Molecular Identification of the Viruses Associated with Sweetpotato Diseases in Côte d’Ivoire

Sweetpotato (Ipomoea batatas) is a staple crop of strategic importance in West Africa, particularly in Côte d’Ivoire. However, its productivity is increasingly under threat due to viral diseases. Given the lack of updated epidemiological data over the past three decades, a nationwide survey was conducted in September 2023 across 94 fields in 83 locations covering seven agroecological zones of the country. A total of 221 symptomatic and asymptomatic leaf samples were analyzed using PCR for DNA viruses and RT-PCR for RNA viruses. The overall viral incidence rate calculated was 65.61%, with significant regional variations (35–97.18%, p < 0.001) and notable differences in the severity of symptoms (p = 0.0095). Agroecological zone I was the most affected, while agroecological zones IV and V were the least impacted. Four viruses were identified: cucumber mosaic virus (CMV), sweet potato leaf curl virus (SPLCV), sweet potato feathery mottle virus (SPFMV), and sweet potato chlorotic stunt virus (SPCSV). No badnaviruses were found. CMV was the most common virus found in single infections (43.44%), followed by SPLCV (5.43%). SPFMV and SPCSV were only observed in mixed infections, particularly CMV/SPLCV (14.03%) and CMV/SPFMV (1.81%). Two triple infections were also detected: SPFMV/SPCSV/CMV and SPFMV/SPLCV/CMV. In total, 34 partial coat protein sequences were obtained (28 SPLCV, 4 SPFMV, 1 CMV, 1 SPCSV). Phylogenetic analysis revealed a high similarity between SPLCV isolates characterized in Côte d’Ivoire and those from Burkina Faso, Europe (Spain, Italy), and the Americas (USA, Puerto Rico) with nucleotide identity values ranging from 98% to 100%. The Côte d’Ivoire SPCSV sequence showed 97.92% nucleotide identity with European isolates, whereas SPFMV sequences exhibited greater diversity (77–89% identity) but clustered within the West African lineage. Sweetpotato viral diseases were detected mostly in mixed-cropping fields (66.85%). This work provides the first epidemiological update on sweetpotato viral diseases since 1987 and the first molecular evidence of the nationwide presence of SPLCV and SPCSV in Côte d’Ivoire.