Frédéric Péréfarres

Muséum National d'Histoire Naturelle, Lutetia Parisorum, Île-de-France, France

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Publications (7)15.22 Total impact

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    ABSTRACT: Biological invasions are the main causes of emerging viral diseases and they favour the co-occurrence of multiple species or strains in the same environment. Depending on the nature of the interaction, co-occurrence can lead to competitive exclusion or coexistence. The successive fortuitous introductions of two strains of Tomato yellow leaf curl virus (TYLCV-Mld and TYLCV-IL) in Réunion Island provided an ideal opportunity to study the invasion of, and competition between, these worldwide emerging pathogens. During a 7-year field survey, we observed a displacement of the resident TYLCV-Mld by the newcomer TYLCV-IL, with TYLCV-Mld remaining mostly in co-infected plants. To understand the factors associated with this partial displacement, biological traits related to fitness were measured. The better ecological aptitude of TYLCV-IL in single infections was demonstrated, which explains its rapid spread. However, we demonstrate that the relative fitness of virus strains can drastically change between single infections and co-infections. An epidemiological model parametrized with our experimental data predicts that the two strains will coexist in the long run through assistance by the fitter strain. This rare case of unilateral facilitation between two pathogens leads to frequency-dependent selection and maintenance of the less fit strain.
    Proceedings of the Royal Society B: Biological Sciences 02/2014; 281(1781):20133374. DOI:10.1098/rspb.2013.3374 · 5.29 Impact Factor
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    ABSTRACT: In the last 20 years, molecular ecology approaches have proven to be extremely useful to identify and assess factors associated with viral emerging diseases, particularly in economically and socially important tropical crops such as maize (maize streak disease) and cassava (cassava mosaic disease). Molecular ecology approaches were applied in Reunion Island to analyze the epidemic of tomato yellow leaf curl disease, which has been affecting the island since the end of the 1990s. Before the invasive biotype B (currently known as Middle East-Asia Minor 1 cryptic species) of Bemisia tabaci spread across the world, Reunion Island (South West Indian Ocean) only hosted an indigenous biotype of B. tabaci, Ms (currently known as Indian Ocean cryptic species). Wild hybrids between invasive and indigenous species were subsequently characterized over multiple generations. Endosymbiont analysis of the hybrid population indicated that matings were non-random. Similarly, while no indigenous begomoviruses have ever been reported on Reunion Island, the two main strains of one of the most damaging and emerging plant viruses in the world, the Mild and Israel strains of the Tomato yellow leaf curl virus (TYLCV-Mld and TYLCV-IL), were introduced in 1997 and 2004 respectively. While these introductions extensively modified the agricultural landscape of Reunion Island, they also provided an invaluable opportunity to study the ecological and genetic mechanisms involved in biological invasion and competition.
    Viruses 12/2012; 4(12):3665-88. DOI:10.3390/v4123665 · 3.28 Impact Factor
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    ABSTRACT: 4 Groupement de Défense des Cultures sous Abri (GDCSA), 98848 Nouméa, Nouvelle-Calédonie; 5 IRD, CBGP, Campus international de Baillarguet, 34988 Montferrier sur Lez, France; 6 Chambre d’Agriculture de la Nouvelle Calédonie, GDS-V, In 2007, severe symptoms of leaf curling and yellowing resembling those of tomato yellow leaf curl disease were observed for the first time on tomato plants (Solanum lycopersicum) with a high incidence in fields and greenhouses in the south western region (Nouméa) of the Pacific island of New Caledonia. Tomato samples with leaf curling and yellowing symptoms were collected in the south west and west of New Caledonia and also Ouvéa (Loyalty Islands), respectively, in November and December 2010 (Table 1). Samples were tested for the presence of begomoviruses using a polymerase chain reaction (PCR) assay with a set of degenerate primers designed to amplify genomic regions of the Old World begomovirus DNA-A component (Delatte et al., 2005). PCR products of the expected sizes were obtained for all the five samples from New Caledonia and for four of the six samples from Ouvéa suggesting the presence of an Old World monopartite begomovirus. PCR positive samples were processed further and full-length viral genomes