Cassava mosaic begomoviruses are a major threat to cassava cultivation in Africa. The virulent Ugandan variant of the East African cassava mosaic virus (EACMV-Ug), which caused substantial damage to cassava production in Uganda in the 1990s and which was previously confined to East and Central Africa, was recently found to be well established in Guinea and Sierra Leone in West Africa. Molecular analysis of cassava leaf samples from a nationwide cassava fields survey conducted in Côte d’Ivoire in 2022 suggested the absence of EACMV-Ug in the country in 2022. Given the proximity of some confirmed EACMV-Ug infected locations in Guinea to Côte d’Ivoire, we conducted another survey in 2025 along the entire western border of Côte d’Ivoire, bordering Guinea and Liberia, to update the status of EACMV-Ug in the country. Molecular analysis of the leaf samples collected confirmed the presence of EACMV-Ug in Côte d’Ivoire for the first time, along with other begomoviruses. The infection rate of EACMV-Ug along the Liberian border was higher (28.85%) than the 17.07% observed along the Guinean border. African cassava mosaic virus (ACMV) and East African cassava mosaic Cameroon virus (EACMCMV) were detected both as a single infection and in double co-infections (ACMV+EACMCMV) in some plants, whereas EACMV-Ug was found as a double co-infection (EACMCMV+EACMV-Ug) and as a triple co-infection (ACMV+EACMCMV+EACMV-Ug). Our results also show that all the cassava varieties grown in the surveyed locations were susceptible to EACMV-Ug. Epidemiological assessment of cassava fields revealed that the incidence and severity of cassava mosaic disease (CMD) were significantly higher along the Liberian border compared to the Guinean border. However, whitefly populations were relatively low across the entire area surveyed. Furthermore, we found that the spread of CMD in the survey area was mainly through the use of infected cassava cuttings for the establishment of new farms. Based on these results, it is imperative to conduct an urgent nationwide cassava fields survey to assess the extent of EACMV-Ug spread in Côte d’Ivoire and implement containment measures to stop further spread.

Yam (Dioscorea 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 Potyvirus yamtesselati (yam mosaic virus, YMV), Potyvirus yamplacidum (yam mild mosaic virus, YMMV), Cucumovirus CMV (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, Dioscorea alata was more widespread (78.03%) than Dioscorea cayenensis-rotundata (21.92%) in the visited fields. Also, D. alata had a highest incidence of YMMV (23.67%) infection than Dioscorea cayenensis-rotundata, while D. cayenensis-rotundata registered the highest incidence of YMV (15.84%) infection compared to D. alata. 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.