Entire genome sequence analysis of genotype IX Newcastle disease viruses reveals their early-genotype phylogenetic position and recent-genotype genome size

Abstract

BackgroundSix nucleotide (nt) insertion in the 5'-noncoding region (NCR) of the nucleoprotein (NP) gene of Newcaslte disease virus (NDV) is considered to be a genetic marker for recent genotypes of NDV, which emerged after 1960. However, F48-like NDVs from China, identified a 6-nt insert in the NP gene, have been previously classified into genotype III or genotype IX.ResultsIn order to clarify their phylogenetic position and explore the origin of NDVs with the 6-nt insert and its significance in NDV evolution, we determined the entire genome sequences of five F48-like viruses isolated in China between 1946 and 2002 by RT-PCR amplification of overlapping fragments of full-length genome and rapid amplification of cDNA ends. All the five NDV isolates shared the same genome size of 15,192-nt with the recent genotype V-VIII viruses whereas they had the highest homology with early genotype III and IV isolates.ConclusionsThe unique characteristic of the genome size and phylogenetic position of F48-like viruses warrants placing them in a separate geno-group, genotype IX. Results in this study also suggest that genotype IX viruses most likely originate from a genotype III virus by insertion of a 6-nt motif in the 5'-NCR of the NP gene which had occurred as early as in 1940 s, and might be the common origin of genotype V-VIII viruses.

Complete Genome and Clinicopathological Characterization of a Virulent Newcastle Disease Virus Isolate from South America

“…However, a complete epidemiological investigation, including sampling of domestic and wild bird species, is needed to define the actual source of the outbreak and origin of the virus. Recent phylogenetic studies have shown that NDV is continuously evolving, with viruses of different genotypes undergoing simultaneous changes in distinct geographic locations (4,5,11,22,25,33,34). The results presented here indicate that NDVPeru/08 has evolved and significantly diverged from viruses representing all known NDV genotypes.…”

Genetic diversity of avian paramyxovirus type 1: Proposal for a unified nomenclature and classification system of Newcastle disease virus genotypes

“…Among these, genotype II comprise mainly viruses of low virulence and strains of this genotype have been used as live vaccines against NDV for more than 40 years . Genotype IX includes the first virulent NDV strain obtained in China in 1948, and viruses of this genotype are still circulating in Asia with sporadic outbreaks being reported in chickens and domestic ducks (Qiu et al, 2011;Wang et al, 2006;Zhang et al, 2011). Genotypes V, VI, VII, VIII and XI emerged after 1960s and are considered ''late'' genotypes (Czeglédi et al, 2006).…”

Newcastle Disease Viruses Causing Recent Outbreaks Worldwide Show Unexpectedly High Genetic Similarity to Historical Virulent Isolates from the 1940s

“…Thus, the data suggest that these recent isolations might represent the reintroduction of already "lost" (not circulating naturally) viral genomes into the environment. The possible source of those field isolates appears to be the virulent strains Texas/GB and F48, both of which have been used as challenge viruses to show the efficacy of ND commercial vaccines before their commercial production and in experimental studies (9,18,46,47).…”

“…Some lentogenic strains of genotype II (e.g., LaSota/1946 and Hitchner/B1/47) were also collected in United States in the 1940s, and since their commercialization they have been used worldwide as live vaccines in poultry (9). Newcastle disease virus strain F48 (according to the number of passages in eggs often designated F48E8 and F48E9) was isolated in China in the 1940s and is designated a member of class II genotype IX (18). During the last 2 decades, isolations of genotype II virulent viruses in Egypt, China, and India have been reported in poultry and wild birds (19)(20)(21).…”