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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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Whon TW, Kim HS, Shin NR, Sung H, Kim MS, Kim JY, Kang W, Kim PS, Hyun DW, Seong HJ, Sul WJ, Roh SW, Bae JW. Calf Diarrhea Caused by Prolonged Expansion of Autochthonous Gut Enterobacteriaceae and Their Lytic Bacteriophages. mSystems 2021; 6:e00816-20. [PMID: 33653940 PMCID: PMC8546982 DOI: 10.1128/msystems.00816-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 02/03/2021] [Indexed: 01/04/2023] Open
Abstract
Neonatal calf diarrhea is a common disease leading to a major economic loss for cattle producers worldwide. Several infectious and noninfectious factors are implicated in calf diarrhea, but disease control remains problematic because of the multifactorial etiology of the disease. Here, we conducted diagnostic multiplex PCR assay and meta-omics analysis (16S rRNA gene-based metataxonomics and untargeted transcriptional profiling) of rectal content of normal and diarrheic beef calves (n = 111). In the diarrheic calf gut, we detected both microbial compositional dysbiosis (i.e., increased abundances of the family Enterobacteriaceae members and their lytic bacteriophages) and functional dysbiosis (i.e., elevated levels of aerobic respiration and virulence potential). The calf diarrheic transcriptome mirrored the gene expression of the bovine host and was enriched in cellular pathways of sulfur metabolism, innate immunity, and gut motility. We then isolated 12 nontoxigenic Enterobacteriaceae strains from the gut of diarrheic calves. Feeding a strain mixture to preweaning mice resulted in a significantly higher level of fecal moisture content, with decreased body weight gain and shortened colon length. The presented findings suggest that gut inflammation followed by a prolonged expansion of nontoxigenic autochthonous Enterobacteriaceae contributes to the onset of diarrhea in preweaning animals.IMPORTANCE Calf diarrhea is the leading cause of death of neonatal calves worldwide. Several infectious and noninfectious factors are implicated in calf diarrhea, but disease control remains problematic because of the multifactorial etiology of the disease. The major finding of the current study centers around the observation of microbial compositional and functional dysbiosis in rectal samples from diarrheic calves. These results highlight the notion that gut inflammation followed by a prolonged expansion of autochthonous Enterobacteriaceae contributes to the onset of calf diarrhea. Moreover, this condition possibly potentiates the risk of invasion of notorious enteric pathogens, including Salmonella spp., and the emergence of inflammation-resistant (or antibiotic-resistant) microbiota via active horizontal gene transfer mediated by lytic bacteriophages.
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Affiliation(s)
- Tae Woong Whon
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, Republic of Korea
| | - Hyun Sik Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Na-Ri Shin
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do, Republic of Korea
| | - Hojun Sung
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Min-Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, Republic of Korea
| | - Joon Yong Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, Republic of Korea
| | - Woorim Kang
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Pil Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Dong-Wook Hyun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Hoon Je Seong
- Department of Systems Biotechnology, Chung-Ang University, Anseong-si, Gyeonggi-do, Republic of Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong-si, Gyeonggi-do, Republic of Korea
| | - Seong Woon Roh
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
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Shi Z, Wang W, Xu Z, Zhang X, Lan Y. Genetic and phylogenetic analyses of the first GIII.2 bovine norovirus in China. BMC Vet Res 2019; 15:311. [PMID: 31477115 PMCID: PMC6720400 DOI: 10.1186/s12917-019-2060-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 08/25/2019] [Indexed: 11/24/2022] Open
Abstract
Background Norovirus (NoV) is recognized as a highly contagious enteric pathogen of mammals, and bovine norovirus (BNoV) is associated with calf diarrhoea and has caused great economic losses in the cattle industry. Results Here, we describe a case of emerging calf diarrhoea on a cattle farm in Henan Province, Central China. BNoV was the only enteric pathogen detected in outbreaks according to tests for enteric viruses, bacteria and parasites. The complete genome of the newly identified strain CH-HNSC-2018 was successfully sequenced and found to be 7342 nucleotides in length. Sequence and phylogenetic analyses revealed that CH-HNSC-2018 belongs to GIII.2 BNoV. Further analysis of the major capsid protein demonstrated that it is separated by specific genetic distances from previous BNoV strains identified in China and has 4 new amino acid (aa) mutations, 134A, 327 T, 380 L and 423A, in the VP1 protein and 11 aa substitutions in the hypervariable P2 subdomain, suggesting that the BNoV strains circulating in China are diverse. Conclusions This is the first detection of GIII.2 BNoV in the VP1 region in China. This report should form a basis for further molecular studies on NoV and bovine enteric viruses in China. Electronic supplementary material The online version of this article (10.1186/s12917-019-2060-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhihai Shi
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China.,Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Zhengzhou, 450002, Henan, China
| | - Wenjia Wang
- College of Pharmaceutical Engineering, Henan University of Animal Husbandry and Economy, Zhengzhou, 450046, Henan, China
| | - Zhaoxue Xu
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China.,Henan Key Laboratory of Farm Animal Breeding and Nutritional Regulation, Zhengzhou, 450002, Henan, China
| | - Xiaozhan Zhang
- College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, 450046, Henan, China.
| | - Yali Lan
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China.
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Shepherd FK, Herrera-Ibata DM, Porter E, Homwong N, Hesse R, Bai J, Marthaler DG. Whole Genome Classification and Phylogenetic Analyses of Rotavirus B strains from the United States. Pathogens 2018; 7:pathogens7020044. [PMID: 29670022 PMCID: PMC6027208 DOI: 10.3390/pathogens7020044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/13/2018] [Accepted: 04/14/2018] [Indexed: 12/17/2022] Open
Abstract
Rotaviruses (RVs) are a major etiological agent of acute viral gastroenteritis in humans and young animals, with rotavirus B (RVB) often detected in suckling and weaned pigs. Group A rotavirus classification is currently based on the two outer capsid proteins, VP7 and VP4, and the middle layer protein, VP6. Using RVB strains generated in this study and reference sequences from GenBank, pairwise identity frequency graphs and phylogenetic trees were constructed for the eleven gene segments of RVB to estimate the nucleotide identity cutoff values for different genotypes and determine the genotype diversity per gene segment. Phylogenetic analysis of VP7, VP4, VP6, VP1–VP3, and NSP1–NSP5 identified 26G, 5P, 13I, 5R, 5C, 5M, 8A, 10N, 6T, 4E, and 7H genotypes, respectively. The analysis supports the previously proposed cutoff values for the VP7, VP6, NSP1, and NSP3 gene segments (80%, 81%, 76% and 78%, respectively) and suggests new cutoff values for the VP4, VP1, VP2, VP3, NSP2, NSP4, and NSP5 (80%, 78%, 79%, 77% 83%, 76%, and 79%, respectively). Reassortment events were detected between the porcine RVB strains from our study. This research describes the genome constellations for the complete genome of Group B rotaviruses in different host species.
