Phylogenetic Analyses of Rotavirus A, B and C Detected on a Porcine Farm in South Africa.
Viruses
; 16(6)2024 Jun 08.
Article
in En
| MEDLINE
| ID: mdl-38932226
ABSTRACT
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.
Key words
Full text:
1
Database:
MEDLINE
Main subject:
Phylogeny
/
Rotavirus Infections
/
Swine Diseases
/
Genome, Viral
/
Rotavirus
/
Farms
/
Genotype
Limits:
Animals
Country/Region as subject:
Africa
Language:
En
Journal:
Viruses
Year:
2024
Type:
Article
Affiliation country:
South Africa