Epidemiological Surveys of Yam Fields in Côte d’Ivoire Revealed the First Detection of YMMV and Evidence of Episomal Badnavirus

Yam (<i>Dioscorea</i> spp.) is a major staple food, contributing significantly to food security and income generation for millions of people worldwide. In 2019, surveys were conducted across the seven agro-ecological zones (AEZs) of Côte d'Ivoire, the third highest producer of yam globally, to ascertain the current status of viral diseases. In the 324 fields surveyed, a total of 1242 yam leaf samples were collected and tested for the presence of <i>Potyvirus yamtesselati</i> (yam mosaic virus, YMV), <i>Potyvirus yamplacidum</i> (yam mild mosaic virus, YMMV), <i>Cucumovirus CMV</i> (cucumber mosaic virus, CMV), and the badnaviruses using PCR, RT-PCR, and RCA followed by Sanger or MinION sequencing. The incidence of yam viral disease varied across the AEZs, with the lowest mean incidence observed in yam farms within the AEZ VII (71.95%) and the highest in AEZ V (88.15%). Viral disease symptom severity was moderate across the country, with more severe symptoms identified in AEZs II and VI. The virus screening revealed a potyvirus detection rate of 35.83% in all the AEZs. YMMV infection (25.12%) is the most prevalent in the samples, followed by YMV infection (15.61%). RCA-MinION sequencing revealed the presence of badnaviruses belonging to the T15 episomal groups K8, K9, and K5. Also, the use of this technique enabled the amplification and sequencing of four full-length episomal badnaviruses, namely Dioscorea bacilliform AL virus in group K8 and Dioscorea bacilliform RT virus in group K5. CMV was not detected in all the samples. It is noteworthy that 22.13% of mixed infections were detected in asymptomatic samples. This study revealed the first occurrence of YMMV in all the AEZs of Côte d'Ivoire. Of the yam species, <i>Dioscorea alata</i> was more widespread (78.03%) than <i>Dioscorea cayenensis-rotundata</i> (21.92%) in the visited fields. Also, <i>D. alata</i> had a highest incidence of YMMV (23.67%) infection than <i>Dioscorea cayenensis-rotundata</i>, while <i>D. cayenensis-rotundata</i> registered the highest incidence of YMV (15.84%) infection compared to <i>D. alata</i>. Phylogenetic analysis of representative of the various viruses detected in the country revealed that the sequences have high diversity for each virus species. This study revealed that viruses infecting yam are widespread and occur in mixed infection, which poses a real threat to yam production in Côte d'Ivoire.