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Elkady G, Chen Y, Hu C, Chen J, Chen X, Guo A. MicroRNA Profile of MA-104 Cell Line Associated With the Pathogenesis of Bovine Rotavirus Strain Circulated in Chinese Calves. Front Microbiol 2022; 13:854348. [PMID: 35516441 PMCID: PMC9062783 DOI: 10.3389/fmicb.2022.854348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Bovine rotavirus (BRV) causes massive economic losses in the livestock industry worldwide. Elucidating the pathogenesis of BRV would help in the development of more effective measures to control BRV infection. The MA-104 cell line is sensitive to BRV and is thereby a convenient tool for determining BRV–host interactions. Thus far, the role of the microRNAs (miRNAs) of MA-104 cells during BRV infection is still ambiguous. We performed Illumina RNA sequencing analysis of the miRNA libraries of BRV-infected and mock-infected MA-104 cells at different time points: at 0 h post-infection (hpi) (just after 90 min of adsorption) and at 6, 12, 24, 36, and 48 hpi. The total clean reads obtained from BRV-infected and uninfected cells were 74,701,041 and 74,184,124, respectively. Based on these, 579 were categorized as known miRNAs and 144 as novel miRNAs. One hundred and sixty differentially expressed (DE) miRNAs in BRV-infected cells in comparison with uninfected MA-104 cells were successfully investigated, 95 of which were upregulated and 65 were downregulated. The target messenger RNAs (mRNAs) of the DE miRNAs were examined by bioinformatics analysis. Functional annotation of the target genes with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) suggested that these genes mainly contributed to biological pathways, endocytosis, apoptotic process, trans-Golgi membrane, and lysosome. Pathways such as the mammalian target of rapamycin (mTOR) (mml-miR-486-3p and mml-miR-197-3p), nuclear factor kappa B (NF-κB) (mml-miR-204-3p and novel_366), Rap1 (mml-miR-127-3p), cAMP (mml-miR-106b-3p), mitogen-activated protein kinase (MAPK) (mml-miR-342-5p), T-cell receptor signaling (mml-miR-369-5p), RIG-I-like receptor signaling (mml-miR-504-5p), AMP-activated protein kinase (AMPK) (mml-miR-365-1-5p), and phosphatidylinositol-3-kinase/protein kinase B (PI3K/Akt) signaling (mml-miR-299-3p) were enriched. Moreover, real-time quantitative PCR (qPCR) verified the expression profiles of 23 selected DE miRNAs, which were consistent with the results of deep sequencing, and the 28 corresponding target mRNAs were mainly of regulatory pathways of the cellular machinery and immune importance, according to the bioinformatics analysis. Our study is the first to report a novel approach that uncovers the impact of BRV infection on the miRNA expressions of MA-104 cells, and it offers clues for identifying potential candidates for antiviral or vaccine strategies.
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Affiliation(s)
- Gehad Elkady
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan, China
- Benha University, Benha, Egypt
| | - Yingyu Chen
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan, China
| | - Changmin Hu
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Jianguo Chen
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Xi Chen
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Aizhen Guo
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Aizhen Guo,
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Pinheiro MS, Dias JBL, Cunha BRAV, Petrucci MP, Travassos CEPF, Mendes GS, Santos N. Rotavirus F and G circulating in chickens in Southeastern Brazil. Trop Anim Health Prod 2022; 54:113. [PMID: 35217986 DOI: 10.1007/s11250-022-03113-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/18/2022] [Indexed: 10/19/2022]
Abstract
Rotavirus (RV) infections represent a significant cause of enteritis and diarrhea in avian species and pose a major concern for the poultry industry. However, the prevalence of rotavirus infections among birds is poorly understood. Stool samples were collected from laying and broiler hens from commercial poultry farms in the states of Rio de Janeiro and Espírito Santo, Southwest region of Brazil, for detection of rotavirus species F and G (RVF and RVG, respectively) by reverse transcription polymerase chain reaction. RV was detected in 11.7% (38/325) of samples: 35 samples were positive for RVF and 3 for RVG. RVF was detected in 15 samples from Rio de Janeiro and 23 samples from Espírito Santo. RVG was detected in 3 samples from Espírito Santo. All the positive samples were from asymptomatic broiler chickens. The prevalence of RV infection in these flocks was high, especially considering that the birds had no apparent clinical disease. Silent circulation in the herds signifies the need for a continuous surveillance program to guide measures to control and prevent this viral infection. Continuous monitoring of pathogens is crucial to ensure greater productivity on poultry farms.
