Molecular Characterisation of Begomoviruses Associated With Chilli Leaf Curl Disease

Abstract

Chilli leaf curl disease is one of the most damaging constraints on chilli and pepper production across South Asia, and the begomoviruses behind it are usually described as if a single named virus were responsible. This narrative review asks how firmly that description is supported. It draws on published work on begomovirus genome organisation, betasatellites and alphasatellites, whitefly transmission, recombination, sequence-based classification and diagnostic methods, and it reports no new sequences or data. The literature shows a disease that is better described as a complex than as a single agent: several begomovirus species, often together with a betasatellite, have been recovered from affected chilli, and recombination blurs the boundaries between them. Which virus appears to be causal therefore depends on where and when plants were sampled, which primers and amplification method were used, and which classification threshold was applied. Reports that rest on a short fragment, or on a single plant per site, can name a virus confidently without being able to exclude its neighbours. The review concludes that the causal agent of chilli leaf curl is best treated as site-dependent, sets out a minimum description that would make molecular reports comparable, and identifies where better sampling and full-genome work would help most.