Caraway yellows virus, a novel nepovirus from Carum carvi

Abstract

A novel nepovirus was identified and characterised from caraway, and tentatively named caraway yellows virus (CawYV). Tubular structures with isomeric virus particles typical for nepoviruses were observed in infected tissues by electron microscopy. The whole genome of CawYV was identified by high throughput sequencing (HTS). It consists of two segments with 8026 nt for RNA1 and 6405 nt for RNA2, excluding the poly(A) tails. CawYV-RNA1 shared closest nt identity to peach rosette mosaic virus (PRMV) with 63%, while RNA2 shared 41.5% with blueberry latent spherical virus (BLSV). The amino acid sequences of the CawYV protease-polymerase (Pro-Pol) and capsid protein (CP) regions share the highest identities with those of the subgroup C nepoviruses. The Pro-Pol region shared highest aa identity with PRMV (80.1%), while the CP region shared 39.6% to soybean latent spherical virus. Phylogenetic analysis of the CawYV-Pro-Pol and -CP aa sequences provided additional evidence of their association with nepoviruses subgroup C. Based on particle morphology, genomic organization and phylogenetic analyses, we propose CawYV as a novel species within the genus Nepovirus subgroup C. Electronic supplementary material The online version of this article (10.1186/s12985-019-1181-1) contains supplementary material, which is available to authorized users.

Metagenomic analysis of nepoviruses: diversity, evolution and identification of a genome region in members of subgroup A that appears to be important for host range

“…Two nepoviruses (GFLV and ArMV) made up the majority of sequences analyzed in this study, while most species were represented by one or a few sequences of either genomic RNAs (Table 1 ). Novel nepoviruses used in this study included MMLRaV [ 31 ], caraway yellows virus [ 12 ], potato virus B [ 4 ], and red clover nepovirus A [ 25 ]. A few new viruses and isolates belonging to the genus Nepovirus have been identified since we last consulted NCBI (January 2020).…”

“…Similarly, diversity studies and phylogenetic analysis have been reported for members of the family Secoviridae , including nepoviruses [ 45 , 51 ]. However, several new nepoviruses have been characterized recently, and the number of complete genome sequences of nepovirus isolates has increased exponentially in the past five years [ 1 , 2 , 4 , 12 , 15 , 18 , 23 – 25 , 41 , 50 , 55 , 56 , 58 ]. In this study, we built on these latest advancements in nepovirus research and carried out metagenomic analysis.…”

Comparative study on three viral enrichment approaches based on RNA extraction for plant virus/viroid detection using high-throughput sequencing

“…No prior knowledge about the pathogen is needed for HTS since all the nucleic acid (viral or non-viral) in the sample can be sequenced. Many previously undescribed viruses and viroids have been discovered using HTS and the number is constantly increasing [ 14 – 17 ]. However, HTS-based approaches for virus/viroid detection is facing several challenges in order to be validated for routine use diagnostic laboratories [ 18 ].…”

Transcriptome analysis reveals the molecular mechanisms of response to an emergent yellow-flower disease in green Chinese prickly ash (Zanthoxylum schinifolium)

“…Tomato black ring virus (TBRV), a typical member of Nepovirus genus within the Secoviridae family, infects a wide range of economically important plants worldwide, including tomato, strawberry, potato, celery, and artichoke 25 . Gaafar et al reported that a caraway yellows virus (CawYV) infection results in systemic yellowing in Caraway 26 . Grapevine fan leaf virus (GFLV), a picorna-like plant virus, is severely in responsible for a widespread disease in vineyards worldwide 27 .…”