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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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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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3
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Chen F, Knutson TP, Ciarlet M, Sturos M, Marthaler DG. Complete genome characterization of a rotavirus B (RVB) strain identified in Alpine goat kids with enteritis reveals inter-species transmission with RVB bovine strains. J Gen Virol 2018. [PMID: 29517476 PMCID: PMC5982130 DOI: 10.1099/jgv.0.001022] [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] [Indexed: 11/18/2022] Open
Abstract
Rotavirus B (RVB) has been associated with enteric disease in many animal species. An RVB strain was identified in pooled intestinal samples from Alpine caprine kids (between 2 and 3 days of age) experiencing high (>90 %) morbidity, and the complete caprine RVB genome was characterized. Histology revealed villus atrophy, the samples tested positive for RVB by real-time RT-PCR and metagenomic next-generation sequencing identified only RVB and orf virus. In the VP4 gene segment, the caprine RVB strain had a higher percentage nucleotide identity to the Indian bovine RVB strains than to the Japanese bovine RVB strains, but the VP7, VP6, VP2, NSP1, NSP2 and NSP5 gene segments of the American caprine RVB strain were genetically related to the Japanese bovine RVB strains. The results indicate a lack of RVB sequences to understand reassortment or the evolutionary relationship of RVB strains from cattle and goats.
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Affiliation(s)
- Fangzhou Chen
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA.,State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Todd P Knutson
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA
| | - Max Ciarlet
- Vaccines Clinical Research and Development, GlaxoSmithKline Vaccines, Cambridge, MA 02139, USA
| | - Matthew Sturos
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA
| | - Douglas G Marthaler
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA.,Veterinary Diagnostic Laboratory, College of Veterinary Medicine, 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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5
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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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6
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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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Morelli M, Ogden KM, Patton JT. Silencing the alarms: Innate immune antagonism by rotavirus NSP1 and VP3. Virology 2015; 479-480:75-84. [PMID: 25724417 PMCID: PMC4940189 DOI: 10.1016/j.virol.2015.01.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 12/23/2014] [Accepted: 01/05/2015] [Indexed: 12/22/2022]
Abstract
The innate immune response involves a broad array of pathogen sensors that stimulate the production of interferons (IFNs) to induce an antiviral state. Rotavirus, a significant cause of childhood gastroenteritis and a member of the Reoviridae family of segmented, double-stranded RNA viruses, encodes at least two direct antagonists of host innate immunity: NSP1 and VP3. NSP1, a putative E3 ubiquitin ligase, mediates the degradation of cellular factors involved in both IFN induction and downstream signaling. VP3, the viral capping enzyme, utilizes a 2H-phosphodiesterase domain to prevent activation of the cellular oligoadenylate synthase (OAS)/RNase L pathway. Computational, molecular, and biochemical studies have provided key insights into the structural and mechanistic basis of innate immune antagonism by NSP1 and VP3 of group A rotaviruses (RVA). Future studies with non-RVA isolates will be essential to understand how other rotavirus species evade host innate immune responses. Rotavirus NSP1 and VP3 directly antagonize host innate immune pathways. NSP1, a putative E3 ubiquitin ligase, mediates turnover of multiple immune factors. VP3, the viral capping enzyme, has phosphodiesterase activity to block OAS/RNase L.
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Affiliation(s)
- Marco Morelli
- Rotavirus Molecular Biology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kristen M Ogden
- Rotavirus Molecular Biology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John T Patton
- Rotavirus Molecular Biology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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Marthaler D, Suzuki T, Rossow K, Culhane M, Collins J, Goyal S, Tsunemitsu H, Ciarlet M, Matthijnssens J. VP6 genetic diversity, reassortment, intragenic recombination and classification of rotavirus B in American and Japanese pigs. Vet Microbiol 2014; 172:359-66. [PMID: 24970362 DOI: 10.1016/j.vetmic.2014.05.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 04/25/2014] [Accepted: 05/03/2014] [Indexed: 01/14/2023]
Abstract
Rotavirus B (RVB) has been identified as a causative agent of diarrhea in rats, humans, cattle, lambs, and swine. Recently, 20 RVB VP7 genotypes were determined based on an 80% nucleotide percent cut-off value. In this study, we sequenced the RVB VP6 gene segment from 80 RVB positive swine samples from the United States and Japan. Phylogenetic analyses, using the 30 available RVB VP6 sequences from GenBank and our 80 novel RVB VP6 sequences, revealed a large genetic diversity of RVB strains, mainly in pigs. For classification purposes, pairwise identity frequency analyses suggested an 81% nucleotide percent cut-off value, resulting in 13 RVB VP6 (I) genotypes. In addition, an intragenic recombinant RVB VP6 segment was identified from Japan. Furthermore, the data indicates frequent reassortment events occurred between the porcine RVB VP7 and VP6 gene segments.
