Uniformity of rotavirus strain nomenclature proposed by the Rotavirus Classification Working Group (RCWG)

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.

[1]  C R Howard,et al.  Rotavirus cross-species pathogenicity: molecular characterization of a bovine rotavirus pathogenic for pigs. , 2001, Virology.

[2]  F. Liprandi,et al.  A novel type of VP4 carried by a porcine rotavirus strain. , 2003, Virology.

[3]  P. Khamrin,et al.  Novel porcine rotavirus of genotype P[27] shares new phylogenetic lineage with G2 porcine rotavirus strain. , 2007, Virology.

[4]  Y. Hoshino,et al.  Whole genome sequence and phylogenetic analyses reveal human rotavirus G3P[3] strains Ro1845 and HCR3A are examples of direct virion transmission of canine/feline rotaviruses to humans. , 2008, Virology.

[5]  R. Peduzzi,et al.  Genotyping of Rotaviruses in Environmental Water and Stool Samples in Southern Switzerland by Nucleotide Sequence Analysis of 189 Base Pairs at the 5′ End of the VP7 Gene , 2000, Journal of Clinical Microbiology.

[6]  G. Kang,et al.  Whole genome characterization of reassortant G10P[11] strain (N155) from a neonate with symptomatic rotavirus infection: Identification of genes of human and animal rotavirus origin , 2009, Journal of Clinical Virology.

[7]  J. Matthijnssens,et al.  Molecular and biological characterization of the 5 human-bovine rotavirus (WC3)-based reassortant strains of the pentavalent rotavirus vaccine, RotaTeq. , 2010, Virology.

[8]  Jelle Matthijnssens,et al.  Evolutionary Dynamics of Human Rotaviruses: Balancing Reassortment with Preferred Genome Constellations , 2009, PLoS pathogens.

[9]  D. Zhou,et al.  Phylogenetic analysis of a human group B rotavirus WH‐1 detected in China in 2002 , 2004, Journal of medical virology.

[10]  Qinghuan Zhao,et al.  Full genomic analysis of human rotavirus strain TB-Chen isolated in China. , 2008, Virology.

[11]  Brian McClain,et al.  X-ray crystal structure of the rotavirus inner capsid particle at 3.8 A resolution. , 2010, Journal of molecular biology.

[12]  J. Matthijnssens,et al.  Rotavirus Strains Isolated in the Democratic Republic of Congo Belong to the DS1-Like Genogroup , 2006 .

[13]  L. Maunula,et al.  Frequent Reassortments May Explain the Genetic Heterogeneity of Rotaviruses: Analysis of Finnish Rotavirus Strains , 2002, Journal of Virology.

[14]  B. Kan,et al.  Molecular characterization of a novel adult diarrhoea rotavirus strain J19 isolated in China and its significance for the evolution and origin of group B rotaviruses. , 2008, The Journal of general virology.

[15]  T. Tatusova,et al.  The Influenza Virus Resource at the National Center for Biotechnology Information , 2007, Journal of Virology.

[16]  J. Farber,et al.  Rotaviruses from Canadian farm samples , 2010, Archives of Virology.

[17]  Jelle Matthijnssens,et al.  Recommendations for the classification of group A rotaviruses using all 11 genomic RNA segments , 2008, Archives of Virology.

[18]  R. Johne,et al.  The Genome Segments of a Group D Rotavirus Possess Group A-Like Conserved Termini but Encode Group-Specific Proteins , 2010, Journal of Virology.

[19]  N. Kobayashi,et al.  Analysis on reassortment of rotavirus NSP1 genes lacking coding region for cysteine-rich zinc finger motif , 1999, Archives of Virology.

[20]  R. Arora,et al.  Full genomic analysis of Indian G1P[8] rotavirus strains. , 2011, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[21]  T. Vesikari,et al.  A Prospective Study of Acute Diarrhoea in Finnish Children from Birth to 2 1/2 Years of Age , 1991, Acta paediatrica Scandinavica.

[22]  L. Saif,et al.  Isolation, characterization, and serial propagation of a bovine group C rotavirus in a monkey kidney cell line (MA104) , 1991, Journal of clinical microbiology.

[23]  J. Matthijnssens,et al.  Whole genome sequencing and phylogenetic analysis of a zoonotic human G8P[14] rotavirus strain. , 2010, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[24]  J. Matthijnssens,et al.  Complete genomic analysis of a Bangladeshi G1P[8] rotavirus strain detected in 2003 reveals a close evolutionary relationship with contemporary human Wa-like strains. , 2010, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[25]  S. M. McDonald,et al.  Complete genome sequence analysis of candidate human rotavirus vaccine strains RV3 and 116E. , 2010, Virology.

