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Diagnostic Approach to Enteric Disorders in Pigs. Animals (Basel) 2023; 13:ani13030338. [PMID: 36766227 PMCID: PMC9913336 DOI: 10.3390/ani13030338] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/21/2023] Open
Abstract
The diagnosis of enteric disorders in pigs is extremely challenging, at any age. Outbreaks of enteric disease in pigs are frequently multifactorial and multiple microorganisms can co-exist and interact. Furthermore, several pathogens, such as Clostridium perfrigens type A, Rotavirus and Lawsonia intracellularis, may be present in the gut in the absence of clinical signs. Thus, diagnosis must be based on a differential approach in order to develop a tailored control strategy, considering that treatment and control programs for enteric diseases are pathogen-specific. Correct sampling for laboratory analyses is fundamental for the diagnostic work-up of enteric disease in pigs. For example, histology is the diagnostic gold standard for several enteric disorders, and sampling must ensure the collection of representative and optimal intestinal samples. The aim of this paper is to focus on the diagnostic approach, from sampling to the aetiological diagnosis, of enteric disorders in pigs due to different pathogens during the different phases of production.
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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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Joshi MS, Arya SA, Shinde MS, Ingle VC, Birade HS, Gopalkrishna V. Rotavirus C infections in asymptomatic piglets in India, 2009-2013: genotyping and phylogenetic analysis of all genomic segments. Arch Virol 2022; 167:2665-2675. [PMID: 36169718 DOI: 10.1007/s00705-022-05607-3] [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: 08/11/2022] [Accepted: 08/17/2022] [Indexed: 12/14/2022]
Abstract
Asymptomatic infection with rotavirus C (RVC) was observed in pigs in India, with a detection rate of 20%. Sequencing of the VP6, VP7, and NSP4 genes of RVC strains identified the genotypes I7/I10, G1, and E5, respectively. Full genome sequencing of one of these strains revealed that the genotypes of the VP4, VP1, VP2, VP3, NSP1, NSP2, NSP3, and NSP5 genes were P1, R1, C1, M3, A1, N5, T5, and H1, respectively. The detection of porcine RVC strains at two different locations in India at different time points strongly suggests that they are circulating continuously in the pig population through asymptomatic infections.
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Affiliation(s)
- Madhuri S Joshi
- Enteric Viruses Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune, 411 001, India.
| | - Shalu A Arya
- Enteric Viruses Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune, 411 001, India
| | - Manohar S Shinde
- Enteric Viruses Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune, 411 001, India
| | - Vijay C Ingle
- Department of Veterinary Microbiology and Animal Biotechnology, Nagpur Veterinary College, Nagpur, India
| | - Hemant S Birade
- Department of Animal Reproduction, Gynaecology and Obstetrics, Krantisinh Nana Patil College of Veterinary Science, Satara, India
| | - Varanasi Gopalkrishna
- Enteric Viruses Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune, 411 001, India
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4
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Analysis of RNA virome in rectal swabs of healthy and diarrheic pigs of different age. Comp Immunol Microbiol Infect Dis 2022; 90-91:101892. [DOI: 10.1016/j.cimid.2022.101892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/23/2022]
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Antibody Response to Rotavirus C Pre-Farrow Natural Planned Exposure to Gilts and Their Piglets. Viruses 2022; 14:v14102250. [PMID: 36298806 PMCID: PMC9610825 DOI: 10.3390/v14102250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022] Open
Abstract
A longitudinal study was conducted to investigate the dynamics of genotype-specific (G6 and P[5]) antibody response to different doses (3, 2 and 1) of rotavirus C (RVC) natural planned exposure (NPE) in gilt serum, colostrum/milk and piglet serum, and compare with antibody response to rotavirus A NPE (RVA genotypes G4, G5, P[7] and P[23]). G6 and P[5] antigens of RVC were expressed in mammalian and bacterial cells, and used to develop individual indirect ELISAs. For both antigens, group 1 with 3 doses of NPE resulted in significantly higher IgG and IgA levels in colostrum compared to other groups. In piglet serum, group 1 P[5] IgG levels were significantly higher than other study groups at day 0 and 7. Piglet serum had higher IgA levels for group 1 piglets compared to other groups for both antigens. A comparison of colostrum antibody levels to rotavirus A (RVA) and RVC revealed that colostrum RVC IgG and IgA titers were lower than RVA titers irrespective of the G and P-type. Next generation sequencing (NGS) detected same RVC genotypes (G6 and P[5]) circulating in the piglet population under the window of lactogenic immunity. We conclude that the low RVC load in NPE material (real-time PCR Ct-values 32.55, 29.32 and 30.30) failed to induce sufficient maternal immunity in gilts (low colostrum RVC antibody levels) and passively prevent piglets from natural RVC infection in the farrowing room. To the best of our knowledge, this is the first study comparing differences in antibody response to porcine RVA and RVC in a commercial setting.
