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In recent decades, a legion of monopartite begomoviruses transmitted by the whitefly Bemisia tabaci has emerged as serious threats to vegetable crops in Africa. Recent studies in Burkina Faso (West Africa) reported the predominance of pepper yellow vein Mali virus (PepYVMLV) and its frequent association with a previously unknown DNA-B component. To understand the role of this DNA-B component in the emergence of PepYVMLV, we assessed biological traits related to virulence, virus accumulation, location in the tissue and transmission. We demonstrate that the DNA-B component is not required for systemic movement and symptom development of PepYVMLV (non-strict association), but that its association produces more severe symptoms including growth arrest and plant death. The increased virulence is associated with a higher viral DNA accumulation in plant tissues, an increase in the number of contaminated nuclei of the phloem parenchyma and in the transmission rate by B. tabaci. Our results suggest that the association of a DNA-B component with the otherwise monopartite PepYVMLV is a key factor of its emergence.

In this report, we present the first description of nine complete genome sequences of a new strain of chayote yellow mosaic virus (ChaYMV, genus Begomovirus, family Geminiviridae), provisionally named Côte d'Ivoire (ChaYMV-CI), isolated from bitter melon (Momordica charantia) leaf samples showing yellow mosaic symptoms collected in the region of Abidjan in Côte d'Ivoire in 2013 and 2019. The nucleotide sequences of ChaYMV-CI DNA-A-like genome share the highest nucleotide sequence identities (91.8–92.5%) with those of ChaYMV isolates from Benin and Cameroon. Phylogenetic analysis confirmed the segregation of ChaYMV isolates into two distinct clades and their affiliation to Old World monopartite begomoviruses. The discovery of a new strain of ChaYMV in West Africa, at the limit of the taxonomic demarcation threshold for begomoviruses (91%), call for further investigations into the molecular diversity, geographical distribution and host range of ChaYMV in Western Africa.

In recent decades, a legion of monopartite begomoviruses transmitted by the whitefly Bemisia tabaci has emerged as serious threats to vegetable crops in Africa. Recent studies in Burkina Faso (West Africa) reported the predominance of pepper yellow vein Mali virus (PepYVMLV) and its frequent association with a previously unknown DNA-B component. To understand the role of this DNA-B component in the emergence of PepYVMLV, we assessed biological traits related to virulence, virus accumulation, location in the tissue and transmission. We demonstrate that the DNA-B component is not required for systemic movement and symptom development of PepYVMLV (non-strict association), but that its association produces more severe symptoms including growth arrest and plant death. The increased virulence is associated with a higher viral DNA accumulation in plant tissues, an increase in the number of contaminated nuclei of the phloem parenchyma and in the transmission rate by B. tabaci. Our results suggest that the association of a DNA-B component with the otherwise monopartite PepYVMLV is a key factor of its emergence.

In this report, we present the first description of nine complete genome sequences of a new strain of chayote yellow mosaic virus (ChaYMV, genus Begomovirus, family Geminiviridae), provisionally named Côte d'Ivoire (ChaYMV-CI), isolated from bitter melon (Momordica charantia) leaf samples showing yellow mosaic symptoms collected in the region of Abidjan in Côte d'Ivoire in 2013 and 2019. The nucleotide sequences of ChaYMV-CI DNA-A-like genome share the highest nucleotide sequence identities (91.8–92.5%) with those of ChaYMV isolates from Benin and Cameroon. Phylogenetic analysis confirmed the segregation of ChaYMV isolates into two distinct clades and their affiliation to Old World monopartite begomoviruses. The discovery of a new strain of ChaYMV in West Africa, at the limit of the taxonomic demarcation threshold for begomoviruses (91%), call for further investigations into the molecular diversity, geographical distribution and host range of ChaYMV in Western Africa.

Next-generation sequencing (NGS), through the implementation of metagenomic protocols,has led to the discovery of thousands of new viruses in the last decade. Nevertheless, these protocolsare still laborious and costly to implement, and the technique has not yet become routine for everydayvirus characterization. Within the context of CRESS DNA virus studies, we implemented twoalternative long-read NGS protocols, one that is agnostic to the sequence (without a priori knowledgeof the viral genome) and the other that use specific primers to target a virus (with a priori). Agnosticand specific long read NGS-based assembled genomes of two capulavirus strains were compared tothose obtained using the gold standard technique of Sanger sequencing. Both protocols allowed thedetection and accurate full genome characterization of both strains. Globally, the assembled genomeswere very similar (99.5–99.7% identity) to the Sanger sequences consensus, but differences in thehomopolymeric tracks of these sequences indicated a specific lack of accuracy of the long reads NGSapproach that has yet to be improved. Nevertheless, the use of the bench-top sequencer has provento be a credible alternative in the context of CRESS DNA virus study and could offer a new range ofapplications not previously accessible.

