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International audience; Cucurbits are widely grown worldwide in diverse agroecosystems, from traditional gardens to soil-less glasshouses. Viruses represent one of the major threats for cucurbit production, affecting both the yield and quality of crops. The number of known cucurbit-infecting virus species has grown from 35 in 1998 to more than 80 in 2018. The prevalence and agronomic impact of these viruses are highly contrasted, and the major problems at the worldwide level are related to circa 10 virus species, both « classic » -i.e known for decades- or recently emerged on a large scale. Among the « old » mosaic-inducing viruses, aphid-transmitted viruses (potyviruses, cucumber mosaic virus) remain agronomically important, particularly in temperate climates. Despite their long-term prevalence and apparent stability, introductions of new strains have been observed in several countries in the last years, probably via commercial exchanges of plant material. Some of these introduced strains have rapidly replaced preexisting virus populations, sometimes resulting in an increased economical impact. In Mediterranean and tropical climates, as well as in heated greenhouses in temperate regions, Bemisia tabaci-transmitted viruses (begomoviruses, ipomoviruses, criniviruses) now constitute major problems. Their rapid emergence can be explained by the combination of changes in climate and cultural practices that favour their natural vectors, and the increased exchanges of plant material that made possible their long-distance spread. Viruses transmitted by seeds or by contact are also easily disseminated worldwide and represent important constraints for exchanges of plants or genetic material. Accurate and regular re-evaluation of the complex viral pathosystem infecting cucurbits in different countries, adaptation of cultural practices and development of resistant cultivars contribute to the continuous arm race against the introductions and local evolution of virus populations.

National audience; Pathogen sequence data have been exploited to infer who infected whom, by using empirical and model-based approaches. Most of these approaches exploit one pathogen sequence per infected host unit (e.g., individual, household, field). However, data collected with deep sequencing techniques, providing a subsample of the pathogen variants at each sampling time, are expected to give more insight on epidemiological links than a single sequence per host unit. A mechanistic viewpoint to transmission and micro-evolution has generally been followed to infer epidemiological links from these data. Here, we investigate an alternative statistical learning approach for estimating epidemiological links, which consists of learning the structure of epidemiological links with a pseudo-evolutionary model and training data before inferring links for the whole data set. We designed the pseudo-evolutionary model as a semi-parametric regression function where the response variable is the set of sequences observed from a recipient host unit and the explanatory variable is the set of sequences observed from a putative source. We derived from this model a penalized pseudo-likelihood that is used for selecting who infected whom or who is closely related to whom, where the penalization is calibrated on training data. In order to assess the efficiency of the pseudo-evolutionary model and the associated inference approach for estimating epidemiological links, we applied it to simulated data generated with diverse sampling efforts, sequencing techniques (corresponding to diverse depths and read lengths), and stochastic models of viral evolution and transmission. Then, we applied it to three real epidemics: swine Influenza, Ebola and a potyvirus of wild salsify. Such an approach has the potential to be particularly valuable in the case of a risk of erroneous mechanistic assumptions and sequencing errors, it is sufficiently parsimonious to allow handling big data sets in the future, and it can be applied to very different contexts from animal, human and plant epidemiology.

National audience

National audience

Cucurbits are widely grown vegetables in different provinces of Turkey. However their production is restricted by pests and pathogens including different plant viruses, among which Zucchini yellow mosaic virus (ZYMV) is particularly damaging. Infections by this virus during the early stages of plant development causes deformation of fruits and significant yield losses. During 2009-2014, 221 cucurbits samples were collected from fields and greenhouses from different provinces of Turkey. Serological testing was performed by double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) for presence of Watermelon mosaic virus (WMV), ZYMV, Cucumber mosaic virus (CMV), Papaya ring spot virus (PRSV), cucumber green mottle mosaic virus (CGMMV) and Squash mosaic virus (SqMV). For molecular analaysis of ZYMV, full-length CP nucleotide sequences were obtained for 45 ZYMV isolates and compared with sequences from worldwide isolates available in databases. The CP coding regions of Turkish ZYMV were 837 nt long and encoded 279 amino acids (aa). Forty two isolates from different regions were classified in the molecular subgroup Al, the most frequent in the Mediterranean Basin, Europe and Africa. Three isolates collected from Antalya region were classified in subgroup A4 and showed 99 % sequence identity with isolates from the same subgroup that have emerged recently in France.

