viruses. Two groups of viruses were selected: (a) the most important viruses contaminating food, based on numbers of publications in the last 5 years and (b) viruses infecting sources of food that might have an impact on human health. RECENT FINDINGS Important foodborne viruses such as norovirus, hepatitis A and rotavirus are usually "only" contaminating food and are detected on the surface of foodstuffs. However, they are threats to human public health and make up for the majority of cases. In contrast, the meaning of viruses born from within the food such as natural animal and plant viruses is still in many cases unknown. An exception is Hepatitis E virus that is endemic in pigs, transmitted via pork meat and is recognised as an emerging zoonosis in industrialised countries. SUMMARY Even though the clinical meaning of "new" foodborne viruses, often detected by next generation sequencing, still needs clarification, the method has great potential to enhance surveillance and detection particularly in view of an increasingly globalised food trade.
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Affiliation(s)
- Claudia Bachofen
- Institute of Virology, Vetsuisse Faculty, University of Zürich, Winterthurerstrasse 266a, 8057 Zürich, Switzerland
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Borda-Molina D, Seifert J, Camarinha-Silva A. Current Perspectives of the Chicken Gastrointestinal Tract and Its Microbiome. Comput Struct Biotechnol J 2018; 16:131-139. [PMID: 30026889 PMCID: PMC6047366 DOI: 10.1016/j.csbj.2018.03.002] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 03/09/2018] [Accepted: 03/12/2018] [Indexed: 12/29/2022] Open
Abstract
The microbial communities inhabiting the gastrointestinal tract (GIT) of chickens are essential for the gut homeostasis, the host metabolism and affect the animals' physiology and health. They play an important role in nutrient digestion, pathogen inhibition and interact with the gut-associated immune system. Throughout the last years high-throughput sequencing technologies have been used to analyze the bacterial communities that colonize the different sections of chickens' gut. The most common methodologies are targeted amplicon sequencing followed by metagenome shotgun sequencing as well as metaproteomics aiming at a broad range of topics such as dietary effects, animal diseases, bird performance and host genetics. However, the respective analyses are still at the beginning and currently there is a lack of information in regard to the activity and functional characterization of the gut microbial communities. In the future, the use of multi-omics approaches may enhance research related to chicken production, animal and also public health. Furthermore, combinations with other disciplines such as genomics, immunology and physiology may have the potential to elucidate the definition of a "healthy" gut microbiota.
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Evolutionary analysis of Porcine circovirus 3 (PCV3) indicates an ancient origin for its current strains and a worldwide dispersion. Virus Genes 2018; 54:376-384. [DOI: 10.1007/s11262-018-1545-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 03/01/2018] [Indexed: 11/27/2022]
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Fernandez-Cassi X, Timoneda N, Gonzales-Gustavson E, Abril JF, Bofill-Mas S, Girones R. A metagenomic assessment of viral contamination on fresh parsley plants irrigated with fecally tainted river water. Int J Food Microbiol 2017. [PMID: 28646670 DOI: 10.1016/j.ijfoodmicro.2017.06.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microbial food-borne diseases are still frequently reported despite the implementation of microbial quality legislation to improve food safety. Among all the microbial agents, viruses are the most important causative agents of food-borne outbreaks. The development and application of a new generation of sequencing techniques to test for viral contaminants in fresh produce is an unexplored field that allows for the study of the viral populations that might be transmitted by the fecal-oral route through the consumption of contaminated food. To advance this promising field, parsley was planted and grown under controlled conditions and irrigated using contaminated river water. Viruses polluting the irrigation water and the parsley leaves were studied by using metagenomics. To address possible contamination due to sample manipulation, library preparation, and other sources, parsley plants irrigated with nutritive solution were used as a negative control. In parallel, viruses present in the river water used for plant irrigation were analyzed using the same methodology. It was possible to assign viral taxons from 2.4 to 74.88% of the total reads sequenced depending on the sample. Most of the viral reads detected in the river water were related to the plant viral families Tymoviridae (66.13%) and Virgaviridae (14.45%) and the phage viral families Myoviridae (5.70%), Siphoviridae (5.06%), and Microviridae (2.89%). Less than 1% of the viral reads were related to viral families that infect humans, including members of the Adenoviridae, Reoviridae, Picornaviridae and Astroviridae families. On the surface of the parsley plants, most of the viral reads that were detected were assigned to the Dicistroviridae family (41.52%). Sequences related to important viral pathogens, such as the hepatitis E virus, several picornaviruses from species A and B as well as human sapoviruses and GIV noroviruses were detected. The high diversity of viral sequences found in the parsley plants suggests that irrigation on fecally-tainted food may have a role in the transmission of a wide diversity of viral families. This finding reinforces the idea that the best way to avoid food-borne viral diseases is to introduce good field irrigation and production practices. New strains have been identified that are related to the Picornaviridae and distantly related to the Hepeviridae family. However, the detection of a viral genome alone does not necessarily indicate there is a risk of infection or disease development. Thus, further investigation is crucial for correlating the detection of viral metagenomes in samples with the risk of infection. There is also an urgent need to develop new methods to improve the sensitivity of current Next Generation Sequencing (NGS) techniques in the food safety area.
