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Xin Z, Li S, Lu X, Liu L, Gao Y, Hu F, Yu K, Ma X, Li Y, Huang B, Wu J, Guo X. Development and Clinical Application of a Molecular Assay for Four Common Porcine Enteroviruses. Vet Sci 2024; 11:305. [PMID: 39057989 PMCID: PMC11281614 DOI: 10.3390/vetsci11070305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
Porcine epidemic diarrhea virus (PEDV), porcine transmissible gastroenteritis virus (TGEV), porcine deltacoronavirus (PDCoV), and porcine rotavirus-A (PoRVA) are the four main pathogens that cause viral diarrhea in pigs, and they often occur in mixed infections, which are difficult to distinguish only according to clinical symptoms. Here, we developed a multiplex TaqMan-probe-based real-time RT-PCR method for the simultaneous detection of PEDV, TGEV, PDCoV, and PoRVA for the first time. The specific primers and probes were designed for the M protein gene of PEDV, N protein gene of TGEV, N protein gene of PDCoV, and VP7 protein gene of PoRVA, and corresponding recombinant plasmids were constructed. The method showed extreme specificity, high sensitivity, and excellent repeatability; the limit of detection (LOD) can reach as low as 2.18 × 102 copies/μL in multiplex real-time RT-PCR assay. A total of 97 clinical samples were used to compare the results of the conventional reverse transcription PCR (RT-PCR) and this multiplex real-time RT-PCR for PEDV, TGEV, PDCoV, and PoRVA detection, and the results were 100% consistent. Subsequently, five randomly selected clinical samples that tested positive were sent for DNA sequencing verification, and the sequencing results showed consistency with the detection results of the conventional RT-PCR and our developed method in this study. In summary, this study developed a multiplex real-time RT-PCR method for simultaneous detection of PEDV, TGEV, PDCoV, and PoRVA, and the results of this study can provide technical means for the differential diagnosis and epidemiological investigation of these four porcine viral diarrheic diseases.
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Affiliation(s)
- Zhonghao Xin
- Key Laboratory of Poultry Disease Diagnosis and Immunity in Shandong Province, Poultry Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.X.); (S.L.); (X.L.); (L.L.); (Y.G.); (F.H.); (K.Y.); (X.M.); (Y.L.); (B.H.)
| | - Shiheng Li
- Key Laboratory of Poultry Disease Diagnosis and Immunity in Shandong Province, Poultry Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.X.); (S.L.); (X.L.); (L.L.); (Y.G.); (F.H.); (K.Y.); (X.M.); (Y.L.); (B.H.)
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010020, China
| | - Xiao Lu
- Key Laboratory of Poultry Disease Diagnosis and Immunity in Shandong Province, Poultry Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.X.); (S.L.); (X.L.); (L.L.); (Y.G.); (F.H.); (K.Y.); (X.M.); (Y.L.); (B.H.)
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010020, China
| | - Liping Liu
- Key Laboratory of Poultry Disease Diagnosis and Immunity in Shandong Province, Poultry Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.X.); (S.L.); (X.L.); (L.L.); (Y.G.); (F.H.); (K.Y.); (X.M.); (Y.L.); (B.H.)
| | - Yuehua Gao
- Key Laboratory of Poultry Disease Diagnosis and Immunity in Shandong Province, Poultry Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.X.); (S.L.); (X.L.); (L.L.); (Y.G.); (F.H.); (K.Y.); (X.M.); (Y.L.); (B.H.)
| | - Feng Hu
- Key Laboratory of Poultry Disease Diagnosis and Immunity in Shandong Province, Poultry Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.X.); (S.L.); (X.L.); (L.L.); (Y.G.); (F.H.); (K.Y.); (X.M.); (Y.L.); (B.H.)
| | - Kexiang Yu
- Key Laboratory of Poultry Disease Diagnosis and Immunity in Shandong Province, Poultry Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.X.); (S.L.); (X.L.); (L.L.); (Y.G.); (F.H.); (K.Y.); (X.M.); (Y.L.); (B.H.)
| | - Xiuli Ma
- Key Laboratory of Poultry Disease Diagnosis and Immunity in Shandong Province, Poultry Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.X.); (S.L.); (X.L.); (L.L.); (Y.G.); (F.H.); (K.Y.); (X.M.); (Y.L.); (B.H.)
| | - Yufeng Li
- Key Laboratory of Poultry Disease Diagnosis and Immunity in Shandong Province, Poultry Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.X.); (S.L.); (X.L.); (L.L.); (Y.G.); (F.H.); (K.Y.); (X.M.); (Y.L.); (B.H.)
| | - Bing Huang
- Key Laboratory of Poultry Disease Diagnosis and Immunity in Shandong Province, Poultry Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.X.); (S.L.); (X.L.); (L.L.); (Y.G.); (F.H.); (K.Y.); (X.M.); (Y.L.); (B.H.)
| | - Jiaqiang Wu
- Shandong Key Laboratory of Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Science, Jinan 250100, China;
| | - Xiaozhen Guo
- Key Laboratory of Poultry Disease Diagnosis and Immunity in Shandong Province, Poultry Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (Z.X.); (S.L.); (X.L.); (L.L.); (Y.G.); (F.H.); (K.Y.); (X.M.); (Y.L.); (B.H.)
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2
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Malik YS, Ansari MI, Karikalan M, Sircar S, Selvaraj I, Ghosh S, Singh K. Molecular Characterization of Rotavirus C from Rescued Sloth Bears, India: Evidence of Zooanthroponotic Transmission. Pathogens 2023; 12:934. [PMID: 37513781 PMCID: PMC10384673 DOI: 10.3390/pathogens12070934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/20/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
The present study reports the detection and molecular characterisation of rotavirus C (RVC) in sloth bears (Melursus ursinus) rescued from urban areas in India. Based on an RVC VP6 gene-targeted diagnostic RT-PCR assay, 48.3% (42/87) of sloth bears tested positive for RVC infection. The VP6, VP7, and NSP4 genes of three sloth bear RVC isolates (UP-SB19, 21, and 37) were further analysed. The VP6 genes of RVC UP-SB21 and 37 isolates were only 37% identical. The sequence identity, TM-score from structure alignment, and selection pressure (dN/dS) of VP6 UP-SB37 with pig and human RVCs isolates were (99.67%, 0.97, and 1.718) and (99.01%, 0.93, and 0.0340), respectively. However, VP6 UP-SB21 has an identity, TM-score, and dN/dS of (84.38%, 1.0, and 0.0648) and (99.63%, 1.0, and 3.7696) with human and pig RVC isolates, respectively. The VP7 genes from UP-SB19 and 37 RVC isolates were 79.98% identical and shared identity, TM-score, and dN/dS of 88.4%, 0.76, and 5.3210, along with 77.98%, 0.77, and 4.7483 with pig and human RVC isolates, respectively. The NSP4 gene of UP-SB37 RVC isolates has an identity, TM-score, and dN/dS of 98.95%, 0.76, and 0.2907, along with 83.12%, 0.34, and 0.2133 with pig and human RVC isolates, respectively. Phylogenetic analysis of the nucleotide sequences of the sloth bear RVC isolates assigned the isolate UP-SB37 to genotype G12, I2 for RVC structural genes VP7 and VP6, and E1 for NSP4 genes, respectively, while isolates UP-SB19 and UP-SB21 were classified as genotype G13 and GI7 based on the structural gene VP7, respectively. The study suggests that the RVCs circulating in the Indian sloth bear population are highly divergent and might have originated from pigs or humans, and further investigation focusing on the whole genome sequencing of the sloth bear RVC isolate may shed light on the virus origin and evolution.