Pathogen sequence data have been exploited to infer who infected whom, by using empirical and model-based approaches. Most of these approaches exploit one pathogen sequence per infected host unit (e.g., individual, household, field). However, data collected with deep sequencing techniques, providing a subsample of the pathogen variants at each sampling time, are expected to give more insight on epidemiological links than a single sequence per host unit. A mechanistic viewpoint to transmission and micro-evolution has generally been followed to infer epidemiological links from these data. Here, we investigate an alternative statistical learning approach for estimating epidemiological links, which consists of learning the structure of epidemiological links with a pseudo-evolutionary model and training data before inferring links for the whole data set. We designed the pseudo-evolutionary model as a semi-parametric regression function where the response variable is the set of sequences observed from a recipient host unit and the explanatory variable is the set of sequences observed from a putative source. We derived from this model a penalized pseudo-likelihood that is used for selecting who infected whom or who is closely related to whom, where the penalization is calibrated on training data. In order to assess the efficiency of the pseudo-evolutionary model and the associated inference approach for estimating epidemiological links, we applied it to simulated data generated with diverse sampling efforts, sequencing techniques (corresponding to diverse depths and read lengths), and stochastic models of viral evolution and transmission. Then, we applied it to three real epidemics: swine Influenza, Ebola and a potyvirus of wild salsify. Such an approach has the potential to be particularly valuable in the case of a risk of erroneous mechanistic assumptions and sequencing errors, it is sufficiently parsimonious to allow handling big data sets in the future, and it can be applied to very different contexts from animal, human and plant epidemiology.

National audience

International audience

National audience; Cucurbits are economically important vegetable in Turkey. Cucurbit crops are seriously affected by many viruses including Cucurbit aphid-borne yellows virus (CABYV). CABYV, a widespread polerovirus causing yellowing symptoms on older leaves that were previously associated to nutritional or physiological disorders. CABYV was first identified in 1988 in France, now, CABYV is widely spread in the whole Mediterranean region (Lecoq and Desbiez 2012). In Turkey, CABY reported firstly by Yardımcı and Özgönen (2007) as serologicaly. The purpose of this study was to characterize the molecular variability of CABYV in Turkey, through determining partial coat protein (CP) nucleotide sequences of (CABYV) isolates of Turkey.

National audience; The cucurbits include several important vegetables to human consumption which are threatened for epidemic diseases such as those caused by begomoviruses. The Old World begomovirus Tomato leet curl New Delhi virus (ToLCNDV) was first described in India and is currently spreading in some Mediterranean countries. Meanwhile, the New World begomovirus Melon chlorotic mosaic virus (MeCMV) has been only described in Venezuela. This work aims to evaluate melon lines in order to look for resistance sources against these viruses.

National audience; Cucurbits are widely grown in different provinces of Turkey. However their production is restricted by plant viruses. ZYMV is one of the most economically important viruses of cucurbit crops worldwide, including in Turkey. Several strains have been defined based on their biological, serological and molecular variability –particularly in the coat protein (CP) coding region. One molecular cluster (A1) appears highly prevalent worldwide, but other clusters (A4, A5) have been observed recently in several European and Mediterranean countries, probably in relation to recent introductions. However the situation in Turkey remains unknown. The aim of this research was thus to characterize the molecular variability of ZYMV in Turkey and look for the presence of emerging strains.

National audience; Watermelon mosaic virus (WMV, genus Potyvirus, family Potyviridae) is a serious pathogen of cucurbit crops with a worldwide distribution. It has a wide host range (>170 species) and it is transmitted non-persistently by several aphid species. Previous molecular analyses based on full-length WMV sequences indicated the presence of 3 major groups, namely G1, G2 & G3. Until 2000 in the Mediterranean basin only G1 and G2 groups were observed, with many G1-G2 recombinants. The third group (G3 or ‘‘EM’’ for emerging) probably originating from Asia was first observed in south-eastern France in 2000. Despite the occurrence of WMV in Greece at least since 1983, no information was available on its genetic variability.

