EVAg

Whilst in the middle of preparing for a lab evaluation, Eric Verdin found the time to have a zoom meeting with EVA. Eric is the head of the Virology Team at the INRAE Plant Pathology Unit (PV). He discussed with us the research themes developed by the team, giving us insight to various aspects of viruses as part of an ecosystem. The Plant Pathology Unit focuses on the phenotypic and genetic characterisation of plant pathogens and studies the conditions enhancing the spread of epidemics. The key biotic and abiotic factors contributing to virus emergence are investigated, while mathematical modelling is used to develop landscape-level control strategies. The research interests of the Virology Team are centered on flower and vegetable crops (mainly cucurbits, such as melon and zucchini, and solanaceous, such as tomato and pepper) that are financially important for the Mediterranean basin. Eight researchers, at all career levels, work towards identifying and characterising emerging viruses in plants, using and developing diagnostic tools in order to understand the epidemiological and evolutionary processes behind viral disease from plant to culture to landscape. In addition to emerging viruses, the main viral models used are Potato virus Y (PVY), watermelon mosaic virus (WMV), zucchini yellow mosaic virus (ZYMV) and cucumber mosaic virus (CMV, not to be confused with cytomegalovirus for human virologists).

The positive side of viruses in an ecosystem:

With viruses being obligate parasites, it is hard to imagine a positive side of viral infection! Nevertheless, a fine balance between mutualistic versus antagonistic symbiosis exists. Take, for instance, the tulip breaking virus (Potyviridae family) which is behind many of the impressive colour patterns this flower can be found in! Infection by certain viruses can indeed be beneficial as, for example, in the case of CMV that confers plant tolerance to drought and freezing temperatures (1, for an overview). Some cryptic viruses, such as the white clover cryptic virus, are integrated in the plant genome and interfere with plant nodulation, a process that enables plant symbiosis with soil bacteria that provide the plant with nitrogen. Upon expression, the virus’ capsid protein regulates nitrogen use, by suppressing root nodulation when sufficient nitrogen is present (2). In other cases, virus infection can act protectively against other diseases, by impacting on the plants ability to produce volatile compounds responsible for attracting certain vectors (e.g., beetles, known vectors of bacterial wilt, are less attracted to ZYMV-infected plants, as opposed to their uninfected counterparts), as has been described in cucurbits (3). Another positive aspect of viruses is their possible use in a cross-protection approach, loosely referred to as plant ‘vaccination’; in the case of pepino mosaic virus (PepMV) or zucchini yellow mosaic virus (ZYMV), infection of plants with viral strains inducing mild symptoms prevents the plants from being infected by strains inducing severe symptoms (4, 5).

Basic concepts behind viral emergence in plants:

The subtle co-existence between viruses and plants can be disrupted, resulting in viral emergence. Identifying and understanding, therefore, the key factors underlying this interaction is critical. The effect of new vectors able to transmit a virus more efficiently, for example, was illustrated by the outbreak of the tomato spotted wilt virus (TSWV) (Orthotospoviridae family) in Europe in the 90s. While TSWV and its native insect vector (thrips) were already present in Europe, the arrival of the Californian thrips, an invasive and very effective vector that spread through the intensive international trade of plants, threw this system out of balance. Another component for viral outbreaks is the appearance of more aggressive variants of a virus, as we all know too well! In the case of WMV infecting zucchini squash, Cécile Desbiez (researcher in PV unit) and collaborators sampled viral isolates in southeastern France. By spatio-temporally characterising these isolates, they showed that new emerging (EM) strains, inducing more severe symptoms on zucchini squash, replaced rapidly and entirely pre-existing classic strains (CL). Emergence of EM stains is likely to have resulted from multiple introductions in the region, rather than mutation of the pre-existing CL strains (6, 7). Finally, human activity has its share in viral outbreaks, with trade and transport of plant materials being a key component of viral spreading at the world scale. Interestingly, fewer incidents of viral infection in greenhouse-grown plants were observed during the SARS-CoV2 pandemic, where movement of people and plant material was drastically reduced. While this remains an empirical correlation in the absence of quantitative data, the limited spread of ToBRFV (tomato brown rugose fruit virus) in France may offer an example. Transmitted through seeds, as well as mechanically, ToBRFV has been emerging in Europe since 2018 affecting tomato and pepper crops. The unusually limited spread of ToBRFV in France, over the last few years, could be partly attributed to the rise of phytosanitary measures combined with fewer people working at a time and, therefore, lower viral transmission rates by hand or plant manipulation.