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Affiliation(s)
- X Fernandez-Cassi
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain.
| | - N Timoneda
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain; Computational Genomics Lab, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain; Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Catalonia, Spain
| | - E Gonzales-Gustavson
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - J F Abril
- Computational Genomics Lab, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain; Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Catalonia, Spain
| | - S Bofill-Mas
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - R Girones
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
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Fu X, Fang B, Ma J, Liu Y, Bu D, Zhou P, Wang H, Jia K, Zhang G. Insights into the epidemic characteristics and evolutionary history of the novel porcine circovirus type 3 in southern China. Transbound Emerg Dis 2017; 65:e296-e303. [PMID: 29178283 DOI: 10.1111/tbed.12752] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Indexed: 01/07/2023]
Abstract
Porcine circovirus type 3 (PCV3) is a newly identified circovirus from swine in the USA, China and Poland. This novel circovirus has been associated with porcine dermatitis and nephropathy syndrome (PDNS), reproductive failure and multisystemic inflammation; moreover, PCV3 poses a potential threat to the swine industry. In this retrospective study, a phylogenetic analysis was conducted to address the epidemiology and evolutionary dynamics of this novel circovirus. The total positive sample rate of PCV3 was 26.7% (76/285) and has increased gradually over the past 3 years. Of these PCV3-positive samples, 22.3% (17/76) were coinfected with PCV2. PCV3 can be detected in multiple sample types with different positive rates, and the positive rate is highest among stillborn. We also divide PCV3 into three clades (PCV3a, PCV3b and PCV3c) based on two amino acid mutations (A24V and R27K) on the cap protein in this study. In addition, the origin of PCV3 was approximately 1966 and may have originated from a bat-associated circovirus. Our results suggested that PCV3 is widely distributed in southern China and has been circulating in swine herds for nearly half a century. PCV3 has evolved into different clades caused by mutations in cap proteins; thus, further research on PCV3 epidemiology should be conducted.
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Affiliation(s)
- X Fu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - B Fang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - J Ma
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Comprehensive Prevention and Control for Severe Clinical Animal Diseases of Guangdong Province, Guangzhou, China
| | - Y Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - D Bu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
| | - P Zhou
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Comprehensive Prevention and Control for Severe Clinical Animal Diseases of Guangdong Province, Guangzhou, China
| | - H Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Comprehensive Prevention and Control for Severe Clinical Animal Diseases of Guangdong Province, Guangzhou, China
| | - K Jia
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Comprehensive Prevention and Control for Severe Clinical Animal Diseases of Guangdong Province, Guangzhou, China
| | - G Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
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Zhai SL, Zhou X, Zhang H, Hause BM, Lin T, Liu R, Chen QL, Wei WK, Lv DH, Wen XH, Li F, Wang D. Comparative epidemiology of porcine circovirus type 3 in pigs with different clinical presentations. Virol J 2017; 14:222. [PMID: 29132394 PMCID: PMC5683367 DOI: 10.1186/s12985-017-0892-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/07/2017] [Indexed: 11/12/2022] Open
Abstract
Background Porcine circovirus type 3 (PCV3), as an emerging circovirus species, was reported to be widely circulating in the United States, China, South Korea and Poland. Previous studies revealed that PCV3 was mainly concentrated in sick animals with respiratory disease, skin disease, reproductive disorders and so on. However, the circulating status of PCV3 in pigs with other clinical presentations (especilly asymptomatic or diarrhea) was not well established. Findings In this study, to conduct a comparative epidemiological survey of PCV3, 80 weaned pig serum samples with severe respiratory disease (SRD), 175 weaned pig serum samples with mild respiratory disease (MRD), 216 asymptomatic weaned pig serum samples, 35 diarrheal weaned pig samples and 35 non-diarrheal weaned pig samples were collected from eight provinces of China. Via qPCR testing, PCV3 was circulating in all sampling provinces, with total positive rates varying from 1.04% to 100%. Interestingly, the PCV3-positive rate was significantly higher in weaned pigs with SRD (63.75%, 51/80) than in those weaned pigs with MRD (13.14%, 23/175) and asymptomatic pigs (1.85%, 4/216) (P < 0.01). Similarly, the PCV3-positive rate was significantly higher in diarrheal weaned pigs (17.14%, 6/35) than in non-diarrheal weaned pigs (2.86%, 1/35) (P < 0.05). Moreover, the lower Ct values of qPCR were frequently found in those weaned pigs or fattening pigs with respiratory disease and diarrhea rather than that in asymptomatic pigs. Sequence analysis showed that low genetic diversity existed among those PCV3 sequences collected from pigs with different clinical presentations. Conclusions The present study further extends evidence that newly described PCV3 widely circulates in six additional provinces of Southern and Northern China and has high similarity to previously reported isolates. As an emerging virus of swine, although the present case-control study reveals that PCV3 has a potential association with swine respiratory disease and diarrhea, further investigations into the pathogenesis are needed to ascertain the role of PCV3 in swine health. Electronic supplementary material The online version of this article (10.1186/s12985-017-0892-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shao-Lun Zhai
- Guangdong Key Laboratory of Animal Disease Prevention, Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China. .,Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA. .,Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, USA.
| | - Xia Zhou
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - He Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Ben M Hause
- Cambridge Technologies, Worthington, MN, 56187, USA
| | - Tao Lin
- Department of Chemistry and Biochemistry, South Dakota State University, Brookings, SD, 57007, USA
| | - Runxia Liu
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA.,Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, USA
| | - Qin-Ling Chen
- Guangdong Key Laboratory of Animal Disease Prevention, Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Wen-Kang Wei
- Guangdong Key Laboratory of Animal Disease Prevention, Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Dian-Hong Lv
- Guangdong Key Laboratory of Animal Disease Prevention, Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Xiao-Hui Wen
- Guangdong Key Laboratory of Animal Disease Prevention, Animal Disease Diagnostic Center, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Feng Li
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA.,Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, USA
| | - Dan Wang
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA.
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