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 production in Ivory Coast is hampered by cassava mosaic disease (CMD), which is caused by several begomovirus species. To increase cassava production and conserve genetic resources, the Centre National de Recherche Agronomique (CNRA) maintains a germplasm collection of 610 cassava accessions of various origins, which is kept in open fields in Bouaké and Man. We carried out an epidemiological assessment of the collection and a molecular characterization of the viruses infecting the CNRA cassava germplasm. The field in Man was less affected by CMD (incidence 49.78%, severity 2.23, whitefly infection 2.23%), despite the abundant whitefly populations (1.34 per plant), compared to Bouaké (incidence 74.54%, severity 2.92, whitefly infection 8.04% and whitefly population of 0.34 per plant). However, the predominant mode of CMD transmission was through infected cassava cuttings at both sites. PCR analysis showed that the East African cassava mosaic Cameroon virus (EACMCMV) was always found in co‐infection with African cassava mosaic virus (ACMV), which also occurred in single infection. Co‐infections of EACMCMV and ACMV were more prevalent in Bouaké (52.64%) than Man (13.87%). Eleven complete genome sequences of cassava mosaic begomoviruses infecting the CNRA germplasm were obtained, and phylogenetic analysis showed that they are closely related to ACMV and EACMCMV isolates from Ghana, Burkina Faso and Nigeria. The results of this study will assist breeders to screen accurately for CMD resistance in progeny resulting from parental lines, enabling the strategic distribution of new clean cassava planting materials to reduce the impact of CMD.

Genetic diversity is very important in crop improvement. This study was carried out to assess the genetic diversity and the number of unique multilocus genotypes (MLGs) in a cassava collection in Burkina Faso. To achieve this objective, 130 cassava accessions were genotyped using 32 simple sequence repeat (SSR) markers. The results revealed that among these markers, twelve (12) were highly informative, with polymorphic information content (PIC) values greater than 0.50; twelve (12) were moderately informative, with PIC values ranging between 0.25 and 0.50; and eight (8) were not very informative, with PIC values lower than 0.25. A moderate level of genetic diversity was found for the population, indicated by the average expected heterozygosity (0.45) and the observed heterozygosity (0.48). About 83.8% of unique multilocus genotypes were found in the cassava collection, indicating that SSR markers seem to be most appropriate for MLG identification. Population structure analysis based on hierarchical clustering identified two subpopulations and the Bayesian approach suggested five clusters. Additionally, discriminant analysis of principal components (DAPC) separated the cassava accessions into 13 subpopulations. A comparison of these results and those of a previous study using single nucleotide polymorphisms (SNP) suggests that each type of marker can be used to assess the genetic structure of cassava grown in Burkina Faso.

Background: Faced with the recrudescence of viral CRESS-DNA plant diseases, the availability of efficient and cost-effective tools for routine diagnosis and genomic characterisation is vital. As these viruses possess circular single-strand DNA genomes, they have been routinely characterised using rolling circle amplification (RCA) coupled with Sanger sequencing. However, while providing the basis of our knowledge of the diverse CRESS-DNA viruses, this approach is laboratory-intensive, time-consuming and ultimately ineffective faced with co-infection or viruses with multiple genomic components, two common characteristics of these viruses. Whereas alternatives have proved effective in some applications, there is a strong need for next-generation sequencing methods suitable for small-scale projects that can routinely produce high quality sequences comparable to the gold standard Sanger sequencing. Results: Here, we present an RCA sequencing diagnostic technique using the latest Oxford Nanopore Technology flongle flow cells. Originally, using the tandem-repeat nature of RCA products, we were able to improve the quality of each viral read and assemble high-quality genomic components. The effectiveness of the method was demonstrated on two plant samples, one infected with the bipartite begomovirus African cassava mosaic virus (ACMV) and the other infected with the nanovirus faba bean necrotic stunt virus (FBNSV), a virus with eight genomic segments. This method allow us to recover all genomic components of both viruses. The assembled genomes of ACMV and FBNSV shared 100% nucleotide identity with those obtained with Sanger sequencing. Additionally, our experiments demonstrated that for similar-sized components, the number of reads was proportional to the segment frequencies measured using qPCR. Conclusion: In this study, we demonstrated an accessible and effective Nanopore-based method for high-quality genomic characterisation of CRESS-DNA viruses, comparable to Sanger sequencing. Face with of increasing challenges posed by viral CRESS-DNA plant diseases, integrating this approach into routine workflows could pave the way for more proactive responses to viral epidemics.

Cassava adaptation to climate change and its resistance to diseases are essential prerequisites for achieving food security in sub-Saharan Africa. The accessions collected from farmers’ fields are very important because they can provide new sources of genetic variability that are essential to achieve this goal. In this study, a panel of 184 accessions collected in Burkina Faso was genotyped using 36 single nucleotide polymorphism (SNP) markers. The accessions and markers that presented with more than 6% missing data were removed from the dataset and the remaining 34 markers and 166 accessions were retained for genetic diversity and population structure assessment. The average values of expected heterozygosity (0.46), observed heterozygosity (0.58), and polymorphic information content (0.36) indicated high genetic diversity within accessions. A complex genetic structure of 166 accessions was observed through the formation of 17 clusters using discriminant analysis of principal components (DAPC) and two clusters using Bayesian analysis. Out of the 166 accessions, 79 were unique multilocus genotypes (MLGs) and 87 were potentially duplicates. From the 79 MLGs, DAPC suggested eight clusters while the Bayesian analysis suggested seven clusters. Clusters shaped by DAPC appeared to be more consistent with a higher probability of assignment of the accessions within the clusters. Principal Coordinate Analysis (PCoA) showed a lack of clustering according to geographical origin. Information related to breeding patterns and geographic origin did not allow for a clear differentiation between the clusters according to the analysis of molecular variance (AMOVA). The results of this study will be useful for cassava germplasm conservation and breeding programs.