Journal Article

Molecular Characterization of Hovenia Dulcis-Associated Virus 1 (HDaV1) and 2 (HDaV2): New Tentative Species within the Order Picornavirales

Resende, Renato O., Boiteux, Leonardo S., Ribeiro, Simone G., Pereira-Carvalho, Rita C., Batista, Josiane G., Lima, Mirtes F., Nery, Flávia M. B., Melo, Fernando L., Orílio, Anelise F.

2020

Overview

In a systematic field survey for plant-infecting viruses, leaf tissues were collected from trees showing virus-like symptoms in Brazil. After viral enrichment, total RNA was extracted and sequenced using the MiSeq platform (Illumina). Two nearly full-length picorna-like genomes of 9534 and 8158 nucleotides were found associated with Hovenia dulcis (Rhamnaceae family). Based upon their genomic information, specific primers were synthetized and used in RT-PCR assays to identify plants hosting the viral sequences. The larger contig was tentatively named as Hovenia dulcis-associated virus 1 (HDaV1), and it exhibited low nucleotide and amino acid identities with Picornavirales species. The smaller contig was related to insect-associated members of the Dicistroviridae family but exhibited a distinct genome organization with three non-overlapping open reading frames (ORFs), and it was tentatively named as Hovenia dulcis-associated virus 2 (HDaV2). Phylogenetic analysis using the amino acid sequence of RNA-dependent RNA polymerase (RdRp) revealed that HDaV1 and HDaV2 clustered in distinct groups, and both viruses were tentatively assigned as new members of the order Picornavirales. HDaV2 was assigned as a novel species in the Dicistroviridae family. The 5′ ends of both viruses are incomplete. In addition, a nucleotide composition analysis (NCA) revealed that HDaV1 and HDaV2 have similarities with invertebrate-infecting viruses, suggesting that the primary host(s) of these novel virus species remains to be discovered.

• Publisher: MDPI AG,MDPI
• Subject: Amino acid sequence / amino acid sequences / amino acids / Brazil / Deoxyribonucleic acid / Dicistroviridae / Dicistroviridae - classification / Dicistroviridae - genetics / Dicistroviridae - isolation & purification / DNA / DNA-directed RNA polymerase / Forests / Genetic testing / genome / Genome, Viral / Genomes / genomics / HDaV1 / HDaV2 / High-Throughput Nucleotide Sequencing / Hovenia dulcis / Invertebrates / leaves / metagenomics / Nucleotide sequence / Nucleotides / Open reading frames / Phylogenetics / Phylogeny / Picornavirales / Picornaviridae - classification / Picornaviridae - genetics / Picornaviridae - isolation & purification / Plant Diseases - virology / Polymerase chain reaction / reverse transcriptase polymerase chain reaction / Rhamnaceae - virology / RNA / RNA-directed RNA polymerase / Species / surveys / Trees / Viral Proteins - genetics / virome / Viruses