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Affiliation(s)
- Yashpal Singh Malik
- ICAR-Indian Veterinary Research Institute, Bareilly 243122, India
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana 141004, India
| | - Mohd Ikram Ansari
- ICAR-Indian Veterinary Research Institute, Bareilly 243122, India
- Department of Biosciences, Integral University, Lucknow 226026, India
| | - Mathesh Karikalan
- Centre for Wildlife Conservation Management and Disease Surveillance, ICAR-Indian Veterinary Research Institute, Bareilly 243122, India
| | - Shubhankar Sircar
- ICAR-Indian Veterinary Research Institute, Bareilly 243122, India
- Department of Animal Sciences, Washington State University, Pullman, WA 99163, USA
| | | | - Souvik Ghosh
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre P.O. Box 334, Saint Kitts and Nevis
| | - Kalpana Singh
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana 141004, India
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Joshi MS, Arya SA, Shinde MS, Ingle VC, Birade HS, Gopalkrishna V. Rotavirus C infections in asymptomatic piglets in India, 2009-2013: genotyping and phylogenetic analysis of all genomic segments. Arch Virol 2022; 167:2665-2675. [PMID: 36169718 DOI: 10.1007/s00705-022-05607-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 08/17/2022] [Indexed: 12/14/2022]
Abstract
Asymptomatic infection with rotavirus C (RVC) was observed in pigs in India, with a detection rate of 20%. Sequencing of the VP6, VP7, and NSP4 genes of RVC strains identified the genotypes I7/I10, G1, and E5, respectively. Full genome sequencing of one of these strains revealed that the genotypes of the VP4, VP1, VP2, VP3, NSP1, NSP2, NSP3, and NSP5 genes were P1, R1, C1, M3, A1, N5, T5, and H1, respectively. The detection of porcine RVC strains at two different locations in India at different time points strongly suggests that they are circulating continuously in the pig population through asymptomatic infections.
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Affiliation(s)
- Madhuri S Joshi
- Enteric Viruses Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune, 411 001, India.
| | - Shalu A Arya
- Enteric Viruses Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune, 411 001, India
| | - Manohar S Shinde
- Enteric Viruses Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune, 411 001, India
| | - Vijay C Ingle
- Department of Veterinary Microbiology and Animal Biotechnology, Nagpur Veterinary College, Nagpur, India
| | - Hemant S Birade
- Department of Animal Reproduction, Gynaecology and Obstetrics, Krantisinh Nana Patil College of Veterinary Science, Satara, India
| | - Varanasi Gopalkrishna
- Enteric Viruses Group, ICMR-National Institute of Virology, 20-A, Dr. Ambedkar Road, Pune, 411 001, India
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Truong TC, Nguyen TH, Kim W. Multiple reassortment and interspecies transmission events contribute to the diversity of porcine-like human rotavirus C strains detected in South Korea. Arch Virol 2022; 167:2163-2171. [PMID: 35840863 DOI: 10.1007/s00705-022-05528-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/25/2022] [Indexed: 11/02/2022]
Abstract
Globally, rotavirus C (RVC) causes diarrhoeal outbreaks, mainly in swine, with sporadic incidents in human, bovine, and canine populations. In this study, two human RVC strains, RVC/Human-wt/KOR/CAU13-1-77/2013 and RVC/Human-wt/KOR/CAU14-1-242/2014, were isolated in South Korea, and their complete genome sequences were compared with those of other human- and animal-origin RVC strains found worldwide. Genetic analysis revealed that these viruses have a G4-P[2]-I2-R2-C2-M3-A2-N2-T2-E2-H2 genotype constellation. Phylogenetic analysis indicated that these Korean RVC strains belong to the M3 lineage of the VP3 gene in human RVC from Japan and China and porcine RVC from Japan. These results suggest that RVC circulates in northeast Asia in both the human and porcine populations. These results also provide evidence of interspecies RVC reassortment events.
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Affiliation(s)
- Thoi Cong Truong
- Department of Microbiology, Chung-Ang University College of Medicine, 06974, Seoul, South Korea
| | | | - Wonyong Kim
- Department of Microbiology, Chung-Ang University College of Medicine, 06974, Seoul, South Korea.
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Hull JJA, Qi M, Montmayeur AM, Kumar D, Velasquez DE, Moon SS, Magaña LC, Betrapally N, Ng TFF, Jiang B, Marthaler D. Metagenomic sequencing generates the whole genomes of porcine rotavirus A, C, and H from the United States. PLoS One 2020; 15:e0244498. [PMID: 33373390 PMCID: PMC7771860 DOI: 10.1371/journal.pone.0244498] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023] Open
Abstract
The genus Rotavirus comprises eight species, designated A to H, and two recently identified tentative species I in dogs and J in bats. Species Rotavirus A, B, C and H (RVA, RVB, RVC and RVH) have been detected in humans and animals. While human and animal RVA are well characterized and defined, complete porcine genome sequences in the GenBank are limited compared to human strains. Here, we used a metagenomic approach to sequence the 11 segments of RVA, RVC and RVH strains from piglets in the United States (US) and explore the evolutionary relations of these RV species. Metagenomics identified Astroviridae, Picornaviridae, Caliciviridae, Coronoviridae in samples MN9.65 and OK5.68 while Picobirnaviridae and Arteriviridae were only identified in sample OK5.68. Whole genome sequencing and phylogenetic analyses identified multiple genotypes with the RVA of strain MN9.65 and OK5.68, with the genome constellation of G5/G9-P[7]/P[13]-I5/I5- R1/R1-C1-M1-A8-N1-T7-E1/E1-H1 and G5/G9-P[6]/P[7]-I5-R1/R1-C1-M1-A8-N1-T1/T7-E1/E1-H1, respectively. The RVA strains had a complex evolutionary relationship with other mammalian strains. The RVC strain OK5.68 had a genome constellation of G9-P[6]-I1-R1-C5-M6-A5-N1-T1-E1-H1, and shared an evolutionary relationship with porcine strains from the US. The RVH strains MN9.65 and OK5.68 had the genome constellation of G5-P1-I1-R1-C1-M1-A5-N1-T1-E4-H1 and G5-P1-I1-R1-C1-M1-A5-N1-T1-E1-H1, indicating multiple RVH genome constellations are circulating in the US. These findings allow us to understand the complexity of the enteric virome, develop improved screening methods for RVC and RVH strains, facilitate expanded rotavirus surveillance in pigs, and increase our understanding of the origin and evolution of rotavirus species.
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Affiliation(s)
- Jennifer J. A. Hull
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Mingpu Qi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas, United States of America
| | - Anna M. Montmayeur
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Deepak Kumar
- Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas, United States of America
| | - Daniel E. Velasquez
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Sung-Sil Moon
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Laura Cristal Magaña
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, United States of America
| | - Naga Betrapally
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, United States of America
| | - Terry Fei Fan Ng
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Baoming Jiang
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
| | - Douglas Marthaler
- Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas, United States of America
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, United States of America
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Costa FB, Flores PS, Amorim AR, Mendes GDS, Santos N. Porcine rotavirus C strains carrying human-like NSP4 and NSP5. Zoonoses Public Health 2020; 67:849-861. [PMID: 32418355 DOI: 10.1111/zph.12713] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 03/24/2020] [Accepted: 04/09/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND Rotavirus C (RVC) is an enteric pathogen that affects humans and animals around the world. METHODS In this study, we characterized the genetic diversity of RVC strains detected in asymptomatic Brazilian pigs by sequencing the NSP4, NSP5 and VP6 genes. RESULTS The results of reverse transcription polymerase chain reaction showed that 53 of 579 samples (9.2%) contained RVC. Positive samples were genotyped by sequencing gene segments NSP4, and NSP5. Most of the RCV strains encountered were classified into typically porcine genotypes: E1-H1. In two strains, BP182 and BP208, the NSP4 gene grouped with E2-RVC human strains with 94.2%-96.5% nucleotide identity, although the NSP5 gene was porcine-like (H1). In strain SD67, the NSP5 gene grouped with human H2-RVC with 92.5%-98.7% nucleotide identity and the NSP4 gene grouped with porcine strains (E1). Two strains (BP208 and SD67) were also genotyped by sequencing gene segment VP6. The VP6 gene grouped with porcine strains, I6 (89.3%-90.2% nucleotide identity) and I5 (88.7%-90.5% nucleotide identity), for strains BP208 and SD67, respectively. CONCLUSIONS These results are indicative of genomic reassortment between RVC strains of human and porcine origin. In recent years, the incidence of RVC infection among humans has increased significantly. It is important to measure the frequency of interspecies transmission in order to monitor the evolution of these viruses and to identify rearranged strains that may lead to an epidemic.
