Plant viral diseases represent a significant burden to plant health, and their highest impact in Mediterranean agriculture is on vegetables grown under intensive horticultural practices. In order to understand better virus evolution and emergence, the most prevalent viruses were mapped in the main cucurbitaceous (melon, squashes) and solanaceous (tomato, pepper) crops and in some wild hosts in the French Mediterranean area, and virus diversity, evolution and population structure were studied through molecular epidemiology approaches. Surveys were performed in summer 2016 and 2017, representing a total of 1530 crop samples and 280 weed samples. The plant samples were analysed using serological and molecular approaches, including high-throughput sequencing (HTS). The viral species and their frequency in crops were quite similar to those of surveys conducted ten years before in the same areas. Contrary to other Mediterranean countries, aphid-transmitted viruses remain the most prevalent in France whereas whitefly-transmitted ones have not yet emerged. However, HTS analysis of viral evolution revealed the appearance of undescribed viral variants, especially for watermelon mosaic virus (WMV) in cucurbits, or variants not present in France before, as for cucumber mosaic virus (CMV) in solanaceous crops. Deep sequencing also revealed complex virus populations within individual plants with frequent recombination or reassortment. The spatial genetic structure of cucurbit aphid-borne yellows virus (CABYV) was related to the landscape structure, whereas in the case of WMV, the recurrence of introduction events and probable human exchanges of plant material resulted in complex spatial pattern of genetic variation.

植物病毒性疾病给植物健康带来了沉重负担，其在地中海农业中的最大影响是在集约化园艺实践下种植的蔬菜。为了更好地了解病毒的进化和出现，在法国地中海地区的主要葫芦科（瓜，南瓜）和茄科（番茄，胡椒）作物以及一些野生宿主中，对最普遍的病毒进行了定位。通过分子流行病学方法研究了种群结构。调查于2016年夏季和2017年进行，代表了1530种农作物样品和280种杂草样品。使用血清学和分子方法，包括高通量测序（HTS），对植物样品进行了分析。作物中的病毒种类及其频率与十年前在同一地区进行的调查非常相似。与其他地中海国家相反，在法国，蚜虫传播的病毒仍然是最流行的，而粉虱传播的病毒尚未出现。但是，HTS对病毒进化的分析揭示了未描述的病毒变体的出现，尤其是葫芦科植物中的西瓜花叶病毒（WMV）或以前在法国不存在的变体，如茄类作物中的黄瓜花叶病毒（CMV）。深度测序还揭示了单个植物内复杂的病毒种群，并具有频繁的重组或重配。葫芦蚜传黄病毒（CABYV）的空间遗传结构与景观结构有关，而在WMV中，