Next-generation sequencing (NGS), through the implementation of metagenomic protocols,has led to the discovery of thousands of new viruses in the last decade. Nevertheless, these protocolsare still laborious and costly to implement, and the technique has not yet become routine for everydayvirus characterization. Within the context of CRESS DNA virus studies, we implemented twoalternative long-read NGS protocols, one that is agnostic to the sequence (without a priori knowledgeof the viral genome) and the other that use specific primers to target a virus (with a priori). Agnosticand specific long read NGS-based assembled genomes of two capulavirus strains were compared tothose obtained using the gold standard technique of Sanger sequencing. Both protocols allowed thedetection and accurate full genome characterization of both strains. Globally, the assembled genomeswere very similar (99.5–99.7% identity) to the Sanger sequences consensus, but differences in thehomopolymeric tracks of these sequences indicated a specific lack of accuracy of the long reads NGSapproach that has yet to be improved. Nevertheless, the use of the bench-top sequencer has provento be a credible alternative in the context of CRESS DNA virus study and could offer a new range ofapplications not previously accessible.

Mostly found in Africa and its surrounding islands, African streak viruses (AfSV) represent the largest group of known mastreviruses. Of the thirteen AfSV species that are known to infect either cultivated or wild Poaceae plant species, six have been identified on Reunion Island. To better characterize AfSV diversity on this island, we undertook a survey of a small agroecosystem using a new metagenomics-based approach involving rolling circle amplification with random PCR amplification tagging (RCA-RA-PCR), high-throughput sequencing (Illumina HiSeq) and the mastrevirus reads classification using phylogenetic placement. Mastreviruses that likely belong to three new species were discovered and full genome sequences of these were determined by Sanger sequencing. The geminivirus-focused metagenomics approach we applied in this study was useful in both the detection of known and novel mastreviruses. The results confirm that Reunion Island is indeed a hotspot of AfSV diversity and that many of the mastrevirus species have likely been introduced multiple times. Applying a similar approach in other natural and agricultural environments should yield sufficient detail on the composition and diversity of geminivirus communities to precipitate major advances in our understanding of the ecology and the evolutionary history of this important group of viruses.

The Mastrevirus genus (Geminiviridae family) contains circular single-stranded DNA viruses transmitted by leafhoppers (in the Cicadellidae family) to a wide range of either monocotyledonous or dicotyledonous host species. Most of the known monocot-infecting mastreviruses have been identified either in Africa or surrounding islands. This group of mastreviruses have collectively been called the “African streak viruses” (AfSV). Of the 13 AfSV species infecting cultivated and wild Poaceae species, six have been identified on Reunion Island. Interestingly, these species were probably introduced at different time and they present with putatively distinct host ranges. Understanding how this virus community operates remains an essential question in the understanding of virus ecology, evolution and emergence. Therefore, to elucidate the diversity, host ranges and structure of mastrevirus communities on Reunion Island, we undertook an extensive survey in a single sampling site of one acre including crop fields, orchards and uncultivated areas. After four sampling campaigns, 2917 samples of 30 cultivated and uncultivated Poaceae species were randomly collected, regardless of their health status. Total plant DNA was isolated and circular viral genomes were amplified by a sequence-independent amplification procedure combining rolling circle amplification, a random amplification tagging (RCA-RA) and high-throughput sequencing (Illumina HiSeq). For every sample, mastrevirus reads were classified using phylogenetic placement within species and strains. Mastrevirus species were confirmed by cloning and Sanger sequencing. Besides uncovering previously undescribed mastrevirus species, our results provide an exhaustive view of the mastrevirus-host association network within an agroecosystem. The topology of this network suggests (1) the co-existence of viruses ranging from generalist to specialist and (2) that certain hosts may act as hubs of virus infection and transmission.

The Mastrevirus genus (Geminiviridae family) contains circular single-stranded DNA viruses transmitted by leafhoppers (in the Cicadellidae family) to a wide range of either monocotyledonous or dicotyledonous host species. Most of the known monocot-infecting mastreviruses have been identified either in Africa or surrounding islands. This group of mastreviruses have collectively been called the “African streak viruses” (AfSV). Of the 13 AfSV species infecting cultivated and wild Poaceae species, six have been identified on Reunion Island. Interestingly, these species were probably introduced at different time and they present with putatively distinct host ranges. Understanding how this virus community operates remains an essential question in the understanding of virus ecology, evolution and emergence. Therefore, to elucidate the diversity, host ranges and structure of mastrevirus communities on Reunion Island, we undertook an extensive survey in a single sampling site of one acre including crop fields, orchards and uncultivated areas. After four sampling campaigns, 2917 samples of 30 cultivated and uncultivated Poaceae species were randomly collected, regardless of their health status. Total plant DNA was isolated and circular viral genomes were amplified by a sequence-independent amplification procedure combining rolling circle amplification, a random amplification tagging (RCA-RA) and high-throughput sequencing (Illumina HiSeq). For every sample, mastrevirus reads were classified using phylogenetic placement within species and strains. Mastrevirus species were confirmed by cloning and Sanger sequencing. Besides uncovering previously undescribed mastrevirus species, our results provide an exhaustive view of the mastrevirus-host association network within an agroecosystem. The topology of this network suggests (1) the co-existence of viruses ranging from generalist to specialist and (2) that certain hosts may act as hubs of virus infection and transmission.