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Kumar D, Shepherd FK, Springer NL, Mwangi W, Marthaler DG. Rotavirus Infection in Swine: Genotypic Diversity, Immune Responses, and Role of Gut Microbiome in Rotavirus Immunity. Pathogens 2022; 11:pathogens11101078. [PMID: 36297136 PMCID: PMC9607047 DOI: 10.3390/pathogens11101078] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/13/2022] [Accepted: 09/17/2022] [Indexed: 11/16/2022] Open
Abstract
Rotaviruses (RVs) are endemic in swine populations, and all swine herds certainly have a history of RV infection and circulation. Rotavirus A (RVA) and C (RVC) are the most common among all RV species reported in swine. RVA was considered most prevalent and pathogenic in swine; however, RVC has been emerging as a significant cause of enteritis in newborn piglets. RV eradication from swine herds is not practically achievable, hence producers’ mainly focus on minimizing the production impact of RV infections by reducing mortality and diarrhea. Since no intra-uterine passage of immunoglobulins occur in swine during gestation, newborn piglets are highly susceptible to RV infection at birth. Boosting lactogenic immunity in gilts by using vaccines and natural planned exposure (NPE) is currently the only way to prevent RV infections in piglets. RVs are highly diverse and multiple RV species have been reported from swine, which also contributes to the difficulties in preventing RV diarrhea in swine herds. Human RV-gut microbiome studies support a link between microbiome composition and oral RV immunogenicity. Such information is completely lacking for RVs in swine. It is not known how RV infection affects the functionality or structure of gut microbiome in swine. In this review, we provide a detailed overview of genotypic diversity of swine RVs, host-ranges, innate and adaptive immune responses to RVs, homotypic and heterotypic immunity to RVs, current methods used for RV management in swine herds, role of maternal immunity in piglet protection, and prospects of investigating swine gut microbiota in providing immunity against rotaviruses.
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Affiliation(s)
- Deepak Kumar
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
- Correspondence: (D.K.); (W.M.); (D.G.M.); Tel.: +1-804-503-1241 (D.K.)
| | - Frances K Shepherd
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55108, USA
| | - Nora L. Springer
- Clinical Pathology, Biomedical and Diagnostic Sciences, College of Veterinary Medicine, University of Tennessee, Knoxville, TN 37996, USA
| | - Waithaka Mwangi
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
- Correspondence: (D.K.); (W.M.); (D.G.M.); Tel.: +1-804-503-1241 (D.K.)
| | - Douglas G. Marthaler
- Indical Inc., 1317 Edgewater Dr #3722, Orlando, FL 32804, USA
- Correspondence: (D.K.); (W.M.); (D.G.M.); Tel.: +1-804-503-1241 (D.K.)
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7
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Development of a Multiplex RT-PCR Assay for Simultaneous Detection of Four Potential Zoonotic Swine RNA Viruses. Vet Sci 2022; 9:vetsci9040176. [PMID: 35448674 PMCID: PMC9029180 DOI: 10.3390/vetsci9040176] [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: 03/03/2022] [Revised: 03/26/2022] [Accepted: 04/04/2022] [Indexed: 11/24/2022] Open
Abstract
Swine viruses like porcine sapovirus (SaV), porcine encephalomyocarditis virus (EMCV), porcine rotavirus A (RVA) and porcine astroviruses (AstV) are potentially zoonotic viruses or suspected of potential zoonosis. These viruses have been detected in pigs with or without clinical signs and often occur as coinfections. Despite the potential public health risks, no assay for detecting them all at once has been developed. Hence, in this study, a multiplex RT-PCR (mRT-PCR) assay was developed for the simultaneous detection of SaV, EMCV, RVA and AstV from swine fecal samples. The PCR parameters were optimized using specific primers for each target virus. The assay’s sensitivity, specificity, reproducibility, and application to field samples have been evaluated. Using a pool of plasmids containing the respective viral target fragments as a template, the developed mRT-PCR successfully detected 2.5 × 103 copies of each target virus. The assay’s specificity was tested using six other swine viruses as a template and did not show any cross-reactivity. A total of 280 field samples were tested with the developed mRT-PCR assay. Positive rates for SaV, EMCV, RVA, and AstV were found to be 24.6% (69/280), 5% (14/280), 4.3% (12/280), and 17.5% (49/280), respectively. Compared to performing separate assays for each virus, this mRT-PCR assay is a simple, rapid, and cost-effective method for detecting mixed or single infections of SaV, EMCV, RVA, and AstV.
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Wang Y, Porter EP, Lu N, Zhu C, Noll LW, Hamill V, Brown SJ, Palinski RM, Bai J. Whole-genome classification of rotavirus C and genetic diversity of porcine strains in the USA. J Gen Virol 2021; 102. [PMID: 33950806 DOI: 10.1099/jgv.0.001598] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rotavirus C (RVC) is associated with acute diarrhoea in both children and young animals. Because of its frequent occurrence, additional sequences have recently been generated. In this study, we sequenced 21 complete genomes from porcine diarrhoea samples and analysed them together with all available reference sequences collected from the GenBank database [National Center for Biotechnology Information (NCBI)]. Based on phylogenetic analysis and genetic distance calculation, the number of each segment was identified as 31G, 26P, 13I, 5R, 5C, 5M, 12A, 10 N, 9T, 8E and 4 H for genotypes encoding VP7, VP4, VP6, VP1, VP2, VP3 and NSP1, NSP2, NSP3, NSP4 and NSP5, respectively. From the analysis, genotypes G19-G31, P[22]-P[26], R5, A9-A12, N9-N10, T7-T9 and E6-E8 were defined as newly identified genotypes, and genotype C6 was combined with C5, and M6 was combined with M1, due to their closely related nature. Estimated with the identity frequency ratio between the intergenotype and intragenotype, the nucleotide identity cutoff values for different genotypes were determined as 85, 85, 86, 84, 83, 84, 82, 87, 84, 81 and 79 % for VP7, VP4, VP6, VP1, VP2, VP3, NSP1, NSP2, NSP3, NSP4 and NSP5, respectively. Genotyping of the 49 US strains indicated possible segment reassortment in 9 of the 11 segments, with the exceptions being VP1 and NSP5, and the most prevalent genotypes for each segment genes in the USA were G6/G5/G21/G9-P5/P4-I6/I5-R1-C5-M1-A8-N1/N10-T1-E1-H1. Our study updated the genotypes of RVC strains and provided more evidence of RVC strain diversity that may be relevant to better understand genetic diversity, and the distribution and evolution of RVC strains.
