Cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) are endemic threats to cassava production, causing significant yield losses. They are caused respectively by begomoviruses and ipomoviruses that are transmitted by whiteflies and infected cuttings. This study aimed to monitor and characterize viruses responsible for these diseases in order to fill existing gaps in understanding their epidemiology in Côte d’Ivoire. Field surveys were conducted in 2016, 2017, and 2020, and no CBSD symptoms were observed. However, an increase in CMD incidence was noted from 45.95% in 2016 to 51.37% in 2020, while CMD severity remained moderate over the years with a mean value of 2.29. The number of whiteflies was relatively low and decreased over the years. Molecular diagnostics carried out on cassava leaf samples allowed the detection of East African cassava mosaic Cameroon virus (EACMCMV) that occurs in single as well as in mixed infection with African cassava mosaic virus (ACMV). Single EACMCMV infection, which was detected only in three agroecological zones of eastern Côte d’Ivoire in 2016, spread throughout the country in 2017 and became more widespread in 2020 with a preponderance in central and southern zones, whereas ACMV and EACMCMV coinfection has spread to the entire zones. Phylogenetic analysis of the viral isolates showed that they are closely related to those from Burkina Faso, Ghana, and Nigeria. This changing population of cassava virus species constitutes a serious threat to cassava cultivation. Understanding the evolutionary dynamics of these viruses could help in adopting better disease management strategies to control the disease.

Begomoviruses are a major threat to cassava production in Africa. Indeed, during the 1990s, the emergence of a recombinant begomovirus (East African cassava mosaic virus-Uganda, EACMV-Ug) resulted in crop devastation and severe famine in Uganda. In 2023, during a pre-survey of cassava farms at Forécariah, South-West Guinea, 22 samples showing peculiar cassava mosaic disease (CMD) symptoms were collected, and subsequent laboratory analysis confirmed the presence of EACMV-Ug in the samples. Deep analysis of DNA-A and DNA-B of the EACMV-Ug isolates from Guinea indicated that they are similar to those associated with the severe CMD epidemic in Uganda in the 1990s. Therefore, a country-wide survey was conducted throughout Guinea in April 2024 to evaluate the extent of the spread of EACMV-Ug in the country and to collect critical CMD epidemiological data. Findings showed a high whitefly population in Lower Guinea averaging 17 per plant; however, the data suggest a spread of EACMV-Ug via infected cuttings. High CMD incidence was found in Lower Guinea and Forest Guinea, whereas the highest CMD severity was observed in Forest Guinea (2.70 ± 0.06) and the lowest CMD severity was found in Middle Guinea (2.20 ± 0.05). Several cases of double and triple infections involving African cassava mosaic virus, East African cassava mosaic virus, East African cassava mosaic Cameroon virus, and EACMV-Ug were observed. EACMV-Ug was detected throughout Guinea, as well as from samples collected in 2022 in Kambia (Sierra Leone). The 63 accessions cultivated in Guinea that were assessed in this study were found susceptible to at least one of the viruses cited above. This study alerts us to an alarming situation in development in West Africa and provides scientific evidence to guide the rapid response needed to contain and stop the progression of EACMV-Ug in West Africa.

Cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) are endemic threats to cassava production. To fill the existing gaps in the understanding of the epidemiology of these diseases in Côte d’Ivoire, nationwide field surveys were conducted in 2016, 2017 and 2020. The leaf samples collected were analysed by PCR. CBSD was not detected in all fields visited. However, an increase of CMD incidence was observed from 45.95% in 2016 to 51.37% in 2020 while CMD severity remained moderate over the years with a mean value of 2.29. Low whiteflies number was observed in field and decreasing over the years. Molecular analysis allowed detection of East African cassava mosaic Cameroon virus (EACMCMV) in single as well as in mixed infection with African cassava mosaic virus (ACMV). Single EACMCMV infection, which was detected only in three agroecological zones of the eastern Côte d’Ivoire in 2016, spread throughout the country in 2017 and became more widespread in 2020 with a preponderance in the central and southern zones, whereas the ACMV+EACMCMV coinfection has spread to the entire zones studied. Knowing the dynamics of the evolution of these viruses across the country, better disease management strategies could be adopted to control the disease.

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.