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Affiliation(s)
- Douglas Marthaler
- University of Minnesota Veterinary Diagnostic Laboratory, Saint Paul, MN, United States.
| | - Tohru Suzuki
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Kurt Rossow
- University of Minnesota Veterinary Diagnostic Laboratory, Saint Paul, MN, United States
| | - Marie Culhane
- University of Minnesota Veterinary Diagnostic Laboratory, Saint Paul, MN, United States
| | - James Collins
- University of Minnesota Veterinary Diagnostic Laboratory, Saint Paul, MN, United States
| | - Sagar Goyal
- University of Minnesota Veterinary Diagnostic Laboratory, Saint Paul, MN, United States
| | - Hiroshi Tsunemitsu
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Max Ciarlet
- Clinical Research and Development, Novartis Vaccines & Diagnostics, Inc., Cambridge, MA, United States
| | - Jelle Matthijnssens
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Belgium
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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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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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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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12
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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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13
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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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14
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Yamamoto D, Ghosh S, Ganesh B, Krishnan T, Chawla-Sarkar M, Alam MM, Aung TS, Kobayashi N. Analysis of genetic diversity and molecular evolution of human group B rotaviruses based on whole genome segments. J Gen Virol 2010; 91:1772-81. [PMID: 20200192 DOI: 10.1099/vir.0.020412-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Group B rotavirus (GBR) is a rare enteric pathogen that causes severe diarrhoea, primarily in adults. Nearly full-length sequences of all 11 RNA segments were determined for human GBRs detected recently in India (IDH-084 in 2007, IC-008 in 2008), Bangladesh (Bang117 in 2003) and Myanmar (MMR-B1 in 2007), and analysed phylogenetically with the sequence data of GBRs reported previously. All RNA segments of GBR strains from India, Bangladesh and Myanmar showed >95 % nucleotide sequence identities. Among the 11 RNA segments, the VP6 and NSP2 genes showed the highest identities (>98 %), whilst the lowest identities were observed in the NSP4 gene (96.1 %), NSP5 gene (95.6 %) and VP8*-encoding region of the VP4 gene (95.9 %). Divergent or conserved regions in the deduced amino acid sequences of GBR VP1-VP4 and NSP1-NSP5 were similar to those in group A rotaviruses (GARs), and the functionally important motifs and structural characteristics in viral proteins known for GAR were conserved in all of the human GBRs. These findings suggest that, whilst the degree of genetic evolution may be dependent on each RNA segment, human GBR may have been evolving in a similar manner to GAR, associated with the similar functional roles of individual viral proteins.
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Affiliation(s)
- Dai Yamamoto
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo, Japan.
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15
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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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16
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Aung TS, Kobayashi N, Nagashima S, Ghosh S, Aung MS, Oo KY, Win N. Detection of group B rotavirus in an adult with acute gastroenteritis in Yangon, Myanmar. J Med Virol 2009; 81:1968-74. [DOI: 10.1002/jmv.21613] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Shen S, Lin PS, Chao YC, Zhang A, Yang X, Lim SG, Hong W, Tan YJ. The severe acute respiratory syndrome coronavirus 3a is a novel structural protein. Biochem Biophys Res Commun 2005; 330:286-92. [PMID: 15781262 PMCID: PMC7092867 DOI: 10.1016/j.bbrc.2005.02.153] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2005] [Indexed: 01/08/2023]
Abstract
The severe acute respiratory syndrome coronavirus (SARS-CoV) 3a protein is one of the opening reading frames in the viral genome with no homologue in other known coronaviruses. Expression of the 3a protein has been demonstrated during both in vitro and in vivo infection. Here we present biochemical data to show that 3a is a novel coronavirus structural protein. 3a was detected in virions purified from SARS-CoV infected Vero E6 cells although two truncated products were present predominantly instead of the full-length protein. In Vero E6 cells transiently transfected with a cDNA construct for expressing 3a, a similar cleavage was observed. Furthermore, co-expression of 3a, membrane and envelope proteins using the baculovirus system showed that both full-length and truncated 3a can be assembled into virus-like particles. This is the first report that demonstrated the incorporation of 3a into virion and showed that the SARS-CoV encodes a novel coronavirus structural protein.