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Affiliation(s)
- Yin Wang
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA
| | - Elizabeth P Porter
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA
| | - Nanyan Lu
- Bioinformatics Center, Kansas State University, Manhattan, KS 66506, USA
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA
| | - Cong Zhu
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA
| | - Lance W Noll
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA
| | - Vaughn Hamill
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA
| | - Susan J Brown
- Bioinformatics Center, Kansas State University, Manhattan, KS 66506, USA
| | - Rachel M Palinski
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA
| | - Jianfa Bai
- Kansas State Veterinary Diagnostic Laboratory, Kansas State University, Manhattan, KS 66506, USA
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
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Indo Y, Kitahara S, Tomokiyo M, Araki S, Islam MA, Zhou B, Albarracin L, Miyazaki A, Ikeda-Ohtsubo W, Nochi T, Takenouchi T, Uenishi H, Aso H, Takahashi H, Kurata S, Villena J, Kitazawa H. Ligilactobacillus salivarius Strains Isolated From the Porcine Gut Modulate Innate Immune Responses in Epithelial Cells and Improve Protection Against Intestinal Viral-Bacterial Superinfection. Front Immunol 2021; 12:652923. [PMID: 34163470 PMCID: PMC8215365 DOI: 10.3389/fimmu.2021.652923] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/20/2021] [Indexed: 12/29/2022] Open
Abstract
Previously, we constructed a library of Ligilactobacillus salivarius strains from the intestine of wakame-fed pigs and reported a strain-dependent capacity to modulate IFN-β expression in porcine intestinal epithelial (PIE) cells. In this work, we further characterized the immunomodulatory activities of L. salivarius strains from wakame-fed pigs by evaluating their ability to modulate TLR3- and TLR4-mediated innate immune responses in PIE cells. Two strains with a remarkable immunomodulatory potential were selected: L. salivarius FFIG35 and FFIG58. Both strains improved IFN-β, IFN-λ and antiviral factors expression in PIE cells after TLR3 activation, which correlated with an enhanced resistance to rotavirus infection. Moreover, a model of enterotoxigenic E. coli (ETEC)/rotavirus superinfection in PIE cells was developed. Cells were more susceptible to rotavirus infection when the challenge occurred in conjunction with ETEC compared to the virus alone. However, L. salivarius FFIG35 and FFIG58 maintained their ability to enhance IFN-β, IFN-λ and antiviral factors expression in PIE cells, and to reduce rotavirus replication in the context of superinfection. We also demonstrated that FFIG35 and FFIG58 strains regulated the immune response of PIE cells to rotavirus challenge or ETEC/rotavirus superinfection through the modulation of negative regulators of the TLR signaling pathway. In vivo studies performed in mice models confirmed the ability of L. salivarius FFIG58 to beneficially modulate the innate immune response and protect against ETEC infection. The results of this work contribute to the understanding of beneficial lactobacilli interactions with epithelial cells and allow us to hypothesize that the FFIG35 or FFIG58 strains could be used for the development of highly efficient functional feed to improve immune health status and reduce the severity of intestinal infections and superinfections in weaned piglets.
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Affiliation(s)
- Yuhki Indo
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Shugo Kitahara
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Mikado Tomokiyo
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Shota Araki
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Md. Aminul Islam
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Department of Medicine, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Binghui Zhou
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Leonardo Albarracin
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Scientific Computing Laboratory, Computer Science Department, Faculty of Exact Sciences and Technology, National University of Tucuman, Tucuman, Argentina
- Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli, (CERELA-CONICET), Tucuman, Argentina
| | - Ayako Miyazaki
- Viral Diseases and Epidemiology Research Division, National Institute of Animal Health, NARO, Tsukuba, Japan
| | - Wakako Ikeda-Ohtsubo
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Tomonori Nochi
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Laboratory of Functional Morphology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Takato Takenouchi
- Animal Bioregulation Unit, Division of Animal Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Hirohide Uenishi
- Animal Bioregulation Unit, Division of Animal Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Hisashi Aso
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Laboratory of Animal Health Science, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Hideki Takahashi
- Laboratory of Plant Pathology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Plant Immunology Unit, International Education and Research Center for Food and Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Shoichiro Kurata
- Laboratory of Molecular Genetics, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Julio Villena
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli, (CERELA-CONICET), Tucuman, Argentina
| | - Haruki Kitazawa
- Food and Feed Immunology Group, Laboratory of Animal Food Function, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
- Livestock Immunology Unit, International Education and Research Center for Food Agricultural Immunology (CFAI), Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
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Sawant PM, Atre N, Kulkarni A, Gopalkrishna V. Detection and molecular characterization of porcine enterovirus G15 and teschovirus from India. Pathog Dis 2021; 78:5874254. [PMID: 32691821 DOI: 10.1093/femspd/ftaa039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/17/2020] [Indexed: 11/13/2022] Open
Abstract
Porcine enterovirus G (EV-G) and teschovirus (PTV) generally cause asymptomatic infections. Although both viruses have been reported from various countries, they are rarely detected from India. To detect these viruses in Western India, fecal samples (n = 26) of diarrheic piglets aged below three months from private pig farms near Pune (Maharashtra) were collected. The samples were screened by reverse transcription-polymerase chain reaction using conserved enterovirus specific primers from 5' untranslated region. For genetic characterization of detected EV-G strain, nearly complete genome, and for PTV, partial VP1 gene were sequenced. EV-G strain showed the highest identity in a VP1 gene at nucleotide (78.61%) and amino acid (88.65%) level with EV-G15, prototype strain. However, its complete genome was homologous with the nucleotide (78.38% identity) and amino acid (91.24% identity) level to Ishi-Ka2 strain (LC316832), unassigned EV-G genotype detected from Japan. The nearly complete genome of EV-G15 consisted of 7398 nucleotides excluding the poly(A) tail and has an open reading frame that encodes a 2170 amino acid polyprotein. Genetic analysis of the partial VP1 gene of teschovirus identified porcine teschovirus 4 (PTV-4) and putative PTV-17 genotype. To the best of our knowledge, this is the first report on nearly full genome characterization of EV-G15, and detection of PTV-4 and putative PTV-17 genotypes from India. Further, detection and characterization of porcine enteroviruses are needed for a comprehensive understanding of their genetic diversity and their association with symptomatic infections from other geographical regions of India.