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Affiliation(s)
- Mariana S Pinheiro
- Instituto de Microbiologia Paulo de Góes, Universidade Federal Do Rio de Janeiro, 21.947-902, Rio de Janeiro, RJ, Brazil
| | - Juliana B L Dias
- Instituto de Microbiologia Paulo de Góes, Universidade Federal Do Rio de Janeiro, 21.947-902, Rio de Janeiro, RJ, Brazil
| | - Beatriz R A V Cunha
- Instituto de Microbiologia Paulo de Góes, Universidade Federal Do Rio de Janeiro, 21.947-902, Rio de Janeiro, RJ, Brazil
| | - Melissa P Petrucci
- Universidade Estadual Do Norte Fluminense Darcy Ribeiro, 28013-602, Campos dos Goytacazes, RJ, Brazil
| | - Carlos E P F Travassos
- Universidade Estadual Do Norte Fluminense Darcy Ribeiro, 28013-602, Campos dos Goytacazes, RJ, Brazil
| | - Gabriella S Mendes
- Instituto de Microbiologia Paulo de Góes, Universidade Federal Do Rio de Janeiro, 21.947-902, Rio de Janeiro, RJ, Brazil
| | - Norma Santos
- Instituto de Microbiologia Paulo de Góes, Universidade Federal Do Rio de Janeiro, 21.947-902, Rio de Janeiro, RJ, Brazil. .,Departamento de Virologia, Centro de Ciências da Saúde, Instituto de Microbiologia Paulo de Góes, Universidade Federal Do Rio de Janeiro, Av. Carlos Chagas Filho - 373, Cidade Universitária, 21.941-902, Rio de Janeiro, RJ, Brazil.
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3
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Elkady G, Zhu J, Peng Q, Chen M, Liu X, Chen Y, Hu C, Chen H, Guo A. Isolation and whole protein characterization of species A and B bovine rotaviruses from Chinese calves. INFECTION GENETICS AND EVOLUTION 2021; 89:104715. [PMID: 33434703 DOI: 10.1016/j.meegid.2021.104715] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 10/14/2020] [Accepted: 01/06/2021] [Indexed: 10/22/2022]
Abstract
Rotaviruses (RVs) account for severe diarrhea in children and young animals globally. In the current study, the fecal samples of diarrheic calves from a beef farm in Inner Mongolia were screened for RVA by ELISA and RT-PCR, followed by culture of three positive RVA samples in the MA-104 cell line. After 10 blind passages, cytopathic effects (CPE) appeared as detachment, granulation, and clustering of the inoculated cells. The virus isolates were identified by RT-PCR (VP6 gene RVA) and ESI-LC-MS/MS for whole protein sequencing. The protein sequences demonstrated the presence of two strains from species A rotavirus and one RVB strain; RVA/Cow-tc/CHN/35333/2019/G6P[5] was mixed with one RVB strain (RVB/Cow-tc/CHN/35334/2019/G5P[3]) in two samples, and RVA/Cow-tc/CHN/10927/2019/G8P[7] was found in one sample. They are of genotype constellations (G6-P[5]-I2-R2-C2-M2-A3-N2-T6-E2-H3), (G8-P[7]-I5-R1-C1- M2-A1-N1-T1-E1-H1), and (G5-P[3]-I3-R5-C5-A5-N4-H5), respectively. Besides, phylogenetic analysis of the obtained sequences demonstrated viral evolution.