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Affiliation(s)
- Frances K Shepherd
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA.
| | - Diana Maria Herrera-Ibata
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
- Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
| | - Elizabeth Porter
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
| | - Nitipong Homwong
- Department of Animal Science, Kasetsart University, Kamphaeng Saen Campus, Kamphaeng Saen, Chatuchak, Bankok 10900, Thailand.
| | - Richard Hesse
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
- Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
| | - Jianfa Bai
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
- Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
| | - Douglas G Marthaler
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
- Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA.
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Vlasova AN, Amimo JO, Saif LJ. Porcine Rotaviruses: Epidemiology, Immune Responses and Control Strategies. Viruses 2017; 9:v9030048. [PMID: 28335454 PMCID: PMC5371803 DOI: 10.3390/v9030048] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 03/13/2017] [Accepted: 03/13/2017] [Indexed: 12/13/2022] Open
Abstract
Rotaviruses (RVs) are a major cause of acute viral gastroenteritis in young animals and children worldwide. Immunocompetent adults of different species become resistant to clinical disease due to post-infection immunity, immune system maturation and gut physiological changes. Of the 9 RV genogroups (A–I), RV A, B, and C (RVA, RVB, and RVC, respectively) are associated with diarrhea in piglets. Although discovered decades ago, porcine genogroup E RVs (RVE) are uncommon and their pathogenesis is not studied well. The presence of porcine RV H (RVH), a newly defined distinct genogroup, was recently confirmed in diarrheic pigs in Japan, Brazil, and the US. The complex epidemiology, pathogenicity and high genetic diversity of porcine RVAs are widely recognized and well-studied. More recent data show a significant genetic diversity based on the VP7 gene analysis of RVB and C strains in pigs. In this review, we will summarize previous and recent research to provide insights on historic and current prevalence and genetic diversity of porcine RVs in different geographic regions and production systems. We will also provide a brief overview of immune responses to porcine RVs, available control strategies and zoonotic potential of different RV genotypes. An improved understanding of the above parameters may lead to the development of more optimal strategies to manage RV diarrheal disease in swine and humans.
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Affiliation(s)
- Anastasia N Vlasova
- Food Animal Health Research Program, CFAES, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH 44691, USA.
| | - Joshua O Amimo
- Department of Animal Production, Faculty of Veterinary Medicine, University of Nairobi, Nairobi 30197, Kenya.
- Bioscience of Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, Nairobi 30709, Kenya.
| | - Linda J Saif
- Food Animal Health Research Program, CFAES, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, OH 44691, USA.
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Hayashi-Miyamoto M, Murakami T, Minami-Fukuda F, Tsuchiaka S, Kishimoto M, Sano K, Naoi Y, Asano K, Ichimaru T, Haga K, Omatsu T, Katayama Y, Oba M, Aoki H, Shirai J, Ishida M, Katayama K, Mizutani T, Nagai M. Diversity in VP3, NSP3, and NSP4 of rotavirus B detected from Japanese cattle. INFECTION GENETICS AND EVOLUTION 2017; 49:97-103. [PMID: 28063924 DOI: 10.1016/j.meegid.2017.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/12/2016] [Accepted: 01/02/2017] [Indexed: 01/24/2023]
Abstract
Bovine rotavirus B (RVB) is an etiological agent of diarrhea mostly in adult cattle. Currently, a few sequences of viral protein (VP)1, 2, 4, 6, and 7 and nonstructural protein (NSP)1, 2, and 5 of bovine RVB are available in the DDBJ/EMBL/GenBank databases, and none have been reported for VP3, NSP3, and NSP4. In order to fill this gap in the genetic characterization of bovine RVB strains, we used a metagenomics approach and sequenced and analyzed the complete coding sequences (CDS) of VP3, NSP3, and NSP4 genes, as well as the partial or complete CDS of other genes of RVBs detected from Japanese cattle. VP3, NSP3, and NSP4 of bovine RVBs shared low nucleotide sequence identities (63.3-64.9% for VP3, 65.9-68.2% for NSP3, and 52.6-56.2% for NSP4) with those of murine, human, and porcine RVBs, suggesting that bovine RVBs belong to a novel genotype. Furthermore, significantly low amino acid sequence identities were observed for NSP4 (36.1-39.3%) between bovine RVBs and the RVBs of other species. In contrast, hydrophobic plot analysis of NSP4 revealed profiles similar to those of RVBs of other species and rotavirus A (RVA) strains. Phylogenetic analyses of all gene segments revealed that bovine RVB strains formed a cluster that branched distantly from other RVBs. These results suggest that bovine RVBs have evolved independently from other RVBs but in a similar manner to other rotaviruses. These findings provide insights into the evolution and diversity of RVB strains.