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Affiliation(s)
- Pradeep Mahadev Sawant
- Enteric Virus Group, ICMR-National Institute of Virology, 20-A, Ambedkar Road, Pune 411001, Maharashtra, India
| | - Nitin Atre
- Bioinformatics Group, ICMR-National Institute of Virology (Pashan Campus), Pune 411021, Maharashtra, India
| | - Abhijeet Kulkarni
- Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, Maharashtra, India
| | - Varanasi Gopalkrishna
- Enteric Virus Group, ICMR-National Institute of Virology, 20-A, Ambedkar Road, Pune 411001, Maharashtra, India
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11
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Virus Metagenomics in Farm Animals: A Systematic Review. Viruses 2020; 12:v12010107. [PMID: 31963174 PMCID: PMC7019290 DOI: 10.3390/v12010107] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 02/07/2023] Open
Abstract
A majority of emerging infectious diseases are of zoonotic origin. Metagenomic Next-Generation Sequencing (mNGS) has been employed to identify uncommon and novel infectious etiologies and characterize virus diversity in human, animal, and environmental samples. Here, we systematically reviewed studies that performed viral mNGS in common livestock (cattle, small ruminants, poultry, and pigs). We identified 2481 records and 120 records were ultimately included after a first and second screening. Pigs were the most frequently studied livestock and the virus diversity found in samples from poultry was the highest. Known animal viruses, zoonotic viruses, and novel viruses were reported in available literature, demonstrating the capacity of mNGS to identify both known and novel viruses. However, the coverage of metagenomic studies was patchy, with few data on the virome of small ruminants and respiratory virome of studied livestock. Essential metadata such as age of livestock and farm types were rarely mentioned in available literature, and only 10.8% of the datasets were publicly available. Developing a deeper understanding of livestock virome is crucial for detection of potential zoonotic and animal pathogens and One Health preparedness. Metagenomic studies can provide this background but only when combined with essential metadata and following the “FAIR” (Findable, Accessible, Interoperable, and Reusable) data principles.
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12
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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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Moutelíková R, Sauer P, Dvořáková Heroldová M, Holá V, Prodělalová J. Emergence of Rare Bovine-Human Reassortant DS-1-Like Rotavirus A Strains with G8P[8] Genotype in Human Patients in the Czech Republic. Viruses 2019; 11:v11111015. [PMID: 31683946 PMCID: PMC6893433 DOI: 10.3390/v11111015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 10/28/2019] [Accepted: 10/30/2019] [Indexed: 01/09/2023] Open
Abstract
Group A Rotaviruses (RVA) are the leading cause of acute gastroenteritis in children and a major cause of childhood mortality in low-income countries. RVAs are mostly host-specific, but interspecies transmission and reassortment between human and animal RVAs significantly contribute to their genetic diversity. We investigated the VP7 and VP4 genotypes of RVA isolated from 225 stool specimens collected from Czech patients with gastroenteritis during 2016–2019. The most abundant genotypes were G1P[8] (42.7%), G3P[8] (11.1%), G9P[8] (9.8%), G2P[4] (4.4%), G4P[8] (1.3%), G12P[8] (1.3%), and, surprisingly, G8P[8] (9.3%). Sequence analysis of G8P[8] strains revealed the highest nucleotide similarity of all Czech G8 sequences to the G8P[8] rotavirus strains that were isolated in Vietnam in 2014/2015. The whole-genome backbone of the Czech G8 strains was determined with the use of next-generation sequencing as DS-1-like. Phylogenetic analysis of all segments clustered the Czech isolates with RVA strains that were formerly described in Southeast Asia, which had emerged following genetic reassortment between bovine and human RVAs. This is the first time that bovine–human DS-1-like G8P[8] strains were detected at a high rate in human patients in Central Europe. Whether the emergence of this unusual genotype reflects the establishment of a new RVA strain in the population requires the continuous monitoring of rotavirus epidemiology.