International audience; Begomoviruses are one of the major constraint for crop production in tropical and subtropical regions. Euphorbia mosaic Venezuela virus (EuMVV) is a begomovirus first reported infecting milkweed (Euphorbia heterophylla) and tomato (Solanum lycopersicum) in Venezuela and displaying mild symptoms of yellowing and curling of leave. In this study seven tomato plants exhibiting begomovirus-like symptoms were collected in a field of Zulia, Venezuela. The samples were analysed by PCR using universal primers for begomoviruses. Begomovirus incidence was confirmed for all samples and sequencing of the expected viral DNA fragments revealed the presence of EuMVV in three samples. One of the EuMVV isolates was highly divergent when compared with previous reported isolates. In order to characterize this EuMMV isolate further assays were carried out to perform full-genome amplification and production of an infectious clone.

Cucurbits are widely grown in different provinces of Turkey. However their production is restricted by plant viruses. ZYMV is one of the most economically important viruses of cucurbit crops worldwide, including in Turkey. Several strains have been defined based on their biological, serological and molecular variability –particularly in the coat protein (CP) coding region. One molecular cluster (A1) appears highly prevalent worldwide, but other clusters (A4, A5) have been observed recently in several European and Mediterranean countries, probably in relation to recent introductions. However the situation in Turkey remains unknown. The aim of this research was thus to characterize the molecular variability of ZYMV in Turkey and look for the presence of emerging strains.

National audience; More than 70 viruses infect cucurbits worldwide. Among the most common and agronomically important are several potyviruses: ZYMV, WMV, PRSV. Besides these viruses that have a worldwide distribution and present distinct biological, serological and molecular features, several viruses closely related to PRSV that could constitute highly divergent strains of this virus or related species have been defined, and could represent new threats for agriculture.

The melon Vat gene confers resistance to the aphid species Aphis gossypii and resistance to non-persistent viruses (CMV, WMV…) when inoculated by this species. It is however ineffective in blocking the transmission of viruses inoculated by other aphid species. Its effect on non-persistent virus epidemics is thus expected to be limited when A. gossypii is not the main aphid species visiting the melon crop. On the contrary, although not documented, its effect on the persistent virus CABYV mainly vectored by A. gossypii is expected to be strong.[br/] The first objective of the study was to evaluate the effect of Vat on virus epidemics and on the genetic structure of virus populations in field conditions.[br/] The second objective was to investigate the benefit of combining Vat resistance and an appropriate management of field margins to regulate the populations of aphids and/or their virus load. Indeed, literature suggests that flower strips can participate in pest biological control by favoring natural enemies, and strips of non-host plants can protect crops from non-persistent viruses by allowing aphids to probe on healthy plants and thus to lose their virus load before reaching the crops.

Surveys were conducted from 2008 to 2010 to identify the viruses infecting cucurbit fields in Adana and Mersin provinces of Cukurova region in Turkey. All cucurbit samples collected from 18 districts were tested for Cucumber mosaic virus (CMV), Cucurbit aphid-borne yellow virus (CABYV), Papaya ringspot virus (PRSV), Squash mosaic virus (SqMV), Zucchini yellow mosaic virus (ZYMV) and Watermelon mosaic virus (WMV) by double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) using polyclonal antisera. Overall, 449 out of 485 samples were found positive for the tested viruses; 327 out of 350 samples in Adana and 122 out of 135 in Mersin were infected at least with one virus. During the entire surveys, 258 of 281 squash samples, 33 of 33 cucumber samples, 84 of 88 melon samples and 74 of 83 watermelon samples were found to have a single or mix virus infection. All six viruses were detected on cucurbits in Adana while all samples from Mersin province were found to be negative for CABY. Sequence analyses indicated that the Turkish ZYMV isolates (ZYMV-TR3, ZYMV-TR15 and ZYMV-TR17) belong to the most common molecular cluster of ZYMV worldwide, including isolates from Europe, Africa, the Middle East, the Indian subcontinent and South America.

Watermelon mosaic virus (WMV, genus Potyvirus, family Potyviridae) is a serious pathogen of cucurbit crops with a worldwide distribution. It has a wide host range (>170 species) and it is transmitted non-persistently by several aphid species. Previous molecular analyses based on full-length WMV sequences indicated the presence of 3 major groups, namely G1, G2 & G3. Until 2000 in the Mediterranean basin only G1 and G2 groups were observed, with many G1-G2 recombinants. The third group (G3 or ‘‘EM’’ for emerging) probably originating from Asia was first observed in south-eastern France in 2000. Despite the occurrence of WMV in Greece at least since 1983, no information was available on its genetic variability.