Mostly found in Africa and its surrounding islands, African streak viruses (AfSV) represent the largest group of known mastreviruses. Of the thirteen AfSV species that are known to infect either cultivated or wild Poaceae plant species, six have been identified on Reunion Island. To better characterize AfSV diversity on this island, we undertook a survey of a small agroecosystem using a new metagenomics-based approach involving rolling circle amplification with random PCR amplification tagging (RCA-RA-PCR), high-throughput sequencing (Illumina HiSeq) and the mastrevirus reads classification using phylogenetic placement. Mastreviruses that likely belong to three new species were discovered and full genome sequences of these were determined by Sanger sequencing. The geminivirus-focused metagenomics approach we applied in this study was useful in both the detection of known and novel mastreviruses. The results confirm that Reunion Island is indeed a hotspot of AfSV diversity and that many of the mastrevirus species have likely been introduced multiple times. Applying a similar approach in other natural and agricultural environments should yield sufficient detail on the composition and diversity of geminivirus communities to precipitate major advances in our understanding of the ecology and the evolutionary history of this important group of viruses.

Background: Cassava mosaic disease (CMD) in Madagascar is caused by a complex of at least six African cassava mosaic geminivirus (CMG) species. This provides a rare opportunity for a comparative study of the evolutionary and epidemiological dynamics of distinct pathogenic crop-infecting viral species that coexist within the same environment. The genetic and spatial structure of CMG populations in Madagascar was studied and Bayesian phylogeographic modelling was applied 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 (SWIO) islands. Results: The isolation and analysis of 279 DNA-A and 117 DNA-B sequences revealed the presence in Madagascar of four prevalent CMG species (South African cassava mosaic virus, SACMV; African cassava mosaic virus, ACMV; East African cassava mosaic Kenya virus, EACMKV; and East African cassava mosaic Cameroon virus, EACMCV), and of numerous CMG recombinants that have, to date, only ever been detected on this island. 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 (consisting of East African cassava mosaic virus, 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. Although there were no statistically supported virus movement events between Madagascar and the other SWIO islands, at least one mainland African ACMV variant likely originated in Madagascar. Conclusions : Our study highlights both the complexity of CMD in Madagascar, and the distinct evolutionary and spatial dynamics of the different viral species that collectively are associated with this disease. Given that more distinct CMG species and recombinants have been found in Madagascar tha

BACKGROUND and OBJECTIVES Cassava 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. We have undertaken (1) to identify the cassava mosaic geminiviruses (CMGs) involved in CMD in Madagascar and their epidemiological characteristics from country-wide surveys, and (2) to study the genetic and spatial structure of Malagasy CMGs populations. MATERIAL and METHODS Altogether 708 cassava leaf samples were collected with and without CMD symptoms from the main cassavagrowing areas of Madagascar during 2009 to 2011. Prevalence and symptom severity of CMD, origin of infection (whitefly or cutting), and abundance of whiteflies were assessed. RESULTS 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. 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 fro

Background: Cassava mosaic disease (CMD) in Madagascar is caused by a complex of at least six African cassava mosaic geminivirus (CMG) species. This provides a rare opportunity for a comparative study of the evolutionary and epidemiological dynamics of distinct pathogenic crop-infecting viral species that coexist within the same environment. The genetic and spatial structure of CMG populations in Madagascar was studied and Bayesian phylogeographic modelling was applied 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 (SWIO) islands. Results: The isolation and analysis of 279 DNA-A and 117 DNA-B sequences revealed the presence in Madagascar of four prevalent CMG species (South African cassava mosaic virus, SACMV; African cassava mosaic virus, ACMV; East African cassava mosaic Kenya virus, EACMKV; and East African cassava mosaic Cameroon virus, EACMCV), and of numerous CMG recombinants that have, to date, only ever been detected on this island. 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 (consisting of East African cassava mosaic virus, 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. Although there were no statistically supported virus movement events between Madagascar and the other SWIO islands, at least one mainland African ACMV variant likely originated in Madagascar. Conclusions : Our study highlights both the complexity of CMD in Madagascar, and the distinct evolutionary and spatial dynamics of the different viral species that collectively are associated with this disease. Given that more distinct CMG species and recombinants have been found in Madagascar tha

BACKGROUND and OBJECTIVES Cassava 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. We have undertaken (1) to identify the cassava mosaic geminiviruses (CMGs) involved in CMD in Madagascar and their epidemiological characteristics from country-wide surveys, and (2) to study the genetic and spatial structure of Malagasy CMGs populations. MATERIAL and METHODS Altogether 708 cassava leaf samples were collected with and without CMD symptoms from the main cassavagrowing areas of Madagascar during 2009 to 2011. Prevalence and symptom severity of CMD, origin of infection (whitefly or cutting), and abundance of whiteflies were assessed. RESULTS 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. 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 fro

In 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.

Cassava 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 dist

Cassava 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 dist

In 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.