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Affiliation(s)
| | - Pavel Sauer
- Institute of Microbiology, University Hospital Olomouc and Faculty of Medicine, Palacký University, 77900 Olomouc, Czech Republic.
| | - Monika Dvořáková Heroldová
- Microbiology Institute of Faculty of Medicine, Masaryk University Brno and University Hospital of St. Anne, 65691 Brno, Czech Republic.
| | - Veronika Holá
- Microbiology Institute of Faculty of Medicine, Masaryk University Brno and University Hospital of St. Anne, 65691 Brno, Czech Republic.
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Wohlgemuth N, Honce R, Schultz-Cherry S. Astrovirus evolution and emergence. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2019; 69:30-37. [PMID: 30639546 PMCID: PMC7106029 DOI: 10.1016/j.meegid.2019.01.009] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 12/19/2022]
Abstract
Astroviruses are small, non-enveloped, positive-sense, single-stranded RNA viruses that belong to the Astroviridae family. Astroviruses infect diverse hosts and are typically associated with gastrointestinal illness; although disease can range from asymptomatic to encephalitis depending on the host and viral genotype. Astroviruses have high genetic variability due to an error prone polymerase and frequent recombination events between strains. Once thought to be species specific, recent evidence suggests astroviruses can spread between different host species, although the frequency with which this occurs and the restrictions that regulate the process are unknown. Recombination events can lead to drastic evolutionary changes and contribute to cross-species transmission events. This work reviews the current state of research on astrovirus evolution and emergence, especially as it relates to cross-species transmission and recombination of astroviruses.
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Affiliation(s)
- Nicholas Wohlgemuth
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, United States
| | - Rebekah Honce
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, United States; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38105, United States
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, United States.
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Simultaneous detection of five pig viruses associated with enteric disease in pigs using EvaGreen real-time PCR combined with melting curve analysis. J Virol Methods 2019; 268:1-8. [PMID: 30844408 DOI: 10.1016/j.jviromet.2019.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/02/2019] [Accepted: 03/02/2019] [Indexed: 12/14/2022]
Abstract
In recent years, a series of porcine diarrhea viruses such as porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), rotaviruses of group A (RVA), rotaviruses of group C (RVC), and porcine circovirus 2 (PCV2) caused enormous economic losses all over the world. While any of these viruses is capable to cause disease alone, there is often concurrent infection with more than one virus on pig farms. In this study, a multiplex real-time PCR method based on EvaGreen fluorescent dye and melting curve analysis was established to simultaneously detect these five viruses in a single closed tube. Five distinct melt peaks were obtained with different melting temperature (Tm) value corresponding to each of the five viruses. This method was highly sensitive to detect and distinguish TGEV, RVA, RVC, PEDV and PCV2 with the limits of detection ranging from 5 to 50 copies/μL. The intra-assay and inter-assay reproducibility were good with coefficient of variation of Tm and cycle threshold values less than 0.32% and 2.86%, respectively. Testing of 90 field samples by the single and multiplex real-time PCR assays demonstrated a concordance of 91.1%. Thus, the EvaGreen multiplex real-time PCR is a rapid, sensitive and low-cost diagnostic tool for differential detection and routine surveillance of TGEV, RVA, RVC, PEDV and PCV2 in pigs.
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16
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Theuns S, Vanmechelen B, Bernaert Q, Deboutte W, Vandenhole M, Beller L, Matthijnssens J, Maes P, Nauwynck HJ. Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus. Sci Rep 2018; 8:9830. [PMID: 29959349 PMCID: PMC6026206 DOI: 10.1038/s41598-018-28180-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/18/2018] [Indexed: 11/13/2022] Open
Abstract
Enteric diseases in swine are often caused by different pathogens and thus metagenomics are a useful tool for diagnostics. The capacities of nanopore sequencing for viral diagnostics were investigated here. First, cell culture-grown porcine epidemic diarrhea virus and rotavirus A were pooled and sequenced on a MinION. Reads were already detected at 7 seconds after start of sequencing, resulting in high sequencing depths (19.2 to 103.5X) after 3 h. Next, diarrheic feces of a one-week-old piglet was analyzed. Almost all reads (99%) belonged to bacteriophages, which may have reshaped the piglet's microbiome. Contigs matched Bacteroides, Escherichia and Enterococcus phages. Moreover, porcine kobuvirus was discovered in the feces for the first time in Belgium. Suckling piglets shed kobuvirus from one week of age, but an association between peak of viral shedding (106.42-107.01 copies/swab) and diarrheic signs was not observed during a follow-up study. Retrospective analysis showed the widespread (n = 25, 56.8% positive) of genetically moderately related kobuviruses among Belgian diarrheic piglets. MinION enables rapid detection of enteric viruses. Such new methodologies will change diagnostics, but more extensive validations should be conducted. The true enteric pathogenicity of porcine kobuvirus should be questioned, while its subclinical importance cannot be excluded.
