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Research Groups Equipe VIP Transmission and evolution of geminiviruses

Transmission and evolution of geminiviruses
Leader of the project: Michel Peterschmitt

Many geminiviruses are ssDNA emerging viruses transmitted by hemipteran insect vectors. This project studies the transmission and evolution of these viruses, from the within host level to the field and landscape.

Staff involved in the project

M. Peterschmitt
Leader of the project

C. Urbino

M. Granier
Assistant engineer
F. Ryckebusch

Background and state of the art

The family Geminiviridae is the most important plant virus family by the number of its species. It is also one of the most important families regarding the number of species having an economic impact and particularly on cassava, cotton and tomato.

Our research on geminiviruses comprises two major fields. (1) We are assessing the potential of evolution of viruses of the genus Begomovirus by recombination and pseudo recombination (Urbino et al., 2013; Urbino et al., 2008; Vuillaume et al., 2011). (2) We are characterizing the mode of transmission of the members of the genus Capulavirus, a genus which we recently identified (Bernardo et al., 2013) and for which we demonstrated an aphid transmission for one of its members, Alfalfa leaf curl virus (Roumagnac et al., 2015).

1. Evolution of begomoviruses

1.1. Assessing the potential of recombination

Tomato is a natural host of a large range of begomoviruses, some of them causing the severe tomato yellow leaf curl symptom (Tylc). Tomato cultivars resistant to Tylc-associated viruses have been bred. The emergence of resistance breaking isolates cannot be excluded because begomoviruses are capable of generating a high genetic diversity by mutations and recombinations. Although geminiviruses have DNA genomes which are replicated with host polymerases, their mutations rate is similar to that of RNA viruses which are replicated with mutation prone virus encoded replicases. We confirmed such a high mutation rate for a member of Tomato yellow leaf curl virus (TYLCV) (Urbino et al., 2008), the most virulent and invasive Tylc associated begomovirus. We showed that genetic diversity can be further increased by recombination. Indeed when TYLCV was coinfected with a representative of Tomato yellow leaf curl Comoros virus (ToLCKMV), a virus exhibiting 20% nt divergence with TYLCV, more than 50% of the genomes isolated at 150 days post inoculation are recombinants (Urbino et al., 2013). Moreover, using a library of TYLCV/ToLCKMV recombinant genomes generated by a random in vitro shuffling with the same parental viruses, we showed that the effect of recombination is rarely lethal or deleterious (Vuillaume et al., 2011).
Symptoms caused by two tomato begomoviruses
TYLCV-ToLCKMV recombinant virus library

Taking advantage of the library of recombinant viruses and the determination of their within-host viral accumulation, we showed for the first time that the genetic determinism of a viral trait can be detected with QTL and FST approaches (Doumayrou et al., 2015).

Following the detection of unexpected symptoms on resistant tomato cultivars in Morocco, we identified a recombinant TYLCV which carried a short genomic fragment inherited from Tomato yellow leaf curl Sardinia virus (TYLCSV), a virus exhibiting 20% nt divergence with TYLCV. The detection of a TYLCV/TYLCSV recombinant in Morocco was expectable and fully consistent with our experimental results, because both parental viruses have been previously reported from Morocco. However, unlike the previous TYLCV/TYLCSV recombinants detected in Spain and Italy, the recombinant exhibited a non-canonical recombinant profile with a short 76 nt TYLCSV fragment and most importantly it replaced the parental viruses in South of Morocco. The emergence dynamic of this recombinant named IS76 was analyzed with more than 800 plants, sampled throughout Morocco between 1998 and 2014. Using full length genome sequences generated in this study or available in Genbank, the date of the recombination event was inferred. The fitness advantage of recombinant IS76 was tested under experimental conditions.

