Complete genome analysis of velogenic Newcastle disease virus reference strain “Chimalhuacan”: evolution of viral lineages in Mexico

Abstract

Newcastle disease virus with velogenic characteristics circulates in the poultry industry in Mexico and various other American countries. In Mexico, vaccine efficacy testing to obtain commercial registration is reliant on a challenge with a velogenic strain known colloquially as Chimalhuacan due to the site where it was isolated. In this paper, we performed a full genome sequencing of the Chimalhuacan strain. The strain belongs to Class II of APMV, particularly genotype V. The viral RNA genome is 15,192 nt in size and contains six genes: 3′ NP-P-M-F-HN-L 5′. The 3′ leader sequence is 55 nt in size and the 5′ trailer sequence 113 nt. The deduced amino acid sequence confirms a velogenic genotype with four basic amino acids at the cleavage site: ¹¹²RRQKR^↓F¹¹⁷. In addition, evolutionary relatedness based on the gene sequence of the fusion protein indicates that this strain is the ancestor of the strains currently circulating in Mexico.