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Affiliation(s)
- Gehad Elkady
- The State Key Laboratory of Agricultural Microbiology, Wuhan 430070, China; College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Hubei Province China, Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Zhu
- The State Key Laboratory of Agricultural Microbiology, Wuhan 430070, China; College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Hubei Province China, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingjie Peng
- Wuhan Keqian Biology Co. Ltd, Wuhan 430023, China
| | - Ming Chen
- The State Key Laboratory of Agricultural Microbiology, Wuhan 430070, China; College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Hubei Province China, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Liu
- College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Hubei Province China, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingyu Chen
- The State Key Laboratory of Agricultural Microbiology, Wuhan 430070, China; College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Hubei Province China, Huazhong Agricultural University, Wuhan 430070, China; National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Changmin Hu
- The State Key Laboratory of Agricultural Microbiology, Wuhan 430070, China
| | - Huanchun Chen
- The State Key Laboratory of Agricultural Microbiology, Wuhan 430070, China; College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Hubei Province China, Huazhong Agricultural University, Wuhan 430070, China; National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Aizhen Guo
- The State Key Laboratory of Agricultural Microbiology, Wuhan 430070, China; College of Veterinary Medicine, Cooperative Innovation Centre of Substantial Pig Production, Hubei Province China, Huazhong Agricultural University, Wuhan 430070, China; National Animal Tuberculosis Para-Reference Laboratory (Wuhan) of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China; Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan 430070, China.
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Malakalinga JJ, Misinzo G, Msalya GM, Kazwala RR. Rotavirus Burden, Genetic Diversity and Impact of Vaccine in Children under Five in Tanzania. Pathogens 2019; 8:pathogens8040210. [PMID: 31671824 PMCID: PMC6963457 DOI: 10.3390/pathogens8040210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 09/27/2019] [Accepted: 10/07/2019] [Indexed: 01/17/2023] Open
Abstract
In Tanzania, rotavirus infections are responsible for 72% of diarrhea deaths in children under five. The Rotarix vaccine was introduced in early 2013 to mitigate rotavirus infections. Understanding the disease burden and virus genotype trends over time is important for assessing the impact of rotavirus vaccine in Tanzania. When assessing the data for this review, we found that deaths of children under five declined after vaccine introduction, from 8171/11,391 (72% of diarrhea deaths) in 2008 to 2552/7087 (36% of diarrhea deaths) in 2013. Prior to vaccination, the prevalence of rotavirus infections in children under five was 18.1–43.4%, 9.8–51%, and 29–41% in Dar es Salaam, Mwanza and Tanga, respectively, and after the introduction of vaccines, these percentages declined to 17.4–23.5%, 16–19%, and 10–29%, respectively. Rotaviruses in Tanzania are highly diverse, and include genotypes of animal origin in children under five. Of the genotypes, 10%, 28%, and 7% of the strains are untypable in Dar es Salaam, Tanga, and Zanzibar, respectively. Mixed rotavirus genotype infection accounts for 31%, 29%, and 12% of genotypes in Mwanza, Tanga and Zanzibar, respectively. The vaccine effectiveness ranges between 53% and 75% in Mwanza, Manyara and Zanzibar. Rotavirus vaccination has successfully reduced the rotavirus burden in Tanzania; however, further studies are needed to better understand the relationship between the wildtype strain and the vaccine strain as well as the zoonotic potential of rotavirus in the post-vaccine era.
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Affiliation(s)
- Joseph J Malakalinga
- Food and Microbiology Laboratory, Tanzania Bureau of Standards, Ubungo Area, Morogoro Road/Sam Nujoma Road, P.O. Box 9524, Dar es Salaam, Tanzania.