[26]  S. Plotkin,et al.  Protective Effect of WC3 Vaccine Against Rotavirus Diarrhea in Infants During a Predominantly Serotype 1 Rotavirus Season , 1988, The Journal of infectious diseases.

[27]  P. Karmakar,et al.  Characterization of VP1, VP2 and VP3 Gene Segments of A Human Rotavirus Closely Related to Porcine Strains , 2006, Virus Genes.

[28]  Songnian Hu,et al.  Whole genome sequencing of lamb rotavirus and comparative analysis with other mammalian rotaviruses , 2009, Virus Genes.

[29]  Jaideep P. Sundaram,et al.  VIGOR, an annotation program for small viral genomes , 2010, BMC Bioinformatics.

[30]  V. Martella,et al.  Molecular characterization of the VP4, VP6, VP7, and NSP4 genes of lapine rotaviruses identified in italy: emergence of a novel VP4 genotype. , 2003, Virology.

[31]  N. Kobayashi,et al.  Full genomic analysis of a simian SA11-like G3P[2] rotavirus strain isolated from an asymptomatic infant: identification of novel VP1, VP6 and NSP4 genotypes. , 2011, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[32]  T. Schumann,et al.  Evidence of interspecies transmission and reassortment among avian group A rotaviruses. , 2008, Virology.

[33]  C. Rupprecht,et al.  Reassortant Group A Rotavirus from Straw-colored Fruit Bat (Eidolon helvum) , 2010, Emerging infectious diseases.

[34]  N. Kobayashi,et al.  Complete genome constellation of a caprine group A rotavirus strain reveals common evolution with ruminant and human rotavirus strains. , 2010, The Journal of general virology.

[35]  N. Kobayashi,et al.  Molecular characterization of a human rotavirus reveals porcine characteristics in most of the genes including VP6 and NSP4 , 2003, Archives of Virology.

[36]  J. Matthijnssens,et al.  Are Human P[14] Rotavirus Strains the Result of Interspecies Transmissions from Sheep or Other Ungulates That Belong to the Mammalian Order Artiodactyla? , 2009, Journal of Virology.

[37]  Manish M Patel,et al.  Zoonotic bovine rotavirus strain in a diarrheic child, Nicaragua. , 2009, Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology.

[38]  N. Kobayashi,et al.  Analysis of genetic diversity and molecular evolution of human group B rotaviruses based on whole genome segments. , 2010, The Journal of general virology.

[39]  K. Bányai,et al.  Genome sequence based molecular epidemiology of unusual US Rotavirus A G9 strains isolated from Omaha, USA between 1997 and 2000. , 2011, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[40]  C. Arias,et al.  In vivo interactions among rotavirus nonstructural proteins , 1998, Archives of Virology.

[41]  D. Belnap,et al.  Sequence analysis of the VP6-encoding genome segment of avian group F and G rotaviruses. , 2011, Virology.

[42]  P. Maes,et al.  RotaC: A web-based tool for the complete genome classification of group A rotaviruses , 2009, BMC Microbiology.

[43]  R. F. Ramig,et al.  Analysis of reassortment of genome segments in mice mixedly infected with rotaviruses SA11 and RRV , 1986, Journal of virology.

[44]  R. Yolken,et al.  Infectious diarrhea of infant rats produced by a rotavirus-like agent , 1984, Journal of virology.

[45]  J. Matthijnssens,et al.  Simian Rotaviruses Possess Divergent Gene Constellations That Originated from Interspecies Transmission and Reassortment , 2009, Journal of Virology.

[46]  R. Johne,et al.  The first complete genome sequence of a chicken group A rotavirus indicates independent evolution of mammalian and avian strains. , 2009, Virology.

[47]  J. Matthijnssens,et al.  Unusual Assortment of Segments in 2 Rare Human Rotavirus Genomes , 2010, Emerging infectious diseases.

[48]  J. Matthijnssens,et al.  Genomic evolution, host-species barrier, reassortment and classification of rotaviruses , 2010 .

[49]  I. Clarke,et al.  Sequence conservation of the major outer capsid glycoprotein of human group C rotaviruses , 1994, Journal of medical virology.

[50]  O. Solberg,et al.  Characterization of novel VP7, VP4, and VP6 genotypes of a previously untypeable group A rotavirus. , 2009, Virology.

[51]  Leonid Zaslavsky,et al.  Virus variation resources at the National Center for Biotechnology Information: dengue virus , 2009, BMC Microbiology.

[52]  K N Shaw,et al.  Validity and reliability of clinical signs in the diagnosis of dehydration in children. , 1997, Pediatrics.

[53]  K. Bányai,et al.  Molecular characterization of a rare, human-porcine reassortant rotavirus strain, G11P[6], from Ecuador , 2009, Archives of Virology.

