Full Genome-Based Classification of Rotaviruses Reveals a Common Origin between Human Wa-Like and Porcine Rotavirus Strains and Human DS-1-Like and Bovine Rotavirus Strains
Jelle Matthijnssens,Max Ciarlet,Erica Heiman,Ingrid Arijs,Thomas Delbeke,Sarah M. McDonald,Enzo A. Palombo,Miren Iturriza-Gomara,Piet Maes,John T. Patton,Mustafizur Rahman,Mustafizur Rahman,Marc Van Ranst +12 more
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TLDR
The novel classification system allows the identification of (i) distinct genotypes, which probably followed separate evolutionary paths; (ii) interspecies transmissions and a plethora of reassortment events; and (iii) certain gene constellations that revealed a common origin between human Wa-like rotavirus strains and porcine rotav virus strains.Abstract:
Group A rotavirus classification is currently based on the molecular properties of the two outer layer proteins, VP7 and VP4, and the middle layer protein, VP6. As reassortment of all the 11 rotavirus gene segments plays a key role in generating rotavirus diversity in nature, a classification system that is based on all the rotavirus gene segments is desirable for determining which genes influence rotavirus host range restriction, replication, and virulence, as well as for studying rotavirus epidemiology and evolution. Toward establishing such a classification system, gene sequences encoding VP1 to VP3, VP6, and NSP1 to NSP5 were determined for human and animal rotavirus strains belonging to different G and P genotypes in addition to those available in databases, and they were used to define phylogenetic relationships among all rotavirus genes. Based on these phylogenetic analyses, appropriate identity cutoff values were determined for each gene. For the VP4 gene, a nucleotide identity cutoff value of 80% completely correlated with the 27 established P genotypes. For the VP7 gene, a nucleotide identity cutoff value of 80% largely coincided with the established G genotypes but identified four additional distinct genotypes comprised of murine or avian rotavirus strains. Phylogenetic analyses of the VP1 to VP3, VP6, and NSP1 to NSP5 genes showed the existence of 4, 5, 6, 11, 14, 5, 7, 11, and 6 genotypes, respectively, based on nucleotide identity cutoff values of 83%, 84%, 81%, 85%, 79%, 85%, 85%, 85%, and 91%, respectively. In accordance with these data, a revised nomenclature of rotavirus strains is proposed. The novel classification system allows the identification of (i) distinct genotypes, which probably followed separate evolutionary paths; (ii) interspecies transmissions and a plethora of reassortment events; and (iii) certain gene constellations that revealed (a) a common origin between human Wa-like rotavirus strains and porcine rotavirus strains and (b) a common origin between human DS-1-like rotavirus strains and bovine rotaviruses. These close evolutionary links between human and animal rotaviruses emphasize the need for close simultaneous monitoring of rotaviruses in animals and humans.read more
Citations
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SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation
TL;DR: Sequence Demarcation Tool (SDT) as discussed by the authors is a free user-friendly computer program that aims to provide a robust and highly reproducible means of objectively using pairwise genetic identity calculations to classify any set of nucleotide or amino acid sequences.
Journal ArticleDOI
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
TL;DR: 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.
Journal ArticleDOI
Recommendations for the classification of group A rotaviruses using all 11 genomic RNA segments.
Jelle Matthijnssens,Max Ciarlet,Mustafizur Rahman,Mustafizur Rahman,Houssam Attoui,Krisztián Bányai,Mary K. Estes,Jon R. Gentsch,Miren Iturriza-Gomara,Carl D. Kirkwood,Vito Martella,Peter P. C. Mertens,Osamu Nakagomi,John T. Patton,Franco Maria Ruggeri,Linda J. Saif,Norma Santos,Andrej Steyer,Koki Taniguchi,Ulrich Desselberger,Marc Van Ranst +20 more
TL;DR: A Rotavirus Classification Working Group (RCWG) including specialists in molecular virology, infectious diseases, epidemiology, and public health was formed, which can assist in the appropriate delineation of new genotypes, thus avoiding duplications and helping minimize errors.
Journal ArticleDOI
Zoonotic aspects of rotaviruses
TL;DR: Genetic heterogeneity in the 11 double stranded RNA segments across different rotavirus strains has provided evidence for frequent intersections between the evolution of human and animal rotaviruses, as a result of multiple, repeated events of interspecies transmission and subsequent adaptation.
Journal ArticleDOI
RotaC: A web-based tool for the complete genome classification of group A rotaviruses
TL;DR: A web-based tool that can be used for fast rotav virus genotype differentiation of all 11 group A rotavirus gene segments according to the new guidelines proposed by the Rotavirus Classification Working Group (RCWG).
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Molecular Evolution and Phylogenetics
Masatoshi Nei,Sudhir Kumar +1 more
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