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.

Cassava (Manihot esculenta Crantz) plays a significant role in the livelihoods of people in Africa, particularly in Côte d’Ivoire. However, its production is threatened by begomoviruses which cause huge yield losses. Some weeds and food crops intercropped with cassava act as reservoirs, thereby facilitating the sustenance and propagation of Cassava mosaic begomoviruses (CMBs), along with other begomoviruses. To effectively manage these diseases, it is imperative to enhance our understanding of the various hosts of cassava viruses in Côte d’Ivoire. Thus, a comprehensive nationwide survey was conducted in 2017 in cassava fields across Côte d’Ivoire, and molecular analyses were performed on the samples collected. The results obtained from this survey indicated that 65 plant species belonging to 31 families were potential alternative hosts for CMBs in Côte d’Ivoire. The molecular analyses revealed that four species, Capsicum annuum, Solanum melongena, Centrosema pubescens, and Asystasia gangetica exhibited differential affinities for both African cassava mosaic virus and East African cassava mosaic Cameroon virus. Additionally, other begomoviruses and new alphasatellites were identified. Soybean chlorotic blotch virus was isolated from C. pubescens while West African Asystasia virus 1, West African Asystasia virus 2, and a new Asystasia yellow mosaic alphasatellite were isolated from A. gangetica which appears to be a plant species that could favor the emergence of new viral species harmful to cassava cultivation. This study offers insights that will inform the development of more effective control methods for sustainable cassava production in Côte d’Ivoire.

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.