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Affiliation(s)
- Sebastiaan Theuns
- Ghent University, Faculty of Veterinary Medicine, Department of Virology, Parasitology and Immunology, Laboratory of Virology, Merelbeke, Belgium.
| | - Bert Vanmechelen
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Clinical Virology, Rega Institute for Medical Research, Leuven, Belgium
| | - Quinten Bernaert
- Ghent University, Faculty of Veterinary Medicine, Department of Virology, Parasitology and Immunology, Laboratory of Virology, Merelbeke, Belgium
| | - Ward Deboutte
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Viral Metagenomics, Rega Institute for Medical Research, Leuven, Belgium
| | - Marilou Vandenhole
- Ghent University, Faculty of Veterinary Medicine, Department of Virology, Parasitology and Immunology, Laboratory of Virology, Merelbeke, Belgium
| | - Leen Beller
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Viral Metagenomics, Rega Institute for Medical Research, Leuven, Belgium
| | - Jelle Matthijnssens
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Viral Metagenomics, Rega Institute for Medical Research, Leuven, Belgium
| | - Piet Maes
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Laboratory of Clinical Virology, Rega Institute for Medical Research, Leuven, Belgium
| | - Hans J Nauwynck
- Ghent University, Faculty of Veterinary Medicine, Department of Virology, Parasitology and Immunology, Laboratory of Virology, Merelbeke, Belgium
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17
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Metagenomics detection and characterisation of viruses in faecal samples from Australian wild birds. Sci Rep 2018; 8:8686. [PMID: 29875375 PMCID: PMC5989203 DOI: 10.1038/s41598-018-26851-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/17/2018] [Indexed: 01/19/2023] Open
Abstract
We present an optimised metagenomics method for detection and characterisation of all virus types including single and double stranded DNA/RNA and enveloped and non-enveloped viruses. Initial evaluation included both spiked and non-spiked bird faecal samples as well as non-spiked human faecal samples. From the non-spiked bird samples (Australian Muscovy duck and Pacific black ducks) we detected 21 viruses, and we also present a summary of a few viruses detected in human faecal samples. We then present a detailed analysis of selected virus sequences in the avian samples that were somewhat similar to known viruses, and had good quality (Q20 or higher) and quantity of next-generation sequencing reads, and was of interest from a virological point of view, for example, avian coronavirus and avian paramyxovirus 6. Some of these viruses were closely related to known viruses while others were more distantly related with 70% or less identity to currently known/sequenced viruses. Besides detecting viruses, the technique also allowed the characterisation of host mitochondrial DNA present and thus identifying host species, while ribosomal RNA sequences provided insight into the "ribosomal activity microbiome"; of gut parasites; and of food eaten such as plants or insects, which we correlated to non-avian host associated viruses.
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18
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Tuanthap S, Phupolphan C, Luengyosluechakul S, Duang-In A, Theamboonlers A, Wattanaphansak S, Vongpunsawad S, Amonsin A, Poovorawan Y. Porcine rotavirus C in pigs with gastroenteritis on Thai swine farms, 2011-2016. PeerJ 2018; 6:e4724. [PMID: 29761045 PMCID: PMC5947060 DOI: 10.7717/peerj.4724] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 04/17/2018] [Indexed: 12/14/2022] Open
Abstract
Swine are economically important food animals, but highly contagious porcine epidemic diarrhea virus (PEDV) and rotavirus can afflict pig herds and contribute significantly to piglet morbidity and mortality. While there have been studies on rotavirus group A (RVA) in Thailand, reports of rotavirus group C (RVC) are limited. Here, we aimed to identify the prevalence of RVC circulating on Thai commercial swine farms. We analyzed 769 feces and intestine mucosal contents of pigs affected with diarrhea between 2011 and 2016 using RT-PCR specific for the PEDV spike (S), rotavirus glycoprotein (G) VP7, and protease-sensitive protein (P) VP4 genes. We found that 6.6% (51/769) of samples tested positive for RVC, of which 11 samples were co-infected with RVA and four samples were co-infected with PEDV. Three samples tested positive for all three viruses. Phylogenetic analysis of the VP7 gene showed that the most frequent RVC genotype was G1, which grouped with the prototypic RVC Cowden strain. While G6 and G9 were also common, G3 was relatively rare. Analysis of the VP4 gene revealed that the most common P type was P[5], followed by P[4], P[7], and P[1]. In all, there were six G/P combinations (G6P[5], G1P[1], G1P[4], G1P[5], G9P[4], and G9P[7]), of which G6P[5] was the most predominant.
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Affiliation(s)
- Supansa Tuanthap
- Inter-Department Program of Biomedical Sciences, Faculty of Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Cherdpong Phupolphan
- The Livestock Animal Hospital, Faculty of Veterinary Science, Chulalongkorn University, Nakorn Pathom, Thailand
| | - Supol Luengyosluechakul
- Department of Veterinary Medicine, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Ausanee Duang-In
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Apiradee Theamboonlers
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Suphot Wattanaphansak
- Department of Veterinary Medicine, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Sompong Vongpunsawad
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Alongkorn Amonsin
- Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Tsuchiaka S, Naoi Y, Imai R, Masuda T, Ito M, Akagami M, Ouchi Y, Ishii K, Sakaguchi S, Omatsu T, Katayama Y, Oba M, Shirai J, Satani Y, Takashima Y, Taniguchi Y, Takasu M, Madarame H, Sunaga F, Aoki H, Makino S, Mizutani T, Nagai M. Genetic diversity and recombination of enterovirus G strains in Japanese pigs: High prevalence of strains carrying a papain-like cysteine protease sequence in the enterovirus G population. PLoS One 2018; 13:e0190819. [PMID: 29324778 PMCID: PMC5764308 DOI: 10.1371/journal.pone.0190819] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/20/2017] [Indexed: 11/18/2022] Open
Abstract
To study the genetic diversity of enterovirus G (EV-G) among Japanese pigs, metagenomics sequencing was performed on fecal samples from pigs with or without diarrhea, collected between 2014 and 2016. Fifty-nine EV-G sequences, which were >5,000 nucleotides long, were obtained. By complete VP1 sequence analysis, Japanese EV-G isolates were classified into G1 (17 strains), G2 (four strains), G3 (22 strains), G4 (two strains), G6 (two strains), G9 (six strains), G10 (five strains), and a new genotype (one strain). Remarkably, 16 G1 and one G2 strain identified in diarrheic (23.5%; four strains) or normal (76.5%; 13 strains) fecal samples possessed a papain-like cysteine protease (PL-CP) sequence, which was recently found in the USA and Belgium in the EV-G genome, at the 2C–3A junction site. This paper presents the first report of the high prevalence of viruses carrying PL-CP in the EV-G population. Furthermore, possible inter- and intragenotype recombination events were found among EV-G strains, including G1-PL-CP strains. Our findings may advance the understanding of the molecular epidemiology and genetic evolution of EV-Gs.