Surveys were conducted from 1992 to 2012 in the major cucurbit growing regions of Sudan to determine the relative incidence of viruses infecting these crops, in order to define adapted control strategies and to identify appropriate resistance sources in germplasm collection. During 2012 survey two new whitefly-borne virus species were identified, a tentative torradovirus from squash: squash chlorotic leaf spot virus (SCLSV) and a tentative ipomovirus from a wild cucurbit Coccinia grandis: coccinia mottle virus (CocMoV).

Begomoviruses are one of the major constraint for crop production in tropical and subtropical regions. Euphorbia mosaic Venezuela virus (EuMVV) is a begomovirus first reported infecting milkweed (Euphorbia heterophylla) and tomato (Solanum lycopersicum) in Venezuela and displaying mild symptoms of yellowing and curling of leave. In this study seven tomato plants exhibiting begomovirus-like symptoms were collected in a field of Zulia, Venezuela. The samples were analysed by PCR using universal primers for begomoviruses. Begomovirus incidence was confirmed for all samples and sequencing of the expected viral DNA fragments revealed the presence of EuMVV in three samples. One of the EuMVV isolates was highly divergent when compared with previous reported isolates. In order to characterize this EuMMV isolate further assays were carried out to perform full-genome amplification and production of an infectious clone.

Surveys were conducted from 2008 to 2010 to identify the viruses infecting cucurbit fields in Adana and Mersin provinces of Cukurova region in Turkey. All cucurbit samples collected from 18 districts were tested for Cucumber mosaic virus (CMV), Cucurbit aphid-borne yellow virus (CABYV), Papaya ringspot virus (PRSV), Squash mosaic virus (SqMV), Zucchini yellow mosaic virus (ZYMV) and Watermelon mosaic virus (WMV) by double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) using polyclonal antisera. Overall, 449 out of 485 samples were found positive for the tested viruses; 327 out of 350 samples in Adana and 122 out of 135 in Mersin were infected at least with one virus. During the entire surveys, 258 of 281 squash samples, 33 of 33 cucumber samples, 84 of 88 melon samples and 74 of 83 watermelon samples were found to have a single or mix virus infection. All six viruses were detected on cucurbits in Adana while all samples from Mersin province were found to be negative for CABY. Sequence analyses indicated that the Turkish ZYMV isolates (ZYMV-TR3, ZYMV-TR15 and ZYMV-TR17) belong to the most common molecular cluster of ZYMV worldwide, including isolates from Europe, Africa, the Middle East, the Indian subcontinent and South America.

Cucurbits are economically important vegetable in Turkey. Cucurbit crops are seriously affected by many viruses including Cucurbit aphid-borne yellows virus (CABYV). CABYV, a widespread polerovirus causing yellowing symptoms on older leaves that were previously associated to nutritional or physiological disorders. CABYV was first identified in 1988 in France, now, CABYV is widely spread in the whole Mediterranean region (Lecoq and Desbiez 2012). In Turkey, CABY reported firstly by Yardımcı and Özgönen (2007) as serologicaly. The purpose of this study was to characterize the molecular variability of CABYV in Turkey, through determining partial coat protein (CP) nucleotide sequences of (CABYV) isolates of Turkey.

