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

Abstract

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.

Identification of dicistro-like viruses in the transcriptome data of Striga asiatica and other plants

“…Dicistroviruses were first isolated in insects and crustaceans, although recent studies have suggested that more diverse organisms might be their natural hosts (Bonning and Miller, 2010;Chiapello et al, 2020;Dastjerdi et al, 2021). The presence of dicistro-like viruses in the S. asiatica sample and other plants raised the possibility that these viruses might be more widely associated with various plants (Nery et al, 2020). To identify their potential viral genome sequences in other plant transcriptome data, the plant transcript contig sequences deposited in the NCBI Transcriptome Sequence Assembly database were searched using the SaDLV1 and SaDLV2 ORF1 polyprotein sequences as queries.…”

“…However, recent studies have demonstrated that dicistroviruses or related viruses are associated with non-arthropod animals, including diverse invertebrates, birds, mammals, and humans (Greninger and Jerome, 2016;Shi et al, 2016;Phan et al, 2018;Dastjerdi et al, 2021). Moreover, dicistrovirus genome sequences have been identified in samples derived from plants and single-celled eukaryotes, suggesting that they might be associated with a wide range of organisms (Chiapello et al, 2020;Nery et al, 2020).…”

Exploring the tymovirids landscape through metatranscriptomics data

“…Phylogenetic relationships suggest that WaCraV1 is likely an invertebrate-infecting virus derived from insect RNA that was eventually co-purified with the targeted plant RNA. The identification of invertebrate-infecting viruses from plant transcriptome datasets was already reported elsewhere suggesting that some undetected invertebrate was contaminating the plant samples [72]. Based on sequence similarities, the distinct genomic organization and phylogenetic relationships WaCraV1, BeeMLV2 and BmMLV should be classified as members of a novel genus within the Tymoviridae family, which could be tentatively named as Inmaculavirus.…”

Geminiviridae and Alphasatellitidae Diversity Revealed by Metagenomic Analysis of Susceptible and Tolerant Tomato Cultivars across Distinct Brazilian Biomes

“…All contigs were compared with the viral RefSEq database available at NCBI (https://www.ncbi.nlm.nih.gov; accessed on 3 April 2024), using the BLASTn and BLASTx algorithms. The procedure was carried out essentially as previously described [20,35]. The read files provided by HTS were mapped to virus-like contigs to obtain the final sequence.…”