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Affiliation(s)
- Fábio Burack Costa
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Patrícia Soares Flores
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Ariane Ribeiro Amorim
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Gabriella da Silva Mendes
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
| | - Norma Santos
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil
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Joshi MS, Walimbe AM, Dilpak SP, Cherian SS, Gopalkrishna V. Whole-genome-based characterization of three human Rotavirus C strains isolated from gastroenteritis outbreaks in Western India and a provisional intra-genotypic lineage classification system. J Gen Virol 2019; 100:1055-1072. [DOI: 10.1099/jgv.0.001284] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Madhuri S. Joshi
- 1 Enteric Viruses Group, ICMR-National Institute of Virology, Pune, India
| | - Atul M. Walimbe
- 2 Bioinformatics Group, ICMR-National Institute of Virology, Pune, India
| | - Sanmati P. Dilpak
- 1 Enteric Viruses Group, ICMR-National Institute of Virology, Pune, India
| | - Sarah S. Cherian
- 2 Bioinformatics Group, ICMR-National Institute of Virology, Pune, India
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8
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Hunnam JC, Sloan S, McCowan CI, Glass E, Walker C. The racing pigeon (Columba livia domestica) industry in Victoria, Australia, and epidemiology of a novel Group A rotavirus outbreak. Transbound Emerg Dis 2019; 66:2058-2066. [PMID: 31140207 DOI: 10.1111/tbed.13254] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/21/2019] [Accepted: 05/20/2019] [Indexed: 01/17/2023]
Abstract
A novel Group A rotavirus, first identified clinically in racing, feral and fancy pigeons in Western Australia, had spread throughout Australia by March 2017. In December 2016, the putative index case of rotavirus in racing pigeons in the state of Victoria was confirmed at a regional bird sale, with rapid spread to peri-urban Melbourne, the capital city. A survey sent to approximately 400 Victorian pigeon fanciers identified eight (of 85 respondents) with a confirmed rotavirus infection in their loft(s). If a fancier had purchased live birds, either from the regional sale or from another source, there was a 13%-38% increased likelihood of the loft subsequently being confirmed rotavirus-positive. An increased loft-level risk of rotavirus was also positively associated with the number of neighbouring lofts within a 5-km radius of a home loft. It was concluded that rotavirus was primarily transmitted beyond the Victorian index case through the movement of live birds into a loft, either deliberately through bird purchase and/or inadvertently through the entry of pigeons from neighbouring lofts. As pigeon racing inherently requires consistent contact between birds from different lofts, vaccination is recommended as a primary method of rotavirus control in this unique industry.
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Affiliation(s)
| | - Sarah Sloan
- Agriculture Victoria, Melbourne, Victoria, Australia
| | | | - Emily Glass
- Department of Primary Industries and Regional Development, Perth, Western Australia, Australia
| | - Colin Walker
- Melbourne Bird Veterinary Clinic, Melbourne, Victoria, Australia
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9
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Trovão NS, Shepherd FK, Herzberg K, Jarvis MC, Lam HC, Rovira A, Culhane MR, Nelson MI, Marthaler DG. Evolution of rotavirus C in humans and several domestic animal species. Zoonoses Public Health 2019; 66:546-557. [PMID: 30848076 DOI: 10.1111/zph.12575] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 12/21/2018] [Accepted: 02/10/2019] [Indexed: 12/19/2022]
Abstract
Rotavirus C (RVC) causes enteric disease in multiple species, including humans, swine, bovines, and canines. To date, the evolutionary relationships of RVC populations circulating in different host species are poorly understood, owing to the low availability of genetic sequence data. To address this gap, we sequenced 45 RVC complete genomes from swine samples collected in the United States and Mexico. A phylogenetic analysis of each genome segment indicates that RVC populations have been evolving independently in human, swine, canine, and bovine hosts for at least the last century, with inter-species transmission events occurring deep in the phylogenetic tree, and none in the last 100 years. Bovine and canine RVC populations clustered together nine of the 11 gene segments, indicating a shared common ancestor centuries ago. The evolutionary relationships of RVC in humans and swine were more complex, due to the extensive genetic diversity and multiple RVC clades identified in pigs, which were not structured geographically. Topological differences between trees inferred for different genome segments occurred frequently, including at nodes deep in the tree, indicating that RVC's evolutionary history includes multiple reassortment events that occurred a long time ago. Overall, we find that RVC is evolving within host-defined lineages, but the evolutionary history of RVC is more complex than previously recognized due to the high genetic diversity of RVC in swine, with a common ancestor dating back centuries. Pigs may act as a reservoir host for RVC, and a source of the lineages identified in other species, including humans, but additional sequencing is needed to understand the full diversity of this understudied pathogen across multiple host species.
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Affiliation(s)
- Nídia S Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland.,Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York.,Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Frances K Shepherd
- Comparative and Molecular Biosciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Katerina Herzberg
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Matthew C Jarvis
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - Ham C Lam
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota.,Minnesota Supercomputing Institute, University of Minnesota, Saint Paul, Minnesota
| | - Albert Rovira
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Marie R Culhane
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
| | - Martha I Nelson
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland
| | - Douglas G Marthaler
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas.,Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota
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Rota RP, Palacios CA, Temprana CF, Argüelles MH, Mandile MG, Mattion N, Laimbacher AS, Fraefel C, Castello AA, Glikmann G. Evaluation of the immunogenicity of a recombinant HSV-1 vector expressing human group C rotavirus VP6 protein. J Virol Methods 2018; 256:24-31. [PMID: 29496429 DOI: 10.1016/j.jviromet.2018.02.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 02/21/2018] [Accepted: 02/25/2018] [Indexed: 12/01/2022]
Abstract
Group C Rotavirus (RVC) has been associated globally with sporadic outbreaks of gastroenteritis in children and adults. RVC also infects animals, and interspecies transmission has been reported as well as its zoonotic potential. Considering its genetic diversity and the absence of effective vaccines, it is important and necessary to develop new generation vaccines against RVC for both humans and animals. The aim of the present study was to develop and characterize an HSV-1-based amplicon vector expressing a human RVC-VP6 protein and evaluate the humoral immune response induced after immunizing BALB/c mice. Local fecal samples positive for RVC were used for isolation and sequencing of the vp6 gene, which phylogenetically belongs to the I2 genotype. We show here that cells infected with the HSV[VP6C] amplicon vector efficiently express the VP6 protein, and induced specific anti-RVC antibodies in mice immunized with HSV[VP6C], in a prime-boost schedule. This work highlights that amplicon vectors are an attractive platform for the generation of safe genetic immunogens against RVC, without the addition of external adjuvants.
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Affiliation(s)
- Rosana P Rota
- Laboratorio de Inmunología y Virología, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Buenos Aires, Argentina
| | - Carlos A Palacios
- Centro de Virología Animal (CEVAN), Instituto de Ciencia y Tecnología Dr. César Milstein, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Saladillo 2468, C1440FFX, Ciudad de Buenos Aires, Argentina
| | - C Facundo Temprana
- Laboratorio de Inmunología y Virología, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Marcelo H Argüelles
- Laboratorio de Inmunología y Virología, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Buenos Aires, Argentina
| | - Marcelo G Mandile
- Laboratorio de Inmunología y Virología, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Nora Mattion
- Centro de Virología Animal (CEVAN), Instituto de Ciencia y Tecnología Dr. César Milstein, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Saladillo 2468, C1440FFX, Ciudad de Buenos Aires, Argentina
| | - Andrea S Laimbacher
- Institute of Virology, University of Zurich, Winterthurerstrasse 266a, CH-8057, Zurich, Switzerland
| | - Cornell Fraefel
- Institute of Virology, University of Zurich, Winterthurerstrasse 266a, CH-8057, Zurich, Switzerland
| | - Alejandro A Castello
- Laboratorio de Inmunología y Virología, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Buenos Aires, Argentina
| | - Graciela Glikmann
- Laboratorio de Inmunología y Virología, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, B1876BXD, Bernal, Buenos Aires, Argentina.
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11
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Bhat S, Kattoor JJ, Malik YS, Sircar S, Deol P, Rawat V, Rakholia R, Ghosh S, Vlasova AN, Nadia T, Dhama K, Kobayashi N. Species C Rotaviruses in Children with Diarrhea in India, 2010-2013: A Potentially Neglected Cause of Acute Gastroenteritis. Pathogens 2018; 7:E23. [PMID: 29462971 PMCID: PMC5874749 DOI: 10.3390/pathogens7010023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 02/10/2018] [Accepted: 02/14/2018] [Indexed: 11/16/2022] Open
Abstract
All over the world, children and adults are severely affected by acute gastroenteritis, caused by one of the emerging enteric pathogens, rotavirus C (RVC). At present, no extensive surveillance program is running for RVC in India, and its prevalence is largely unknown except cases of local outbreaks. Here, we intended to detect the presence of RVC in diarrheic children visiting or admitted to hospitals in Haldwani (state of Uttarakhand, India), a city located in the foothills of the Himalayas. During 2010-2013, we screened 119 samples for RVC by an RVC VP6 gene-specific RT-PCR. Of these, 38 (31.93%) were found positive, which is higher than the incidence rates reported so far from India. The phylogenetic analysis of the derived nucleotide sequences from one of the human RVC (HuRVC) isolates, designated as HuRVC/H28/2013/India, showed that the study isolate belongs to genotype I2, P2 and E2 for RVC structural genes 6 and 4 (VP6, and VP4) and non-structural gene 4 (NSP4), respectively. Furthermore, the VP6 gene of HuRVC/H28/2013/India shows the highest similarity to a recently-reported human-like porcine RVC (PoRVC/ASM140/2013/India, KT932963) from India suggesting zoonotic transmission. We also report a full-length NSP4 gene sequence of human RVC from India. Under the One-health platforms there is a need to launch combined human and animal RVC surveillance programs for a better understanding of the epidemiology of RVC infections and for implementing control strategies.Reoviridae, possess 11 double-stranded segments of RNA that encode six structural viral proteins (VP1, VP2, VP3, VP4, VP6, VP7) and five/six non-structural proteins (NSP1-NSP5/6) [7]. Based on the antigenic properties of the major inner capsid protein (VP6), RVs are subdivided into eight well-characterized species (A-H) and two putative species viz. I and J [8-10]. Humans and other mammalian species are affected by species A, B, C and H rotaviruses and birds by species D, F and G, and species E has been reported exclusively in pigs [7,8,11-17]. The newly-proposed species I is reported in dogs [18] and cats [19], whereas species J is found in bats [10].