International audience

International audience

International audience; In 2014, a total of 108 symptomatic watermelon samples were collected in Greece and analyzed by DAS-ELISA using polyclonal antisera (INRA, Montfavet) against the most common aphid-transmitted viruses. Cucumber mosaic virus (CMV) was detected in eight of 108 plants tested. Five of these plants collected at Lesvos were also infected with Watermelon mosaic virus (WMV), whereas three plants from Prohoma had single infections. Five samples with severe stunting and yellowing collected at Asenovgrad (Bulgaria) in 2013 and tested by DAS-ELISA for the above viruses hosted CMV and Cucurbit aphid-borne yellows virus (CABYV). To confirm CMV presence in watermelon, a nested RT-PCR assay was carried out first with the degenerated primers CMVup624a (5′-ATGGACAAATCTGRATC- 3′) and CMVdo1244a (5′-TGRTGCTCRAYGTCKACATGA-3′) followed by CMVup624b (5′-GGACAAA TCTGRA TCTCCCAA TGC-3′) and CMVdo1244b (5′- TGCTCRAYGTCRACATGAAG-3′) that amplify a 622 bp region from the viral coat protein gene. Total RNA (Chatzinasiou et al., 2010, method A) extracted from all ELISA- positive watermelon samples from both countries and from two healthy watermelon plants was used as template in nested RT-PCR. A product of the expected size was amplified from all serologically CMV-positive samples, but not from the healthy ones. The Greek CMV isolates from Lesvos (LN810059) and Prohoma (LN810060) showed 99% nucleotide sequence identity with potato (AB448694) and tomato (EF153734) CMV isolates from Syria and India, while the Bulgarian isolate (LN810058) showed 99% nucleotide sequence identity with an Indian cucumber isolate (JF279608). Phylogenetic analysis indicated that the Greek CMV isolate (LN810059) belongs to sub-group IA, while the Bulgarian isolate and a Greek isolate (LN810060) belong to sub-group IB. To our knowledge this is the first report of CMV infecting watermelons in Greece and Bulgaria.

National audience

A watermelon mosaic virus isolate (WMV-Tr) was obtained from a naturally infected watermelon (Citrullus lanatus (Thunb.) Matsum. and Nakai) plant with mosaic, mottle and leaf deformation symptoms collected in the major cucurbit-growing area in Adana province of Turkey during a survey conducted in May 2009. DAS-ELISA and RT-PCR showed the presence of watermelon mosaic virus (WMV, Potyvirus) in the sample. WMV-Tr was characterized biologically and its partial coat protein genome sequence was established. WMV-Tr had biological properties similar to those reported for the WMV isolates from different parts of the world. WMV-Tr belonged to molecular group 3, containing Asian isolates of WMV as well as isolates currently emerging in different parts of the world including Europe. This suggests recent emergence of Group 3 isolates in Turkey.

International audience; A watermelon mosaic virus isolate (WMV-Tr) was obtained from a naturally infected watermelon (Citrullus lanatus (Thunb.) Matsum. and Nakai) plant with mosaic, mottle and leaf deformation symptoms collected in the major cucurbit-growing area in Adana province of Turkey during a survey conducted in May 2009. DAS-ELISA and RT-PCR showed the presence of watermelon mosaic virus (WMV, Potyvirus) in the sample. WMV-Tr was characterized biologically and its partial coat protein genome sequence was established. WMV-Tr had biological properties similar to those reported for the WMV isolates from different parts of the world. WMV-Tr belonged to molecular group 3, containing Asian isolates of WMV as well as isolates currently emerging in different parts of the world including Europe. This suggests recent emergence of Group 3 isolates in Turkey.

National audience

International audience; Although the biological variability of Watermelon mosaic virus is limited, isolates from the three main molecular groups differ in their ability to infect systemically Chenopodium quinoa. Mutations were introduced in a motif of three or five amino acids located in the N-terminal part of the coat protein, and differing in isolates from group 1 (motif: lysine-glutamic acid-alanine (Lys-Glu-Ala) or KEA, systemic on C. quinoa), group 2 (Lys-Glu-Thr or KET, not systemic on C. quinoa) and group 3 (KEKET, not systemic on C. quinoa). Mutagenesis of KEKET in an isolate from group 3 to KEA or KEKEA was sufficient to make the virus systemic on C. quinoa, whereas mutagenesis to KET had no effect. Introduction of a KEA motif in Zucchini yellow mosaic virus coat protein also resulted in systemic infection on C. quinoa. These mutations had no obvious effect on the disorder profile or potential post-translational modifications of the coat protein as determined in silico.

