Prevalence, molecular characterization and phylogenetic analysis of Newcastle disease virus isolated from domestic poultry during 2019-2024 in Egypt.

The current study aimed to determine the current status, genetic diversity, and molecular characterization of Newcastle disease viruses (NDV) isolated from chicken in Egypt during the period between 2019 and 2024. Out of 739 samples examined, 101 (14%) tested positive for NDV by real-time reverse transcription polymerase chain reaction (RT-qPCR). Positive cases were confirmed in 17 out of the 24 governorates studied which accounts for 71% of the locations where samples were collected. The majority of these cases (82 out of 664) were from chicken farms with 18 cases from other poultry species. Forty seven out of the 101 NDV isolates from chicken were selected for partial F gene sequence analysis. Based on F gene partial sequence analysis, 44 strains from chicken were classified as NDV genotype VII which is prevalent in poultry species in Egypt, and three isolates were categorized as Class II closely related to LaSota vaccine strains. However, the complete genomic sequencing of F gene revealed that all five isolates were associated with sub genotype VII.1.1. The avirulent strains of the viruses displayed the 112GRQGRL117 motif, while the virulent strains revealed the 112RRQKRF117 motif. Mutations were also found in the F gene which encompassed a region of the effect, such as the cleavage site, the cystoplasmic domains, and the HR domains. Investigation of the glycosylation site revealed that six N-linked glycosylation motifs were located in the F gene at residues 85, 191, 366, 447, 471, and 541 and in the HR domains 191 and 471. This study concludes the requirement of strict biosecurity measures combined with updated vaccination strategies to control NDV in poultry.