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Affiliation(s)
| | - Toshiaki Murakami
- Ishikawa Hokubu Livestock Hygiene Service Center, Nanao, Ishikawa 929-2126, Japan
| | - Fujiko Minami-Fukuda
- Ishikawa Hokubu Livestock Hygiene Service Center, Nanao, Ishikawa 929-2126, Japan
| | - Shinobu Tsuchiaka
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Mai Kishimoto
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Kaori Sano
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Yuki Naoi
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Keigo Asano
- Department of Bioproduction Science, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
| | - Toru Ichimaru
- Department of Health and Medical Sciences, Ishikawa Prefectural Nursing University, Kahoku, Ishikawa 929-1210, Japan
| | - Kei Haga
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo 208-0011, Japan; Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Minato, Tokyo 108-8641, Japan
| | - Tsutomu Omatsu
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Yukie Katayama
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Mami Oba
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Hiroshi Aoki
- Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Musashino, Tokyo 180-8602, Japan
| | - Junsuke Shirai
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan; Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Motohiko Ishida
- Department of Bioproduction Science, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
| | - Kazuhiko Katayama
- Department of Virology II, National Institute of Infectious Diseases, Musashimurayama, Tokyo 208-0011, Japan; Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Graduate School of Infection Control Sciences, Minato, Tokyo 108-8641, Japan
| | - Tetsuya Mizutani
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Makoto Nagai
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan; Department of Bioproduction Science, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan.
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Otto PH, Rosenhain S, Elschner MC, Hotzel H, Machnowska P, Trojnar E, Hoffmann K, Johne R. Detection of rotavirus species A, B and C in domestic mammalian animals with diarrhoea and genotyping of bovine species A rotavirus strains. Vet Microbiol 2015. [DOI: 10.1016/j.vetmic.2015.07.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Esona MD, Gautam R, Tam KI, Williams A, Mijatovic-Rustempasic S, Bowen MD. Multiplexed one-step RT-PCR VP7 and VP4 genotyping assays for rotaviruses using updated primers. J Virol Methods 2015; 223:96-104. [PMID: 26231786 DOI: 10.1016/j.jviromet.2015.07.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 06/23/2015] [Accepted: 07/24/2015] [Indexed: 12/25/2022]
Abstract
The current two-step VP7 and VP4 genotyping RT-PCR assays for rotaviruses have been linked consistently to genotyping failure in an estimated 30% of RVA positive samples worldwide. We have developed a VP7 and VP4 multiplexed one-step genotyping assays using updated primers generated from contemporary VP7 and VP4 sequences. To determine assay specificity and sensitivity, 17 reference virus strains, 6 non-target gastroenteritis viruses and 725 clinical samples carrying the most common VP7 (G1, G2, G3, G4, G9, and G12) and VP4 (P[4], P[6], P[8], P[9] and P[10]) genotypes were tested in this study. All reference RVA strain targets yielded amplicons of the expected sizes and non-target genotypes and gastroenteritis viruses were not detected by either assay. Out of the 725 clinical samples tested, the VP7 and VP4 assays were able to assigned specific genotypes to 711 (98.1%) and 714 (98.5%), respectively. The remaining unassigned samples were re-tested for RVA antigen using EIA and qRT-PCR assays and all were found to be negative. The overall specificity, sensitivity and limit of detection of the VP7 assay were in the ranges of 99.0-100%, 94.0-100% and 8.6×10(1) to 8.6×10(2) copies of RNA/reaction, respectively. For the VP4 assay, the overall specificity, sensitivity and limit of detection assay were in the ranges of 100%, 94.0-100% and ≤1 to 8.6×10(2) copies of RNA/reaction, respectively. Here we report two highly robust, accurate, efficient, affordable and documentable gel-based genotyping systems which are capable of genotyping 97.8% of the six common VP7 and 98.3% of the five common VP4 genotypes of RVA strains which are responsible for approximately 88.2% of all RVA infections worldwide.
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Affiliation(s)
- Mathew D Esona
- Gastroenteritis and Respiratory Viruses Laboratory Branch, Division of Viral Diseases, NCIRD, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.
| | - Rashi Gautam
- Gastroenteritis and Respiratory Viruses Laboratory Branch, Division of Viral Diseases, NCIRD, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Ka Ian Tam
- Gastroenteritis and Respiratory Viruses Laboratory Branch, Division of Viral Diseases, NCIRD, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | | | - Slavica Mijatovic-Rustempasic
- Gastroenteritis and Respiratory Viruses Laboratory Branch, Division of Viral Diseases, NCIRD, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Michael D Bowen
- Gastroenteritis and Respiratory Viruses Laboratory Branch, Division of Viral Diseases, NCIRD, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
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Suzuki T, Soma J, Miyazaki A, Tsunemitsu H. Phylogenetic analysis of nonstructural protein 5 (NSP5) gene sequences in porcine rotavirus B strains. INFECTION GENETICS AND EVOLUTION 2012; 12:1661-8. [DOI: 10.1016/j.meegid.2012.06.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 06/22/2012] [Accepted: 06/28/2012] [Indexed: 01/05/2023]
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10
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Marthaler D, Rossow K, Gramer M, Collins J, Goyal S, Tsunemitsu H, Kuga K, Suzuki T, Ciarlet M, Matthijnssens J. Detection of substantial porcine group B rotavirus genetic diversity in the United States, resulting in a modified classification proposal for G genotypes. Virology 2012; 433:85-96. [PMID: 22877843 PMCID: PMC7111968 DOI: 10.1016/j.virol.2012.07.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2012] [Revised: 06/27/2012] [Accepted: 07/04/2012] [Indexed: 02/05/2023]
Abstract
Rotavirus (RV) is an important cause of gastrointestinal disease in animals and humans. In this study, we developed an RT-PCR to detect RV group B (RVB) and characterized the VP7 (G) gene segment detected in porcine samples. One hundred seventy three samples were tested for RV group A (RVA), RVB, and C (RVC) by RT-PCR and examined for RV-like lesion using histopathology. A majority (86.4%) of the samples had mixed RV infections and co-infections of RVA/RVB/RVC were detected at a higher rate (24.3%) than previously reported. RVB was identified in 46.8% of the 173 samples. An adapted VP7 classification was developed using previously published (n=57) and newly sequenced (n=68) RVB strains, resulting in 20 G genotypes based on an 80% nucleotide identity cutoff value. Our results revealed a broad genetic diversity of porcine RVB strains, suggesting RVB has been the cause of common/pre-existing, yet undiagnosed, disease in pigs.
