Characterization of yam mosaic viruses from Brazil reveals a new phylogenetic group and possible incursion from the African continent

White yam (Dioscorea rotundata) plants exhibiting virus-like symptoms are co-infected with a new potyvirus and a new crinivirus in Ethiopia

White yam (Dioscorea rotundata) plants collected from farmers' fields and planted at the Areka Agricultural Research Center, Southern Ethiopia, displayed mosaic, mottling, and chlorosis symptoms. To determine the presence of viral pathogens, an investigation for virome characterization was conducted by Illumina high-throughput sequencing. The bioinformatics analysis allowed the assembly of five viral genomes, which according to the ICTV criteria were assigned to a novel potyvirus (3 genome sequences) and a novel crinivirus (2 genome sequences). The potyvirus showed ~ 66% nucleotide (nt) identity in the polyprotein sequence to yam mosaic virus (NC004752), clearly below the demarcation criteria of 76% identity. For the crinivirus, the RNA 1 and RNA 2 shared the highest sequence identity to lettuce chlorosis virus, and alignment of the aa sequence of the RdRp, CP and HSP70h (~ 49%, 45% and 76% identity), considered for the demarcation criteria, revealed the finding of a novel virus species. The names Ethiopian yam virus (EYV) and Yam virus 1 (YV-1) are proposed for the two tentative new virus species.

Improved Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) for the Rapid and Sensitive Detection of Yam mosaic virus

Yam (Dioscorea spp.) productivity is constrained significantly by the lack of a formal seed system. Vegetative propagation, through tuber setts as 'seed' yams, encourages the recycling of virus-infected planting materials, contributing to high virus incidence and yield losses. Efforts are ongoing to increase the production of high-quality seed yams in a formal seed system to reduce virus-induced yield losses and enhance the crop's productivity and food security. Specific and sensitive diagnostic tests are imperative to prevent the multiplication of virus-infected materials contributing to a sustainable seed yam certification system. During routine indexing of yam accessions, discrepancies were observed between the results obtained from the reverse transcription loop-mediated isothermal amplification (RT-LAMP) test and those from reverse transcription polymerase chain reaction (RT-PCR); RT-LAMP failed to detect Yam mosaic virus (YMV) in some samples that tested positive by RT-PCR. This prompted the design of a new set of LAMP primers, YMV1-OPT primers. These primers detected as little as 0.1 fg/µL of purified RNA obtained from a YMV-infected plant, a sensitivity equivalent to that obtained with RT-PCR. RT-LAMP using YMV1-OPT primers is recommended for all future virus-indexing of seed yams for YMV, offering a rapid, sensitive, and cost-effective approach.

Molecular diversity of yam virus Y and identification of banana mild mosaic virus isolates infecting yam (Dioscorea spp.)

Two members of the family Betaflexiviridae associated with yam (Dioscorea spp.) have been described so far: yam latent virus (YLV) and yam virus Y (YVY). However, their geographical distribution and molecular diversity remain poorly documented. Using a nested RT-PCR assay, we detected YVY in D. alata, D. bulbifera, D. cayenensis, D. rotundata, and D. trifida in Guadeloupe, and in D. rotundata in Côte d'Ivoire, thus extending the known host range of this virus and geographical distribution. Using amplicon sequencing, we determined that the molecular diversity of YVY in the yam samples analyzed in this work ranged between 0.0 and 29.1% and that this diversity is partially geographically structured. We also identified three isolates of banana mild mosaic virus (BanMMV) infecting D. alata in Guadeloupe, providing the first evidence for BanMMV infection in yam.

Epidemiology of Yam Viruses in Guadeloupe: Role of Cropping Practices and Seed-Tuber Supply

The epidemiology of yam viruses remains largely unexplored. We present a large-scale epidemiological study of yam viruses in Guadeloupe based on the analysis of 1124 leaf samples collected from yams and weeds. We addressed the prevalence of cucumber mosaic virus (CMV), Cordyline virus 1 (CoV1), Dioscorea mosaic associated virus (DMaV), yam asymptomatic virus 1 (YaV1), yam mosaic virus (YMV), yam mild mosaic virus (YMMV), badnaviruses, macluraviruses and potexviruses, and the key epidemiological drivers of these viruses. We provide evidence that several weeds are reservoirs of YMMV and that YMMV isolates infecting weeds cluster together with those infecting yams, pointing to the role of weeds in the epidemiology of YMMV. We report the occurrence of yam chlorotic necrosis virus (YCNV) in Guadeloupe, the introduction of YMMV isolates through the importation of yam tubers, and the absence of vertical transmission of YaV1. We identified specific effects on some cropping practices, such as weed management and the use of chemical pesticides, on the occurrence of a few viruses, but no crop-related factor had a strong or general effect on the overall epidemiology of the targeted viruses. Overall, our work provides insights into the epidemiology of yam viruses that will help design more efficient control strategies.

Viruses of Yams (Dioscorea spp.): Current Gaps in Knowledge and Future Research Directions to Improve Disease Management

Viruses are a major constraint for yam production worldwide. They hamper the conservation, movement, and exchange of yam germplasm and are a threat to food security in tropical and subtropical areas of Africa and the Pacific where yam is a staple food and a source of income. However, the biology and impact of yam viruses remains largely unknown. This review summarizes current knowledge on yam viruses and emphasizes gaps that exist in the knowledge of the biology of these viruses, their diagnosis, and their impact on production. It provides essential information to inform the implementation of more effective virus control strategies.