Biological invasions are major threats to biodiversity and the main causes of emerging viral diseases. The ongoing spread of Tomato yellow leaf curl virus is a major concern to the sustainable tomato production throughout the world. The two main strains of TYLCV have been successively introduced in Reunion Island providing a fortuitous field experiment to study the invasion and competition of these two emerging strains in a tropical and insular environment. In this study, a seven-year field survey was performed following the introduction of the Israel strain of TYLCV (TYLCV-IL) into a niche occupied by the Mild strain of TYLCV (TYLCV-Mld). A displacement of the resident TYLCV-Mld by the newcomer TYLCV-IL was observed in this short period. To understand the factors associated with this displacement, biological traits related to fitness were measured to compare these strains. Besides demonstrating a better ecological aptitude of TYLCV-IL, which explains its rapid spread and increasing prevalence, the first estimate of the number of viral particles efficiently transmitted by an insect vector for a circulative virus was obtained. However, TYLCV-Mld persistence in the field (especially in mixed infections with TYLCV-IL) spurred further experiments regarding the effects of the mixed infections on these biological traits. Our study revealed complex interplay between these two strains of one of the most emergent plant virus following their successive introductions in the insular and tropical environment of Reunion Island. This rare case of unilateral facilitation between two pathogens led to the epidemiological rescue and maintenance of the less fit strain. (Texte intégral)

Cassava (Manihot esculenta) is a major food source for over 200 million sub-Saharan Africans. Unfortunately, its cultivation is severely hampered by cassava mosaic disease (CMD). Caused by a complex of bipartite cassava mosaic geminiviruses (CMG) species (Family: Geminivirideae; Genus: Begomovirus) CMD has been widely described throughout Africa and it is apparent that CMGs are expanding their geographical distribution. Determining where and when CMG movements have occurred could help curtail its spread and reveal the ecological and anthropic factors associated with similar viral invasions. We applied Bayesian phylogeographic inference and recombination analyses to available and newly described CMG sequences to reconstruct a plausible history of CMG diversification and migration between Africa and South West Indian Ocean (SWIO) islands. The isolation and analysis of 114 DNA-A and 41 DNA-B sequences demonstrated the presence of three CMG species circulating in the Comoros and Seychelles archipelagos (East African cassava mosaic virus, EACMV; East African cassava mosaic Kenya virus, EACMKV; and East African cassava mosaic Cameroon virus, EACMCV). Phylogeographic analyses suggest that CMG's presence on these SWIO islands is probably the result of at least four independent introduction events from mainland Africa occurring between 1988 and 2009. Amongst the islands of the Comoros archipelago, two major migration pathways were inferred: One from Grande Comore to Mohéli and the second from Mayotte to Anjouan. Numerous re-assortments events were detected between EACMV and EACMKV, which seem to almost freely interchange their genome components. Rapid and extensive virus spread within the SWIO islands was demonstrated for three CMG complex species. Strong evolutionary or ecological interaction between CMG species may explain both their propensity to exchange components and the absence of recombination with non-CMG begomoviruses. Our results suggest an important role of anthr

Biological invasions are major threats to biodiversity and the main causes of emerging viral diseases. The ongoing spread of Tomato yellow leaf curl virus is a major concern to the sustainable tomato production throughout the world. The two main strains of TYLCV have been successively introduced in Reunion Island providing a fortuitous field experiment to study the invasion and competition of these two emerging strains in a tropical and insular environment. In this study, a seven-year field survey was performed following the introduction of the Israel strain of TYLCV (TYLCV-IL) into a niche occupied by the Mild strain of TYLCV (TYLCV-Mld). A displacement of the resident TYLCV-Mld by the newcomer TYLCV-IL was observed in this short period. To understand the factors associated with this displacement, biological traits related to fitness were measured to compare these strains. Besides demonstrating a better ecological aptitude of TYLCV-IL, which explains its rapid spread and increasing prevalence, the first estimate of the number of viral particles efficiently transmitted by an insect vector for a circulative virus was obtained. However, TYLCV-Mld persistence in the field (especially in mixed infections with TYLCV-IL) spurred further experiments regarding the effects of the mixed infections on these biological traits. Our study revealed complex interplay between these two strains of one of the most emergent plant virus following their successive introductions in the insular and tropical environment of Reunion Island. This rare case of unilateral facilitation between two pathogens led to the epidemiological rescue and maintenance of the less fit strain. (Texte intégral)

Cassava (Manihot esculenta) is a major food source for over 200 million sub-Saharan Africans. Unfortunately, its cultivation is severely hampered by cassava mosaic disease (CMD). Caused by a complex of bipartite cassava mosaic geminiviruses (CMG) species (Family: Geminivirideae; Genus: Begomovirus) CMD has been widely described throughout Africa and it is apparent that CMGs are expanding their geographical distribution. Determining where and when CMG movements have occurred could help curtail its spread and reveal the ecological and anthropic factors associated with similar viral invasions. We applied Bayesian phylogeographic inference and recombination analyses to available and newly described CMG sequences to reconstruct a plausible history of CMG diversification and migration between Africa and South West Indian Ocean (SWIO) islands. The isolation and analysis of 114 DNA-A and 41 DNA-B sequences demonstrated the presence of three CMG species circulating in the Comoros and Seychelles archipelagos (East African cassava mosaic virus, EACMV; East African cassava mosaic Kenya virus, EACMKV; and East African cassava mosaic Cameroon virus, EACMCV). Phylogeographic analyses suggest that CMG's presence on these SWIO islands is probably the result of at least four independent introduction events from mainland Africa occurring between 1988 and 2009. Amongst the islands of the Comoros archipelago, two major migration pathways were inferred: One from Grande Comore to Mohéli and the second from Mayotte to Anjouan. Numerous re-assortments events were detected between EACMV and EACMKV, which seem to almost freely interchange their genome components. Rapid and extensive virus spread within the SWIO islands was demonstrated for three CMG complex species. Strong evolutionary or ecological interaction between CMG species may explain both their propensity to exchange components and the absence of recombination with non-CMG begomoviruses. Our results suggest an important role of anthr