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Affiliation(s)
- Sudipta Bhat
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, India.
| | - Jobin Jose Kattoor
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, India.
| | - Yashpal Singh Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, India.
| | - Shubhankar Sircar
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, India.
| | - Pallavi Deol
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, India.
| | - Vinita Rawat
- Department of Microbiology, Government Medical College, Haldwani, Nainital, Uttarakhand 263 139, India.
| | - Ritu Rakholia
- Department of Pediatrics, Government Medical College, Haldwani, Nainital, Uttarakhand 263 139, India.
| | - Souvik Ghosh
- Department of Biomedical Sciences, One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, P.O. Box 334, Basseterre, St. Kitts, West Indies.
| | - 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.
| | - Touil Nadia
- Laboratoire de Biosécurité et de Recherche, Hôpital Militaire d'Instruction Med V de Rabat; 110 000 Morocco.
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243 122, India.
| | - Nobumichi Kobayashi
- Sapporo Medical University School of Medicine, Chuo-Ku, Sapporo 060-8556, Japan.
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12
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Suzuki T, Hasebe A. A provisional complete genome-based genotyping system for rotavirus species C from terrestrial mammals. J Gen Virol 2017; 98:2647-2662. [DOI: 10.1099/jgv.0.000953] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Tohru Suzuki
- Division of Viral Disease and Epidemiology, National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Ayako Hasebe
- Gifu Prefectural Central Livestock Health and Sanitation Office, Gifu, Japan
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13
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Tiku VR, Jiang B, Kumar P, Aneja S, Bagga A, Bhan MK, Ray P. First study conducted in Northern India that identifies group C rotavirus as the etiological agent of severe diarrhea in children in Delhi. Virol J 2017; 14:100. [PMID: 28558823 PMCID: PMC5450416 DOI: 10.1186/s12985-017-0767-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/22/2017] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Group C Rotavirus (RVC) is an enteric pathogen responsible for acute gastroenteritis in children and adults globally. At present there are no surveillance studies on group C Rotaviruses in India and therefore their prevalence in India remains unknown. The present study aimed to evaluate group C rotavirus infection among <5 years old children hospitalized with acute gastroenteritis in New Delhi. METHODS A total of 350 fecal specimens were collected during September 2013 to November 2014 from <5 years old diarrheal patients admitted at KSCH hospital, Delhi. The samples found negative for group A rotavirus (N = 180) by Enzyme immunoassay were screened for group C rotavirus by RT-PCR with VP6, VP7 and VP4 gene specific primers. The PCR products were further sequenced (VP6, VP7, VP4) and analyzed to ascertain their origin and G and P genotypes. RESULTS Six out of 180 (group A rotavirus negative) samples were found positive for group C rotavirus by VP6 gene specific RT-PCR, of which 3 were also found positive for VP7 and VP4 genes. Phylogenetic analysis of VP7 and VP4 genes of these showed them to be G4 and P[2] genotypes. Overall, the nucleotide sequence data (VP6, VP7 and VP4) revealed a close relationship with the human group C rotavirus with no evidence of animal ancestry. Interestingly, the nucleotide sequence analysis of various genes also indicated differences in their origin. While the identity matrix of VP4 gene (n = 3) showed high amino acid sequence identity (97.60 to 98.20%) with Korean strain, the VP6 gene (n = 6) showed maximum identity with Nigerian strain (96.40 to 97.60%) and VP7 gene (n = 3) with Bangladeshi and USA strains. This is true for all analyzed samples. CONCLUSION Our study demonstrated the group C rotavirus as the cause of severe diarrhea in young children in Delhi and provides insights on the origin of group C rotavirus genes among the local strains indicating their source of transmission. Our study also highlights the need for a simple and reliable diagnostic test that can be utilized to determine the disease burden due to group C rotavirus in India.
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Affiliation(s)
| | - Baoming Jiang
- Centers for Disease Control and Prevention, Atlanta, USA
| | - Praveen Kumar
- Kalawati Saran Children's Hospital, Lady Hardinge Medical College, New Delhi, India
| | - Satender Aneja
- Kalawati Saran Children's Hospital, Lady Hardinge Medical College, New Delhi, India
| | - Arvind Bagga
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Maharaj Kishen Bhan
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Pratima Ray
- Department of Biotechnology, Faculty of Science, Jamia Hamdard University, Hamdard Nagar, New Delhi, 110062, India.
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14
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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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15
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Niira K, Ito M, Masuda T, Saitou T, Abe T, Komoto S, Sato M, Yamasato H, Kishimoto M, Naoi Y, Sano K, Tuchiaka S, Okada T, Omatsu T, Furuya T, Aoki H, Katayama Y, Oba M, Shirai J, Taniguchi K, Mizutani T, Nagai M. Whole genome sequences of Japanese porcine species C rotaviruses reveal a high diversity of genotypes of individual genes and will contribute to a comprehensive, generally accepted classification system. INFECTION GENETICS AND EVOLUTION 2016; 44:106-113. [PMID: 27353186 DOI: 10.1016/j.meegid.2016.06.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 12/16/2022]
Abstract
Porcine rotavirus C (RVC) is distributed throughout the world and is thought to be a pathogenic agent of diarrhea in piglets. Although, the VP7, VP4, and VP6 gene sequences of Japanese porcine RVCs are currently available, there is no whole-genome sequence data of Japanese RVC. Furthermore, only one to three sequences are available for porcine RVC VP1-VP3 and NSP1-NSP3 genes. Therefore, we determined nearly full-length whole-genome sequences of nine Japanese porcine RVCs from seven piglets with diarrhea and two healthy pigs and compared them with published RVC sequences from a database. The VP7 genes of two Japanese RVCs from healthy pigs were highly divergent from other known RVC strains and were provisionally classified as G12 and G13 based on the 86% nucleotide identity cut-off value. Pairwise sequence identity calculations and phylogenetic analyses revealed that candidate novel genotypes of porcine Japanese RVC were identified in the NSP1, NSP2 and NSP3 encoding genes, respectively. Furthermore, VP3 of Japanese porcine RVCs was shown to be closely related to human RVCs, suggesting a gene reassortment event between porcine and human RVCs and past interspecies transmission. The present study demonstrated that porcine RVCs show greater genetic diversity among strains than human and bovine RVCs.
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Affiliation(s)
- Kazutaka Niira
- Tochigi Prefectural South District Animal Hygiene Service Center, Tochigi, Tochigi 328-0002, Japan
| | - Mika Ito
- Ishikawa Nanbu Livestock Hygiene Service Center, Kanazawa, Ishikawa 920-3101, Japan
| | - Tsuneyuki Masuda
- Kurayoshi Livestock Hygiene Service Center, Kurayoshi, Tottori 682-0017, Japan
| | - Toshiya Saitou
- Tochigi Prefectural Central District Animal Hygiene Service Center, Utsunomiya, Tochigi 321-0905, Japan
| | - Tadatsugu Abe
- Tochigi Prefectural Central District Animal Hygiene Service Center, Utsunomiya, Tochigi 321-0905, Japan
| | - Satoshi Komoto
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, Japan
| | - Mitsuo Sato
- Tochigi Prefectural Central District Animal Hygiene Service Center, Utsunomiya, Tochigi 321-0905, Japan
| | - Hiroshi Yamasato
- Kurayoshi Livestock Hygiene Service Center, Kurayoshi, Tottori 682-0017, 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
| | - 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
| | - 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
| | - Shinobu Tuchiaka
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Takashi Okada
- Research and Education Center for Prevention of Global Infectious Disease of Animal, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, 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
| | - Tetsuya Furuya
- 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
| | - Hiroshi Aoki
- Faculty of Veterinary Science, Nippon Veterinary and Life Science University, Musashino, Tokyo 180-8602, 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
| | - 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
| | - Koki Taniguchi
- Department of Virology and Parasitology, Fujita Health University School of Medicine, Toyoake, Aichi 470-1192, 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 Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.