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Affiliation(s)
- Douglas Marthaler
- University of Minnesota Veterinary Diagnostic Laboratory College of Veterinary Medicine 1333 Gortner Ave Saint Paul, MN 55108, United States.
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Lahon A, Walimbe AM, Chitambar SD. Full genome analysis of group B rotaviruses from western India: genetic relatedness and evolution. J Gen Virol 2012; 93:2252-2266. [PMID: 22815276 DOI: 10.1099/vir.0.043497-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
To date, full-genome sequences of only seven human group B rotavirus (RVBs) strains have been described. Such data on more RVBs are necessary to establish the evolutionary relationship and ecological features of RVBs from different geographical regions. The present study was aimed at determining the full-length sequences of all 11 genes of 13 human RVB strains detected during 1995-2010 in sporadic and outbreak cases of acute gastroenteritis from four different cities of western India. This study also included estimation of evolutionary rates and site-specific selection pressure analysis for all gene segments. Nucleotide/deduced amino acid sequence analyses of structural and non-structural genes showed 95.1-99.8/94.1-100 % identity with the counterparts of RVB strains isolated in India, Bangladesh and Myanmar. Phylogenetic analyses of all gene segments revealed formation of a monophyletic clade of the western Indian RVB strains, reflecting their highly conserved nature. All gene segments were also found to be under negative/purifying selection pressure. These data suggest that RVB is circulating in the natural host as a series of stable viral clones. Estimates of rates of nucleotide substitution in all RVBs ranged from 1.36-4.78×10(-3) substitutions per site per year. The rate for human RVB VP7 and NSP2 genes were comparable, respectively, with the evolution kinetics of genotype G9/G12 and N1 group A rotavirus strains. The time of the most recent common ancestor of the extant human RVBs was estimated to be during 1915-1974. Evolutionary and genetic analyses carried out in this study provide data that is useful for the elucidation of evolutionary relationship/timescale, stasis or dynamics existing in the RVB population.
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Affiliation(s)
- Anismrita Lahon
- Enteric Viruses Group, National Institute of Virology, 20-A, Dr. Ambedkar Road, PO Box 11, Pune 411001, India
| | - Atul M Walimbe
- Bionformatics Group, National Institute of Virology, 20-A, Dr. Ambedkar Road, PO Box 11, Pune 411001, India
| | - Shobha D Chitambar
- Enteric Viruses Group, National Institute of Virology, 20-A, Dr. Ambedkar Road, PO Box 11, Pune 411001, India
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12
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Suzuki T, Soma J, Kuga K, Miyazaki A, Tsunemitsu H. Sequence and phylogenetic analyses of nonstructural protein 2 genes of species B porcine rotaviruses detected in Japan during 2001–2009. Virus Res 2012; 165:46-51. [DOI: 10.1016/j.virusres.2012.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 12/20/2011] [Accepted: 01/01/2012] [Indexed: 01/10/2023]
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13
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Suzuki T, Kuga K, Miyazaki A, Tsunemitsu H. Genetic divergence and classification of non-structural protein 1 among porcine rotaviruses of species B. J Gen Virol 2011; 92:2922-2929. [DOI: 10.1099/vir.0.036426-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Porcine rotavirus B (RVB) has frequently been detected in diarrhoea of suckling and weaned pigs. Moreover, epidemiological studies using ELISA have demonstrated high antibody prevalence in sera from sows, indicating that RVB infections are widespread. Because it is difficult to propagate RVBs serially in cell culture, genetic analysis of RNA segments of porcine RVBs other than those encoding VP7 and NSP2 has been scarcely performed. We conducted sequence and phylogenetic analyses focusing on non-structural protein 1 (NSP1), using 15 porcine RVB strains isolated from diarrhoeic faeces collected around Japan. Sequence analysis showed that the porcine NSP1 gene contains two overlapping ORFs. Especially, peptide 2 of NSP1 retains highly conserved cysteine and histidine residues among RVBs. Comparison of NSP1 nucleotide and deduced amino acid sequences from porcine RVB strains demonstrated low identities to those from other RVB strains. Phylogenetic analysis of RVB NSP1 revealed the presence of murine, human, ovine, bovine and porcine clusters. Furthermore, the NSP1 genes of porcine RVBs were divided into three genotypes, suggesting the possibility that porcine species might be an original host of RVB infection. Of nine strains common to those used in our previous study, only one strain was classified into a different genotype from the others in the analysis of VP7, in contrast to the analysis of NSP1, where all belonged to the same cluster. This fact suggests the occurrence of gene reassortment among porcine RVBs. These findings should provide more beneficent information to understand the evolution and functions of RVBs.
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Affiliation(s)
- Tohru Suzuki
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-0856, Japan
| | - Kazufumi Kuga
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-0856, Japan
| | - Ayako Miyazaki
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-0856, Japan
| | - Hiroshi Tsunemitsu
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-0856, Japan
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14
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Matthijnssens J, Ciarlet M, McDonald SM, Attoui H, Bányai K, Brister JR, Buesa J, Esona MD, Estes MK, Gentsch JR, Iturriza-Gómara M, Johne R, Kirkwood CD, Martella V, Mertens PPC, Nakagomi O, Parreño V, Rahman M, Ruggeri FM, Saif LJ, Santos N, Steyer A, Taniguchi K, Patton JT, Desselberger U, Van Ranst M. Uniformity of rotavirus strain nomenclature proposed by the Rotavirus Classification Working Group (RCWG). Arch Virol 2011; 156:1397-413. [PMID: 21597953 DOI: 10.1007/s00705-011-1006-z] [Citation(s) in RCA: 740] [Impact Index Per Article: 56.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 04/19/2011] [Indexed: 12/31/2022]
Abstract
In April 2008, a nucleotide-sequence-based, complete genome classification system was developed for group A rotaviruses (RVs). This system assigns a specific genotype to each of the 11 genome segments of a particular RV strain according to established nucleotide percent cutoff values. Using this approach, the genome of individual RV strains are given the complete descriptor of Gx-P[x]-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx. The Rotavirus Classification Working Group (RCWG) was formed by scientists in the field to maintain, evaluate and develop the RV genotype classification system, in particular to aid in the designation of new genotypes. Since its conception, the group has ratified 51 new genotypes: as of April 2011, new genotypes for VP7 (G20-G27), VP4 (P[28]-P[35]), VP6 (I12-I16), VP1 (R5-R9), VP2 (C6-C9), VP3 (M7-M8), NSP1 (A15-A16), NSP2 (N6-N9), NSP3 (T8-T12), NSP4 (E12-E14) and NSP5/6 (H7-H11) have been defined for RV strains recovered from humans, cows, pigs, horses, mice, South American camelids (guanaco), chickens, turkeys, pheasants, bats and a sugar glider. With increasing numbers of complete RV genome sequences becoming available, a standardized RV strain nomenclature system is needed, and the RCWG proposes that individual RV strains are named as follows: RV group/species of origin/country of identification/common name/year of identification/G- and P-type. In collaboration with the National Center for Biotechnology Information (NCBI), the RCWG is also working on developing a RV-specific resource for the deposition of nucleotide sequences. This resource will provide useful information regarding RV strains, including, but not limited to, the individual gene genotypes and epidemiological and clinical information. Together, the proposed nomenclature system and the NCBI RV resource will offer highly useful tools for investigators to search for, retrieve, and analyze the ever-growing volume of RV genomic data.
