The Effect of Vaccination on the Evolution and Population Dynamics of Avian Paramyxovirus-1

Abstract

Newcastle Disease Virus (NDV) is a pathogenic strain of avian paramyxovirus (aPMV-1) that is among the most serious of disease threats to the poultry industry worldwide. Viral diversity is high in aPMV-1; eight genotypes are recognized based on phylogenetic reconstruction of gene sequences. Modified live vaccines have been developed to decrease the economic losses caused by this virus. Vaccines derived from avirulent genotype II strains were developed in the 1950s and are in use globally, whereas Australian strains belonging to genotype I were developed as vaccines in the 1970s and are used mainly in Asia. In this study, we evaluated the consequences of attenuated live virus vaccination on the evolution of aPMV-1 genotypes. There was phylogenetic incongruence among trees based on individual genes and complete coding region of 54 full length aPMV-1 genomes, suggesting that recombinant sequences were present in the data set. Subsequently, five recombinant genomes were identified, four of which contained sequences from either genotype I or II. The population history of vaccine-related genotype II strains was distinct from other aPMV-1 genotypes; genotype II emerged in the late 19th century and is evolving more slowly than other genotypes, which emerged in the 1960s. Despite vaccination efforts, genotype II viruses have experienced constant population growth to the present. In contrast, other contemporary genotypes showed population declines in the late 1990s. Additionally, genotype I and II viruses, which are circulating in the presence of homotypic vaccine pressure, have unique selection profiles compared to nonvaccine-related strains. Collectively, these data show that vaccination with live attenuated viruses has changed the evolution of aPMV-1 by maintaining a large effective population size of a vaccine-related genotype, allowing for coinfection and recombination of vaccine and wild type strains, and by applying unique selective pressures on viral glycoproteins.

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

“…Their use might lead to incorrect results and conclusions. The substitution rate for genotype II estimated in the present study is consistent with a previously reported data by Chong et al (22); however, the authors did not consider the possibility that some of the viruses used in their analysis would have been escapes; thus, results are in disagreement with the rates of evolution estimated previously for class II NDV isolates. Previous studies using large data sets for the full fusion gene coding sequence and the complete NDV genomes have shown that the annual rate of change for Newcastle disease virus is approximately 10 Ϫ3 .…”

“…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). Isolates of genotype II are reported occasionally, and surprisingly, it has been reported that they have lower substitution rates in their genomic sequences than do other genotypes (22). In the last decade, virulent viruses of genotype IX have also been isolated frequently from poultry and wild birds in China (23,24).…”

Intragenic Recombination as a Mechanism of Genetic Diversity in Bluetongue Virus

“…Accumulated data have shown that homologous recombination can occur between double-or negative-stranded RNA viruses that undergo "caged replication" (12,13,15,19,41,57). However, the mechanism resulting in homologous recombination in these viruses is still unknown.…”

High Genetic Diversity of Newcastle Disease Virus in Poultry in West and Central Africa: Cocirculation of Genotype XIV and Newly Defined Genotypes XVII and XVIII

“…Sequences were identified as true recombinant when P values were Ͻ0.001 for at least two tests. All putative recombinant sequences were removed from the data set, as well as the recombinants identified based on complete genome analyses by Chong et al (25) and Diel et al (9). The final data set contained 896 previously published sequences and 96 obtained in this study.…”