- Southern African Centre for Infectious Disease Surveillance (SACIDS), Africa Centre of Excellence for Infectious Diseases of Humans and Animals in Eastern and Southern Africa (ACE), Sokoine University of Agriculture (SUA), P.O. Box 3297, Chuo Kikuu, SUA, Morogoro, Tanzania.
| | - Gerald Misinzo
- Southern African Centre for Infectious Disease Surveillance (SACIDS), Africa Centre of Excellence for Infectious Diseases of Humans and Animals in Eastern and Southern Africa (ACE), Sokoine University of Agriculture (SUA), P.O. Box 3297, Chuo Kikuu, SUA, Morogoro, Tanzania.
| | - George M Msalya
- Department of Animal, Aquaculture and Range Sciences, College of Agriculture, Sokoine University of Agriculture, P.O. Box 3004, Morogoro, Tanzania.
| | - Rudovick R Kazwala
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3021, Morogoro, Tanzania.
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5
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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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Kondakova OA, Nikitin NA, Trifonova EA, Atabekov JG, Karpova OV. Rotavirus Vaccines: New Strategies and Approaches. ACTA ACUST UNITED AC 2018. [DOI: 10.3103/s0096392517040071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Molinari BLD, Possatti F, Lorenzetti E, Alfieri AF, Alfieri AA. Unusual outbreak of post-weaning porcine diarrhea caused by single and mixed infections of rotavirus groups A, B, C, and H. Vet Microbiol 2016; 193:125-32. [DOI: 10.1016/j.vetmic.2016.08.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 08/13/2016] [Accepted: 08/16/2016] [Indexed: 02/06/2023]
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8
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Genomic Sequence of the First Porcine Rotavirus Group H Strain in the United States. GENOME ANNOUNCEMENTS 2016; 4:4/2/e01763-15. [PMID: 26966223 PMCID: PMC4786673 DOI: 10.1128/genomea.01763-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The genomic sequence of a rotavirus group H was identified in the intestine of a diarrheal pig in the United States, designated RVH/Pig-wt/USA/MN9.65/2008/GxP[x].
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Marton S, Mihalov-Kovács E, Dóró R, Csata T, Fehér E, Oldal M, Jakab F, Matthijnssens J, Martella V, Bányai K. Canine rotavirus C strain detected in Hungary shows marked genotype diversity. J Gen Virol 2015; 96:3059-3071. [PMID: 26297005 DOI: 10.1099/jgv.0.000237] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Species C rotaviruses (RVC) have been identified in humans and animals, including pigs, cows and ferrets. In dogs, RVC strains have been reported anecdotally on the basis of visualization of rotavirus-like virions by electron microscopy combined with specific electrophoretic migration patterns of the genomic RNA segments. However, no further molecular characterization of these viruses was performed. Here, we report the detection of a canine RVC in the stool of a dog with enteritis. Analysis of the complete viral genome uncovered distinctive genetic features of the identified RVC strain. The genes encoding VP7, VP4 and VP6 were distantly related to those of other RVC strains and were putatively classified as G10, P8 and I8, respectively. The new strain was named RVC/Dog-wt/HUN/KE174/2012/G10P[8]. Phylogenetic analyses revealed that canine RVC was most closely related to bovine RVC strains with the exception of the NSP4 gene, which clustered together with porcine RVC strains. These findings provide further evidence for the genetic diversity of RVC strains.