Cassava mosaic disease (CMD) caused by cassava mosaic geminiviruses (CMGs, Geminiviridae) is a major threat on cassava production throughout Africa. In Madagascar, severe symptoms with high prevalence of CMD were observed. From 700 mostly symptomatic cassava leaves, we undertook molecular characterization of the CMGs involved. The PCR diagnosis confirmed the presence of CMGs in Madagascar and six species were detected with the frequent occurrence of mixed infections. Based on rolling circle amplification, cloning and sequencing, we obtained full genome sequences of 281 DNA-A and 119 DNA-B of CMGs. DNA-A sequences were most closely related to those of African cassava mosaic virus (ACMV), South African cassava mosaic virus (SACMV), East African cassava mosaic virus (EACMV), East African cassava mosaic Cameroon virus (EACMCV), East African cassava mosaic Kenya virus (EACMKV) and a new species named cassava mosaic Madagascar virus (CMMGV). DNAB sequences were most closely related to those of ACMV, EACMKV, EACMCV and CMMGV. Phylogenetic reconstruction allowed to assess the geographical structure of CMG populations and to determine the recent history of CMG migrations in Madagascar. Taken together, our results point to Madagascar as a potential major center of begomovirus diversity.

Cassava mosaic disease (CMD) is a major constraint on cassava cultivation in Africa. The disease is endemic and is caused by seven distinct cassava mosaic geminiviruses (CMGs), some of them including several variants. From cassava leaf samples presenting CMD symptoms collected in Burkina Faso, four DNA-A begomovirus components were cloned and sequenced, showing 99.9% nucleotide identity among them. These isolates are most closely related to African cassava mosaic virus (ACMV) but share less than 89% nucleotide identity (taxonomic threshold) with any previously described begomovirus. A DNA-B genomic component, sharing 93% nucleotide identity with DNA-B of ACMV, was also characterized. Since all genomic components have a typical genome organization of Old World bipartite begomoviruses, this new species was provisionally named African cassava mosaic Burkina Faso virus (ACMBFV). Recombination analysis of the new virus demonstrated an interspecies recombinant origin, with major parents related to West African isolates of ACMV, and minor parents related to Tomato leaf curl Cameroon virus and Cotton leaf curl Gezira virus. This is the first report of an ACMV-like recombinant begomovirus arisen by interspecific recombination between bipartite and monopartite African begomoviruses. (Texte intégral)

Background: Cassava mosaic disease (CMD) is a major constraint on cassava cultivation in Africa. The disease is endemic and is caused by seven distinct cassava mosaic geminiviruses (CMGs), some of them including several variants. Findings: From cassava leaf samples presenting CMD symptoms collected in Burkina Faso, four DNA-A begomovirus components were cloned and sequenced, showing 99.9% nucleotide identity among them. These isolates are most closely related to African cassava mosaic virus (ACMV) but share less than 89% nucleotide identity (taxonomic threshold) with any previously described begomovirus. A DNA-B genomic component, sharing 93% nucleotide identity with DNA-B of ACMV, was also characterized. Since all genomic components have a typical genome organization of Old World bipartite begomoviruses, this new species was provisionally named African cassava mosaic Burkina Faso virus (ACMBFV). Recombination analysis of the new virus demonstrated an interspecies recombinant origin, with major parents related to West African isolates of ACMV, and minor parents related to Tomato leaf curl Cameroon virus and Cotton leaf curl Gezira virus. Conclusion: This is the first report of an ACMV-like recombinant begomovirus arisen by interspecific recombination between bipartite and monopartite African begomoviruses.

Cassava mosaic disease (CMD) caused by cassava mosaic geminiviruses (CMGs, Geminiviridae) is a major threat on cassava production throughout Africa. In Madagascar, severe symptoms with high prevalence of CMD were observed. From 700 mostly symptomatic cassava leaves, we undertook molecular characterization of the CMGs involved. The PCR diagnosis confirmed the presence of CMGs in Madagascar and six species were detected with the frequent occurrence of mixed infections. Based on rolling circle amplification, cloning and sequencing, we obtained full genome sequences of 281 DNA-A and 119 DNA-B of CMGs. DNA-A sequences were most closely related to those of African cassava mosaic virus (ACMV), South African cassava mosaic virus (SACMV), East African cassava mosaic virus (EACMV), East African cassava mosaic Cameroon virus (EACMCV), East African cassava mosaic Kenya virus (EACMKV) and a new species named cassava mosaic Madagascar virus (CMMGV). DNAB sequences were most closely related to those of ACMV, EACMKV, EACMCV and CMMGV. Phylogenetic reconstruction allowed to assess the geographical structure of CMG populations and to determine the recent history of CMG migrations in Madagascar. Taken together, our results point to Madagascar as a potential major center of begomovirus diversity.

