GENOTYPING AND GENETIC EVOLUTION ANALYSIS OF NEWLY ISOLATED NEWCASTLE DISEASE VIRUS IN EGYPT

Abstract

In spite of enormous vaccination programs that were implemented in the Egyptian poultry farms, Newcastle Disease Virus (NDV) remains one of the major concerns to the poultry industry. Therefore, molecular analysis for the circulating NDV strains is crucial to monitor their genetic evolution. Twenty-three tracheal samples were collected from vaccinated broiler, layer and breeder flocks suffered from respiratory, nervous symptoms and drop in egg production between October 2019 and December 2020. Only ten samples (10/23; 43.5%) showed HA activity after propagation into ECE while only six samples were positive for Avian avulavirus 1 based on real time RT-PCR. Nucleotide sequences for both F and HN genes showed high similarity to recently reported Egyptian NDV isolates. Sequencing for the F protein cleavage site showed the typical sequence of velogenic NDV strains (112R-R/K-Q-K-R↓F117). Deduced amino acid analyses for the cleavage site, fusion peptide, glycosylation sites, heptad repeat region and transmembrane domain of F protein were conducted along with the transmembrane domain of HN protein that showed different substitutions in comparison with the commonly used vaccine strains. Phylogenetic analyses for the reported isolates in this study based on the full-length F gene revealed their clustering within sub-genotype VII.1.1. 3D protein structural modelling suggested that amino acids substitutions within the fusion peptide sequences result in conformational changes in the F protein structure. In conclusion, NDV continues to evolve and further in vivo studies are strongly recommended to define the precise efficacy of applied NDV vaccines against the circulating strains in Egypt.