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16
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Theuns S, Conceição-Neto N, Zeller M, Heylen E, Roukaerts IDM, Desmarets LMB, Van Ranst M, Nauwynck HJ, Matthijnssens J. Characterization of a genetically heterogeneous porcine rotavirus C, and other viruses present in the fecal virome of a non-diarrheic Belgian piglet. INFECTION GENETICS AND EVOLUTION 2016; 43:135-45. [PMID: 27184192 PMCID: PMC7172746 DOI: 10.1016/j.meegid.2016.05.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 04/15/2016] [Accepted: 05/12/2016] [Indexed: 12/31/2022]
Abstract
Next-generation sequencing (NGS) technologies are becoming increasingly accessible, leading to an expanded interest in the composition of the porcine enteric virome. In the present study, the fecal virome of a non-diarrheic Belgian piglet was determined. Although the virome of only a single piglet was analyzed, some interesting data were obtained, including the second complete genome of a pig group C rotavirus (RVC). This Belgian strain was only distantly related to the only other completely characterized pig RVC strain, Cowden. Its relatedness to RVC strains from other host species was also analyzed and the porcine strain found in our study was only distantly related to RVCs detected in humans and cows. The gene encoding the outer capsid protein VP7 belonged to the rare porcine G3 genotype, which might be serologically distinct from most other pig RVC strains. A putative novel RVC VP6 genotype was identified as well. A group A rotavirus strain also present in this fecal sample contained the rare pig genotype combination G11P[27], but was only partially characterized. Typical pig RVA genotypes I5, A8, and T7 were found for the viral proteins VP6, NSP1, and NSP3, respectively. Interestingly, the fecal virome of the piglet also contained an astrovirus and an enterovirus, of which the complete genomes were characterized. Results of the current study indicate that many viruses may be present simultaneously in fecal samples of non-diarrheic piglets. In this study, these viruses could not be directly associated with any disease, but still they might have had a potential subclinical impact on pig growth performance. The fast evolution of NGS will be a powerful tool for future diagnostics in veterinary practice. Its application will certainly lead to better insights into the relevance of many (sub)clinical enteric viral infections, that may have remained unnoticed using traditional diagnostic techniques. This will stimulate the development of new and durable prophylactic measures to improve pig health and production. The virome of a non-diarrheic Belgian piglet was determined. Porcine group C and A rotaviruses, and an astrovirus and enterovirus were found. The second complete genome of a pig group C rotavirus was fully characterized. The Belgian rotavirus C strain was only distantly related to pig strain Cowden. A putative novel genotype of VP6 of the RVC strains was detected.
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Affiliation(s)
- Sebastiaan Theuns
- Ghent University, Faculty of Veterinary Medicine, Department of Virology, Parasitology and Immunology, Laboratory of Virology, Merelbeke B-9820, Belgium.
| | - Nádia Conceição-Neto
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, B-3000 Leuven, Belgium; KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Clinical Virology, B-3000, Leuven, Belgium
| | - Mark Zeller
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, B-3000 Leuven, Belgium
| | - Elisabeth Heylen
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, B-3000 Leuven, Belgium
| | - Inge D M Roukaerts
- Ghent University, Faculty of Veterinary Medicine, Department of Virology, Parasitology and Immunology, Laboratory of Virology, Merelbeke B-9820, Belgium
| | - Lowiese M B Desmarets
- Ghent University, Faculty of Veterinary Medicine, Department of Virology, Parasitology and Immunology, Laboratory of Virology, Merelbeke B-9820, Belgium
| | - Marc Van Ranst
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Clinical Virology, B-3000, Leuven, Belgium
| | - Hans J Nauwynck
- Ghent University, Faculty of Veterinary Medicine, Department of Virology, Parasitology and Immunology, Laboratory of Virology, Merelbeke B-9820, Belgium
| | - Jelle Matthijnssens
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Laboratory of Viral Metagenomics, B-3000 Leuven, Belgium
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17
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Medici MC, Tummolo F, Martella V, Arcangeletti MC, De Conto F, Chezzi C, Fehér E, Marton S, Calderaro A, Bányai K. Analysis of the full genome of human group C rotaviruses reveals lineage diversification and reassortment. J Gen Virol 2016; 97:1888-1898. [PMID: 27154899 DOI: 10.1099/jgv.0.000497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Group C rotaviruses (RVC) are enteric pathogens of humans and animals. Whole-genome sequences are available only for few RVCs, leaving gaps in our knowledge about their genetic diversity. We determined the full-length genome sequence of two human RVCs (PR2593/2004 and PR713/2012), detected in Italy from hospital-based surveillance for rotavirus infection in 2004 and 2012. In the 11 RNA genomic segments, the two Italian RVCs segregated within separate intra-genotypic lineages showed variation ranging from 1.9 % (VP6) to 15.9 % (VP3) at the nucleotide level. Comprehensive analysis of human RVC sequences available in the databases allowed us to reveal the existence of at least two major genome configurations, defined as type I and type II. Human RVCs of type I were all associated with the M3 VP3 genotype, including the Italian strain PR2593/2004. Conversely, human RVCs of type II were all associated with the M2 VP3 genotype, including the Italian strain PR713/2012. Reassortant RVC strains between these major genome configurations were identified. Although only a few full-genome sequences of human RVCs, mostly of Asian origin, are available, the analysis of human RVC sequences retrieved from the databases indicates that at least two intra-genotypic RVC lineages circulate in European countries. Gathering more sequence data is necessary to develop a standardized genotype and intra-genotypic lineage classification system useful for epidemiological investigations and avoiding confusion in the literature.
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Affiliation(s)
- Maria Cristina Medici
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Fabio Tummolo
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Vito Martella
- Department of Veterinary Medicine, University Aldo Moro of Bari, Valenzano, Italy
| | - Maria Cristina Arcangeletti
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Flora De Conto
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Carlo Chezzi
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Enikő Fehér
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Szilvia Marton
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Adriana Calderaro
- Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
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Doan YH, Haga K, Fujimoto A, Fujii Y, Takai-Todaka R, Oka T, Kimura H, Yoshizumi S, Shigemoto N, Okamoto-Nakagawa R, Shirabe K, Shinomiya H, Sakon N, Katayama K. Genetic analysis of human rotavirus C: The appearance of Indian-Bangladeshi strain in Far East Asian countries. INFECTION GENETICS AND EVOLUTION 2016; 41:160-173. [PMID: 27071530 DOI: 10.1016/j.meegid.2016.03.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/17/2016] [Accepted: 03/25/2016] [Indexed: 11/30/2022]
Abstract
Rotaviruses C (RVCs) circulate worldwide as an enteric pathogen in both humans and animals. Most studies of their genetic diversity focus on the VP7 and VP4 genes, but the complete genomes of 18 human RVCs have been described in independent studies. The genetic background of the Far East Asian RVCs is different than other human RVCs that were found in India and Bangladesh. Recently, a RVC detected in 2010 in South Korea had genetic background similar to the Indian-Bangladeshi RVCs. This study was undertaken to determine the whole genome of eight Japanese RVCs detected in 2005-2012, and to compare them with other human and animal global RVCs to better understand the genetic background of contemporary Far East Asian RVC. By phylogenetic analysis, the human RVCs appeared to be distinct from animal RVCs. Among human RVCs, three lineage constellations had prolonged circulation. The genetic background of the Far East Asian RVC was distinguished from Indian-Bangladeshi RVC as reported earlier. However, we found one Japanese RVC in 2012 that carried the genetic background of Indian-Bangladeshi RVC, whereas the remaining seven Japanese RVCs carried the typical genetic background of Far East Asian RVC. This is the first report of the Indian-Bangladeshi RVC in Japan. With that observation and the reassortment event of human RVCs in Hungary, our study indicates that the RVCs are spreading from one region to another.
