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J. Virol. doi:10.1128/JVI.02257-07
Copyright (c) 2008, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Full Genome-Based Classification of Rotaviruses Reveals Common Origin between Human Wa-like and Porcine rotavirus strains and Human DS-1-like and Bovine Rotavirus strains

Laboratory of Clinical & Epidemiological Virology, Department of Microbiology & Immunology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium; Vaccine & Biologics - Clinical Research, Merck & Co., Inc., North Wales, Pennsylvania 19454, USA; Laboratory of Infectious Diseases, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892; Environment and Biotechnology Centre, Faculty of Life and Social Sciences, Swinburne University of Technology, Hawthorn, Victoria, Australia; Enteric Virus Unit, Virus Reference Department, Centre for Infections, Health Protection Agency, London, United Kingdom; Laboratory of Virology, ICDDR,B: Mohakhali, Dhaka-1212, Bangladesh

^* To whom correspondence should be addressed. Email: jelle.matthijnssens{at}uz.kuleuven.ac.be.

	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. Towards establishing such a classification system, gene sequences encoding VP1-VP3, VP6, and NSP1-NSP5 were determined for human and animal rotavirus strains belonging to different G and P genotypes in addition to those available in databases, and were used to define phylogenetic relationships among all rotavirus genes. Based on these phylogenetic analyses, appropriate identity cut-off values were determined for each gene. For the VP4 gene, a nucleotide identity cut-off value of 80% completely correlated with the 27 established P genotypes. For the VP7 gene, a nucleotide identity cut-off 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-VP3, VP6, and NSP1-NSP5 genes showed the existence of four, five, six, eleven, fourteen, five, seven, eleven, and six genotypes, respectively, based on nucleotide identity cut-off 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 1) a common origin between human Wa-like rotavirus strains and porcine rotavirus strains, and 2) a common origin between human DS-1-like rotavirus strains and bovine rotaviruses. These close evolutionary links between human and animal rotaviruses emphasise the need for close simultaneous monitoring of rotaviruses in animals and humans.

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