Distribution and evolution of the major viruses infecting cucurbitaceous and solanaceous crops in the French Mediterranean area

• Published in: Virus research Vol. 286; p. 198042
• Main Authors: Desbiez, Cécile, Wipf-Scheibel, Catherine, Millot, Pauline, Berthier, Karine, Girardot, Grégory, Gognalons, Patrick, Hirsch, Judith, Moury, Benoît, Nozeran, Karine, Piry, Sylvain, Schoeny, Alexandra, Verdin, Eric
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01.09.2020; Elsevier
• Subjects: Epidemiology; Evolution; Life Sciences; Melon; Microbiology and Parasitology; Pepper; Phytopathology and phytopharmacy; Potyvirus; Recombination; Tomato; Vegetal Biology; Virology; Recombination; Pepper; Evolution; Potyvirus; Tomato; Epidemiology; Melon
• ISSN: 0168-1702; 1872-7492
• DOI: 10.1016/j.virusres.2020.198042

•We characterized viruses infecting cucurbitaceous and solanaceous crops in France.•Aphid- and thrips-transmitted viruses remain the most prevalent viruses so far.•New WMV and CMV strains have been introduced in France in the last decade.•Recombination and reassortment are frequent.•The frequency of introductions is a major driver of population genetic structure. 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.