Detection of multiple potential alternative hosts of begomoviruses in Madagascar, using multiplexed parallel amplicon pyrosequencing. [O.08]

International audienceIn the last decades, begomoviruses emerged as probably the most economically important crop pathogens. Despites the hypothesis that uncultivated hosts, such as wild plants or weeds, provide alternative hosts during intercropping periods, few studies effectively identified the plant species involved. Here, we used multiple parallel-sequencing of a conserved region of begomovirus genome, using newly designed primers, to identify the presence of begomoviruses in a large number of wild plants and crops in Madagascar and sub-Saharan African countries. Whereas our primers set successfully amplified begomoviruses in a wide range of plant species and families, we focused our analyses on Madagascan samples, and identified four distinct Operational Taxonomic Units (OTUs), that infect both crop and weeds. While one of these OTUs likely represents an example of a malvaceous-adapted virus which acquired the ability to infect bean, three closely related OTUs, largely prevalent on tomato, were found infecting weeds. One of these tomato-associated OTU in particular, related to variants of tomato leaf curl Madagascar virus, was found in eight distinct plant species, suggesting its evolution as a generalist pathogen. Despites several biases associated to the use of primers designed from known sequences, and the need to confirm our results with the cloning of complete sequences, our study has unravelled the complexity of the relationships between begomoviruses and their hosts and raised some exciting questions on the niche partitioning of begomoviruses in natural and cultivated ecosystems. (Résumé d'auteur

Asystasia mosaic Madagascar virus: A novel bipartite begomovirus infecting the weed Asystasia gangetica# in Madagascar

International audienceHere, we describe for the first time the complete genome sequence of a new bipartite begomovirus in Madagascar isolated from the weed Asystasia gangetica (Acanthaceae), for which we propose the tentative name asystasia mosaic Madagascar virus (AMMGV). DNA-A and -B nucleotide sequences of AMMGV were only distantly related to known begomovirus sequence and shared highest nucleotide sequence identity of 72.9 % (DNA-A) and 66.9 % (DNA-B) with a recently described bipartite begomovirus infecting Asystasia sp. in West Africa. Phylogenetic analysis demonstrated that this novel virus from Madagascar belongs to a new lineage of Old World bipartite begomoviruses. (Résumé d'auteur

Molecular characterization of a new alphasatellite associated with a cassava mosaic geminivirus in Madagascar

Two complete nucleotide sequences of an alphasatellite isolated from a cassava plant with mosaic disease symptoms in Madagascar are described and analyzed. While the helper begomovirus was identified as an isolate of East African cassava mosaic Kenya virus (EACMKV), its associated alphasatellite was most closely related (80 % nucleotide sequence identity) to cotton leaf curl Gezira alphasatellite. These satellite molecules have typical features of alphasatellites, with a single gene in the virion sense, an A-rich region and a stem-loop structure. According to the proposed species demarcation threshold of alphasatellites (83 % nucleotide identity), they are isolates of a new species for which we propose the name "Cassava mosaic alphasatellite". (Résumé d'auteur

Molecular epidemiology, genetic diversity and dissemination routes of CMGs in sub-Saharan Africa and the south-west Indian Ocean islands. [S05-10]

International audienceCassava cultivation is associated with a wide range of diseases that seriously undermine the food and economic security in African countries. The most notable of these is CMD, caused by a complex of cassava mosaic geminiviruses (CMGs; Geminiviridae, Begomovirus). To better understand the epidemiology of CMD as a major constraint of cassava production, we investigated a large-scale plant epidemiological survey in Central African Republic (CAR) and Madagascar. CMD was shown to be the most serious constraint to cassava in both countries with an average incidence of 85% in CAR (Harimalala et al., Plant Pathol. 2015; Zinga et al., Crop Protection 2013). Importantly, 94% and 95% of diseased plants collected in CAR and Madagascar, respectively, had cutting-derived CMD infection, suggesting that farmers mostly use virus-infected cuttings for planting. Molecular diagnosis revealed that the causal agents of CMD in CAR, Chad (Zinga et al., NDR 2012), and Burkina Faso (Tiendrébéogo et al., Plant Pathol. 2009) are ACMV and/or EACMV-UG. We also demonstrated that 58% of CMD samples of CAR present mixed infections (ACMV and EACMV-UG) and that the severity of symptoms was significantly higher in these samples (Zinga et al., NDR 2013). Molecular diagnosis of CMGs in Madagascar revealed an unprecedented diversity of six species: ACMV, EACMCV, EACMKV, EACMV, SACMV, and CMMGV (Harimalala et al., Plant Pathol. 2015; Harimalala et al., Arch. Virol. 2012). Distinct geographical distributions were observed for the six species in Madagascar. While ACMV was more prevalent in the central highlands, EACMV and EACMKV were prevalent in lowlands and coastal regions. Molecular diagnosis revealed that mixed infection (up to four co-infected viruses) occurred in 21% of the samples and was associated with higher symptom severity scores. All our results suggest that mixed infection and synergism between CMGs could be an important feature in the low yields of cassava plants in these countries, similar to the severe CMD epidemics reported in East Africa. Given the sampling locations, sampling dates, and full genome sequences of hundreds of CMG isolates sampled during 1996–2009, we statistically retraced the historical migration routes of these viruses across sub-Saharan Africa and the SWIO islands (De Bruyn et al., BMC Evol. Biol. 2012). Phylogeographic analyses suggest that presence of CMGs on these islands is likely the result of recent introductions from mainland Africa between 1988 and 2009. Our results suggest that anthropic factors may play a major role in the spread of CMGs, as the principal axes of viral migration correspond with major routes of human movement and commercial trade. (Texte intégral

Cassava mosaic disease in Madagascar: complex epidemiology and evolutionary dynamics of cassava mosaic geminiviruses

International audienceCassava is the staple food for hundreds of millions of people in Africa but its cultivation is seriously constrained by cassava mosaic disease (CMD) in Madagascar and in Africa in general. In this study, we first identified the cassava mosaic geminiviruses (CMGs) involved in CMD in Madagascar and their associated epidemiological characteristics from countrywide surveys. Molecular diagnosis of CMGs in Madagascar revealed an unprecedented diversity and co-occurrence of six CMGs. Distinct geographical distributions were observed for the six viruses. While EACMCV and SACMV were widespread, ACMV was more prevalent in the central highlands, and EACMV and EACMKV were prevalent in lowlands and coastal regions. PCR diagnosis revealed that mixed infection (up to four co-infected viruses) occurred in 21% of the samples and were associated with higher symptom severity scores. Pairwise comparisons of virus associations showed that EACMCV was found in mixed infections more often than expected while ACMV and SACMV were mostly found in single infections. Even if the whitefly vector Bemisia tabaci was more abundant in lowland and coastal areas, infected cuttings remain the primary source of CMD propagation (95%) in Madagascar. Secondly, the genetic and spatial structure of CMGs populations was studied and we applied Bayesian phylogeographic modelling to infer the origins of Madagascan CMG populations within the epidemiological context of related populations situated on mainland Africa and other south western Indian Ocean islands. SACMV and ACMV, the two most prevalent viruses, displayed low degrees of genetic diversity and have most likely been introduced to the island only once. By contrast, EACMV-like CMG populations (EACMV, EAMCKV, EACMCV and complex recombinants of these) were more diverse, more spatially structured, and displayed evidence of at least three independent introductions from mainland Africa. Our study highlights both the complexity of CMD on Madagascar, and the distinct evolutionary and spatial dynamics of the different viral species that collectively are associated with this disease. (Résumé d'auteur