Phylogenetic Analysis of Virulent Newcastle Disease Virus Recently Isolated from Broiler Farms

Abstract

Newcastle disease (ND) is a highly contagious viral disease that causing high economic losses among poultry farms. The disease is caused by Newcastle disease virus (NDV) that frequently reported in Egypt although of intensive vaccination. Continuous genetic characterization of the virus along with detection of genetic variations in relation to the vaccine strains, are important for proper disease control. Clinical samples were collected from broiler farms in six Egyptian governorates during 2020−2022. NDV was isolated on embryonated chicken egg and identified by real time reverse transcriptase-PCR. Nineteen NDV isolates namely (HS1NDV−HS19NDV) were identified by RT-PCR and deposited on GeneBank database under the accession nos. (OP588159−OP588177). All the isolates found to be velogenic according to the amino acid sequences of the cleavage sits (GRRQKRF). In addition these strains were assigned under genotype VII and sub-genotype VII.1.1. In relation to vaccine strains, comparison of amino acids deduced from partially sequenced fusion gene revealed amino acid substitutions in fusion peptides that are essential in initiation of viral fusion with the host cell membrane. Moreover, HS3NDV had one amino acid substitution that was found in HR1 which shares in formation of the conserved six-helix bundles, that their assembly is tightly joined to the membrane fusion.