were successfully amplified from six samples (Table 1) by rolling-circle amplification, cloned using XmnI restriction enzyme and sequenced (Shepherd et al., 2008). The complete DNA-A genome sequences obtained (EMBL-GenBank-DDBJ Accession Nos. HE603241-HE603246), showed the highest pairwise sequence identity of 97.6 to 99.4% (BLAST, NCBI) with isolates of the Israel strain of Tomato yellow leaf curl virus (TYLCV-IL) from Spain ([SP:Alm], AJ489258) and Reunion ([RE:SGi:RE4:04], AM409201). The new sequences were aligned with representative sequences of TYLCV strains using MUSCLE (using default settings) in MEGA5 (Tamura et al., 2011). A maximum-likelihood (ML) phylogenetic tree (Fig. 1) was constructed from the full alignment using PHYML with GTR+G4 selected as the best model of sequence evolution by RDP3 (Martin et al., 2010). The ML phylogenetic tree confirmed the relationship of New Caledonia and Ouvéa isolates of TYLCV-IL with the isolates of Spain [SP:Alm] and Reunion [RE:SGi:RE4:04] (Fig. 1). Surprisingly despite the proximity of New Caledonia and Ouvéa to Australia, the New Caledonian TYLCV isolates seem to have a different origin/source of introduction to those recently described from Australia [AU:Bri1:06] and [AU:Bun1:06] (Van Brunschot et al., 2010). This divergence suggests that the epidemic of TYLCD in New Caledonia and Loyalty Islands seems not directly associated with the introduction of TYLCV-IL in Australia where the first symptoms of TYLCD were described in 2006. To our knowledge, this is the first report of the Old World TYLCV implicated in yellow leaf curl disease on tomato in New Caledonia and Loyalty Islands. This description confirms the invasion and the dissemination of the Israel strain, also called "severe" strain, of TYLCV in the Pacific region, and represents a new record of first importance for the regional management of emerging crop diseases and regulatory institutions.
    06/2012; 25025(6-25):2044-588006. DOI:10.5197/j.2044-0588.2012.025.006
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    12/2011; accepted. DOI:10.5197/j.2044-0588.2011.024.019
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    ABSTRACT: In the 2000s, tobacco plantations on the Comoros Islands were afflicted with a previously unobserved tobacco leaf curl disease characterised by symptoms of severe leaf curling and deformation. Previous molecular characterization of potential viral pathogens revealed a complex of African monopartite tobacco leaf curl begomovirus (TbLCVs). Our molecular investigation allowed the characterization of a new monopartite virus involved in the disease: tomato leaf curl Namakely virus (ToLCNamV). Agroinoculation experiments indicated that TbLCVs and tomato leaf curl viruses (ToLCVs) can infect both tomato and tobacco but that infectivity and symptom expression fluctuate depending on the virus and the plant cultivar combination.
    Archives of Virology 12/2011; 157(3):545-50. DOI:10.1007/s00705-011-1199-1 · 2.28 Impact Factor
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    ABSTRACT: 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. Real-time PCRs were optimized for accurate detection and quantification over a range of 2 × 10(9) to 2 × 10(3) copies of genomic viral DNA/μL for TYLCV-Mld, TYLCV-IL and PYMV-B and 2 × 10(8) to 2 × 10(3) copies of genomic viral DNA/μL 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. To detect and quantify a wide range of begomoviruses, five duplex real-time PCRs were developed in association with a novel strategy for the quantification standard. These assays should be of a great interest for breeding programs and epidemiological surveys to monitor viral populations.
    Virology Journal 08/2011; 8(1):389. DOI:10.1186/1743-422X-8-389 · 2.09 Impact Factor
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    ABSTRACT: Yellow vein disease (YVD) is a major problem in pepper in West Africa. Despite the recent implication of a begomovirus in YVD in Mali and in Burkina Faso, the aetiology of the disease remains unclear. Using symptomatic samples from the main vegetable cultivation regions in Burkina Faso, 10 full-length DNA-A-like begomovirus sequences were obtained, each showing 98% nucleotide identity to pepper yellow vein Mali virus (PepYVMV). The host range was determined after construction of a viral clone for agroinfection. Severe symptoms developed in tomato and Nicotiana benthamiana. By contrast, no symptoms developed in either commercial or local pepper cultivars, demonstrating that the aetiology of YVD is not only associated with the presence of PepYVMV.
    Archives of Virology 11/2010; 156(3):483-7. DOI:10.1007/s00705-010-0854-2 · 2.28 Impact Factor