Two Novel Negative-Sense RNA Viruses Infecting Grapevine Are Members of a Newly Proposed Genus within the Family Phenuiviridae.

Alfredo Diaz-Lara,Kristian Stevens,Bryce W Falk,Sandra Thuy Vu,Maher Al Rwahnih,Joshua Kohl,Deborah Golino,Min Sook Hwang,Francesco Di Serio,Beatriz Navarro

doi:10.3390/v11080685

Abstract

Two novel negative-stranded (ns)RNA viruses were identified by high throughput sequencing in grapevine. The genomes of both viruses, named grapevine Muscat rose virus (GMRV) and grapevine Garan dmak virus (GGDV), comprise three segments with each containing a unique gene. Based on sequence identity and presence of typical domains/motifs, the proteins encoded by the two viruses were predicted to be: RNA-dependent RNA polymerase (RdRp), nucleocapsid protein (NP), and putative movement protein (MP). These proteins showed the highest identities with orthologs in the recently discovered apple rubbery wood viruses 1 and 2, members of a tentative genus (Rubodvirus) within the family Phenuiviridae. The three segments of GMRV and GGDV share almost identical sequences at their 5′ and 3′ termini, which are also complementary to each other and may form a panhandle structure. Phylogenetics based on RdRp, NP and MP placed GMRV and GGDV in the same cluster with rubodviruses. Grapevine collections were screened for the presence of both novel viruses via RT-PCR, identifying infected plants. GMRV and GGDV were successfully graft-transmitted, thus, they are the first nsRNA viruses identified and transmitted in grapevine. Lastly, different evolutionary scenarios of nsRNA viruses are discussed.

Highlights

The phylum Negarnaviricota, composed of viruses with negative-strandedRNA genome, includes species characterized by (i) non-segmented or segmented genomes, (ii) the presence or absence of a membrane enveloping the capsid, and (iii) a diverse host range including plants and animals [1,2].Examples of nsRNA viruses associated with economically important diseases in plants are rose rosette virus [3], rice stripe virus (RSV) [4], citrus psorosis virus [5], and blueberry mosaic associated virus [6].Historically, only a relatively small number of nsRNA viruses infecting plants as their primary host have been reported [7]
Analysis of high throughput sequencing (HTS) data (Table S2) generated from the transcriptome of two asymptomatic grapevine selections revealed the presence of different viruses and viroids
The Garan dmak grapevine was found infected by grapevine rupestris stem pitting-associated virus (GRSPaV), Australian grapevine viroid (AGVd), grapevine yellow speckle viroid 1 (GYSVd-1), and hop stunt viroid (HSVd)

Summary

Introduction

Only a relatively small number of nsRNA viruses infecting plants as their primary host have been reported [7]. In the last few years, the use of high throughput sequencing (HTS) technology has allowed the identification and characterization of new nsRNA viruses in pistachio [8], citrus [9,10], watermelon [11], and apple [12]. Most of these novel nsRNA viruses were classified under the family Phenuiviridae (order Bunyavirales).

Methods

Results

Conclusion