Phylogenetic Analyses of Rotavirus A, B and C Detected on a Porcine Farm in South Africa

Rotaviruses (RVs) are known to infect various avian and mammalian hosts, including swine. The most common RVs associated with infection in pigs are A, B, C and H (RVA-C; RVH). In this study we analysed rotavirus strains circulating on a porcine farm in the Western Cape province of South Africa over...

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Bibliographic Details
Published in:	Viruses Vol. 16; no. 6; p. 934
Main Authors:	Strydom, Amy, Segone, Neo, Coertze, Roelof, Barron, Nikita, Strydom, Muller, O'Neill, Hester G
Format:	Journal Article
Language:	English
Published:	Switzerland MDPI AG 08-06-2024 MDPI
Subjects:	Analysis Animals Care and treatment Cattle Classification Diagnosis Epidemiology Farms Feces - virology Genome, Viral Genomes Genotype Genotype & phenotype Genotypes Health aspects Hogs Houses Infectious Medicine Infektionsmedicin P-type reassortment Phylogenetics Phylogeny porcine rotavirus Proteins Reassortant Viruses - classification Reassortant Viruses - genetics Reassortant Viruses - isolation & purification Rotavirus Rotavirus - classification Rotavirus - genetics Rotavirus - isolation & purification rotavirus A rotavirus A, B, C Rotavirus infections Rotavirus Infections - epidemiology Rotavirus Infections - veterinary Rotavirus Infections - virology South Africa South Africa - epidemiology Strains (organisms) Swine Swine Diseases - epidemiology Swine Diseases - virology Taxonomy Viruses Whole Genome Sequencing South Africa St Louis Missouri United States > US Africa porcine rotavirus South Africa P-type reassortment rotavirus A, B, C
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Summary:	Rotaviruses (RVs) are known to infect various avian and mammalian hosts, including swine. The most common RVs associated with infection in pigs are A, B, C and H (RVA-C; RVH). In this study we analysed rotavirus strains circulating on a porcine farm in the Western Cape province of South Africa over a two-year period. Whole genomes were determined by sequencing using Illumina MiSeq without prior genome amplification. Fifteen RVA genomes, one RVB genome and a partial RVC genome were identified. Phylogenetic analyses of the RVA data suggested circulation of one dominant strain (G5-P[6]/P[13]/P[23]-I5-R1-C1-M1-A8-N1-T7-E1-H1), typical of South African porcine strains, although not closely related to previously detected South African porcine strains. Reassortment with three VP4-encoding P genotypes was detected. The study also reports the first complete RVB genome (G14-P[5]-I13-R4-C4-M4-A10-T4-E4-H7) from Africa. The partial RVC (G6-P[5]-IX-R1-C1-MX-A9-N6-T6-EX-H7) strain also grouped with porcine strains. The study shows the continued circulation of an RVA strain, with a high reassortment rate of the VP4-encoding segment, on the porcine farm. Furthermore, incidents of RVB and RVC on this farm emphasize the complex epidemiology of rotavirus in pigs.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1999-4915 1999-4915
DOI:	10.3390/v16060934