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Affiliation(s)
- Yen Hai Doan
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kei Haga
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Akira Fujimoto
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshiki Fujii
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Reiko Takai-Todaka
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tomoichiro Oka
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Naoki Shigemoto
- Hiroshima Prefectural Technology Research Institute, Hiroshima, Japan
| | | | - Komei Shirabe
- Yamaguchi Prefectural Institute of Public Health and Environment, Yamaguchi, Japan
| | - Hiroto Shinomiya
- Ehime Prefectural Institute of Public Health and Environmental Science, Ehime, Japan
| | - Naomi Sakon
- Osaka Prefectural Institute of Public Health, Osaka, Japan
| | - Kazuhiko Katayama
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan.
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Zhirakovskaia E, Tikunov A, Klemesheva V, Loginovskikh N, Netesov S, Tikunova N. First genetic characterization of rotavirus C in Russia. INFECTION GENETICS AND EVOLUTION 2016; 39:1-8. [DOI: 10.1016/j.meegid.2016.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 12/18/2015] [Accepted: 01/04/2016] [Indexed: 11/26/2022]
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Dóró R, Farkas SL, Martella V, Bányai K. Zoonotic transmission of rotavirus: surveillance and control. Expert Rev Anti Infect Ther 2015; 13:1337-50. [DOI: 10.1586/14787210.2015.1089171] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Lobo PDS, Guerra SDFDS, Siqueira JAM, Soares LDS, Gabbay YB, Linhares AC, Mascarenhas JDP. Phylogenetic analysis of human group C rotavirus in hospitalized children with gastroenteritis in Belém, Brazil. J Med Virol 2015; 88:728-33. [PMID: 26369400 DOI: 10.1002/jmv.24379] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2015] [Indexed: 11/10/2022]
Abstract
Group C rotavirus (RVC) is potentially an important pathogen associated with acute gastroenteritis (AG), especially in outbreaks. This study aims to detect and molecularly characterize RVC in hospitalized children with AG in Belém, Brazil. From May 2008 to April 2011, 279 stools were subjected to reverse-transcription polymerase chain reaction targeting VP7, VP6, VP4, and NSP4 genes. RVC positivity rate was 2.1% (6/279) and phylogenetic analysis of positive samples yields genotype G4-P[2]-I2-E2. No evidence of zoonotic transmission and VP7 gene demonstrated close relationship with Asian strains. RVC surveillance is worth to expand information on evolutionary and epidemiological features of this virus.
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Complete Genome Sequence of Rotavirus Group C Isolated in South Korea. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01068-15. [PMID: 26404599 PMCID: PMC4582575 DOI: 10.1128/genomea.01068-15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Rotavirus group C is the major etiological agent associated with acute gastroenteritis in all human age groups. Here, we report the complete genome sequence of human group C rotavirus (GpC-RV) isolated in South Korea.
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23
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Whole-Genome Sequences of Two Rare Human Group C Rotavirus Strains Isolated from Two Cases of Acute Gastroenteritis. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01014-15. [PMID: 26358598 PMCID: PMC4566180 DOI: 10.1128/genomea.01014-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
This is a report of the complete genomic sequences of two rare group C rotavirus strains RVC/SZ94/CHN/2011 and RVC/SZ272/CHN/2011, isolated from two cases of acute gastroenteritis in Shenzhen, southern China, in 2011. These two strains display a close genetic relationship to 2007 Chinese strain YNR001 and 2008 Japanese strain BK0830.
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24
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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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25
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Dhama K, Saminathan M, Karthik K, Tiwari R, Shabbir MZ, Kumar N, Malik YS, Singh RK. Avian rotavirus enteritis - an updated review. Vet Q 2015; 35:142-58. [PMID: 25917772 DOI: 10.1080/01652176.2015.1046014] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Rotaviruses (RVs) are among the leading causes of enteritis and diarrhea in a number of mammalian and avian species, and impose colossal loss to livestock and poultry industry globally. Subsequent to detection of rotavirus in mammalian hosts in 1973, avian rotavirus (AvRV) was first reported in turkey poults in USA during 1977 and since then RVs of group A (RVA), D (RVD), F (RVF) and G (RVG) have been identified around the globe. Besides RVA, other AvRV groups (RVD, RVF and RVG) may also contribute to disease. However, their significance has yet to be unraveled. Under field conditions, co-infection of AvRVs occurs with other infectious agents such as astroviruses, enteroviruses, reoviruses, paramyxovirus, adenovirus, Salmonella, Escherichia coli, cryptosporidium and Eimeria species prospering severity of disease outcome. Birds surviving to RV disease predominantly succumb to secondary bacterial infections, mostly E. coli and Salmonella spp. Recent developments in molecular tools including state-of-the-art diagnostics and vaccine development have led to advances in our understanding towards AvRVs. Development of new generation vaccines using immunogenic antigens of AvRV has to be explored and given due importance. Till now, no effective vaccines are available. Although specific as well as sensitive approaches are available to identify and characterize AvRVs, there is still need to have point-of-care detection assays to review disease burden, contemplate new directions for adopting vaccination and follow improvements in public health measures. This review discusses AvRVs, their epidemiology, pathology and pathogenesis, immunity, recent trends in diagnostics, vaccines, therapeutics as well as appropriate prevention and control strategies.
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Affiliation(s)
- Kuldeep Dhama
- a Division of Pathology , Indian Veterinary Research Institute , Izatnagar , Bareilly 243122 , India
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26
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Moutelíková R, Prodělalová J, Dufková L. Diversity of VP7, VP4, VP6, NSP2, NSP4, and NSP5 genes of porcine rotavirus C: phylogenetic analysis and description of potential new VP7, VP4, VP6, and NSP4 genotypes. Arch Virol 2015; 160:1715-27. [PMID: 25951969 DOI: 10.1007/s00705-015-2438-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 04/23/2015] [Indexed: 11/30/2022]
Abstract
Rotavirus C (RVC) is a cause of gastroenteritis in swine and has a worldwide distribution. A total of 448 intestinal or faecal samples from pigs of all ages were tested for viruses causing gastroenteritis. RVC was detected in 118 samples (26.3%). To gain information on virus diversity, the complete coding nucleotide sequences of the VP7, VP4, VP6, NSP2, NSP4, and NSP5 genes of seven RVC strains were determined. Phylogenetic analysis of VP7 nucleotide sequence divided studied Czech strains into six G genotypes (G1, G3, G5-G7, and a newly described G10 genotype) based on an 85% identity cutoff value at the nucleotide level. Analysis of the VP4 gene revealed low nucleotide sequence identities between two Czech strains and other porcine (72.2-75.3%), bovine (74.1-74.6%), and human (69.1-69.3%) RVC strains. Thus, we propose that those two Czech porcine strains comprise a new RVC VP4 genotype, P8. Analysis of the VP6 gene showed 79.9-86.8% similarity at the nucleotide level between the Czech strains and other porcine RVC strains. According to the 87% identity cutoff value, we propose the existence of three new RVC VP6 genotypes, I8-I10. Analysis of the NSP4 gene divided porcine RVC strains into two clusters (the E1 genotype and the new E4 genotype, based on an 85% nucleotide sequence identity cutoff value). Our results indicate a degree of high genetic heterogeneity, not only in the variable VP7 and VP4 genes encoding the outer capsid proteins, but also in more-conserved genes encoding the inner capsid protein VP6 and the non-structural proteins NSP2, NSP4, and NSP5. This emphasizes the need for a whole-genome-sequence-based classification system.
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Affiliation(s)
- Romana Moutelíková
- Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic,
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27
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Marton S, Deák J, Dóró R, Csata T, Farkas SL, Martella V, Bányai K. Reassortant human group C rotaviruses in Hungary. INFECTION GENETICS AND EVOLUTION 2015; 34:410-4. [PMID: 25958136 DOI: 10.1016/j.meegid.2015.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 04/09/2015] [Accepted: 05/06/2015] [Indexed: 10/23/2022]
Affiliation(s)
- Szilvia Marton
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Judith Deák
- Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary
| | - Renáta Dóró
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Tünde Csata
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Szilvia L Farkas
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Vito Martella
- Department of Veterinary Medicine, University of Bari Aldo Moro, Valenzano, Italy
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21, H-1143 Budapest, Hungary.
