First Report of Yambean Mosaic Virus on Vanilla in New Caledonia

In July 2023, mosaic symptoms on leaves of vanilla (Vanilla planifolia) were observed in three plots, with an incidence of c. 7%, on a farm in Païta in the South Province of New Caledonia (Figure 1). The symptoms, similar to the mosaic symptoms of potyvirus-infected vanilla plants (Grisoni et al. 2010), suggested the possible involvement of a potyvirus. Among the seven Potyvirus species that infect vanilla, bean common mosaic virus (P. phaseovulgaris), dasheen mosaic virus (P. dasheenis), watermelon mosaic virus (P. citrulli) and Wisteria vein mosaic virus (P. wisteriae) have been detected on vanilla in Pacific regions (Grisoni et al. 2006). To verify the identity of the causal agent, symptom-bearing leaf samples from one plant from each plot were tested (NC46, NC49 and NC50). Total RNA was extracted using a RNeasy Plant Mini Kit (Qiagen, France). For the detection of potyviruses, the SuperScript III One-Step RT-PCR kit (Invitrogen, France) was used with degenerate primers CIFor and CIRev designed to amplify the potyviral CI region (Ha et al. 2008). RT-PCR products of the expected size were obtained for the three samples. To confirm the diagnosis, the RT-PCR products were directly and bi-directionally sequenced and contigs assembled using DNABaser (Heracle BioSoft, Romania). Identical sequences of 565 bp were obtained (MEGA12; Kumar et al. 2024) (GenBank Accession Nos. PX400203-PX400205). The sequences showed the highest nucleotide identities with isolate DSMZ PV-0784 (97.2%, PV780754) of unknown origin and a Brazilian isolate BR6 (97.0%, MZ018226) of yambean mosaic virus (YBMV; P. pachyrizus). To obtain a full genome sequence of the New Caledonian isolate of YBMV, ribodepletion on total RNA extraction and Illumina RNA sequencing (2 × 150 bp) were performed by Azenta (Leipzig, Germany) for the NC50 sample. A total of c. 20.1 million of paired reads was obtained. After de novo assembly using MEGAHIT v1.2.9 (Li et al. 2015), a quasi-complete genome sequence of 10,015 nucleotides of YBMV (isolate NC50-2023; PX409851) with a mean coverage of c. ×10,300 was obtained. The sequence shares the highest nucleotide identity (96.1% with 93% query cover) with isolate DSMZ PV-0784 of YBMV (PV780754). A phylogenetic reconstruction with publicly available complete genome sequences of potyviruses confirmed that the New Caledonian isolate is genetically related to YBMV isolates (MEGA12; Figure 2). Interestingly, it is genetically more closely related to the South American isolates than to the neighbouring Australian isolate, suggesting different routes of introduction. A second sequence of 7096 nucleotides was obtained showing the highest nucleotide identity (94.5% with 100% query cover) with Vanilla latent virus (Allexivirus latensvanillae; MF150239), causing asymptomatic infections (Grisoni et al. 2017). To our knowledge, this is the first description of YBMV both in New Caledonia and on vanilla. Given the economic and cultural importance of vanilla cultivation in Pacific islands, its predominant vegetative mode of propagation and the associated risk of viral disease transmission, this report is of great significance for managing the health of vanilla in Pacific countries, and warrants urgent attention from regulatory institutions. This study was co-funded by the European Union (European Regional Development Fund), the Conseil Régional de La Réunion, CIRAD and the Ministère Européen des Affaires Etrangères (NAAP project), and conducted at the Plant Protection Platform (3P, IBISA).