Population structure of Cydia pomonella granulovirus isolates revealed by quantitative analysis of genetic variation

Abstract

Genetic diversity of viruses is driven by genomic mutations and selection through its host, resulting in differences in virulence as well as host responses. For baculoviruses, which are naturally occurring pathogens of insects and which are frequently sprayed on hundred thousands to millions of hectares as biocontrol agents of insect pests, the phenomenon of virus-host co-evolution is of particular scientific interest and economic importance because high virulence of baculovirus products is essential and emergence of host resistance needs to be avoided as much as possible. In the present study, the population structure of twenty isolates of the Cydia pomonella granulovirus (CpGV), including twelve isolates from different geographic origins and eight commercial formulations, were studied on the basis of next generation sequencing data and by analyzing the distribution of single nucleotide polymorphisms (SNPs). An entirely consensus sequence free quantitative SNP analysis was applied for the identification of 753 variant SNP sites being specific for single as well as groups of CpGV isolates. Based on the quantitative SNP analysis, homogenous, heterogenous as well as mixed isolates were identified and their proportions of genotypes were deciphered, revealing a high genetic diversity of CpGV isolates from around the world. Based on hierarchical clustering on principal components (HCPC) six distinct isolate/group clusters were identified, representing the proposed main phylogenetic lineages of CpGV but comprising full genome information from virus mixtures. The relative location of different isolates in HCPC reflected the proportion of variable compositions of different genotypes. The established methods provide novel analysis tools to decipher the molecular complexity of genotype mixtures in baculovirus isolates, thus depicting the population structure of baculovirus isolates in a more adequate form than consensus based analyses.

Patterns in Genotype Composition of Indian Isolates of the Bombyx mori Nucleopolyhedrovirus and Bombyx mori Bidensovirus

“…Thus far, the genome description of BmNPV isolates was mainly restricted to consensus sequences that reflected the majority nucleotide composition of an isolate [ 9 , 40 ]. New approaches in baculovirus genomics have aimed to decipher the genetic composition of isolates and allowed the differentiation and bioinformatic presentation of complex genotype mixtures [ 25 , 26 , 37 , 41 ]. Here, this approach was successfully transferred to an alphabaculovirus in the example of BmNPV.…”

“…The terminology of homogenous, heterogeneous and mixed isolates was first introduced for the Cydia pomonella granulovirus (CpGV), a baculovirus of the genus Betabaculovirus [ 25 , 42 ]. Similar to BmNPV-My, the Mexican and Canadian isolates CpGV-M and CpGV-S, respectively, were identified as highly pure in their genotype composition, since variable SNP positions were missing [ 25 , 43 ].…”

“…The terminology of homogenous, heterogeneous and mixed isolates was first introduced for the Cydia pomonella granulovirus (CpGV), a baculovirus of the genus Betabaculovirus [ 25 , 42 ]. Similar to BmNPV-My, the Mexican and Canadian isolates CpGV-M and CpGV-S, respectively, were identified as highly pure in their genotype composition, since variable SNP positions were missing [ 25 , 43 ]. The English isolate CpGV-E2 was identified as highly heterogeneous, since a clear demarcation of a certain genotype was not possible ([ 25 , 28 ], whereas other CpGV isolates appeared to be mixtures of rather pure genotypes [ 25 , 28 ].…”

“…Similar to BmNPV-My, the Mexican and Canadian isolates CpGV-M and CpGV-S, respectively, were identified as highly pure in their genotype composition, since variable SNP positions were missing [ 25 , 43 ]. The English isolate CpGV-E2 was identified as highly heterogeneous, since a clear demarcation of a certain genotype was not possible ([ 25 , 28 ], whereas other CpGV isolates appeared to be mixtures of rather pure genotypes [ 25 , 28 ]. Although the SNP patterns of BmNPV-De and BmNPV-Ja suggest that both isolates are mixtures of two main variants, the underlying major genotypes of BmNPV-De and BmNPV-Ja were unknown, which was reflected by SNP positions being specific for none of the BmNPV isolates included in this study.…”

“…Thus far, whole genome analysis of BmNPV/BomaNPV and BmBDV allowed the establishment of consensus genomes of these viruses that reflect the entity of the sequenced virus populations. Recent analyses focusing on the population structure of baculoviruses showed that the genotypic composition of single virus isolates can be rather complex [ 24 , 25 , 26 ]. Genetic diversity was determined by detecting single nucleotide polymorphisms (SNPs) and the frequencies of alternative occurring nucleotide variants in these positions, which allowed for the differentiation of homogeneous, heterogeneous and mixed isolates [ 24 , 25 , 26 ].…”