Strategies for plant resistance deployment:

Effective treatment of viral disease in plants, grown in greenhouses or in open fields, is mostly unfeasible due to a number of reasons. On one hand, the plant cell wall does not facilitate the entry of small molecules (potential antivirals) inside the cell. Even if this intrinsic difficulty could be circumvented, the scale and frequency of potential treatments (whole greenhouses or plots, production basins including wild areas) is not manageable. On the other hand, and most importantly, the potential environmental impact of large-scale use of small molecules, as well as the risk of resistance development in plant viruses (but also in human or animal viruses) make plant treatment rather risky. Subsequently, countermeasures are mostly focused on prophylaxis. Controls of plant and seed entry, tool disinfection and vector control by pesticides or integrated pest management, altogether provide a first line of prevention. Additionally, environmentally friendly and long-term sustainable approaches include the use of ‘bait’ plants to attract certain vectors, crop mixture and rotation, at the landscape level, as well as the use of resistant plants. Nevertheless, the interplay between plant resistance and breakdown can be tricky. Aiming to pinpoint the molecular components underlying resistance breaking, Cécile Desbiez and collaborators found that melon cultivars tolerant to Cucumber vein yellowing virus (CVYV, potyviridae family), were protected against a wide range of CVYV isolates. On the contrary, CVYV-resistant cultivars were susceptible to resistance breakdown provoked by a point mutation in the viral genome, corresponding to the viral protein genome-linked (8). This illustrates how, when too specific, resistance is likely to deteriorate with the emergence of new viral mutants.

The need for spatiotemporal modelling:

As the multifactorial nature of plant resistance durability is becoming increasingly clearer, the combination of resistance genes at different spatio-temporal scales is a promising approach to improve resistance to viruses at the landscape scale. Combining different resistance genes in a single plant species (pyramiding strategy), different resistant cultivars or species within the same field (mixture strategy) or in alternation (rotation strategy), as well as mosaic landscapes, composed of diverse plant species and resistance profiles, is likely to reinforce the global ability of our crops to resist viruses. Mathematical modelling proves to be a useful tool for designing such strategies and assessing their long-term sustainability. Landsepi (https://cran.r-project.org/web/packages/landsepi/index.html), designed by Loup Rimbaud (researcher in PV unit) and collaborators, is a stochastic simulation tool taking into account landscape geometry and distribution of cultivars, as well as the spread and evolution of a pathogen over time (9). Currently used to study rust fungi of cereal crops, Landsepi is undergoing further development for resistant banana crops against cercosporiosis (Guadeloupe), and for resistant grapevine crops against mildew (France). This simulation tool illustrates how mathematical modelling can be used to optimize plant resistance deployment strategy.

The development of spatial statistics tools, such as MAPI (Mapping Average Pairwise Information-MAPI) engineered by Karine Berthier (researcher in PV unit) and collaborators, provides new approaches for studying the spatial genetic structure of virus populations, in order to further understand the relationship between virus dispersal and landscape structure (10). For example, MAPI was successfully combined with machine learning algorithms (Random Forest) to show strong differences in the spatial genetic structure of two aphid-borne cucurbit-infecting viruses that are widespread in the French Mediterranean area; one with a persistent transmission (cucurbit aphid-borne yellows virus, CABYV) and one with a non-persistent transmission (WMV). The spatial genetic structure of CABYV was clearly related to landscape features that are likely to impact vector dispersal (e.g. presence of permanent crops vs. forests), whereas for WMV, the recurrence of introduction events and probable human exchanges of plant material resulted in a complex spatial pattern of genetic variation that could not be explained by landscape heterogeneity.