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Affiliation(s)
- Jelle Matthijnssens
- Laboratory of Clinical & Epidemiological Virology, Department of Microbiology & Immunology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium.
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15
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Saiada F, Rahman HNA, Moni S, Karim MM, Pourkarim MR, Azim T, Rahman M. Clinical presentation and molecular characterization of group B rotaviruses in diarrhoea patients in Bangladesh. J Med Microbiol 2010; 60:529-536. [PMID: 21183601 DOI: 10.1099/jmm.0.025981-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A total of 1106 stool samples collected from diarrhoea patients admitted to Dhaka hospital of the International Centre for Diarrhoeal Disease Research, Bangladesh, during January-December 2008 were analysed for the presence of rotavirus-specific RNA by PAGE. The group B-specific RNA migration pattern was detected in 26 patients (2.4%) and group A-specific pattern in 259 patients (23.4%). Clinical data from group A and group B rotavirus-infected patients indicated that episodes did not differ much in the prevalence of diarrhoea, number of stools, outcome or differences in gender. However, abdominal pain was more common in group B rotavirus infections (36 vs 15%, P=0.02) and the virus was responsible for more severe dehydration compared with group A-infected patients (12 vs 3%, P=0.04). Sequence analyses of VP4, VP7 and NSP2 indicated that an Indian-Bangladeshi lineage of the virus, which is different from both the prototype (Chinese) lineage and from the animal group B rotaviruses, has been circulating in Bangladesh. Continuous monitoring of group B rotaviruses both in hospitals and in the community will be helpful to determine the true burden of group B rotaviruses.
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Affiliation(s)
- Farjana Saiada
- Virology Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B), Mohakhali, Dhaka 1212, Bangladesh
| | - H N Ashiqur Rahman
- Virology Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B), Mohakhali, Dhaka 1212, Bangladesh
| | - Sayra Moni
- Virology Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B), Mohakhali, Dhaka 1212, Bangladesh
| | - M Manjurul Karim
- Department of Microbiology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Mahmoud Reza Pourkarim
- Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
| | - Tasnim Azim
- Virology Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B), Mohakhali, Dhaka 1212, Bangladesh
| | - Mustafizur Rahman
- Virology Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B), Mohakhali, Dhaka 1212, Bangladesh
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16
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Rose TL, Miagostovich MP, Leite JPG. Rotavirus A genotype G1P[8]: a novel method to distinguish wild-type strains from the Rotarix® vaccine strain. Mem Inst Oswaldo Cruz 2010; 105:1068-72. [DOI: 10.1590/s0074-02762010000800021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Accepted: 10/27/2010] [Indexed: 11/21/2022] Open
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17
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Médici KC, Barry AF, Alfieri AF, Alfieri AA. Genetic analysis of the porcine group B rotavirus NSP2 gene from wild-type Brazilian strains. Braz J Med Biol Res 2010; 43:13-6. [PMID: 20069262 DOI: 10.1590/s0100-879x2010000100003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2009] [Accepted: 12/07/2009] [Indexed: 11/22/2022] Open
Abstract
Group B rotaviruses (RV-B) were first identified in piglet feces, being later associated with diarrhea in humans, cattle, lambs, and rats. In human beings, the virus was only described in China, India, and Bangladesh, especially infecting adults. Only a few studies concerning molecular analysis of the RV-B NSP2 gene have been conducted, and porcine RV-B has not been characterized. In the present study, three porcine wild-type RV-B strains from piglet stool samples collected from Brazilian pig herds were used for analysis. PAGE results were inconclusive for those samples, but specific amplicons of the RV-B NSP2 gene (segment 8) were obtained in a semi-nested PCR assay. The three porcine RV-B strains showed the highest nucleotide identity with the human WH1 strain and the alignments with other published sequences resulted in three groups of strains divided according to host species. The group of human strains showed 92.4 to 99.7% nucleotide identity while the porcine strains of the Brazilian RV-B group showed 90.4 to 91.8% identity to each other. The identity of the Brazilian porcine RV-B strains with outer sequences consisting of group A and C rotaviruses was only 35.3 to 38.8%. A dendrogram was also constructed to group the strains into clusters according to host species: human, rat, and a distinct third cluster consisting exclusively of the Brazilian porcine RV-B strains. This is the first study of the porcine RV-B NSP2 gene that contributes to the partial characterization of this virus and demonstrates the relationship among RV-B strains from different host species.
