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Pathogens 2018, 7(2), 44; https://doi.org/10.3390/pathogens7020044

Whole Genome Classification and Phylogenetic Analyses of Rotavirus B strains from the United States

1
Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55108, USA
2
Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
3
Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506, USA
4
Department of Animal Science, Kasetsart University, Kamphaeng Saen Campus, Kamphaeng Saen, Chatuchak, Bankok 10900, Thailand
*
Author to whom correspondence should be addressed.
Received: 16 March 2018 / Revised: 13 April 2018 / Accepted: 14 April 2018 / Published: 18 April 2018
(This article belongs to the Special Issue Rotavirus Epidemiology: Host, Climate and Vaccine Influences)
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Abstract

Rotaviruses (RVs) are a major etiological agent of acute viral gastroenteritis in humans and young animals, with rotavirus B (RVB) often detected in suckling and weaned pigs. Group A rotavirus classification is currently based on the two outer capsid proteins, VP7 and VP4, and the middle layer protein, VP6. Using RVB strains generated in this study and reference sequences from GenBank, pairwise identity frequency graphs and phylogenetic trees were constructed for the eleven gene segments of RVB to estimate the nucleotide identity cutoff values for different genotypes and determine the genotype diversity per gene segment. Phylogenetic analysis of VP7, VP4, VP6, VP1–VP3, and NSP1–NSP5 identified 26G, 5P, 13I, 5R, 5C, 5M, 8A, 10N, 6T, 4E, and 7H genotypes, respectively. The analysis supports the previously proposed cutoff values for the VP7, VP6, NSP1, and NSP3 gene segments (80%, 81%, 76% and 78%, respectively) and suggests new cutoff values for the VP4, VP1, VP2, VP3, NSP2, NSP4, and NSP5 (80%, 78%, 79%, 77% 83%, 76%, and 79%, respectively). Reassortment events were detected between the porcine RVB strains from our study. This research describes the genome constellations for the complete genome of Group B rotaviruses in different host species. View Full-Text
Keywords: rotavirus B virus; phylogenetic analysis; classification; whole genome sequencing rotavirus B virus; phylogenetic analysis; classification; whole genome sequencing
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Shepherd, F.K.; Herrera-Ibata, D.M.; Porter, E.; Homwong, N.; Hesse, R.; Bai, J.; Marthaler, D.G. Whole Genome Classification and Phylogenetic Analyses of Rotavirus B strains from the United States. Pathogens 2018, 7, 44.

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