Identification and Characterization of a Novel Emaravirus From Grapevine Showing Chlorotic Mottling Symptoms

Abstract

A novel negative-sense, single-stranded (ss) RNA virus was identified in a “Shennong Jinhuanghou” (SJ) grapevine showing severe chlorotic mottling symptoms by integrating high-throughput sequencing (HTS) and conventional Sanger sequencing of reverse transcription polymerase chain reaction (RT-PCR) products. The virus was provisionally named as “grapevine emaravirus A” (GEVA). GEVA had a genome comprising five genomic RNA segments, each containing a single open reading frame on the viral complementary strand and two untranslated regions with complementary 13- nt stretches at the 5′ and 3′ terminal ends. RNA1 (7,090 nt), RNA2 (2,097 nt), RNA3 (1,615 nt), and RNA4 (1,640 nt) encoded putative proteins P1–P4 that, based on their conserved motifs, were identified as the RNA-dependent RNA polymerase, glycoprotein, nucleocapsid protein, and movement protein, respectively. However, the functional role of protein P5 encoded by RNA5 (1,308 nt) could not be determined. Phylogenetic trees constructed based on amino acids of P1 to P4, allocated GEVA in clade I, together with other species-related emaraviruses. These data support the proposal that GEVA is a representative member of a novel species in the genus Emaravirus of the family Fimoviridae. Moreover, when GEVA was graft-transmitted to SJ and “Beta” grapevines, all grafted plants showed the same symptoms, similar to those observed in the source of the inoculum. This is the first report to our knowledge of an emaravirus infecting grapevine and its possible association with chlorotic mottling symptoms.

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“…4a,c,f). Phylogenetic analyses with known fimoviruses revealed that ArtV1 is related to Perilla mosaic virus, making it the fourth member of the divergent phylogroup IV of Fimoviridae ( i.e., a clade of phylogenetically-related fimoviruses) [62, 63] (Fig. 4i).…”

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“…In contrast with RNA1-4, from which the putative proteins derived included recognizable functional domains, RNA5 encodes a protein of unknown function. It was not unusual in other emaraviruses that the role of P5 with a similar molecular weight but no sequence homology with each other is still to be determined (Buzkan et al, 2019 ; Wang et al, 2020 ; Fan et al, 2021 ; Rabbidge et al, 2021 ).…”

The Complex World of Emaraviruses – Challenges, Insights and Prospects

“…In China, AcCRaV and Actinidia virus 2 (AcV-2), both infecting kiwifruits, have been found in several provinces [52,54]. Further emaraviruses including JYMaV [55], PerMV [110], LiCRaV [62], Camellia chlorotic ringspot virus 1 (CaCRSV-1) and Camellia chlorotic ringspot virus 2 (CaCRSV-2) [59], PCLSaV [31], chrysanthemum mosaic-associated virus (ChMaV) [64,111], Japanese star anise ringspot-associated virus (JSARaV) [71], Vitis emaravirus (VEV) [67,68], alfalfa ringspot-associated virus (ARaV) [66], Ailanthus crinkle leaf-associated emaravirus (ACrLaV) [74] and PloAEV that infect important commercial fruits, ornamental crops and trees have been described in China and Japan. From other parts of the world there is limited information on emaraviruses diversity and distribution.…”

“…In a nursery in Liaoning (China) Fan et al [68] detected grapevine emaravirus A (GEVA) on the grapevine cultivar "Shennong Jinhuanghou" (Vitis vinifera L.) showing chlorotic mottling symptoms. GEVA contains five RNAs and could be graft-transmitted to healthy grapevines.…”