Partial nucleotide sequence analysis of the VP6 gene from rotavirus species A, D, and F identified in diarrheic broiler chickens

Rotavirus (RV) causes viral enteric diseases in several livestock species. It is a non-enveloped, icosahedral virus with 11 segments of double-stranded RNA genome encoding six structural proteins (VP). VP6, the most abundant protein, is located in the middle layer of the RV capsid and is commonly used for detection and classification of RV species. Avian RVs are classified into four species: RVA, RVD, RVF, and RVG, with RVA being the most frequently reported in avian hosts, though it remains little studied. We aimed to identify RV species and possible co-infections, characterize the VP6 gene in fecal samples previously confirmed as RV-positive by silver-stained polyacrylamide gel electrophoresis, and to evaluate their phylogenetic and diversity relationships. The sampling included 55 RV-positive fecal samples from 1–2-week-old broiler chickens exhibiting diarrhea and clinical signs of malabsorption syndrome. Nucleic acids were extracted and subjected to reverse transcription-polymerase chain reaction assays targeting the VP6 gene of RVA, RVD, RVF, and RVG. Amplified products were sequenced, and 33 nucleotide (nt) sequences were submitted for phylogenetic analysis. RVA, RVD, and RVF species were identified in 10 (18.2%), 17 (30.9%), and 28 (50.9%) of the fecal samples, respectively. Only one RV species was identified in each fecal sample. RVG VP6 gene was not amplified in any of the fecal samples. Phylogenetic analysis revealed that the 10 RVA strains clustered within genotype I11. RVD and RVF strains showed 87.7–90.1% and 87.9–98.4% nt identity, respectively. Molecular characterization of circulating RV strains in avian species aids in understanding the epidemiology of these infections.