Diversity and evolution of the Cydia pomonella granulovirus

Eight new field isolates of Cydia pomonella granulovirus (CpGV) originating in Iran and Georgia and one English CpGV isolate were analysed for restriction fragment length polymorphisms (RFLPs) and by partial genome amplification and sequencing. According to the observed RFLPs, most of the predominant genotypes of these isolates could be assigned to those present in previously found isolates originating from Mexico (CpGV-M), England (CpGV-E) and Russia (CpGV-R). We suggest that these isolates should be designated genome A, B and C types, respectively. A fourth genome type was identified in three isolates and is designated D type. The isolates with A, B and D type genomes contained four open reading frames (ORFs) (ORF63-CRF66) not present in C type genomes. The lack of these ORFs in other granuloviruses suggests that the C type genome is evolutionarily ancestral to the other genome types. The B and D type genomes contained an additional insertion of a non-protein coding region of 0.7 kb, which was at different genome locations. Analysis of the partial gene sequences of late expression factor 8 (lef-8), lef-9 and polyhedrin/granulin (polh/gran) genes revealed single nucleotide polymorphisms (SNPs) that corresponded to the RFLP types. Phylogenetic analyses based on these SNPs corroborated the proposed ancestry of the C type genome. C type viruses were also less virulent to neonate codling moth larvae than the other virus types. In conclusion, the known diversity of CpGV isolates can be described by four major genome types, which appear to exist in different isolates as genotype mixtures.