All and all, the Virology team (PV unit) led by Eric Verdin combines an array of experimental, statistical and modelling approaches and is multi-faceted in its research themes that range from the characterisation of emerging viral diseases to the understanding of epidemic processes at the field and landscape scales, as well as the sustainable management of plant disease. Their joining the EVA consortium in 2020, together with other plant virus partner, has enabled the enrichment of the EVA online catalogue with relevant products, while giving us the opportunity to look at plants and their viruses from a different perspective!

Text by Semeli Platsaki, PhD

References:

1. Roossinck M. J., 2011. The good viruses: viral mutualistic symbioses. Nature Reviews 9, 99-108. doi: 10.1038/nrmicro2491
   
2. Nakatsukasa-Akune M., Yamashita K., Shimoda Y., Uchiumi T., Abe M., Aoki T., Kamizawa A., Ayabe S., Higashi S., and Suzuki A. 2005. Suppression of Root Nodule Formation by Artificial Expression of the TrEnodDR1 (Coat Protein of White clover cryptic virus 1) Gene in Lotus japonicus. MPMI 18, 1069–1080. doi: 10.1094/MPMI-18-1069
   
3. Shapiro L. R., Salvaudon L., Mauck K. E., Pulido H., DeMoraes C. M., Stephenson A. G., Mescher M. C. 2013. Disease interactions in a shared host plant: effects of pre-existing viral infection on cucurbit plant defense responses and resistance to bacterial wilt disease. PLoS One 8, e77393. doi: 10.1371/journal.pone.0077393
   
4. Hanssen I. M., Gutiérrez-Aguirre I., Paeleman A., Goen K., Wittemans L., Lievens B., Vanachter A. C. R. C., Ravnikar M., Thomma B. P. H. J. 2010. Cross-protection or enhanced symptom display in greenhouse tomato co-infected with different Pepino mosaic virus isolates. Plant Pathology 59, 13–21. doi: 10.1111/j.1365-3059.2009.02190.x
   
5. Perring, T. M., Farrar C. A., Blua M., J., Wang H. L, Gonsalves D., 1995. Cross protection of cantaloupe with a mild strain of zucchini yellow mosaic virus: effectiveness and application. Crop Protection 14, 601-606. doi: 10.1016/0261-2194(95)00030-5
   
6. Desbiez C., Joannon B., Wipf-Scheibel C., Chandeysson C., Lecoq H. 2009. Emergence of new strains of Watermelon mosaic virus in South-eastern France: Evidence for limited spread but rapid local population shift. Virus Research 141, 201-208. doi: 10.1016/j.virusres.2008.08.018
   
7. Desbiez C., Wipf-Scheibel C., Millot P., Berthier K., Girardot G., Gognalons P., Hirsch J., Moury B., Nozeran K., Piry S., Schoeny A., Verdin E. 2020. Distribution and evolution of the major viruses infecting cucurbitaceous and solanaceous crops in the French Mediterranean area. Virus Research 286, 198042. doi: 10.1016/j.virusres.2020.198042
   
8. Desbiez C., Domingo-Calap M. L., Pitrat M., Wipf-Scheibel C., Girardot G., Ferriol I., Lopez-Moya J. J., Lecoq H. 2022. Specificity of Resistance and Tolerance to Cucumber Vein Yellowing Virus in Melon Accessions and Resistance Breaking with a Single Mutation in VPg. Phytopathology 112,1185-1191. doi: 10.1094/PHYTO-06-21-0263-R
   
9. Rimbaud L., Papaïx J., Rey J-F., Barrett L. G., Thrall P. H., 2018. Assessing the durability and efficiency of landscape-based strategies to deploy plant resistance to pathogens. PLOS Computational Biology. doi: 10.1371/journal.pcbi.1006067
10. Piry S., Chapuis M-P ., Gauffre B., Papaïx J., Cruaud A., Berthier K., 2016. Mapping Averaged Pairwise Information (MAPI): a new exploratory tool to uncover spatial structure. Methods in Ecology and Evolution. doi: 10.1111/2041-210X.12616
    

--

Have you read our newsletter? Click here!