High levels of genetic variation within core Helicoverpa armigera nucleopolyhedrovirus genes.

It is well documented that baculovirus populations contain many genotypic variants, but little is known about the degree of genetic variation in specific baculovirus genes. Helicoverpa armigera nucleopolyhedrovirus (HearNPV) was used as a model system for studying genetic variation in nucleopolyhedrovirus genes. Next generation sequencing (NGS) was used to identify single-nucleotide polymorphisms (SNPs) within a core baculovirus gene (DNA polymerase) and two core lepidopteran-specific baculovirus genes (dbp1 and me53) in HearNPV populations. Analysis of the NGS data identified 60 SNPs within the 3063 bp DNA polymerase gene, 13 SNPs within the 972 bp dbp1 gene, and 25 SNPs within the 1080 bp me53 gene. Depending on the gene, between 31 and 35% of the SNPs were non-synonymous and may, thus, affect the biological functioning of the encoded proteins. The number and homogenous distribution of SNPs found suggest that nucleotide substitution is a major contributor to HearNPV genetic diversity. Denaturing gradient gel electrophoresis (DGGE) assays were used to provide an additional method for evaluating HearNPV genetic variation. Since each of the gene-specific DGGE assays produced unique banding profiles containing numerous bands of differing relative intensities, the DGGE experiments confirmed that there was a high degree of genetic variation in core HearNPV genes and provided information on the relative frequency distribution of genetic variants in the population. The amount of gene-specific genetic variation detected in this study significantly exceeds that reported in other HearNPV studies, suggesting that NGS and DGGE may be useful techniques for studying genetic variation in other baculoviruses.