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: (112)RRQKR(↓)F(117). 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.

Epidemiology, control, and prevention of Newcastle disease in endemic regions: Latin America

“…Since the 1970s, viruses of genotype V have been frequently reported in Central America including the countries of Honduras (2000 and 2007), Nicaragua (2001), and Belize (2008) suggesting that this genotype may have become established in some unknown reservoir (Susta et al 2014 ; Brown et al 2018 ). In North America, the frequent outbreaks in Mexico resulted in the isolation of virulent NDV strains from genotype V in 1988, 1996, 2000, 2001, 2005, and 2008 to 2011 (Absalón et al 2014 ). On both Central and North American continents, genotype V strains are the predominant NDV found, with reports of isolations in both wild birds and poultry (Cardenas Garcia et al 2013 ; Susta et al 2014 ).…”

“…The genetic variation of genotype V viruses is quite significant, making it possible to identify three subgenotypes: Va, Vb, and Vc (Fig. 1 ) (Absalón et al 2014 ; Susta et al 2014 ; Dimitrov et al 2016c ). The analyses of nucleotide sequence of the fusion protein (F) genes provide evidence of genetic differences between the three subgenotypes.…”

“…It is worth emphasizing that the most frequent genotypes affecting poultry farms in Latin America correspond to genotypes V, VI, VII, XII, and XVI (Fig. 1 ) (Absalón et al 2012a , 2014 ; Susta et al 2014 ; Dimitrov et al 2016c ).

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