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Transcription profile and genomic 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 genomic 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.

Maximum likelihood phylogeny analysis of four different wild type populations of OrNV based on their complete genome sequence consensus generated two major clades. These data show that samples from Solomon Islands and Philippines are closely related to each other while samples from PNG and Fiji are separated from them and located in another clade (Figure 1). The phylogenic analysis of field-collected O. rhinoceros based on the host partial CoxI gene revealed three major mitochondrial lineages, CRB-G, CRB-S and CRB-PNG. All O. rhinoceros individuals collected from PNG (Kimbe, New Britain) and Fiji belonged to the mitochondrial lineages CRB-PNG and CRB-S, respectively. The individuals from the Philippines and the recently invaded Solomon Islands belonged to the CRB-G clade (Figure 1C). The virus strains from the Solomon Islands and the Philippines also belonged to one major clade (Figure 1B). Harmonious topologies of both host and OrNV strains provide evidence of co-divergence of OrNV strains with their O. rhinoceros hosts.

The source of the virus found in our 2019 collection from the Solomon Islands is not known; it could have been introduced deliberately as a biological control agent or along with an incursion of infected beetles from neighbouring islands (CRB-PNG from PNG). However, due to the high level of similarity and lack of any evidence that OrNV (Philippines strain) was introduced into the country as a biological control agent, our work suggests that the OrNV came to the Solomon Islands with an incursion of infected CRB-G that originated in Southeast Asia.


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