Cassava mosaic disease (CMD) is a major constraint on cassava cultivation in Africa. The disease is endemic and is caused by seven distinct cassava mosaic geminiviruses (CMGs), some of them including several variants. From cassava leaf samples presenting CMD symptoms collected in Burkina Faso, four DNA-A begomovirus components were cloned and sequenced, showing 99.9% nucleotide identity among them. These isolates are most closely related to African cassava mosaic virus (ACMV) but share less than 89% nucleotide identity (taxonomic threshold) with any previously described begomovirus. A DNA-B genomic component, sharing 93% nucleotide identity with DNA-B of ACMV, was also characterized. Since all genomic components have a typical genome organization of Old World bipartite begomoviruses, this new species was provisionally named African cassava mosaic Burkina Faso virus (ACMBFV). Recombination analysis of the new virus demonstrated an interspecies recombinant origin, with major parents related to West African isolates of ACMV, and minor parents related to Tomato leaf curl Cameroon virus and Cotton leaf curl Gezira virus. This is the first report of an ACMV-like recombinant begomovirus arisen by interspecific recombination between bipartite and monopartite African begomoviruses. (Texte intégral)

Background: Cassava mosaic disease (CMD) is a major constraint on cassava cultivation in Africa. The disease is endemic and is caused by seven distinct cassava mosaic geminiviruses (CMGs), some of them including several variants. Findings: From cassava leaf samples presenting CMD symptoms collected in Burkina Faso, four DNA-A begomovirus components were cloned and sequenced, showing 99.9% nucleotide identity among them. These isolates are most closely related to African cassava mosaic virus (ACMV) but share less than 89% nucleotide identity (taxonomic threshold) with any previously described begomovirus. A DNA-B genomic component, sharing 93% nucleotide identity with DNA-B of ACMV, was also characterized. Since all genomic components have a typical genome organization of Old World bipartite begomoviruses, this new species was provisionally named African cassava mosaic Burkina Faso virus (ACMBFV). Recombination analysis of the new virus demonstrated an interspecies recombinant origin, with major parents related to West African isolates of ACMV, and minor parents related to Tomato leaf curl Cameroon virus and Cotton leaf curl Gezira virus. Conclusion: This is the first report of an ACMV-like recombinant begomovirus arisen by interspecific recombination between bipartite and monopartite African begomoviruses.

Genetic recombination is an important process during the evolution of many virus species and occurs particularly frequently amongst begomoviruses in the single stranded DNA virus family, Geminiviridae. As in many other recombining viruses it is apparent that non-random recombination breakpoint distributions observable within begomovirus genomes sampled from nature are the product of variations both in basal recombination rates across genomes and in the over-all viability of different recombinant genomes. Whereas factors influencing basal recombination rates might include local degrees of sequence similarity between recombining genomes, nucleic acid secondary structures and genomic sensitivity to nuclease attack or breakage, the viability of recombinant genomes could be influenced by the degree to which their co-evolved protein-protein and protein-nucleotide and nucleotide-nucleotide interactions are disreputable by recombination. Here we investigate patterns of recombination that occur over 120 day long experimental infections of tomato plants with the begomoviruses Tomato yellow leaf curl virus and Tomato leaf curl Comoros virus. We show that patterns of sequence exchange between these viruses can be extraordinarily complex and present clear evidence that factors such as local degrees of sequence similarity but not genomic secondary structure strongly influence where recombination breakpoints occur. It is also apparent from our experiment that over-all patterns of recombination are strongly influenced by selection against individual recombinants displaying disrupted intra-genomic interactions such as those required for proper protein and nucleic acid folding. Crucially, we find that selection favoring the preservation of co-evolved longer-range proteinprotein and protein DNA interactions is so strong that its imprint can even be used to identify the exact sequence tracts involved in these interactions.

Background: Begomovirus is a genus of phytopathogenic single-stranded DNA viruses, transmitted by the whitefly Bemisia tabaci. This genus includes emerging and economically significant viruses such as those associated with Tomato Yellow Leaf Curl Disease, for which diagnostic tools are needed to prevent dispersion and new introductions. Five real-time PCRs with an internal tomato reporter gene were developed for accurate detection and quantification of monopartite begomoviruses, including two strains of the Tomato yellow leaf curl virus (TYLCV; Mld and IL strains), the Tomato leaf curl Comoros virus-like viruses (ToLCKMV-like viruses) and the two molecules of the bipartite Potato yellow mosaic virus. These diagnostic tools have a unique standard quantification, comprising the targeted viral and internal report amplicons. These duplex real-time PCRs were applied to artificially inoculated plants to monitor and compare their viral development. Results: Real-time PCRs were optimized for accurate detection and quantification over a range of 2 × 109 to 2 × 103 copies of genomic viral DNA/?L for TYLCV-Mld, TYLCV-IL and PYMV-B and 2 × 108 to 2 × 103 copies of genomic viral DNA/?L for PYMV-A and ToLCKMV-like viruses. These real-time PCRs were applied to artificially inoculated plants and viral loads were compared at 10, 20 and 30 days post-inoculation. Different patterns of viral accumulation were observed between the bipartite and the monopartite begomoviruses. Interestingly, PYMV accumulated more viral DNA at each date for both genomic components compared to all the monopartite viruses. Also, PYMV reached its highest viral load at 10 dpi contrary to the other viruses (20 dpi). The accumulation kinetics of the two strains of emergent TYLCV differed from the ToLCKMV-like viruses in the higher quantities of viral DNA produced in the early phase of the infection and in the shorter time to reach this peak viral load. Conclusions: To detect and quantify a wide range of begomovi