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Affiliation(s)
- K C Médici
- Laboratório de Virologia Animal, Departamento de Medicina Veterinária Preventiva, Universidade Estadual de Londrina, Londrina, PR, Brasil
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18
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Molecular characterization of the VP1, VP2, VP4, VP6, NSP1 and NSP2 genes of bovine group B rotaviruses: identification of a novel VP4 genotype. Arch Virol 2009; 155:159-67. [DOI: 10.1007/s00705-009-0555-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 10/22/2009] [Indexed: 11/26/2022]
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19
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Kuga K, Miyazaki A, Suzuki T, Takagi M, Hattori N, Katsuda K, Mase M, Sugiyama M, Tsunemitsu H. Genetic diversity and classification of the outer capsid glycoprotein VP7 of porcine group B rotaviruses. Arch Virol 2009; 154:1785-95. [PMID: 19821067 DOI: 10.1007/s00705-009-0517-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2009] [Accepted: 09/09/2009] [Indexed: 11/27/2022]
Abstract
We determined the nucleotide sequences of the outer capsid glycoprotein (VP7) genes of 38 porcine group B rotaviruses (GBRs) from feces of pigs at 27 farms in Japan between 2000 and 2007. Substantial diversity among porcine GBR VP7 genes was observed, with up to 42.4% difference in nucleotides and 49.8% in amino acids. On comparison of VP7 genes, porcine GBRs were clearly distinct from the published corresponding genes from human, bovine and murine GBRs (53.7-70.8% identity in nucleotides and 45.8-73.4% identity in amino acids). Phylogenetic analysis showed that the VP7s of GBRs could be divided into five genotypes: the murine strain was genotype 1, human strains were genotype 2, bovine and some porcine strains were genotype 3, and other porcine strains belonged to genotype 4 or 5. In addition, GBR VP7s in genotypes 3 and 5 were further divided into four and five clusters, respectively. No relationship between VP7 genotype and double-stranded RNA migration patterns of porcine GBRs in polyacrylamide gel electrophoresis were observed. However, an antigen enzyme-linked immunosorbent assay using antiserum to recombinant bovine GBR VP6 did not react with fecal samples containing one cluster of genotype 5 of porcine GBRs. The abundant divergence of porcine GBR VP7 genes suggests that porcine species might be an original natural host of GBR infection and that different serotypes might exist among porcine GBRs. To our knowledge, this is the first report to describe the gene sequences and typing of porcine GBR VP7s.
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Affiliation(s)
- Kazufumi Kuga
- Research Team for Viral Diseases, National Institute of Animal Health, Tsukuba, Ibaraki, 3050856, Japan
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20
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Detection and genotyping of human rotavirus VP4 and VP7 genes by reverse transcriptase PCR and reverse hybridization. J Clin Microbiol 2009; 47:2704-12. [PMID: 19553575 DOI: 10.1128/jcm.00378-09] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rotavirus infections can be diagnosed in stool samples by serological and molecular methods. We developed a novel reverse transcriptase PCR (RT-PCR) method for the amplification of rotavirus RNA and a reverse hybridization assay on a strip to detect amplimers and identify the specific G and P genotypes present in human stool specimens. An additional aim was to permit specific identification of the rotavirus G1P[8] strain, used in the Rotarix vaccine. Novel broad-spectrum PCR primers were developed for both VP4 and VP7, permitting the amplification of a wide range of rotavirus genotypes. Primer sets comprise mixtures of defined primer sequences. For the identification of G and P genotypes, two reverse hybridization strip assays were developed. Both the VP4 and the VP7 strip contain universal probes for the detection of VP4 and VP7 sequences, irrespective of the G or P genotype. The VP4 strip contains type-specific probes for P[4], P[6], P[8], P[9], and P[10]. The VP7 strip contains type-specific probes for G1, G2, G3, G4, G5, G6, G8, and G9. In addition, probes to distinguish between wild-type G1 and G1 vaccine strain sequences were present. Testing by analysis of multiple reference strains confirmed that both RT-PCR methods allowed the detection of a broad spectrum of genotypes. RT-PCR for VP7 was more sensitive than RT-PCR for VP4, but all samples identified as positive for rotavirus antigen by an enzyme-linked immunosorbent assay (ELISA) were also positive for both VP4 and VP7. The high specificity of the reverse hybridization method was confirmed by sequence analysis as well as by type-specific PCR, and the vaccine strain could also be specifically identified. The reverse hybridization method permits accurate identification of mixed infections with different genotypes. Rotavirus genotypes for which no type-specific probes were present on the strip were adequately identified by the universal detection probes. The assay was formally validated by analyses of specificity, sensitivity, precision, accuracy, and robustness. In a panel of 149 ELISA-positive stool samples, comparison with conventional type-specific RT-PCR methods revealed the superiority of the novel method, mainly in cases of mixed rotavirus infections. This novel method permits highly accurate detection and identification of human rotavirus infections in stool samples. This validated assay could be useful for large-scale epidemiological and clinical trials.
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21
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Park SI, Jeong C, Kim HH, Park SH, Park SJ, Hyun BH, Yang DK, Kim SK, Kang MI, Cho KO. Molecular epidemiology of bovine noroviruses in South Korea. Vet Microbiol 2007; 124:125-33. [PMID: 17466472 PMCID: PMC7117243 DOI: 10.1016/j.vetmic.2007.03.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2006] [Revised: 03/07/2007] [Accepted: 03/22/2007] [Indexed: 11/24/2022]
Abstract
Since the prevalence of bovine norovirus (BNoV) and their genetic diversity have only been reported in the USA, England, Germany and The Netherlands, this study examined the prevalence and genetic diversity of BNoVs in diarrheic calves in South Korea using 645 diarrheic fecal specimens from calves by RT-PCR and nested PCR assays. Overall, 9.3% of the diarrheic fecal samples tested positive for BNoVs by either RT-PCR or nested PCR, of which 5.9% samples also tested positive for other enteric pathogens including the bovine coronavirus, bovine viral diarrhea virus, bovine torovirus, bovine groups A, B and C rotaviruses, bovine enteric Nebraska-like calicivirus and Escherichia coli. The genetic diversity was determined by direct sequencing of the partial RdRp region of 12 BNoVs detected from the fecal samples by nested PCR. Among the BNoVs examined, one Korean BNoV strain had the highest nucleotide (86.8%) and amino acid (99.1%) identity with the genotype 1 BNoV (GIII-1) strain, while the remaining 11 Korean BNoVs shared a higher nucleotide (88.0-90.5%) and amino acid (93.5-99.1%) identity with the genotype 2 BNoV (GIII-2) strains. The phylogenetic data for the nucleotide and amino acid sequences also demonstrated that one Korean BNoV strain clustered with GIII-1 but the remaining eleven strains clustered with GIII-2. In conclusion, BNoV infections are endemic and there are two distinct genotypes with GIII-2 being the main genotype circulating in the calf population in South Korea.
