Characterization of New Isolates of Apricot vein clearing-associated virus and of a New Prunus-Infecting Virus: Evidence for Recombination as a Driving Force in Betaflexiviridae Evolution

  title={Characterization of New Isolates of Apricot vein clearing-associated virus and of a New Prunus-Infecting Virus: Evidence for Recombination as a Driving Force in Betaflexiviridae Evolution},
  author={Armelle Marais and Chantal Faure and Eldar Mustafayev and Thierry Candresse},
  journal={PLoS ONE},
Double stranded RNAs from Prunus samples gathered from various surveys were analyzed by a deep-sequencing approach. Contig annotations revealed the presence of a potential new viral species in an Azerbaijani almond tree (Prunus amygdalus) and its genome sequence was completed. Its genomic organization is similar to that of the recently described Apricot vein clearing associated virus (AVCaV) for which two new isolates were also characterized, in a similar fashion, from two Japanese plums… 

Figures and Tables from this paper

Molecular Characterization of a Novel Species of Capillovirus from Japanese Apricot (Prunus mume)

Considering the species demarcation criteria in the family and phylogenetic analyses, this virus should be considered as representing a new viral species in the genus Capillovirus, for which the name of Mume virus A is proposed.

Identification of a novel robigovirus and a Prunus-infecting tepovirus in Pyrus communis and their transmissibility on Malus spp.

This study expands the list of viruses infecting pome fruit trees and augments the knowledge on the molecular diversity and host range evolution of betaflexiviruses.

A Virus in American Blackcurrant (Ribes americanum) with Distinct Genome Features Reshapes Classification in the Tymovirales

Data strongly suggest that RAVA is a novel virus that should be classified as a species in a new genus in the Betaflexiviridae or a new family within the order Tymovirales.

New Insights into Asian Prunus Viruses in the Light of NGS-Based Full Genome Sequencing

Critical genome information of Asian prunus virus 1, APV2 and APV3 is provided, showing that the unusually long 3’ non-coding region (3' NCR) is highly variable and a hot spot for indel polymorphisms.


Next generation sequencing (NGS) of total RNAs from a wild cherry tree revealed a multiple virus infection and evidence was obtained supporting the recombinant nature of two Slovak isolates and for the presence of “non-cherry” group isolates of CVA in several cherry host plants.

Partial biological and molecular characterization of a novel citrivirus from Nandina domestica

Computer-based analysis suggests that this novel virus isolated from Nandina domestica ‘Firepower’ in Auckland, New Zealand is the result of recombination between CLBV-Act and an unknown virus, highlighting the importance of this phenomenon for betaflexivirus evolution.

Small RNA NGS Revealed the Presence of Cherry Virus A and Little Cherry Virus 1 on Apricots in Hungary

C Cherry virus A (CVA) and little cherry virus 1 (LChV-1) are identified for the first time in Hungary using next generation sequencing of small RNAs to investigate their phylogenetic relationships.

Virus classification based on in-depth sequence analyses and development of demarcation criteria using the Betaflexiviridae as a case study.

Current issues concerning classification of viruses in the family Betaflexiviridae in the era of high-throughput sequencing are critically addressed and an updated set of demarcation criteria based on a process involving pairwise identity analyses and phylogenetics are proposed.



Characterization by Deep Sequencing of Prunus virus T, a Novel Tepovirus Infecting Prunus Species.

The name Prunus virus T (PrVT) is proposed for the new virus, considered as a new member of the genus Tepovirus, even if the level of nucleotide identity with PVT is borderline with the genus demarcation criteria for the family Betaflexiviridae.

Molecular characterization of banana virus X (BVX), a novel member of the Flexiviridae family

Comparative sequence analysis showed that BVX is only distantly related to other members of the Flexiviridae family, in which it appears to define a new genus.

Characterization by deep sequencing of divergent plum bark necrosis stem pitting-associated virus (PBNSPaV) isolates and development of a broad-spectrum PBNSPaV detection assay.

Complete sequencing of the divergent isolates allowed the development of a more broad-spectrum detection test targeting a conserved region in the P61 gene and indicate a much broader diversity of PBNSPaV than previously thought.

Characterization of the complete genome of a novel citrivirus infecting Actinidia chinensis

A ssRNA virus from kiwifruit (Actinidia spp.) was identified as a member of the family Betaflexiviridae andylogenetic analysis of the entire genome indicated it was a novel members of the genus Citrivirus.

Genetic characterization of novel putative rhabdovirus and dsRNA virus from Japanese persimmon.

The virus formed a distinct cluster in the genus Cytorhabdovirus with lettuce necrotic yellows virus, lettuce yellow mottle virus and strawberry crinkle virus in a phylogenetic tree based on the L protein (RNA-dependent RNA polymerase, RdRp) and formed a possible new genus cluster with two insect viruses and one plant virus.

Association of Little cherry virus 1 (LChV1) with the Shirofugen stunt disease and characterization of the genome of a divergent LChV1 isolate.

The failure to detect any other viral agent in the V2356 SSD source and the identification of LchV1 in a second, independent, source of the disease suggests that LChV1 isolates could be responsible for the SSD syndrome.

Development of a polyvalent RT‐PCR detection assay covering the genetic diversity of Cherry capillovirus A

Comparison of existing detection techniques using a panel of CVA isolates representative of the various phylogenetic groups indicated that dot-blot hybridization assays show high polyvalence but may lack the sensitivity to detect CVA in some samples.