Le gombo (Abelmoschus esculentus, Malvaceae) est une plante légumière originaire d'Afrique de première importance pour sa richesse en vitamines et en sels minéraux. Cependant, la maladie de l'enroulement foliaire du gombo (OLCD) constitue une contrainte majeure pour sa production dans les régions tropicales. L'impact de la maladie a été évalué au Burkina Faso pour quatre accessions du cultivar local 'Man Yanga' et quatre cultivars commerciaux (Clemson spineless, Indiana, Lima et Volta) au champ en 2007 et 2008 (Tiendrébéogo et al., Crop Protection, 2010). Il résulte une très forte incidence et sévérité de la maladie observées chez les accessions du cultivar local (respectivement 69-73% et 58%) comparativement aux cultivars commerciaux (respectivement 9-16% et 40%). De plus, l'impact de la maladie sur le rendement (nombre de fruits par plante, longueur, diamètre et poids du fruit) a été étudié, nous amenant au constat suivant : des pertes de rendement significativement plus importantes ont été observées pour le cultivar local (26-55%) comparativement aux cultivars commerciaux (4,4-9,6%) Les pertes économiques moyennes à l'hectare ont été estimées à 11100 et 1950 dollars, respectivement chez le cultivar local et les cultivars commerciaux. Notre étude agronomique a permis de démontrer l'impact négatif de l'OLCD sur la production du gombo au Burkina Faso, la sensibilité du cultivar local et l'intérêt de diffuser du matériel amélioré. La collecte de feuilles de gombo symptomatiques réalisée dans les grandes régions productrices du gombo au Burkina Faso a permis de diagnostiquer la présence d'un bégomovirus monopartite associé à un complexe d'ADN satellites (Tiendrébéogo et al., Virology Journal, 2010). Vingt-trois génomes complets d'isolats du Cotton leaf curl Gezira virus (CLCuGV) ont été clonés et séquencés. Dans un même temps, six betasatellites correspondant au Cotton leaf curl Gezira betasatellite (CLCuGB), un alphasatellite variant du Cotton leaf curl Gezira alphas

Les bégomovirus (Geminiviridae) transmis par l'aleurode Bemisia tabaci sont responsables de nombreuses maladies virales d'importance économique, notamment en ce qui concerne la culture du manioc, essentielle en Afrique. A Madagascar, la maladie de la mosaïque du manioc (CMD) est une préoccupation agronomique majeure, le manioc constituant une denrée de réserve et une base alimentaire pour la population paysanne. Face à l'incidence élevée de la maladie et à la sévérité des symptômes observés sur le terrain, nous avons entrepris une caractérisation moléculaire des bégomovirus bipartites (CMGs) impliqués dans la CMD. Depuis 2006, nous avons récolté plus de 300 échantillons foliaires de manioc symptomatique à travers le pays. Pour l'ensemble des échantillons, des amorces PCR universelles ont d'une part démontré la présence de bégomovirus ; d'autre part, le design et l'utilisation d'amorces PCR spécifiques ont permis d'identifier la présence inédite de quatre espèces de CMGs à Madagascar, à savoir l'African cassava mosaic virus (ACMV), l'East African cassava mosaic virus (EACMV), l'East African cassava mosaic Kenya virus (EACMKV) et le South African cassava mosaic virus (SACMV). Par ailleurs, 35% des échantillons se sont révélés être co-infectés par deux (26%), trois (8%), voire quatre (1%) espèces de CMGs, ceci se traduisant à l'échelle du pays par un large chevauchement des aires de répartition des espèces de CMGs. Afin de caractériser les relations phylogénétiques entre les CMGs malgaches et leurs liens de parenté avec les isolats africains, nous avons entrepris de cloner et séquencer à large échelle leurs ADN-A et ADN-B. Les premières séquences de génomes complets (102 ADN-A et 12 ADN-B) confirment la présence des trois principaux génotypes de CMGs connus (ACMV, EACMV et SACMV) à Madagascar, ainsi que d'une nouvelle espèce virale nommée provisoirement South East African cassava mosaic virus (SEACMV). En conclusion, le territoire malgache semble héberger des CMGs d'un

