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Oryctes rhinoceros nudivirus

ABSTRACT: Oryctes rhinoceros nudivirus Raw sequence reads

PROVIDER: PRJNA413966 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6161627_1.fastq.gz	Fastqsanger.gz
	SRR6161627_2.fastq.gz	Fastqsanger.gz

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Genomic structural and transcriptional variation of Oryctes rhinoceros nudivirus (OrNV) in Coconut Rhinoceros Beetle

Project description: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.

2020-08-26 | GSE152658 | GEO

Oryctes rhinoceros nudivirus isolate:LiboV

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Genomic structural and transcriptional variation of Oryctes rhinoceros nudivirus (OrNV) in Coconut Rhinoceros Beetle

Project description:Genomic structural and transcriptional variation of Oryctes rhinoceros nudivirus (OrNV) in Coconut Rhinoceros Beetle

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Oryctes rhinoceros breed:Oil Palm

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Oryctes rhinoceros breed:Wild

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Confirmation of Oryctes rhinoceros nudivirus infections in G-haplotype coconut rhinoceros beetles (Oryctes rhinoceros) from Palauan PCR-positive populations.

Project description:Coconut rhinoceros beetle (CRB), Oryctes rhinoceros, is a pest of palm trees in the Pacific. Recently, a remarkable degree of palm damage reported in Guam, Hawaii, Papua New Guinea and Solomon Islands has been associated with a particular haplotype (clade I), known as "CRB-G". In the Palau Archipelago, both CRB-G and another haplotype (clade IV) belonging to the CRB-S cluster coexist in the field. In this study, more than 75% of pheromone trap-captured adults of both haplotypes were Oryctes rhinoceros nudivirus (OrNV)-positive by PCR. No significant difference in OrNV prevalence between the haplotypes was detected. In PCR-positive CRB-G tissue specimens from Palau, viral particles were observed by electron microscopy. Hemocoel injection of CRB larvae with crude virus homogenates from these tissues resulted in viral infection and mortality. OrNV isolated from Palauan-sourced CRB was designated as OrNV-Palau1. Both OrNV-Palau1 and OrNV-X2B, a CRB biological control isolate released in the Pacific, were propagated using the FRI-AnCu-35 cell line for production of inoculum. However, the OrNV-Palau1 isolate exhibited lower viral production levels and longer larval survival times compared to OrNV-X2B in O. rhinoceros larvae. Full genome sequences of the OrNV-Palau1 and -X2B isolates were determined and found to be closely related to each other. Altogether these results suggest CRB adults in Palau are infected with a less virulent virus, which may affect the nature and extent of OrNV-induced pathology in Palauan populations of CRB.

| S-EPMC8452681 | biostudies-literature

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