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Phylogenetic analysis of human group C rotavirus circulating in Brazil reveals a potential unique NSP4 genetic variant and high similarity with Asian strains. Mol Genet Genomics 2014; 290:969-86. [PMID: 25501310 DOI: 10.1007/s00438-014-0971-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 11/25/2014] [Indexed: 01/23/2023]
Abstract
Group C rotaviruses (RVC) cause gastroenteritis in humans and animals worldwide, and the evidence for a possible zoonotic role has been recently provided. To gain information on the genetic diversity and relationships between human and animal RVC, we sequenced the VP4, VP7, and NSP4 genes of 12, 19, and 15 human strains, respectively, detected in São Paulo state during historical (1988 and 1993) and recent (2007 and 2008) Brazilian rotavirus surveillance. All RVC strains analyzed in the present study grouped into human genotype (G4-P[2]-E2), and did not show any evidence of animal ancestry. Phylogenetic analysis showed that RVC samples detected in 1988 and 1993 clustered together with strains from distinct continents, indicating that historical RVC strains circulating in São Paulo were closely related to those strains circulating worldwide. All three genes (VP7, VP4 and NSP4) of São Paulo RVC strains isolated in 2007-2008 exhibited close phylogenetic relationship with human RVC strains isolated in China and Japan, suggesting that they are genetically linked, and that a gene flow could be occurring between this Asian countries and Brazil. We identified two distinct clusters in the NSP4 phylogenetic tree. One cluster formed exclusively by human Brazilian strains detected in 1997 and 2003-2004 in Rio de Janeiro, Bahia, and Rio Grande do Sul states (Subgroup II) previously described in a different study, that displayed low sequence identities to other human strains formerly published, and to the Brazilian RVC strains (Subgroup I) characterized in the present study. These data suggests the circulation of two genetic profiles of the NSP4 gene in Brazil. High sequence diversity in NSP4 gene was previously reported in Asia, and additional diversity in NSP4 RVC strains spreading in the world should be expected. More in-depth molecular and epidemiological analysis of human RVC throughout the world will be needed to understand their diversity and clarify their evolution, as well as to develop classifications schemes.
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Analysis of genetic divergence among strains of porcine rotavirus C, with focus on VP4 and VP7 genotypes in Japan. Virus Res 2014; 197:26-34. [PMID: 25499298 DOI: 10.1016/j.virusres.2014.12.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 12/01/2014] [Accepted: 12/02/2014] [Indexed: 11/20/2022]
Abstract
Porcine rotavirus C (RVC) has been often detected in sporadic cases or outbreaks of diarrhoea in suckling and weaned pigs. Surveillance studies of RVCs have demonstrated high prevalence in the United States, and Japan, and some other countries. To date, the zoonotic impact and pathogenicity of RVCs are not well understood, and only a few complete sequences of RVCs are available. The aim of this study was to perform sequence and phylogenetic analyses for the VP4 and VP7 genes of the 22 porcine RVCs identified in Japan from 2002 to 2010. The genetic classification of the VP4 genes of the 22 porcine RVCs revealed the presence of six clusters including one cluster each from human and bovine RVCs with a cut-off value of 80%. In addition, VP7 genes of the 22 porcine RVCs were grouped into four of the seven known clusters on the basis of cut-off values of 85% at the nucleotide level reported previously. The data presented here demonstrate that multiple porcine RVC strains with distinctive genotypes based on a combination of the VP4 and VP7 genes are widely distributed and circulated among farms throughout Japan. According to establishment of dual genetic classification for VP4 and VP7 genotypes of porcine RVCs, furthermore, we discovered a possible event of gene reassortment between different rotavirus strains from the same farm. Our findings should advance the understanding of the evolution and pathogenicity of RVCs.
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30
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Phylogenetic characterization of VP6 gene (inner capsid) of porcine rotavirus C collected in Japan. INFECTION GENETICS AND EVOLUTION 2014; 26:223-7. [PMID: 24929122 DOI: 10.1016/j.meegid.2014.05.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 05/16/2014] [Accepted: 05/22/2014] [Indexed: 11/22/2022]
Abstract
Porcine rotavirus C (RVC) has been often detected in sporadic cases or outbreaks of diarrhea in suckling and weaned pigs. Previous surveillance studies using both enzyme-linked immunosorbent assays and reverse-transcription polymerase chain reaction in some countries including Japan and the United States have demonstrated a high prevalence of porcine RVCs. In order to understand the phylogenetic relatedness of RVCs, we performed genetic analysis of VP6 gene encoding inner capsid protein by using 22 porcine RVC strains collected in Japan from 2002 to 2010. Comparative analyses of the VP6 nucleotide and amino acid sequences from these porcine RVCs exhibited lower sequence identities than those from human and bovine RVCs. The phylogenetic analysis of VP6 gene of RVC indicated the presence of seven clusters (tentatively assigned I1-I7) according to host species with cut-off values of 87% at the nucleotide level, and VP6 genes of porcine RVCs were divided into five genotypes. These findings indicate that multiple porcine RVC strains with distinctive genotypes are broadly spreading and circulating among farms in Japan. Our data may provide important insights in understanding evolutionary dynamics of RVCs.
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Lorenzetti E, Stipp DT, Possatti F, Campanha JE, Alfieri AF, Alfieri AA. Diarrhea outbreaks in suckling piglets due to rotavirus group C single and mixed (rotavirus groups A and B) infections. PESQUISA VETERINARIA BRASILEIRA 2014. [DOI: 10.1590/s0100-736x2014000500001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Porcine group A rotavirus (PoRVA) is a major cause of neonatal diarrhea in suckling and recently weaned piglets worldwide. The involvement of non-group A rotavirus in cases of neonatal diarrhea in piglets are sporadic. In Brazil there are no reports of the porcine rotavirus group C (PoRVC) as etiologic agent of the diarrhea outbreaks in piglets. The aim of this study was to describe the identification of rotavirus group C in single and in mixed infection with rotavirus groups A and B in three neonatal diarrhea outbreaks in suckling (<21-day-old) piglets, with 70% to 80% and 20% to 25% of morbidity and lethality rates, respectively, in three pig herds located in the state of Santa Catarina, Brazil. The diagnosis of PoRV in the diarrheic fecal samples was performed using polyacrylamide gel electrophoresis (PAGE) to identify the presence of porcine rotavirus groups A, B (PoRVB), and C, and by RT-PCR (PoRVA and PoRVC) and semi-nested (SN)-PCR (PoRVB) to partially amplify the VP4 (VP8*)-VP7, NSP2, and VP6 genes of PoRVA, PoRVB, and PoRVC, respectively. One RT-PCR (PoRVA and PoRVC) and SN-PCR (PoRVB) product of each group of rotavirus of each diarrhea outbreak was submitted to nucleotide (nt) sequence analysis. Based on the PAGE technique, 4 (25%) and 1 (6.25%) of the 16 diarrheic fecal samples evaluated in the first outbreak presented PoRVA and PoRVC electropherotype, respectively, and 11 (68.75%) were negative. In the second outbreak, 3 (42.85%) of the 7 fecal samples evaluated presented PoRVA electropherotype, and in 3 (42.85%) and in 1 (14.3%) fecal samples were detected inconclusive and negative results, respectively. Three (30%) of the 10 fecal samples of the third outbreak presented PoRVC electropherotype; 5 (50%) and 2 (20%) samples showed negative and inconclusive results, respectively. Based on the RT-PCR and SN-PCR assays in the first neonatal diarrhea outbreak, PoRVC was detected in 13 (81.2%) of the 16 diarrheic fecal samples evaluated. PoRVC single infection was identified in 4 (25%) of these samples and mixed infections with PoRVA and PoRVB in 9 (56.2%) fecal samples. All of the seven diarrheic fecal samples evaluated from the second neonatal diarrhea outbreak were positive for PoRVC, whereas its mixed infection with other PoRV groups was detected in 4 (57.2%) samples. In the third outbreak, PoRVC in single infection was detected in all of the 10 diarrheic fecal samples analyzed. In the nt sequence analysis, the PoRVA strains of the first and second outbreaks demonstrated higher nt identity with G4P[6] and G9P[23] genotypes, respectively. The PoRVB strains (first and second outbreaks) and the PoRVC strains (first, second, and third outbreaks) showed higher nt identity and clustered in the phylogenetic tree with PoRVB and PoRVC strains that belong to the N4 and I1 genotypes, respectively. This is the first description in Brazil of the involvement of PoRVC in the etiology of diarrhea outbreaks in suckling piglets. The results of this study demonstrated that PoRVC, in both single and mixed infections, is an important enteropathogen involved in neonatal diarrhea outbreaks in piglets and that the use of more sensitive diagnostic techniques allows the identification of mixed infections involving two or even three groups of PoRV, which may be more common than previously reported.