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Affiliation(s)
- Shinobu Tsuchiaka
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Yuki Naoi
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Ryo Imai
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Tsuneyuki Masuda
- Kurayoshi Livestock Hygiene Service Center, Kurayoshi, Tottori, Japan
| | - Mika Ito
- Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa, Japan
| | | | - Yoshinao Ouchi
- Kenpoku Livestock Hygiene Service Center, Mito, Ibaraki, Japan
| | - Kazuo Ishii
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Shoichi Sakaguchi
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Tsutomu Omatsu
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Yukie Katayama
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Mami Oba
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Junsuke Shirai
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Yuki Satani
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Yanagido, Gifu, Japan
| | - Yasuhiro Takashima
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Yanagido, Gifu, Japan
- Education and Research Center for Food Animal Health, Gifu University (GeFAH), Gifu, Japan
- Center for Highly Advanced Integration of Nano and Life Sciences, Gifu University (G-CHAIN), Gifu, Japan
| | - Yuji Taniguchi
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Yanagido, Gifu, Japan
| | - Masaki Takasu
- Department of Veterinary Medicine, Faculty of Applied Biological Sciences, Gifu University, Yanagido, Gifu, Japan
| | - Hiroo Madarame
- Laboratory of Small Animal Clinics, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Fujiko Sunaga
- Department of Veterinary Medicine, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Hiroshi Aoki
- Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Musashino, Tokyo, Japan
| | - Shinji Makino
- Department of Microbiology and Immunology, The University of Texas Medical Branch at Galveston, Galveston, Texas, United States of America
| | - Tetsuya Mizutani
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
- * E-mail: (TM); (MN)
| | - Makoto Nagai
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
- Department of Bioproduction Science, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
- * E-mail: (TM); (MN)
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20
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Conceição-Neto N, Theuns S, Cui T, Zeller M, Yinda CK, Christiaens I, Heylen E, Van Ranst M, Carpentier S, Nauwynck HJ, Matthijnssens J. Identification of an enterovirus recombinant with a torovirus-like gene insertion during a diarrhea outbreak in fattening pigs. Virus Evol 2017; 3:vex024. [PMID: 28924489 PMCID: PMC5591953 DOI: 10.1093/ve/vex024] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Diarrhea outbreaks in pig farms have raised major concerns in Europe and USA, as they can lead to dramatic pig losses. During a suspected outbreak in Belgium of porcine epidemic diarrhea virus (PEDV), we performed viral metagenomics to assess other potential viral pathogens. Although PEDV was detected, its low abundance indicated that other viruses were involved in the outbreak. Interestingly, a porcine bocavirus and several enteroviruses were most abundant in the sample. We also observed the presence of a porcine enterovirus genome with a gene insertion, resembling a C28 peptidase gene found in toroviruses, which was confirmed using re-sequencing, bioinformatics, and proteomics approaches. Moreover, the predicted cleavage sites for the insertion suggest that this gene was being expressed as a single protein, rather than a fused protein. Recombination in enteroviruses has been reported as a major mechanism to generate genetic diversity, but gene insertions across viral families are rather uncommon. Although such inter-family recombinations are rare, our finding suggests that these events may significantly contribute to viral evolution.
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Affiliation(s)
- Nádia Conceição-Neto
- Laboratory of Viral Metagenomics, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Clinical Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium
| | - Sebastiaan Theuns
- Laboratory of Virology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - Tingting Cui
- Laboratory of Virology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - Mark Zeller
- Laboratory of Viral Metagenomics, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium
| | - Claude Kwe Yinda
- Laboratory of Viral Metagenomics, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium.,Laboratory of Clinical Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium
| | - Isaura Christiaens
- Laboratory of Virology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - Elisabeth Heylen
- Laboratory of Viral Metagenomics, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium
| | - Marc Van Ranst
- Laboratory of Clinical Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium
| | - Sebastien Carpentier
- Laboratory of Tropical Crop Improvement, Division of Crop Biotechnics, KU Leuven - University of Leuven, B-3000 Leuven, Belgium.,Facility for Systems Biology Based Mass Spectrometry (SYBIOMA), KU Leuven - University of Leuven, B-3000 Leuven, Belgium
| | - Hans J Nauwynck
- Laboratory of Virology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - Jelle Matthijnssens
- Laboratory of Viral Metagenomics, Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium
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21
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Knutson TP, Velayudhan BT, Marthaler DG. A porcine enterovirus G associated with enteric disease contains a novel papain-like cysteine protease. J Gen Virol 2017; 98:1305-1310. [PMID: 28590234 PMCID: PMC5656790 DOI: 10.1099/jgv.0.000799] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Identification of unknown pathogens in pigs displaying enteric illness is difficult due to the large diversity of bacterial and viral species found within faecal samples. Current methods often require bacterial or viral isolation, or testing only a limited number of known species using quantitative PCR analysis. Herein, faeces from two 25-day-old piglets with diarrhoea from Texas, USA, were analysed by metagenomic next-generation sequencing to rapidly identify possible pathogens. Our analysis included a bioinformatics pipeline of rapid short-read classification and de novo genome assembly which resulted in the identification of a porcine enterovirus G (EV-G), a complete genome with substantial nucleotide differences (>30 %) among current sequences, and a novel non-structural protein similar in sequence to the Torovirus papain-like cysteine protease (PLpro). This discovery led to the identification and circulation of an EV-G with a novel PLpro in the USA that has not been previously reported.