Detection of the genetic determinism of a viral accumulation by QTL approach

1.2. Assessing the potential of pseudo-recombination
Begomoviruses (family Geminiviridae) are frequently detected with half genome size defective DNAs, and for some of them with alpha- and betasatellite DNAs of similar size. Except some begomoviruses, like Cotton leaf curl virus (CLCuV) which rely on a betasatellite for a full symptomatic infection in their natural host, most of the begomoviruses which were frequently detected with satellites do not rely on them for infectivity. The alphasatellite was rarely proved to have an impact on the helper virus but the betasatellite was often shown to increase its virulence. The association of TYLCV with satellites was only reported for a TYLCV strain isolated from Oman but the Mediterranean IL and Mld strains of TYLCV were experimentally proven to transreplicate readily satellite DNAs. As betasatellites dramatically increase the virulence of TYLCV, the potential economic impact of betasatellites on tomato was assessed by testing various factors involved in the potential maintenance of TYLCV-satellite association: (i) the relative intra-plant accumulation of TYLCV and the satellites, (ii) the frequency of host cells co-infected with TYLCV and the satellites, and (iii) the transmission efficiency of satellites by the natural whitefly vector of TYLCV, Bemisia tabaci.
Besides the specific question of the possible maintenance of satellites with TYLCV, the results of our study are expected to provide a new insight on the interactions between begomovirus and satellites, at the plant, cellular and molecular levels.

Healthy tomato plant TYLCV-infected tomato plant TYLCV-Betasatellite infected tomato plant

2- Characterizing the mode of transmission of capulaviruses by aphids

Two highly divergent geminiviruses, Euphorbia caput-medusae latent virus (EcmLV) and French bean severe leaf curl virus (FbSLCV), were discovered in South Africa and India, respectively (Bernardo et al., 2013). Based on genomic sequence divergence, genome organization, and the typical twinned quasi-icosahedral particles detected with EcmLV (Roumagnac et al., 2015), we classified them into a new geminivirus genus named Capulavirus.
Recently, we identified a third capulavirus, Alfalfa leaf curl virus (ALCV), and showed that it is transmitted by Aphis craccivora. As, ALCV is the first reported aphid-transmitted geminivirus, we are presently characterizing the transmission parameters of this new mode of transmission.

Virions of Euphorbia caput medusae latent capulavirus
Aphis craccivora

Recent publication

Doumayrou, J., Thébaud, G., Vuillaume, F., Peterschmitt, M., and Urbino, C. (2015). Mapping genetic determinants of viral traits with FST and quantitative trait locus (QTL) approaches. Virology 484, 346-353.

Roumagnac, P., Granier, M., Bernardo, P., Deshoux, M., Ferdinand, R., Galzi, S., Fernandez, E., Julian, C., Abt, I., Filloux, D., Mesleard, F., Varsani, A., Blanc, S., Martin, D. P., and Peterschmitt, M. (2015). Alfalfa Leaf Curl Virus: an Aphid-Transmitted Geminivirus. Journal of Virology 89(18), 9683-8.

Urbino, C., Gutierrez, S., Antolik, A., Bouazza, N., Doumayrou, J., Granier, M., Martin, D. P., and Peterschmitt, M. (2013). Within-Host Dynamics of the Emergence of Tomato Yellow Leaf Curl Virus Recombinants. PLoS ONE 8(3).

Bernardo, P., Golden, M., Akram, M., Naimuddin, Nadarajan, N., Fernandez, E., Granier, M., Rebelo, A. G., Peterschmitt, M., Martin, D. P., and Roumagnac, P. (2013). Identification and characterisation of a highly divergent geminivirus: Evolutionary and taxonomic implications. Virus Research 177(1), 35-45.

Vuillaume, F., Thebaud, G., Urbino, C., Forfert, N., Granier, M., Froissart, R., Blanc, S., and Peterschmitt, M. (2011). Distribution of the Phenotypic Effects of Random Homologous Recombination between Two Virus Species. Plos Pathogens 7(5).

Urbino, C., Thebaud, G., Granier, M., Blanc, S., and Peterschmitt, M. (2008). A novel cloning strategy for isolating, genotyping and phenotyping genetic variants of geminiviruses. Virology Journal 5, 10.