Outbreak of Cucumber Mosaic Virus Subgroup IB in Pepper from the Espelette Area (Basque Country, Southwestern France) and First Report of Five Taxa as Natural Hosts of CMV

Abstract

To better understand the emergence of cucumber mosaic virus (CMV) in the protected designation of origin of Espelette pepper (southwestern France), more than 7,300 samples were collected in and around 36 pepper fields in 2021 and 2022 and diagnosed using ELISA, RT-PCR, and partial Sanger sequencing of viral RNAs. This allowed the identification of five new host genera or species among the natural hosts of CMV: Arum italicum, Cerastium glomeratum, Hyacinthoides sp., Lysimachia arvensis, and Trifolium incarnatum. A CMV variant belonging to subgroup IB and presenting a low molecular diversity was highly prevalent in the pepper crops (78% of the pepper samples) as well as in naturally growing plants (8% of the non-pepper samples) within the fields. CMV isolates from group II were detected in a single pepper plant as well as in Hyacinthoides sp. (three samples), Capsella bursa-pastoris (two samples), and Stachys arvensis (one sample). To our knowledge, this is the second report of the occurrence of subgroup IB of CMV in France. Investigation of old pepper samples indicated that it has been present at least since 2009.