Genetic recombination is an important process during the evolution of many virus species and occurs particularly frequently amongst begomoviruses in the single stranded DNA virus family, Geminiviridae. As in many other recombining viruses it is apparent that non-random recombination breakpoint distributions observable within begomovirus genomes sampled from nature are the product of variations both in basal recombination rates across genomes and in the over-all viability of different recombinant genomes. Whereas factors influencing basal recombination rates might include local degrees of sequence similarity between recombining genomes, nucleic acid secondary structures and genomic sensitivity to nuclease attack or breakage, the viability of recombinant genomes could be influenced by the degree to which their co-evolved protein-protein and protein-nucleotide and nucleotide-nucleotide interactions are disreputable by recombination. Here we investigate patterns of recombination that occur over 120 day long experimental infections of tomato plants with the begomoviruses Tomato yellow leaf curl virus and Tomato leaf curl Comoros virus. We show that patterns of sequence exchange between these viruses can be extraordinarily complex and present clear evidence that factors such as local degrees of sequence similarity but not genomic secondary structure strongly influence where recombination breakpoints occur. It is also apparent from our experiment that over-all patterns of recombination are strongly influenced by selection against individual recombinants displaying disrupted intra-genomic interactions such as those required for proper protein and nucleic acid folding. Crucially, we find that selection favoring the preservation of co-evolved longer-range proteinprotein and protein DNA interactions is so strong that its imprint can even be used to identify the exact sequence tracts involved in these interactions.

Background: Begomovirus is a genus of phytopathogenic single-stranded DNA viruses, transmitted by the whitefly Bemisia tabaci. This genus includes emerging and economically significant viruses such as those associated with Tomato Yellow Leaf Curl Disease, for which diagnostic tools are needed to prevent dispersion and new introductions. Five real-time PCRs with an internal tomato reporter gene were developed for accurate detection and quantification of monopartite begomoviruses, including two strains of the Tomato yellow leaf curl virus (TYLCV; Mld and IL strains), the Tomato leaf curl Comoros virus-like viruses (ToLCKMV-like viruses) and the two molecules of the bipartite Potato yellow mosaic virus. These diagnostic tools have a unique standard quantification, comprising the targeted viral and internal report amplicons. These duplex real-time PCRs were applied to artificially inoculated plants to monitor and compare their viral development. Results: Real-time PCRs were optimized for accurate detection and quantification over a range of 2 × 109 to 2 × 103 copies of genomic viral DNA/?L for TYLCV-Mld, TYLCV-IL and PYMV-B and 2 × 108 to 2 × 103 copies of genomic viral DNA/?L for PYMV-A and ToLCKMV-like viruses. These real-time PCRs were applied to artificially inoculated plants and viral loads were compared at 10, 20 and 30 days post-inoculation. Different patterns of viral accumulation were observed between the bipartite and the monopartite begomoviruses. Interestingly, PYMV accumulated more viral DNA at each date for both genomic components compared to all the monopartite viruses. Also, PYMV reached its highest viral load at 10 dpi contrary to the other viruses (20 dpi). The accumulation kinetics of the two strains of emergent TYLCV differed from the ToLCKMV-like viruses in the higher quantities of viral DNA produced in the early phase of the infection and in the shorter time to reach this peak viral load. Conclusions: To detect and quantify a wide range of begomovi

Le gombo (Abelmoschus esculentus, Malvaceae) est une plante légumière originaire d'Afrique de première importance pour sa richesse en vitamines et en sels minéraux. Cependant, la maladie de l'enroulement foliaire du gombo (OLCD) constitue une contrainte majeure pour sa production dans les régions tropicales. L'impact de la maladie a été évalué au Burkina Faso pour quatre accessions du cultivar local 'Man Yanga' et quatre cultivars commerciaux (Clemson spineless, Indiana, Lima et Volta) au champ en 2007 et 2008 (Tiendrébéogo et al., Crop Protection, 2010). Il résulte une très forte incidence et sévérité de la maladie observées chez les accessions du cultivar local (respectivement 69-73% et 58%) comparativement aux cultivars commerciaux (respectivement 9-16% et 40%). De plus, l'impact de la maladie sur le rendement (nombre de fruits par plante, longueur, diamètre et poids du fruit) a été étudié, nous amenant au constat suivant : des pertes de rendement significativement plus importantes ont été observées pour le cultivar local (26-55%) comparativement aux cultivars commerciaux (4,4-9,6%) Les pertes économiques moyennes à l'hectare ont été estimées à 11100 et 1950 dollars, respectivement chez le cultivar local et les cultivars commerciaux. Notre étude agronomique a permis de démontrer l'impact négatif de l'OLCD sur la production du gombo au Burkina Faso, la sensibilité du cultivar local et l'intérêt de diffuser du matériel amélioré. La collecte de feuilles de gombo symptomatiques réalisée dans les grandes régions productrices du gombo au Burkina Faso a permis de diagnostiquer la présence d'un bégomovirus monopartite associé à un complexe d'ADN satellites (Tiendrébéogo et al., Virology Journal, 2010). Vingt-trois génomes complets d'isolats du Cotton leaf curl Gezira virus (CLCuGV) ont été clonés et séquencés. Dans un même temps, six betasatellites correspondant au Cotton leaf curl Gezira betasatellite (CLCuGB), un alphasatellite variant du Cotton leaf curl Gezira alphas