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Affiliation(s)
| | - Danilo T. Stipp
- Universidade Estadual de Londrina, Brazil; Universidade Federal da Paraíba, Brazil
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Mawatari T, Hirano K, Tsunemitsu H, Suzuki T. Whole-genome analysis of bovine rotavirus species C isolates obtained in Yamagata, Japan, 2003–2010. J Gen Virol 2014; 95:1117-1125. [DOI: 10.1099/vir.0.062166-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
An epidemic of diarrhoea in adult cows occurred at a total of 105 dairy farms in Yamagata Prefecture, Japan, between 2003 and 2010. Reverse transcription-PCR diagnostic tests revealed the presence of bovine rotavirus species C (RVCs) in samples from each of six farms (5.7 %). In this study, we determined the full-length nucleotide sequences of 11 RNA segments from six bovine RVC strains and investigated genetic diversity among them, including two bovine RVC strains identified in a previous study. Comparisons of all segmental nucleotide and the deduced amino acid sequences among bovine RVCs indicated high identities across all genes except for the VP4 gene. Phylogenetic analysis of each gene revealed that the six bovine RVCs belonged to a bovine cluster distinct from human and porcine RVCs. Bovine RVC strains could be clearly divided into two lineages of the VP4 genes. The nucleotide sequence identity for VP4 genes between lineage I and II was 83.7–84.8 %. Moreover, bovine RVC strains belonging to lineage I exhibited one amino acid deletion and three amino acid insertions, which differed for those strains belonging to lineage II. Our data suggest that multiple bovine RVCs originated from a common ancestor, but had different genetic backgrounds, not only in Yamagata Prefecture but also in the rest of Japan.
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Affiliation(s)
- Takahiro Mawatari
- Yamagata Prefectural Central Livestock Health and Sanitation Office, Yamagata, 990-2161 Japan
| | - Kaori Hirano
- Yamagata Prefectural Central Livestock Health and Sanitation Office, Yamagata, 990-2161 Japan
| | - Hiroshi Tsunemitsu
- Dairy Hygiene Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Hokkaido, 062-0045 Japan
| | - Tohru Suzuki
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, 305-0856 Japan
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Moutelíková R, Prodělalová J, Dufková L. Prevalence study and phylogenetic analysis of group C porcine rotavirus in the Czech Republic revealed a high level of VP6 gene heterogeneity within porcine cluster I1. Arch Virol 2013; 159:1163-7. [PMID: 24212886 DOI: 10.1007/s00705-013-1903-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 10/18/2013] [Indexed: 12/15/2022]
Abstract
Group C rotavirus (RVC) has been described to be a causative agent of gastroenteritis in humans and animals. In the current study, the presence of porcine RVC was confirmed in 25.6 % of 293 porcine faecal samples collected from seven Czech farms. A significantly larger (p < 0.05) number of RVC-positive samples was detected in groups of finisher pigs and post-weaning piglets (4-12 weeks of age). Phylogenetic analysis of nine RVC-positive Czech strains and their comparison with available sequence data for the gene encoding RVC group antigen VP6 revealed two separate lineages within porcine cluster I1.
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Affiliation(s)
- Romana Moutelíková
- Department of Virology, Veterinary Research Institute, Hudcova 70, 621 00, Brno, Czech Republic,
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Kumazaki M, Usuku S. Epidemiological and genetic analysis of human group C rotaviruses isolated from outbreaks of acute gastroenteritis in Yokohama, Japan, between 2006 and 2012. Arch Virol 2013; 159:761-71. [PMID: 24154950 DOI: 10.1007/s00705-013-1894-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 10/10/2013] [Indexed: 02/01/2023]
Abstract
Group C rotavirus (GCRV) infection has been described in several parts of the world, predominantly as sporadic cases of acute gastroenteritis. Little is known about the yearly changes in the GCRV strains from diarrheal outbreaks. Stool samples collected from outbreaks of acute gastroenteritis in Yokohama, Japan, between 2006 and 2012 that were negative for norovirus, sapovirus, and group A rotavirus, were screened for GCRV using a reverse passive hemagglutination method. The GCRV strains were characterized by nucleotide sequence and phylogenetic analysis of their VP6, VP7, VP4, and NSP4 genes. Samples from nine of 735 outbreaks in Yokohama (1 %) contained GCRV, and eight of these outbreaks occurred in primary schools. The nucleotide sequences of the strains detected in this study were more closely related to Asian strains than to those from other regions of the world. The nucleotide sequences of the VP7 gene in these nine strains differed, and yearly changes were observed in the amino acid sequences of the VP4 genes. Phylogenetic trees constructed using the nucleotide sequences of the VP6, VP7, VP4, and NSP4 genes showed that sublineage S1 has divided into S1-1 and S1-2 in the VP4 gene only. Our results confirm that the prevalent strains of GCRV change yearly in Yokohama. This is the first study to demonstrate GCRV-associated gastroenteritis outbreaks in Yokohama, Japan.
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Affiliation(s)
- Makoto Kumazaki
- Department of Testing and Research, Yokohama City Institute of Health, Takigashira 1-2-17, Isogo-ku, Yokohama, Kanagawa, 235-0012, Japan,
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Baek IH, Than VT, Kim H, Lim I, Kim W. Full genomic characterization of a group C rotavirus isolated from a child in south Korea. J Med Virol 2013; 85:1478-84. [DOI: 10.1002/jmv.23587] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2013] [Indexed: 11/11/2022]
Affiliation(s)
- In Hyuk Baek
- Department of Microbiology and Research Center for Medical Sciences; Chung-Ang University College of Medicine; Seoul South Korea
| | - Van Thai Than
- Department of Microbiology and Research Center for Medical Sciences; Chung-Ang University College of Medicine; Seoul South Korea
| | - Hakyoung Kim
- Department of Pediatrics; Chung-Ang University College of Medicine; Seoul South Korea
| | - Inseok Lim
- Department of Pediatrics; Chung-Ang University College of Medicine; Seoul South Korea
| | - Wonyong Kim
- Department of Microbiology and Research Center for Medical Sciences; Chung-Ang University College of Medicine; Seoul South Korea
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Soma J, Tsunemitsu H, Miyamoto T, Suzuki G, Sasaki T, Suzuki T. Whole-genome analysis of two bovine rotavirus C strains: Shintoku and Toyama. J Gen Virol 2013; 94:128-135. [DOI: 10.1099/vir.0.046763-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rotavirus C (RVC) has been detected frequently in epidemic cases and/or outbreaks of diarrhoea in humans and animals worldwide. Because it is difficult to cultivate RVCs serially in cell culture, the sequence data available for RVCs are limited, despite their potential economical and epidemiological impact. Although whole-genome sequences of one porcine RVC and seven human RVC strains have been analysed, this has not yet been done for a bovine RVC strain. In the present study, we first determined the nucleotide sequences for five as-yet underresearched genes, including the NSP4 gene, from a cultivable bovine RVC, the Shintoku strain, identified in Hokkaido Prefecture, Japan, in 1991. In addition, we elucidated the ORF sequences of all segments from another bovine RVC, the Toyama strain, detected in Toyama Prefecture, Japan, in 2010, in order to investigate genetic divergence among bovine RVCs. Comparison of segmental nucleotide and deduced amino acid sequences among RVCs indicates high identity among bovine RVCs and low identity between human and porcine RVCs. Phylogenetic analysis of each gene showed that the two bovine RVCs belong to a cluster distinct from human and porcine RVCs. These data demonstrate that RVCs can be classified into different genotypes according to host species. Moreover, RVC NSP1, NSP2 and VP1 amino acid sequences contain a unique motif that is highly conserved among rotavirus A (RVA) strains and, hence, several proteins from bovine RVCs are suggested to play important roles that are similar to those of RVAs.
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Affiliation(s)
- Junichi Soma
- Research and Development Section, Institute of Animal Health, JA Zen-noh (National Federation of Agricultural Cooperative Associations), Chiba 285-0043, Japan
| | - Hiroshi Tsunemitsu
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki 305-0856, Japan
| | - Takeshi Miyamoto
- Toyama Prefectural Tobu Livestock Hygiene Service Center, Toyama 939-3536, Japan
| | - Goro Suzuki
- Research and Development Section, Institute of Animal Health, JA Zen-noh (National Federation of Agricultural Cooperative Associations), Chiba 285-0043, Japan
| | - Takashi Sasaki
- Research and Development Section, Institute of Animal Health, JA Zen-noh (National Federation of Agricultural Cooperative Associations), Chiba 285-0043, Japan
| | - Tohru Suzuki
- Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki 305-0856, Japan
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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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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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