International audience; Cucurbit crops are cultivated throughout the world. Melon (Cucumis melo L.), cucumber (Cucumis sativus L.), watermelon (Citrullus lanatus (Thumb.) Mat. et Nak.), squash and pumpkin (Cucurbita spp.) are the major crops. In Latin America and the Caribbean islands (LAC) cucurbits are consumed as a part of the daily diet since pre-Columbian times, when some species such as Cucurbita pepo L., Cucurbita moschata Duch. and Cucurbita maxima Duch. were domesticated by American Indians. In LAC, cucurbit crops have become export commodities and a source of income for several countries, in addition to their role in local consumption. The increase of area devoted to cucurbit crops and the intensification of production has led to the emergence of severe viral epidemics that threaten the sustainability of these cultures. This paper reviews the cucurbit viruses described in the region and their impact. In addition, the potential of different measures to control the most frequent cucurbit viruses in LAC is discussed.

International audience; Watermelon mosaic virus (WMV) and Zucchini yellow mosaic virus (ZYMV) are among the major cucurbit-infecting viruses worldwide. In France, WMV has a high prevalence every year throughout the growing season; ZYMV, although it can present locally a very high agronomic impact, induces epidemics that are very irregular both in spatial distribution and timing of infection. Large-scale epidemiological surveys followed by molecular analysis of all collected samples were performed during 5 years in France, and revealed the recent appearance of new, “emerging” (EM) isolates of both viruses in south-eastern France. In the case of WMV, four subgroups of EM isolates were defined, probably resulting from several recent introductions. They presented a strong geographic structure that remained stable over 5 years, and tended to replace rapidly the original “classic” isolates in areas where both types of strains were present. For ZYMV, at least two subgroups of new isolates were also detected in the last years, although the geographic structure of infections and evolution of populations was less obvious than for WMV. In order to characterize the evolution of viral populations and study the mechanisms favouring or limiting viral emergence and spread, several complementary approaches were developed: multilocal and multiscale epidemiological studies, molecular analyses and population genetics, as well as estimation of viral fitness in experimental condition and modeling. The risks of emergence of recombinants between “classic” and EM populations in the few years following their contact were also assessed.

International audience; Watermelon mosaic virus (WMV, Potyvirus) is very common in France where it has been present for at least 40 years. Since the early 2000s, new “emerging” (EM) strains of WMV, highly divergent molecularly from the “classic” (CL) strains present before and probably originating from recent introductions, were detected in southeastern France. Since both types of strains did not appear to be present in the same geographic locations before, this situation constituted a unique opportunity to study the frequency of appearance and the potential spread of recombinants in the few years following the introduction of the new strains. Analyzing isolates from experimental plots in Montfavet (Southeastern France) as well as from epidemiological surveys performed from 2004 to 2008 all around France (about 2000 WMV isolates) revealed at least 7 independent recombination events, either between CL and EM strains or between different EM subgroups. Most recombinants were found in a few plants from the same field, but, with one notable exception, did not seem to spread or be maintained locally for several years. Mixed infections of CL and EM isolates were also performed in experimental conditions in order to compare the frequency and nature of recombination events to those of natural situation. The fitness of natural recombinants relative to potential “parental” strains was also tested in controlled conditions. The epidemiological and evolutionary consequences of recombination in WMV populations will be discussed. This work represents one of the first estimation for the frequency of appearance of recombinants in natural populations of a plant RNA virus.

International audience; Zucchini yellow mosaic virus (ZYMV) causes locally severe but sporadic epidemics in France, contrasting with other non-persistent aphid-borne viruses such as Watermelon mosaic virus (WMV) or Cucumber mosaic virus (CMV) which occur much more regularly. In order to better understand parameters that could explain this particular behavior, ZYMV occurrence and spread were monitored over a four-year period in a multilocal layout. The layout included four identical zucchini squash plots, planted on the same day with the same batch of seedlings and located 0.5 to 4 km apart. ZYMV, WMV, CMV and Cucurbit aphid-borne yellows virus (CABYV) epidemics were monitored within each plot at weekly intervals using DAS-ELISA and ZYMV populations were characterized by direct sequencing of the N-terminal part of the coat protein after RT-PCR amplification. ZYMV occurred irregularly, and, depending on the plot, developed either early, late or no epidemics. Three out of the five different strain types known from France were observed in the layout throughout the four years, but generally a single very homogeneous population (often composed of a single haplotype) was observed per plot. Only in one occasion, two distinct populations were detected in the same plot, and with different haplotypes for each population. These results will be discussed in relation with the potential of ZYMV dissemination by aphids, the origin of primary inoculum and the potential interactions between different virus populations.