Complete genome sequence of Oryctes rhinoceros nudivirus isolated from the coconut rhinoceros beetle in Solomon Islands

• Published in: Virus research 2020-03, Vol.278, p.197864-197864, Article 197864
• Main Authors: Etebari, Kayvan, Filipović, Igor, Rašić, Gordana, Devine, Gregor J., Tsatsia, Helen, Furlong, Michael J.
• Format: Article
• Language: English
• Subjects: Animals; Biological Control Agents; Coconut rhinoceros beetles; Cocos; Coleoptera - virology; Female; Genome; Genome, Viral; Melanesia; Nudiviridae - genetics; Open Reading Frames; Oryctes rhinoceros; Oryctes rhinoceros nudivirus (OrNV); Oxford Nanopore Technologies (ONT) sequencing; Scarabaeidae; Sequence Analysis, DNA; Solomon Islands; Whole Genome Sequencing
• ISSN: 0168-1702; 1872-7492
• DOI: 10.1016/j.virusres.2020.197864

The complete circular genome of the virus consisted of 125,917 nucleotides, encoding 130 open reading frames. The SI isolate of OrNV is 1,698 bp shorter than Ma07. Highlighted arrangement that differs between the original (Ma07) and the new isolate (Solomon Islands isolate) contains four genes within a putative inversion, and two hypothetical proteins (gp129 and gp130) that are not present in the new assembly (they are identified as duplicated versions of gp135 and gp136). [Display omitted] •The complete circular genome of the virus consisted of 125,917 nucleotides.•This virus encoding 130 open reading frames.•The cluster analysis shows more similarity between isolate sequenced from Solomon Island and Philippines.•We found 43 EcoRI, 27 HindIII, 21 BamHI and 7 PstI cleavage sites. Oryctes rhinoceros nudivirus (OrNV) has been an effective biocontrol agent against the insect pest Oryctes rhinoceros (Coleoptera: Scarabaeidae) for decades, but there is evidence that resistance could be evolving in some host populations. We detected OrNV infection in O. rhinoceros from Solomon Islands and used Oxford Nanopore Technologies (ONT) long-read sequencing to determine the full length of the virus genomic sequence isolated from an individual belonging to a mitochondrial lineage (CRB-G) that was previously reported as resistant to OrNV. The complete circular genome of the virus consisted of 125,917 nucleotides, 1.698 bp shorter than the originally-described full genome sequence of Ma07 strain from Malaysia. We found 130 out of 139 previously annotated ORFs (seven contained interrupted/non-coding sequences, two were identified as duplicated versions of the existing genes), as well as a putatively inverted regions containing four genes. These results demonstrate the usefulness of a long-read sequencing technology for resolving potential structural variations when describing new virus isolates. While the Solomon Islands isolate exhibited 99.41 % nucleotide sequence identity with the originally described strain, we found several genes, including a core gene (vlf-1), that contained multiple amino acid insertions and/or deletions as putative polymorphisms of large effect. Our complete annotated genome sequence of a newly found isolate in Solomon Islands provides a valuable resource to help elucidate the mechanisms that compromise the efficacy of OrNV as a biocontrol agent against the coconut rhinoceros beetle.