Spatial Distribution and Genetic Characterization of Pepper Yellow Leaf Curl Virus Infecting Chili (Capsicum annuum) in Lampung Province, Indonesia.

Abstract

Chili pepper (Capsicum annuum) is a major horticultural commodity in Indonesia whose productivity is constrained by viral diseases, particularly pepper yellow leaf curl virus (PepYLCV). This study investigated the spatial distribution, symptomatology, incidence, severity, and genetic diversity of PepYLCV in seven primary chili‑producing districts of Lampung Province, namely North, Central, South, and West Lampung, Pesawaran, Pringsewu, and Tanggamus. Field surveys combined with molecular diagnostics demonstrated widespread PepYLCV infection, with disease incidence reaching 91% and 85% and disease severity 79% and 77% in Tanggamus and West Lampung, respectively. Symptom expression, including leaf curling, yellow mosaic, leaf size reduction, and stunting, varied among agroecosystems. Infection by PepYLCV was confirmed through PCR using begomovirus‑specific primers, and partial nucleotide sequences of the replication‑associated (AC1/AC2) and coat protein (AV1) genes showed 86-94% identity with PepYLCV isolates in GenBank, indicating close relatedness within the Indonesian PepYLCV complex. Phylogenetic analyses grouped all Lampung isolates in a well‑supported clade (bootstrap 99-100%) distinct from foreign begomoviruses, and the pronounced genetic homogeneity is consistent with efficient regional spread mediated by the whitefly Bemisia tabaci. Collectively, these findings demonstrate that PepYLCV constitutes a serious constraint to chili production in Lampung and poses a risk of further dissemination to other production centers, underscoring the need for integrated disease management through vector suppression, deployment of PepYLCV‑resistant cultivars, and strategic development of mild strain cross‑protection.