Uniformity of rotavirus strain nomenclature proposed by the Rotavirus Classification Working Group (RCWG).
Jelle Matthijnssens,Max Ciarlet,Sarah M. McDonald,Houssam Attoui,Krisztián Bányai,J. Rodney Brister,Javier Buesa,Mathew D. Esona,Mary K. Estes,Jon R. Gentsch,Miren Iturriza-Gomara,Reimar Johne,Carl D. Kirkwood,Vito Martella,Peter P. C. Mertens,Osamu Nakagomi,Viviana Parreño,Mustafizur Rahman,Franco Maria Ruggeri,Linda J. Saif,Norma Santos,Andrej Steyer,Koki Taniguchi,John T. Patton,Ulrich Desselberger,Marc Van Ranst +25 more
TLDR
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.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.read more
Citations
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Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
Nuala A. O'Leary,Mathew W. Wright,J. Rodney Brister,Stacy Ciufo,Diana Haddad,Richard McVeigh,Bhanu Rajput,Barbara Robbertse,Brian Smith-White,Danso Ako-adjei,Alexander Astashyn,Azat Badretdin,Yiming Bao,Olga Blinkova,Vyacheslav Brover,Vyacheslav Chetvernin,Jinna Choi,Eric Cox,Olga Ermolaeva,Catherine M. Farrell,Tamara Goldfarb,Tripti Gupta,Daniel H. Haft,Eneida L. Hatcher,Wratko Hlavina,Vinita Joardar,Vamsi K. Kodali,Wenjun Li,Donna Maglott,Patrick Masterson,Kelly M. McGarvey,Michael R. Murphy,Kathleen O'Neill,Shashikant Pujar,Sanjida H. Rangwala,Daniel Rausch,Lillian D. Riddick,Conrad L. Schoch,Andrei Shkeda,Susan S. Storz,Hanzhen Sun,Françoise Thibaud-Nissen,Igor Tolstoy,Raymond E. Tully,Anjana R. Vatsan,Craig Wallin,David Webb,Wendy Wu,Melissa J. Landrum,Avi Kimchi,Tatiana Tatusova,Michael DiCuccio,Paul Kitts,Terence Murphy,Kim D. Pruitt +54 more
TL;DR: The approach to utilizing available RNA-Seq and other data types in the authors' manual curation process for vertebrate, plant, and other species is summarized, and a new direction for prokaryotic genomes and protein name management is described.
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NCBI Viral Genomes Resource
TL;DR: The NCBI Viral Genomes Resource is a reference resource designed to bring order to this sequence shockwave and improve usability of viral sequence data.
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VP6-sequence-based cutoff values as a criterion for rotavirus species demarcation.
TL;DR: Indirect immunofluorescence techniques targeting the rotavirus (RV) protein VP6 are used to differentiate RV species and a potential new RV species, ADRV-N, has been described.
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Virus Variation Resource - improved response to emergent viral outbreaks.
Eneida L. Hatcher,Sergey A. Zhdanov,Yiming Bao,Olga Blinkova,Eric P. Nawrocki,Yuri Ostapchuck,Alejandro A. Schäffer,J. Rodney Brister +7 more
TL;DR: This manuscript describes a series of features and functionalities recently added to the Virus Variation Resource, a value-added viral sequence data resource hosted by the National Center for Biotechnology Information.
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Human Intestinal Enteroids: a New Model To Study Human Rotavirus Infection, Host Restriction, and Pathophysiology
Kapil Saxena,Sarah E. Blutt,Khalil Ettayebi,Xi Lei Zeng,James R. Broughman,Sue E. Crawford,Umesh C. Karandikar,Narayan P. Sastri,Margaret E. Conner,Antone R. Opekun,David Y. Graham,Waqar A. Qureshi,Vadim Sherman,Jennifer Foulke-Abel,Julie In,Olga Kovbasnjuk,Nicholas C. Zachos,Mark Donowitz,Mary K. Estes +18 more
TL;DR: This research establishes HIEs as nontransformed cell culture models to understand human intestinal physiology and pathophysiology and the epithelial response, including host restriction of gastrointestinal infections such as HRV infection.
References
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The International Committee on Taxonomy of Viruses
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