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.

Sweetpotato is a key staple crop in tropical and subtropical regions. Its vegetative propagation makes it a persistent reservoir, facilitating the emergence and spread of complex infections. Understanding its virome is crucial for disease management and food security. We investigated the sweetpotato virome in Burkina Faso using rolling circle amplification and Oxford Nanopore sequencing. Eight symptomatic leaf samples, previously undiagnosed using conventional methods, were analysed. Bioinformatic pipelines were employed followed by phylogenetic comparisons. Two viruses known to infect sweetpotato, namely sweet potato leaf curl virus (SPLCV) and sweet potato leaf curl deltasatellite 3 (SPLCD3), were consistently detected in all samples. Additionally, pepper yellow vein Mali virus (PepYVMV), cotton leaf curl Gezira alphasatellite (CLCuGeA) and cotton leaf curl Gezira betasatellite (CLCuGeB) were identified for the first time in this crop. Phylogenetic analysis confirmed their genetic proximity to isolates from tomato, okra and pepper. Their co-occurrence with SPLCV and SPLCD3 indicates a complex viral landscape that could influence disease severity. This study highlights the underestimated role of sweetpotato as a viral reservoir, influencing virus evolution and transmission. Further studies should assess their pathogenicity, co-infection dynamics and vector-mediated transmission to improve crop productivity.

A study was conducted in Sierra Leone to identify cassava plants that are asymptomatic and symptomatic to cassava mosaic disease (CMD) and collect planting materials for field trial establishment; determine the prevalence of CMD caused by African cassava mosaic virus (ACMV) and East African cassava mosaic virus (EACMV) using the Nuru App and virus indexing techniques; and assess selected agronomic traits in cassava. A total of 80 cassava farms spanning four provinces (Southern, Eastern, Northern, and North-West) were surveyed in April 2022. Findings showed that the cassava variants of the experiment and locations significantly (p < 0.001) affected CMD incidence, severity, growth, and fresh storage root yield traits. The CMD incidence (87.0%) and whitefly abundance (144.8) were highest, and the CMD severity was moderate (4.0) for the plants derived from cuttings obtained from symptomatic Cocoa mother plants, while plants derived from cuttings of improved mother plants exhibited no visible symptoms of the disease and the lowest population (45.1) of whiteflies. The Nuru app is inefficient for phenotypically detecting CMD at 3 months after planting (MAP), while at 6, 9 and 12 MAP, the app efficiently detected the disease using a molecular analysis technique. Resistant, non-diseased plants derived from cuttings obtained from SLICASS 4 mother plants produced the highest fresh storage root yield (54.9 t ha⁻¹). The highest storage root yield loss was recorded in the plants obtained from cuttings of symptomatic variety Cocoa mother plants harvested at Matotoka grassland ecology, Bombali District (90.2%), while those harvested from cuttings of asymptomatic variety Cocoa mother plants grown at the four test environments had a similar storage root yield loss ranging from 40.3 to 46.2%. Findings suggest the importance of genetic variability, environmental adaptation, utilization of diseased-free materials, and phytosanitation as disease management strategies for increased production. These findings provide important insights into the distribution, impact, and spread of CMD and whitefly abundance in the studied areas in Sierra Leone that could be exploited for cassava production, productivity, conservation, and population improvement.

Whitefly Bemisia tabaci (Gennadium, Hemiptera) causes severe damage to cassava plants through excessive feeding on leaves and transmitting viruses, such as African cassava mosaic virus (ACMV), East African cassava mosaic virus (EACMV), and ipomoviruses that cause cassava brown streak disease. Currently, little is known about the molecular diversity and distribution of whitefly species in the major cassava-growing zones of Nigeria. This study aimed to address the knowledge gap by assessing the genetic diversity, distribution, and associated cassava mosaic begomoviruses (CMBs) in whiteflies across South West and North Central, Nigeria. Whitefly samples were systematically collected from cassava plants during georeferenced epidemiological surveys in 2017, 2020, and 2022. The samples were genotyped using the mitochondrial cytochrome oxidase I (mtCOI) marker, and CMBs were detected by PCR with virus-specific primers. Phylogenetic analyses revealed four distinct genetic groups of B. tabaci: Sub-Saharan Africa 1 (SSA1; 84.8%), SSA2 (1.4%), SSA3 (13.1%), and Mediterranean (MED) (0.7%). The SSA1 group was the predominant and most widely distributed genotype across the surveyed zones, with three subgroups identified: SSA1-SG1, SSA1-SG3, and SSA1-SG5. The second most frequently identified genotype, SSA3, was restricted to the North Central zone, along with the SSA2 group, which was only identified in two North Central states (Niger and Plateau). African cassava mosaic virus (ACMV) was detected in SSA1-SG1, SSA1-SG5, and SSA3, whereas EACMV was found in only the SSA1-SG3. The findings of this study will aid in developing better whitefly management strategies to reduce the impact of CMD on cassava production in Nigeria.

The dearth of information on the extent of genetic variability in cassava limits the genetic improvement of cassava in Sierra Leone. This study aimed at assessing the genetic variability and relationships within 103 cassava genotypes using agro-morphological and culinary markers. A field trial was conducted in the School of Agriculture and Food Sciences research site. The experiment was laid out in an augmented randomized block design. Morphological classification based on qualitative and quantitative traits categorized the germplasm into three different groups. A total of ten principal components (PCs) in the qualitative and six PCs in the quantitative trait sets accounted for 66.74% and 67.27% of the total genetic variation, respectively. Traits with significantly strong and positive correlations included presence of fruit (PFRT) and presence of seeds (PSE) (r = 0.86 ***), root yield per plant (RYPP) and number of storage roots (NSR) (r = 0.76 ***), RYPP and number of commercial roots (NCR) (r = 0.68 ***), length of leaf lobes (LLL) and width of leaf lobes (WLL) (r = 0.66 ***), and between NSR and NCR (r = 0.84 ***). The cooking time, cooking percentage, texture, mealiness, taste, and aroma varied widely among the accessions. The findings established that the cassava germplasm possesses useful genetic variability that could be exploited through selection for short-term release programs, genetic conservation of the valuable germplasm, and genetic improvement of the crop.

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.