Identification and Characterization of a Novel Robigovirus Species from Sweet Cherry in Turkey

Abstract

High throughput sequencing of total RNA isolated from symptomatic leaves of a sweet cherry tree (Prunus avium cv. 0900 Ziraat) from Turkey identified a new member of the genus Robigovirus designated cherry virus Turkey (CVTR). The presence of the virus was confirmed by electron microscopy and overlapping RT-PCR for sequencing its whole-genome. The virus has a ssRNA genome of 8464 nucleotides which encodes five open reading frames (ORFs) and comprises two non-coding regions, 5′ UTR and 3′ UTR of 97 and 296 nt, respectively. Compared to the five most closely related robigoviruses, RdRp, TGB1, TGB2, TGB3 and CP share amino acid identities ranging from 43–53%, 44–60%, 39–43%, 38–44% and 45–50%, respectively. Unlike the four cherry robigoviruses, CVTR lacks ORFs 2a and 5a. Its genome organization is therefore more similar to African oil palm ringspot virus (AOPRV). Using specific primers, the presence of CVTR was confirmed in 15 sweet cherries and two sour cherries out of 156 tested samples collected from three regions in Turkey. Among them, five samples were showing slight chlorotic symptoms on the leaves. It seems that CVTR infects cherry trees with or without eliciting obvious symptoms, but these data should be confirmed by bioassays in woody and possible herbaceous hosts in future studies.

Identification of Divergent Isolates of Banana Mild Mosaic Virus and Development of a New Diagnostic Primer to Improve Detection

“…The percentage identities of RdRp and CP nucleic acid and the translated amino acid sequences confirmed that both contigs are independent full genomes of BanMMV [ 33 ].…”

“…The particles were approximately 580 nm in size, suggestive of members of the family Betaflexiviridae. Like all virions of the latter family, these particles showed a diameter ranging from 10 to 15 nm [ 33 ].…”

Identification of Pomegranate as a New Host of Passiflora Edulis Symptomless Virus (PeSV) and Analysis of PeSV Diversity

“…Based on the assembled contigs, two primer pairs amplifying partial sequences of the NIa-Pro (6564F: 5 -TTT GGT TTT CGT CAC TGG AT-3 /7030R: 5 -GTG ACT GGT GTG AAG TAG TT-3 ) and of the coat protein (CP) regions (8985F: 5 -CTGGATGTGATTGAGTTACC-3'/9753R: 5 -CAAGAGGTTTTCATGCCAG-3 ) were designed to confirm the HTS-assembled sequences and fulfillment of the survey. Reaction ingredients, conditions, and thermal cycling for RT-PCR were as described previously [21]. The amplified fragments were cleaned up using PCR purification kit (Qiagen) and directly sequenced in both directions by Medsantek (Istanbul, Turkey).…”

Identification of a Novel Quinvirus in the Family Betaflexiviridae That Infects Winter Wheat

“…The subfamily Quinvirinae contains three genera – Carlavirus , Foveavirus and, Robigovirus – and three floating species, including Banana mild mosaic virus (recently proposed genus “Banmivirus”), Banana virus X , and Sugarcane striate mosaic associated virus (proposed genus “Sustrivirus”; Candresse et al, 2021 ). Quinviruses have a plus-sense RNA genome (5.8–9.0 kb; 5' capped and 3' polyadenylated ends) with six open reading frames (ORFs) for carlaviruses or five ORFs for the other two genera and floating species, with some exceptions ( Caglayan et al, 2019 ; Zheng et al, 2020 ). Members of the Quinvirinae encode the so-called triple-gene block (TGB) for cell-to-cell movement in the leaf epidermis, and are clearly differentiated from the members of the subfamily Trivirinae , whose genomes encode a single movement protein (the 30K superfamily).…”