[54]  Wonyong Kim,et al.  Complete genomic characterization of cell culture adapted human G12P[6] rotaviruses isolated from South Korea , 2011, Virus Genes.

[55]  T. Vesikari,et al.  Rotavirus disease in Finnish children: use of numerical scores for clinical severity of diarrhoeal episodes. , 1990, Scandinavian journal of infectious diseases.

[56]  R. Glass,et al.  Global mortality associated with rotavirus disease among children in 2004. , 2009, The Journal of infectious diseases.

[57]  M. Georges-Courbot,et al.  Evaluation of the efficacy of a low-passage bovine rotavirus (strain WC3) vaccine in children in Central Africa. , 1991, Research in virology.

[58]  N. Kobayashi,et al.  Full genomic analysis and possible origin of a porcine G12 rotavirus strain RU172 , 2010, Virus Genes.

[59]  L. Saif,et al.  Sequence conservation of gene 8 between human and porcine group C rotaviruses and its relationship to the VP7 gene of group A rotaviruses. , 1991, Virology.

[60]  J. Matthijnssens,et al.  Evolutionary History and Global Spread of the Emerging G12 Human Rotaviruses , 2007, Journal of Virology.

[61]  R. Glass,et al.  Genomic characterization of human rotavirus G10 strains from the African Rotavirus Network: relationship to animal rotaviruses. , 2011, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[62]  Mamta,et al.  Whole Genomic Characterization of Human Group C Rotaviruses : 1 Identification of two lineages in VP 3 gene , 2010 .

[63]  C. Rao,et al.  Sequence analysis of VP4 and VP7 genes of nontypeable strains identifies a new pair of outer capsid proteins representing novel P and G genotypes in bovine rotaviruses. , 2000, Virology.

[64]  K. Bányai,et al.  Molecular analysis of the VP7 gene of pheasant rotaviruses identifies a new genotype, designated G23 , 2009, Archives of Virology.

[65]  Jean Cohen,et al.  Sequences of the four larger proteins of a porcine group C rotavirus and comparison with the equivalent group A rotavirus proteins. , 1992, Virology.

[66]  P. Khamrin,et al.  Molecular characterization of a rare G3P[3] human rotavirus reassortant strain reveals evidence for multiple human‐animal interspecies transmissions , 2006, Journal of medical virology.

[67]  J. Matthijnssens,et al.  Full Genomic Analysis of Human Rotavirus Strain B4106 and Lapine Rotavirus Strain 30/96 Provides Evidence for Interspecies Transmission , 2006, Journal of Virology.

[68]  N. Kobayashi,et al.  Whole genomic characterization of a human rotavirus strain B219 belonging to a novel group of the genus rotavirus , 2008, Journal of medical virology.

[69]  R. Arora,et al.  Molecular characterization of a rare G1P[19] rotavirus strain from India: evidence of reassortment between human and porcine rotavirus strains. , 2009, Journal of medical microbiology.

[70]  N. Ito,et al.  Sequential analysis of nonstructural protein NSP4s derived from Group A avian rotaviruses. , 2002, Virus research.

[71]  N. Kobayashi,et al.  Full genomic analyses of two human G2P[4] rotavirus strains detected in 2005: identification of a caprine-like VP3 gene. , 2011, The Journal of general virology.

[72]  U. Liebert,et al.  Molecular Characteristics of German G8P[4] Rotavirus Strain GER1H-09 Suggest that a Genotyping and Subclassification Update Is Required for G8 , 2009, Journal of Clinical Microbiology.

[73]  N. Kobayashi,et al.  Whole-genome characterization of human group C rotaviruses: identification of two lineages in the VP3 gene. , 2011, The Journal of general virology.

[74]  M. Dyall-Smith,et al.  Cloning and sequence of UK bovine rotavirus gene segment 7: marked sequence homology with simian rotavirus gene segment 8. , 1983, Nucleic acids research.

[75]  J. Matthijnssens,et al.  G8Rotavirus Strains Isolated in the Democratic Republic of Congo Belong to the DS-1-Like Genogroup , 2006, Journal of Clinical Microbiology.

[76]  N. Ito,et al.  Whole genome characterization of new bovine rotavirus G21P[29] and G24P[33] strains provides evidence for interspecies transmission. , 2011, The Journal of general virology.

[77]  L. A. Ball,et al.  The Universal Taxonomy of Viruses in Theory and Practice , 2005 .

[78]  H. Greenberg,et al.  Variation in Antagonism of the Interferon Response to Rotavirus NSP1 Results in Differential Infectivity in Mouse Embryonic Fibroblasts , 2009, Journal of Virology.