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Affiliation(s)
- Todd P Knutson
- Veterinary Diagnostic Laboratory, Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN 55108, USA
| | - Binu T Velayudhan
- Texas A&M Veterinary Medical Diagnostic Laboratory, Amarillo, TX 79106, USA
| | - Douglas G Marthaler
- Veterinary Diagnostic Laboratory, Department of Veterinary Population Medicine, University of Minnesota, St Paul, MN 55108, USA
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Abstract
Bluetongue virus (BTV) is the type species of genus Orbivirus within family Reoviridae. Bluetongue virus is transmitted between its ruminant hosts by the bite of Culicoides spp. midges. Severe BT cases are characterized by symptoms including hemorrhagic fever, particularly in sheep, loss of productivity, and death. To date, 27 BTV serotypes have been documented. These include novel isolates of atypical BTV, which have been almost fully characterized using deep sequencing technologies and do not rely on Culicoides vectors for their transmission among hosts. Due to its high economic impact, BT is an Office International des Epizooties (OIE) listed disease that is strictly controlled in international commercial exchanges. During the 20th century, BTV has been endemic in subtropical regions. In the last 15 years, novel strains of nine "typical" BTV serotypes (1, 2, 4, 6, 8, 9, 11, 14, and 16) invaded Europe, some of which caused disease in naive sheep and unexpectedly in bovine herds (particularly serotype 8). Over the past few years, three novel "atypical" serotypes (25-27) were characterized during sequencing studies of animal samples from Switzerland, Kuwait, and France, respectively. Classical serotype-specific inactivated vaccines, although expensive, were very successful in controlling outbreaks as shown with the northern European BTV-8 outbreak which started in the summer of 2006. Technological jumps in deep sequencing methodologies made rapid full characterizations of BTV genome from isolates/tissues feasible. Next-generation sequencing (NGS) approaches are powerful tools to study the variability of BTV genomes on a fine scale. This paper provides information on how NGS impacted our knowledge of the BTV genome.
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Bányai K, Kemenesi G, Budinski I, Földes F, Zana B, Marton S, Varga-Kugler R, Oldal M, Kurucz K, Jakab F. Candidate new rotavirus species in Schreiber's bats, Serbia. INFECTION GENETICS AND EVOLUTION 2016; 48:19-26. [PMID: 27932285 PMCID: PMC7106153 DOI: 10.1016/j.meegid.2016.12.002] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/30/2016] [Accepted: 12/01/2016] [Indexed: 11/05/2022]
Abstract
The genus Rotavirus comprises eight species designated A to H and one tentative species, Rotavirus I. In a virus metagenomic analysis of Schreiber's bats sampled in Serbia in 2014 we obtained sequences likely representing novel rotavirus species. Whole genome sequencing and phylogenetic analysis classified the representative strain into a tentative tenth rotavirus species, we provisionally called Rotavirus J. The novel virus shared a maximum of 50% amino acid sequence identity within the VP6 gene to currently known members of the genus. This study extends our understanding of the genetic diversity of rotaviruses in bats. Viral metagenomic analysis identified numerous eukaryotic viruses in bat guano. Whole genome sequencing was performed to characterize a novel rotavirus strain. This novel rotavirus strain likely represents a new rotavirus species, provisionally named Rotavirus J.
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Affiliation(s)
- Krisztián Bányai
- Lendület Pathogen Discovery Research Group, Institute for Veterinary Medical Research, Centre for Agricultural Research, HAS-Centre for Agricultural Research, Budapest, Hungary.
| | - Gábor Kemenesi
- Virological Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Ivana Budinski
- Department of Genetic Research, Institute for Biological Research "Siniša Stanković", University of Belgrade, Belgrade, Serbia
| | - Fanni Földes
- Virological Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Brigitta Zana
- Virological Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Szilvia Marton
- Lendület Pathogen Discovery Research Group, Institute for Veterinary Medical Research, Centre for Agricultural Research, HAS-Centre for Agricultural Research, Budapest, Hungary
| | - Renáta Varga-Kugler
- Lendület Pathogen Discovery Research Group, Institute for Veterinary Medical Research, Centre for Agricultural Research, HAS-Centre for Agricultural Research, Budapest, Hungary
| | - Miklós Oldal
- Virological Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Kornélia Kurucz
- Virological Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Ferenc Jakab
- Virological Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary.
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