Molecular pathotyping and phylogenesis of the first Newcastle disease virus strain isolated from backyard chickens in Qatar.

Abstract

The first Newcastle disease virus (NDV) field strain (NDV-QC08), previously isolated and identified in Qatar, was further subjected to molecular characterization and phylogenic analysis at passage levels two. Initial amplification and detection of the complementary DNA (cDNA) fragment of the NDV RNA amnioallantoic fluid (AAF) extract demonstrated the positive virus identity using real-time reverse transcriptase chain reaction (RRT-PCR). Partial sequence of the totally amplified 216 bp of the functional cleavage region encoding the F gene retrieved (112)R-R-Q-K-R-F(117) amino acid motif indicating the velogenic nature of the strain, and confirming the previously investigated in-vivo pathotyping. Phylogenic analysis and genotypic clustering studies classified the strain under NDV subgenotype VIId.