Sequencing and phylogenetic characterization of a novel RNA virus genome from Harmonia axyridis

• Published in: Molecular biology reports Vol. 47; no. 5; pp. 4015 - 4019
• Main Authors: Liu, Yingjie, Ren, Guangwei, Jiang, Lianqiang, Feng, Changchun, Liu, Dongyang, Liu, Yongjie, Xu, Pengjun
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01.05.2020; Springer Nature B.V
• Subjects: Amino Acid Sequence - genetics; Amino acids; Animal Anatomy; Animal Biochemistry; Animals; Base Sequence - genetics; Biomedical and Life Sciences; Coleoptera - genetics; Coleoptera - virology; DNA helicase; DNA-directed RNA polymerase; Genome, Viral - genetics; Genomes; Harmonia axyridis; Histology; Life Sciences; Morphology; Open reading frames; Open Reading Frames - genetics; Pests; Phylogenetics; Phylogeny; Polypeptides; Probiotics; RNA helicase; RNA polymerase; RNA viruses; RNA Viruses - classification; RNA Viruses - genetics; RNA Viruses - isolation & purification; RNA, Viral - genetics; RNA-directed RNA polymerase; Short Communication; Viral Proteins - genetics; Viruses; Whole Genome Sequencing - methods; Insect virus; Genome; Harmonia axyridis virus 1; Phylogenetic characterization; Harmonia axyridis
• ISSN: 0301-4851; 1573-4978
• DOI: 10.1007/s11033-020-05418-2

As a natural predator of many insect pests on its native Asian range, Harmonia axyridis remains amongst the insects whose pathogenic or beneficial microorganisms are yet to be studied. The genome nucleotide (nt) and amino acid sequences of open reading frames (ORFs) of the novel RNA virus were identified. Neighbor-joining (NJ) were constructed using MEGA7 software packages with nt sequences and conserved amino acid sequences of predicted RNA-dependent RNA polymerase (RdRp).The complete genome of a novel virus named Harmonia axyridis virus 1 was determined by RNA-seq and rapid amplification of cDNA ends from H . axyridis , which had a single-stranded RNA genome of 8868 nts in length and contains two putative ORFs. ORF1 encodes a polypeptide of 2182 amino acids, which contained conserved domains for 2 picornavirus-like capsid proteins and one RNA helicase. ORF2 encodes a polypeptide of 655 amino acids, which contained 1 RdRp domain. Phylogenetic analysis of whole genome nt sequences and RdRp deduced amino acid sequences suggested that the virus clustered with several unclassified Hubei picorna-like virus. To our knowledge, this is the first full annotated genome of a novel member of the unclassified group of RNA viruses, infecting H . axyridis in natural field conditions.