Analysis of the Fusion Protein Cleavage Site of Newcastle disease virus Isolates from India Reveals Preliminary Evidence for the Existence of II, VI and VII Genotypes

Abstract

Newcastle disease virus (NDV) has been a threat to poultry industry in most of the developing countries with a wide variety of avian species being susceptible, coupled with the presence of mobile wild bird reservoirs contributing not only to the vast genomic diversity of this virus but also to the diagnostic failures. NDV of multiple genotypes (I-XI) is known to be prevalent and reported worldwide. However, there is a paucity of information on the circulating genotypes of NDV in India. This study utilized the fusion protein cleavage site (FPCS) sequence to determine the different genotypes of NDV circulating in India. Our results indicate that majority of NDV isolates from southern states of India namely, Tamil Nadu, Kerala and Karnataka were found to belong to genotype II. However, some of the strains from Tamil Nadu and most from Uttar Pradesh belong to genotype groups VI and VII. Interestingly, three isolates recovered from Tamil Nadu grouped with genotype IV viruses (namely Herts/33) which had not been hitherto reported to GenBank since 1989. This preliminary information points to the existence of multiple genotypes and also the need for efficacy studies with vaccines incorporating multiple genotypes in controlling virulent NDV (vNDV) outbreaks in India.

Keywords: APMV-1; Class II-APMV; FPCS; Genotype; Pathotyping.

Fig. 1

Phylogenetic relationship of various Indian isolates of Newcastle disease virus based on the 374-nucleotide sequence of the fusion protein gene. A rooted consensus tree drawn to scale using neighbour-joining method was obtained with the evolutionary distances inferred by using the based a Kimura-2 parameter method and gamma distribution model with evolutionary rate differences among sites, that also allowed some sites to be evolutionarily invariable (K2 + G + I). Bootstrap consensus value was inferred from 1000 replications. There were 389 positions in the final dataset. Evolutionary analysis was conducted in MEGA5. The Indian isolates of NDV were found to be of three major genotypes namely II, VII and VI. Most of the isolates from North India (from UP) are found to group with the genotype VI strains (IT-1/2000-AF293350, IT-112/04-AF218127 & ZA-25/93-AF136758) while the strains from South India (from Tamil Nadu and Kerala) grouped with the genotype II strains (Lasota, Beaudette-C)