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Affiliation(s)
- Shuo Shen
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Pi-Shiu Lin
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan, ROC
| | - Yu-Chan Chao
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei 115, Taiwan, ROC
| | - Aihua Zhang
- Wuhan Institute of Biological Products, Wuhan 430060, PR China
| | - Xiaoming Yang
- Wuhan Institute of Biological Products, Wuhan 430060, PR China
| | - Seng Gee Lim
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Wanjin Hong
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Yee-Joo Tan
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
- Corresponding author. Fax: + 65 67791117
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18
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Shen S, Law Y, Liu D. A single amino acid mutation in the spike protein of coronavirus infectious bronchitis virus hampers its maturation and incorporation into virions at the nonpermissive temperature. Virology 2004; 326:288-98. [PMID: 15302214 PMCID: PMC7126609 DOI: 10.1016/j.virol.2004.06.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2004] [Revised: 05/25/2004] [Accepted: 06/03/2004] [Indexed: 11/22/2022]
Abstract
The spike (S) glycoprotein of coronavirus is responsible for receptor binding and membrane fusion. A number of variants with deletions and mutations in the S protein have been isolated from naturally and persistently infected animals and tissue cultures. Here, we report the emergence and isolation of two temperature sensitive (ts) mutants and a revertant in the process of cold-adaptation of coronavirus infectious bronchitis virus (IBV) to a monkey kidney cell line. The complete sequences of wild type (wt) virus, two ts mutants, and the revertant were compared and variations linked to phenotypes were mapped. A single amino acid reversion (L294-to-Q) in the S protein is sufficient to abrogate the ts phenotype. Interestingly, unlike wt virus, the revertant grows well at and below 32 degrees C, the permissive temperature, as it carries other mutations in multiple genes that might be associated with the cold-adaptation phenotype. If the two ts mutants were allowed to enter cells at 32 degrees C, the S protein was synthesized, core-glycosylated and at least partially modified at 40 degrees C. However, compared with wt virus and the revertant, no infectious particles of these ts mutants were assembled and released from the ts mutant-infected cells at 40 degrees C. Evidence presented demonstrated that the Q294-to-L294 mutation, located at a highly conserved domain of the S1 subunit, might hamper processing of the S protein to a matured 180-kDa, endo-glycosidase H-resistant glycoprotein and the translocation of the protein to the cell surface. Consequently, some essential functions of the S protein, including mediation of cell-to-cell fusion and its incorporation into virions, were completely abolished.
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Affiliation(s)
| | | | - D.X Liu
- Corresponding author. Institute of Molecular and Cell Biology, 30 Medical Drive, 117609, Singapore. Fax: +65-67791117.
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19
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Barman P, Ghosh S, Das S, Varghese V, Chaudhuri S, Sarkar S, Krishnan T, Bhattacharya SK, Chakrabarti A, Kobayashi N, Naik TN. Sequencing and sequence analysis of VP7 and NSP5 genes reveal emergence of a new genotype of bovine group B rotaviruses in India. J Clin Microbiol 2004; 42:2816-8. [PMID: 15184480 PMCID: PMC427839 DOI: 10.1128/jcm.42.6.2816-2818.2004] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2003] [Revised: 02/17/2004] [Accepted: 03/09/2004] [Indexed: 11/20/2022] Open
Abstract
Three bovine group B rotavirus strains were detected from diarrheic calves during a surveillance study of rotaviral diarrhea in West Bengal, India. The sequence analysis of VP7 and NSP5 genes of these strains demonstrates a high degree of sequence variation from other group B rotavirus strains, indicating the emergence of a new genotype.
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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, Calcutta 700010, India
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20
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Abstract
Vaccination is the current strategy for control and prevention of severe rotavirus infections, a major cause of acute, dehydrating diarrhoea in young children worldwide. Public health interventions aimed at improving water, food and sanitation are unlikely adequately to control the disease. The development of vaccines against severe rotavirus diarrhoea is based upon homotypic or heterotypic protection provided against either a single common G serotype (monovalent vaccines) or against multiple serotypes (multivalent vaccines). Rotavirus strain surveillance has a high priority in disease control programmes worldwide. The continued identification of the most common G and P serotypes for inclusion in vaccines is an important priority. And subsequent to the introduction of a vaccine candidate, not only monitoring of circulating strains is recommended, but also surveillance of potential reassortment of animal rotavirus genes from the vaccine into human rotavirus strains is critical. Conventional methods used in the characterisation of rotavirus strains, such as enzyme immunoassay serotyping and reverse‐transcription PCR‐based genotyping often fail to identify uncommon and newly appearing strains. The application of newer molecular approaches, including sequencing and oligonucleotide microarray hybridisation, may be required to characterise such strains. The present paper presents a brief overview of the variety of standard methods available, followed by suggestions for a systematic approach for routine rotavirus strain surveillance as well as for characterisation of incompletely typed rotavirus strains. Improved detection and characterisation of incompletely typed strains will help to develop a comprehensive strain surveillance that may be required for tailoring effective rotavirus vaccines. Published in 2004 by John Wiley & Sons, Ltd.