[79]  Q. Hu,et al.  Full genomic analysis of a porcine–bovine reassortant G4P[6] rotavirus strain R479 isolated from an infant in China , 2010, Journal of medical virology.

[80]  M. Estes,et al.  Cloning of bovine rotavirus (RF strain): nucleotide sequence of the gene coding for the major capsid protein. , 1984, Virology.

[81]  M. Barro,et al.  Genome heterogeneity of SA11 rotavirus due to reassortment with "O" agent. , 2007, Virology.

[82]  J. Matthijnssens,et al.  Rotavirus disease and vaccination: impact on genotype diversity. , 2009, Future microbiology.

[83]  T. Dermody,et al.  Dual selection mechanisms drive efficient single-gene reverse genetics for rotavirus , 2010, Proceedings of the National Academy of Sciences.

[84]  K. Bányai,et al.  Identification of a novel VP4 genotype carried by a serotype G5 porcine rotavirus strain. , 2006, Virology.

[85]  K. Bányai,et al.  Sequencing and phylogenetic analysis of the coding region of six common rotavirus strains: Evidence for intragenogroup reassortment among co‐circulating G1P[8] and G2P[4] strains from the United States , 2011, Journal of medical virology.

[86]  J. Matthijnssens,et al.  Multiple reassortment and interspecies transmission events contribute to the diversity of feline, canine and feline/canine-like human group A rotavirus strains. , 2011, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[87]  J. Nicolas,et al.  Serological characterization of human reassortant rotaviruses , 1986, Journal of virology.

[88]  H. Ito,et al.  Complete nucleotide sequence of a group A avian rotavirus genome and a comparison with its counterparts of mammalian rotaviruses. , 2001, Virus research.

[89]  J. Matthijnssens,et al.  Zoonotic aspects of rotaviruses. , 2010, Veterinary microbiology.

[90]  J. Matthijnssens,et al.  Two out of the 11 genes of an unusual human G6P[6] rotavirus isolate are of bovine origin. , 2008, The Journal of general virology.

[91]  N. Kobayashi,et al.  Full genomic analyses of human rotavirus G4P[4], G4P[6], G9P[19] and G10P[6] strains from North-eastern India: evidence for interspecies transmission and complex reassortment events. , 2011, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[92]  N. Kobayashi,et al.  Full genomic analysis of a G8P[1] rotavirus strain isolated from an asymptomatic infant in Kenya provides evidence for an artiodactyl‐to‐human interspecies transmission event , 2011, Journal of medical virology.

[93]  David H. L. Bishop,et al.  The International Committee on Taxonomy of Viruses , 1995 .

[94]  Karina Yusim,et al.  The hepatitis C sequence database in Los Alamos , 2007, Nucleic Acids Res..

[95]  V. Martella,et al.  Identification of a G2-like porcine rotavirus bearing a novel VP4 type, P[32] , 2010, Veterinary research.

[96]  H. Greenberg,et al.  Genetic mapping indicates that VP4 is the rotavirus cell attachment protein in vitro and in vivo , 1996, Journal of virology.

[97]  I. Clarke,et al.  Human group C rotavirus: completion of the genome sequence and gene coding assignments of a non-cultivatable rotavirus. , 2002, Virus research.

[98]  N. Kobayashi,et al.  Sequencing and Sequence Analysis of VP7 and NSP5 Genes Reveal Emergence of a New Genotype of Bovine Group B Rotaviruses in India , 2004, Journal of Clinical Microbiology.

[99]  E. V. Makeyev,et al.  Cloning and sequence analysis of dsRNA segments 5, 6 and 7 of a novel non-group A, B, C adult rotavirus that caused an outbreak of gastroenteritis in China. , 2004, Virus research.

[100]  J. Matthijnssens,et al.  Genetic heterogeneity in human G6P[14] rotavirus strains detected in Hungary suggests independent zoonotic origin. , 2009, The Journal of infection.

[101]  J. Matthijnssens,et al.  Reassortment of Human Rotavirus Gene Segments into G11 Rotavirus Strains , 2010, Emerging infectious diseases.

[102]  A. Steyer,et al.  Molecular characterization of a new porcine rotavirus P genotype found in an asymptomatic pig in Slovenia. , 2007, Virology.

[103]  Mustafizur,et al.  Full Genome-Based Classification of Rotaviruses Reveals Common Origin , 2008 .

[104]  R. F. Ramig.  Isolation and genetic characterization of temperature-sensitive mutants that define five additional recombination groups in simian rotavirus SA11. , 1983, Virology.

[105]  J. Matthijnssens,et al.  A feline rotavirus G3P[9] carries traces of multiple reassortment events and resembles rare human G3P[9] rotaviruses. , 2011, The Journal of general virology.