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Affiliation(s)
- Sang-Ik Park
- Bio-therapy Human Resources Center, College of Veterinary Medicine, Chonnam National University, Gwangju 500-757, South Korea
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22
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Rahman M, Hassan ZM, Zafrul H, Saiada F, Banik S, Faruque ASG, Delbeke T, Matthijnssens J, Van Ranst M, Azim T. Sequence analysis and evolution of group B rotaviruses. Virus Res 2007; 125:219-25. [PMID: 17292993 DOI: 10.1016/j.virusres.2007.01.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2006] [Revised: 01/10/2007] [Accepted: 01/12/2007] [Indexed: 11/25/2022]
Abstract
Human group B rotaviruses were isolated from hospitalized patients in Bangladesh between July 2003 and December 2004. Phylogenetic analyses of the gene segments encoding the hemagglutinin (VP4), glycoprotein (VP7) and RNA-binding protein (NSP2) of group B rotaviruses showed that Bangladeshi strains were more similar to the Indian strains than to the prototype Chinese strains. Moreover, all human strains were clustered together and were distantly related to the animal strains. With limited sequence data, the evolutionary rate of the glycoproteins (VP7) of human group B rotaviruses was estimated to be 1.57x10(-3) nucleotide substitutions/(siteyear), which was comparable to other rapidly evolving RNA viruses. The most recent common ancestor (MRCA) of the extant human group B rotaviruses was calculated to date to around 1976.
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Affiliation(s)
- Mustafizur Rahman
- Laboratory of Virology, ICDDR,B, GPO Box-128, Dhaka 1000, Bangladesh.
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GHOSH S, VARGHESE V, SINHA M, KOBAYASHI N, NAIK T. Evidence for interstate transmission and increase in prevalence of bovine group B rotavirus strains with a novel VP7 genotype among diarrhoeic calves in Eastern and Northern states of India. Epidemiol Infect 2007; 135:1324-30. [PMID: 17291375 PMCID: PMC2870693 DOI: 10.1017/s0950268806007813] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
During a surveillance study (2003-2005) in a cattle market in Kolkata city, state of West Bengal, Eastern India, 34 (13.0%) of 260 calves with diarrhoea were positive for group B rotaviruses (GBR) by RNA electrophoresis in polyacrylamide gels. Analysis of the partial VP7 gene sequence of 28 of the 34 GBR strains revealed maximum identities (97.7-99.5% at nucleotide level and 97.8-100% at amino-acid level) with the novel bovine GBR 'Kolkata strains' reported in an earlier surveillance study (1.5%, n=192, 2001-2002) from the same cattle market, and shared low identities of 73.7-78.9% and 80.8-89.6%; 62.6-66.2% and 59.8-65.4%; 58.9-62.2% and 48.6-54.9% at nucleotide and amino-acid level with other bovine, human, and murine GBR. The GBR-infected calves were traced to districts in neighbouring states of West Bengal. Therefore, the present study reports a rapid increase in prevalence (13.0% in 2003-2005 against 1.5% in 2001-2002) of novel GBR strains among calves with diarrhoea, and provides evidence for interstate transmission of GBR.
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Affiliation(s)
- S. GHOSH
- Division of Virology, National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
| | - V. VARGHESE
- Division of Virology, National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
| | - M. SINHA
- Division of Virology, National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
| | - N. KOBAYASHI
- Department of Hygiene, Sapporo Medical University School of Medicine, Chuo-Ku, Sapporo, Japan
| | - T. N. NAIK
- Division of Virology, National Institute of Cholera and Enteric Diseases, Beliaghata, Kolkata, India
- Author for correspondence: Dr T. N. Naik, Division of Virology, National Institute of Cholera and Enteric Diseases, P-33 C.I.T. Road, Scheme XM, Beliaghata, Kolkata-700010, West Bengal, India. (or)
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24
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Park SJ, Jeong C, Yoon SS, Choy HE, Saif LJ, Park SH, Kim YJ, Jeong JH, Park SI, Kim HH, Lee BJ, Cho HS, Kim SK, Kang MI, Cho KO. Detection and characterization of bovine coronaviruses in fecal specimens of adult cattle with diarrhea during the warmer seasons. J Clin Microbiol 2006; 44:3178-88. [PMID: 16954245 PMCID: PMC1594715 DOI: 10.1128/jcm.02667-05] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bovine coronavirus (BCoV) is an etiological agent associated with winter dysentery (WD), prevalent in adult cattle during the winter. Although we previously detected, isolated, and characterized BCoV strains from adult cattle with WD (WD-BCoV strains) during the winter in South Korea, the precise epidemiology, as well as the causative agent of diarrhea in adult cattle in the warmer seasons, has not been examined. We examined 184 diarrheic fecal specimens collected from 75 herds of adult cattle from seven provinces during the spring (warm), autumn (warm), and summer (hot) seasons. Bovine coronavirus-positive reactions were detected for 107 (58.2%) diarrheic fecal samples (in 47/75 herds). Of these 107 positive samples, 90 fecal samples from 33 herds tested positive for BCoV alone and 17 fecal samples from 14 herds also tested positive for other pathogens. Biological comparisons between the 9 BCoV strains isolated in this study and the 10 previously isolated WD-BCoV strains revealed that there was no receptor-destroying enzyme (RDE) activity against mouse erythrocytes in the 9 BCoV strains but the 10 WD-BCoV strains had high RDE activity. Phylogenetic analysis of the spike (S) and hemagglutinin/esterase (HE) proteins revealed that all the Korean BCoVs clustered together regardless of season and were distinct from the other known BCoVs, suggesting a distinct evolutionary pathway for the Korean BCoVs. These and previous results revealed a high prevalence and widespread geographical distribution of BCoV, suggesting that this virus is endemic in adult cattle with diarrhea in all seasons in South Korea.