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Affiliation(s)
- Thea K Fischer
- Centre for International Health, University of Bergen, Norway, Laboratorio National de Saúde Publica, Bissau, Guinea-Bissau and Department of Epidemiology Research, Danish Epidemiology Science Centre, Copenhagen, Denmark.
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21
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Shen S, Wen ZL, Liu DX. Emergence of a coronavirus infectious bronchitis virus mutant with a truncated 3b gene: functional characterization of the 3b protein in pathogenesis and replication. Virology 2003; 311:16-27. [PMID: 12832199 PMCID: PMC7125764 DOI: 10.1016/s0042-6822(03)00117-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The subgenomic RNA 3 of IBV has been shown to be a tricistronic mRNA, encoding three products in IBV-infected cells. To explore if the least expressed ORF, ORF 3b, which encodes a nonstructural protein, is evolutionarily conserved and functionally indispensable for viral propagation in cultured cells, the Beaudette strain of IBV was propagated in chicken embryonated eggs for three passages and then adapted to a monkey kidney cell line, Vero. The 3b gene of passage 3 in embryonated eggs and passages 7, 15, 20, 25, 30, 35 50, and 65 in Vero cells were amplified by reverse transcription-polymerase chain reaction and sequenced. The results showed that viral RNA extracted from passages 35, 50, and 65 contained a single A insertion in a 6A stretch of the 3b gene between nucleotides 24075 and 24080, whereas the early passages carried the normal 3b gene. This insertion resulted in a frameshift event and therefore, if expressed, a C-terminally truncated protein. We showed that the frameshifting product, cloned in a plasmid, was expressed in vitro and in cells transfected with the mutant construct. The normal product of the 3b gene is 64 amino acids long, whereas the frameshifting product is 34 amino acids long with only 17 homogeneous amino acid residues at the N-terminal half. Immunofluorescent studies revealed that the normal 3b protein was localized to the nucleus and the truncated product showed a "free" distribution pattern, indicating that the C-terminal portion of 3b was responsible for its nuclear localization. Comparison of the complete genome sequences (27.6 kb) of isolates p20c22 and p36c12 (from passages 20 and 36, respectively) revealed that p36c12 contains three amino acid substitutions, two in the 195-kDa protein (encoded by gene 1) and one in the S protein, in addition to the frameshifting 3b product. Further characterization of the two isolates demonstrated that p36c12 showed growth advantage over p20c22 in both Vero cells and chicken embryos and was more virulent in chicken embryos than p20c22. These results suggest that the 3b gene product is not essential for the replication of IBV.
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Affiliation(s)
- S Shen
- Institute of Molecular and Cell Biology, National University of Singapore, 117604, Singapore
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22
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Shen S, Liu DX. Characterization of temperature-sensitive (ts) mutants of coronavirus infectious bronchitis virus (IBV). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2002; 494:557-62. [PMID: 11774524 DOI: 10.1007/978-1-4615-1325-4_82] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- S Shen
- Institute of Molecular Agrobiology, 1 Research Linke, National University of Singapore, Singapore 117604
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23
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Kobayashi N, Naik TN, Kusuhara Y, Krishnan T, Sen A, Bhattacharya SK, Taniguchi K, Alam MM, Urasawa T, Urasawa S. Sequence analysis of genes encoding structural and nonstructural proteins of a human group B rotavirus detected in Calcutta, India. J Med Virol 2001; 64:583-8. [PMID: 11468747 DOI: 10.1002/jmv.1089] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Nucleotide sequences of RNA segments encoding structural proteins(VP4, VP6, and VP7) and nonstructural proteins(NSP1 and NSP3) of a human group B rotavirus CAL-1, which was detected in Calcutta, India, were determined and their relatedness with cognate genes of other group B rotaviruses was analyzed. The CAL-1 genes showed generally high sequence identities (more than 90%) to those of human group B rotavirus, adult diarrheal rotavirus (ADRV) in China, while identities with bovine, murine, and ovine viruses were considerably lower (58-73%). Among RNA segments analyzed, sequence identity of the VP6 gene was relatively high compared with other gene segments. In the CAL-1 VP7 sequence, many characteristics were shared by ADRV, but not by other animal group B rotaviruses. In contrast, VP4 and NSP3 of CAL-1 were single amino acid and 23 amino acids longer than those of ADRV strain, respectively, due to differences of a few nucleotides. These findings suggested that human group B rotaviruses CAL-1 and ADRV might have originated from a common ancestral virus distinct from animal group B rotaviruses reported so far, while some notable sequence differences indicated the distinct nature of these viruses.
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Affiliation(s)
- N Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, S-1, W-17, Chuo-ku, Sapporo, Japan.
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