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Affiliation(s)
- Szilvia Marton
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest 1143, Hungary
| | - Eszter Mihalov-Kovács
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest 1143, Hungary
| | - Renáta Dóró
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest 1143, Hungary
| | - Tünde Csata
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest 1143, Hungary
| | - Enikő Fehér
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest 1143, Hungary
| | - Miklós Oldal
- Virological Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary.,Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Ferenc Jakab
- Virological Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary.,Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Jelle Matthijnssens
- KU Leuven-University of Leuven, Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Vito Martella
- Department of Veterinary Public Health, University of Bari, S.p. per Casamassima km 3, 70010 Valenzano, Bari, Italy
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, Budapest 1143, Hungary
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Molinari BLD, Alfieri AF, Alfieri AA. Genetic variability of VP6, VP7, VP4, and NSP4 genes of porcine rotavirus group H detected in Brazil. Virus Res 2014; 197:48-53. [PMID: 25499297 DOI: 10.1016/j.virusres.2014.12.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 12/02/2014] [Accepted: 12/02/2014] [Indexed: 12/31/2022]
Abstract
Rotaviruses (RV) are a common cause of viral gastroenteritis in humans and animals. Despite the seven groups/species of RV (A-G), recently it was proposed the creation of a new RV group/specie H (RVH) based on VP6 sequence analysis. In this study we determined the VP6, VP7, VP4, and NSP4 nucleotide and deduced amino acid sequences of 6 (BR59-BR64) RVH-positive stool specimens obtained from piglets with diarrhea in Mato Grosso do Sul, Central-West region of Brazil in 2012, using RT-PCR assay. Based on the high sequence identities (>99%) of the VP6, VP4, VP7, and NSP4 genes among 5 of the studied fecal specimens (BR59-BR63), they are considered the same local rotavirus strain denominated RVH/BRA-1. In contrast, once that the fecal sample BR64 showed a relatively high difference (81.6% nt identity and 83.4% aa identity) in the VP7 sequence when compared to the other 5 specimens it was named RVH/BRA-2 strain. Comparative phylogenetic analysis showed that the 6 RVH strains do not cluster together with any available sequences of members of the established RV groups (RVA-RVG), however, seem to be related to RVB and RVG. These results confirm the presence of RVH in Brazil, demonstrate their genetic diversity, and provide new data that will assist in understanding the viral phylogeny and epidemiology, as well as the explanation of patterns of viral evolution and biological properties of RVH.
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Affiliation(s)
- Bruna Letícia Domingues Molinari
- Laboratory of Animal Virology, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Londrina, Parana, Brazil
| | - Alice Fernandes Alfieri
- Laboratory of Animal Virology, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Londrina, Parana, Brazil
| | - Amauri Alcindo Alfieri
- Laboratory of Animal Virology, Department of Veterinary Preventive Medicine, Universidade Estadual de Londrina, Londrina, Parana, Brazil.
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Abstract
Gut health is very important to get maximum returns in terms of weight gain and egg production. Enteric diseases such as poult enteritis complex (PEC) in turkeys do not allow their production potential to be achieved to its maximum. A number of viruses, bacteria, and protozoa have been implicated but the primary etiology has not been definitively established. Previously, electron microscopy was used to detect the presence of enteric viruses, which were identified solely on the basis of their morphology. With the advent of rapid molecular diagnostic methods and next generation nucleic acid sequencing, researchers have made long strides in identification and characterization of viruses associated with PEC. The molecular techniques have also helped us in identification of pathogens which were previously not known. Regional and national surveys have revealed the presence of several different enteric viruses in PEC including rotavirus, astrovirus, reovirus and coronavirus either alone or in combination. There may still be unknown pathogens that may directly or indirectly play a role in enteritis in turkeys. This review will focus on the role of turkey coronavirus, rotavirus, reovirus, and astrovirus in turkey enteritis.