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Affiliation(s)
- Su-Jin Park
- Biotherapy Human Resources Center, College of Veterinary Medicine, Chonnam National University, Gwangju 500-757, South Korea
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25
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Barman P, Ghosh S, Samajdar S, Mitra U, Dutta P, Bhattacharya SK, Krishnan T, Kobayashi N, Naik TN. RT-PCR based diagnosis revealed importance of human group B rotavirus infection in childhood diarrhoea. J Clin Virol 2006; 36:222-7. [PMID: 16765641 DOI: 10.1016/j.jcv.2006.02.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2005] [Revised: 12/27/2005] [Accepted: 02/20/2006] [Indexed: 12/01/2022]
Abstract
BACKGROUND Human group B rotavirus was first identified as causative agent of a large outbreak of severe gastroenteritis affecting more than 1 million people, predominantly adults in China in 1982-1983. In spite of serological evidences for the presence of group B rotavirus in many countries of the world, the virus has been detected only from China, India and Bangladesh, where most of the cases were from adults. OBJECTIVES To ascertain the role of group B rotavirus as an aetiological agent of diarrhoea among children in Kolkata, India. STUDY DESIGN An active surveillance was conducted for rotavirus infection in children in a leading referral paediatric hospital and a few samples were also collected from adults of another hospital in Kolkata, India over a period of 3 years (2002-2004). After primary screening of rotaviruses by RNA electrophoresis in polyacrylamide gel, 200 of 412 samples negative by PAGE were screened by reverse transcription polymerase chain reaction for group B rotaviruses. The group B rotavirus positives samples were also confirmed by dot-blot hybridization. RESULT During the study period, we detected 37 (18.5%) sporadic cases of human group B rotavirus infection in children below 3 years of age of which 15 (7.5%) showed mixed infection with group A rotaviruses by RT-PCR. In dot-blot hybridization studies the RNA of all rotavirus positive samples hybridized with the nonisotopic psoralen-biotin labeled total RNA probe generated from a human group B rotavirus CAL-1 strain confirming the samples as group B rotaviruses. CONCLUSION The shift in age preference of group B rotavirus infection from adult to children and mixed infection of group B and group A rotaviruses reveals the importance of group B rotavirus as an etiological agent of childhood diarrhoea. Therefore, future vaccination strategy should include both group A and B rotaviruses to control rotavirus diarrhoea.
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Affiliation(s)
- P Barman
- Division of Virology, National Institute of Cholera and Enteric Diseases, P-33 CIT Road, Scheme XM, Beliaghata, Kolkata-700010, West Bengal, India
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Ghosh S, Varghese V, Samajdar S, Bhattacharya SK, Kobayashi N, Naik TN. Molecular characterization of a porcine Group A rotavirus strain with G12 genotype specificity. Arch Virol 2006; 151:1329-44. [PMID: 16502286 DOI: 10.1007/s00705-005-0714-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2005] [Accepted: 12/19/2005] [Indexed: 10/25/2022]
Abstract
A porcine Group A rotavirus strain (RU172) was detected and molecularly characterized during a surveillance study conducted for rotavirus infection in a pig farm located in a suburban area of Kolkata City, India. The G12 genotype specificity of RU172 was revealed by PCR-based genotyping assays following addition of a G12 type-specific primer (designed in our laboratory to pick up G12 isolates from field samples) and was confirmed by sequence analysis of the VP7-encoding gene. The RU172 strain exhibited maximum VP7 identities of 93.6% to 94.5% with human G12 strains at the deduced amino acid level. In spite of its G12 genotype nature, RU172 appeared to be distinct from human G12 rotaviruses and, on phylogenetic analysis, formed a separate lineage with human G12 strains. Among the other gene segments analyzed, RU172 belonged to NSP4 genotype B, had a NSP5 and VP6 of porcine origin, and shared maximum VP4 identities with porcine P[7] rotaviruses (94.3%-95.4% at the deduced amino acid level). Therefore, to the best of our knowledge, this is the first report of detection of an animal rotavirus strain with G12 genotype specificity. Detection of strains like RU172 provides vital insights into the genomic diversity of Group A rotaviruses of man and animals.
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Affiliation(s)
- S Ghosh
- Division of Virology, National Institute of Cholera and Enteric Diseases, Beliaghata, India
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Kang G, Kelkar SD, Chitambar SD, Ray P, Naik T. Epidemiological profile of rotaviral infection in India: challenges for the 21st century. J Infect Dis 2005; 192 Suppl 1:S120-6. [PMID: 16088795 PMCID: PMC2464020 DOI: 10.1086/431496] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Rotaviruses cause acute viral gastroenteritis worldwide. It has been estimated that, each year, 440,000 deaths that occur among children are attributed to rotavirus infection, mainly in developing countries. In India, the diversity of rotaviruses reported during the 1980s and 1990s emphasizes the need for surveillance of cocirculating strains, to follow the rapid changes in circulation and to detect novel strains. METHODS We analyzed data from published epidemiological studies, to collate available information on serotyping and genotyping of rotaviruses before the initiation of a national rotavirus surveillance program. The studies included 18 Indian cities and were performed during 1996-2001. RESULTS Rotaviruses were detected in 23.4% of patients with diarrhea who presented to the hospital. There were marked geographic differences in virus circulation, with G1 being the single most common G type identified in all parts of India, except for western India. Group B rotaviruses were reported from Kolkata and Pune. Human infections with strains G6, G8, G10, and G9P[19], which may occur as a result of zoonotic transmission of bovine and porcine rotaviruses, were reported from western, southern, and eastern India. CONCLUSIONS The remarkable diversity of rotaviruses circulating in India highlights the need for uniform, widespread surveillance for rotaviruses before the initiation and during the implementation of immunization programs.
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Affiliation(s)
- Gagandeep Kang
- Department of Gastrointestinal Sciences, Christian Medical College, Vellore, India.
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