Genomic structural and transcriptional variation of Oryctes rhinoceros nudivirus (OrNV) in Coconut Rhinoceros Beetle
Oryctes rhinoceros nudivirus (OrNV) is a dsDNA virus which has been used as a biocontrol agent to suppress Coconut Rhinoceros Beetle (Oryctes rhinoceros) in Southeast Asia and the Pacific Islands. Recently a new wave of O. rhinoceros incursions in Oceania is thought to be related to the presence of low virulence isolates of OrNV or virus tolerant haplotypes of beetles. Here, chronically infected beetles were collected from the Philippines, Fiji, PNG and the Solomon Islands (SI). RNAseq was performed to investigate the global viral gene expression profiles and comparative genomic analysis of structural variations. Maximum likelihood phylogenic analysis indicated that OrNV strains from the SI and the Philippines are closely related to while OrNV strains from PNG and Fiji formed a distinct adjacent clade. We detected several polymorphic sites with a frequency higher than 35% in 892 positions of the viral genome. Non-synonymous mutations were detected in several hypothetical proteins, and 15 nudivirus core genes such as gp034, lef-8, lef-4 and vp91. We found limited evidence of variation in viral gene expression among geographic populations. Only a few genes such as gp01, gp022 and gp107 were differentially expressed among different strains. Additionally, small RNA sequencing from SI population suggests that OrNV is targeted by the host RNA interference (RNAi) response with abundant 21nt small RNAs. Some of these structural changes are specific to the geographic population and could be related to particular phenotypic characteristics of the strain, such as viral pathogenicity or transmissibility, and this requires further investigation. Overall design: Adult female Coconut Rhinoceros Beetles (O. rhinoceros) were collected from the Philippines (Los Baños) and three different South Pacific countries, Fiji (Sigatoka, Viti Levu), Papua New Guinea (Kimbe, New Britain) and Solomon Islands (Honiara, Guadalcanal) using traps baited with aggregation pheromone (Oryctalure, P046-Lure, ChemTica Internacional, S. A., Heredia Costa Rica) between June-October 2019. We have 11 OrNV infected beetles in this study.