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Lachapelle V, Sohal JS, Lambert MC, Brassard J, Fravalo P, Letellier A, L’Homme Y. Genetic diversity of group A rotavirus in swine in Canada. Arch Virol 2014; 159:1771-9. [DOI: 10.1007/s00705-013-1951-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 11/13/2013] [Indexed: 12/31/2022]
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Marthaler D, Rossow K, Culhane M, Collins J, Goyal S, Ciarlet M, Matthijnssens J. Identification, phylogenetic analysis and classification of porcine group C rotavirus VP7 sequences from the United States and Canada. Virology 2013; 446:189-98. [DOI: 10.1016/j.virol.2013.08.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 04/03/2013] [Accepted: 08/01/2013] [Indexed: 12/18/2022]
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14
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Kuzuya M, Fujii R, Hamano M, Kida K, Mizoguchi Y, Kanadani T, Nishimura K, Kishimoto T. Prevalence and molecular characterization of G1P[8] human rotaviruses possessing DS-1-like VP6, NSP4, and NSP5/6 in Japan. J Med Virol 2013; 86:1056-64. [DOI: 10.1002/jmv.23746] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2013] [Indexed: 01/17/2023]
Affiliation(s)
- Mitsutaka Kuzuya
- Department of Virology; Okayama Prefectural Institute for Environmental Science and Public Health; Okayama Japan
| | - Ritsushi Fujii
- Department of Virology; Okayama Prefectural Institute for Environmental Science and Public Health; Okayama Japan
| | - Masako Hamano
- Department of Virology; Okayama Prefectural Institute for Environmental Science and Public Health; Okayama Japan
| | - Koji Kida
- Department of Virology; Okayama Prefectural Institute for Environmental Science and Public Health; Okayama Japan
| | - Yoshinori Mizoguchi
- Department of Virology; Okayama Prefectural Institute for Environmental Science and Public Health; Okayama Japan
| | - Tomohisa Kanadani
- Okayama Medical Center of National Hospital Organization; Okayama; Japan
| | - Keiko Nishimura
- Okayama Medical Center of National Hospital Organization; Okayama; Japan
| | - Toshio Kishimoto
- Department of Virology; Okayama Prefectural Institute for Environmental Science and Public Health; Okayama Japan
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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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16
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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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17
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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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18
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VP6-sequence-based cutoff values as a criterion for rotavirus species demarcation. Arch Virol 2012; 157:1177-82. [PMID: 22430951 DOI: 10.1007/s00705-012-1273-3] [Citation(s) in RCA: 304] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 12/15/2011] [Indexed: 10/28/2022]
Abstract
Indirect immunofluorescence techniques targeting the rotavirus (RV) protein VP6 are used to differentiate RV species. The ICTV recognizes RV species A to E and two tentative species, F and G. A potential new RV species, ADRV-N, has been described. Phylogenetic trees and pairwise identity frequency graphs were constructed with more than 400 available VP6 sequences and seven newly determined VP6 sequences of RVD strains. All RV species were separated into distinct phylogenetic clusters. An amino acid sequence cutoff value of 53% firmly permitted differentiation of RV species, and ADRV-N was tentatively assigned to a novel RV species H (RVH).
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19
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Kuzuya M, Fujii R, Hamano M, Kida K, Kanadani T, Nishimura K, Kishimoto T. Molecular characterization of OP354-like P[8] (P[8]b subtype) human rotaviruses a species isolated in Japan. J Med Virol 2012; 84:697-704. [DOI: 10.1002/jmv.23224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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20
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Ghosh S, Kobayashi N. Whole-genomic analysis of rotavirus strains: current status and future prospects. Future Microbiol 2011; 6:1049-65. [DOI: 10.2217/fmb.11.90] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Studies on genetic diversity of rotaviruses have been primarily based on the genes encoding the antigenically significant VP7 and VP4 proteins. Since the rotavirus genome has 11 segments of RNA that are vulnerable to reassortment events, analyses of the VP7 and VP4 genes may not be sufficient to obtain conclusive data on the overall genetic diversity, or true origin of strains. In the last few years following the advent of the whole-genome-based genotype classification system, the whole genomes of at least 167 human group A rotavirus strains have been analyzed, providing a plethora of new and important information on the complex origin of strains, inter- and intra-genogroup reassortment events, animal–human reassortment events, zoonosis, and genetic linkages involving different group A rotavirus gene segments. In addition, the whole genomes of a limited number of human group B, C and novel group rotavirus strains have been analyzed. This article briefly reviews the available data on whole-genomic analysis of human rotavirus strains. The significance and future prospects of whole-genome-based studies are also discussed.
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Affiliation(s)
- Souvik Ghosh
- Department of Hygiene, Sapporo Medical University School of Medicine, S 1, W 17, Chuo-Ku, Sapporo, Hokkaido 060-8556, Japan
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21
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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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