Netla, Vamsidhar Reddy, Hiremath, Shridhar, Muttappagol, Mantesh, Vinay Kumar, H D, Prasanna, S. Koti, Kumar, T. L. Mohan, Basha, C. R. Jahir, Venkataravanappa, V., Shankarappa, K. S., Maruthi, M. N. ORCID: https://orcid.org/0000-0002-8060-866X and Reddy, C. N. Lakshminarayana (2025) Virome analysis of field-collected chilli samples reveals diverse viruses. Virology Journal, 22:116. ISSN 1743-422X (Online) (doi:10.1186/s12985-025-02713-x)

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Abstract

Background: Chilli (Capsicum annuum L.), an important spice crop, is susceptible to diverse viral infections. Traditional detection methods including PCR and its variants had difficulty in identifying the complete spectrum of viruses, especially in mixed infections. High-throughput sequencing (HTS) has emerged as a successful tool for comprehensive virome analyses, enabling the identification of the known and novel viruses in the infected samples. Using HTS, we investigated virome analyses to identify known and novel viruses in chilli.
Methods: In 2021–22, 19 leaf samples were collected from chili plants in farmer fields in Karnataka, India, showing symptoms such as leaf curling, vein banding, mosaic, mottling, filiform, leathery, dull-colored, and bunchy leaves. Total RNA was extracted, pooled at equimolar concentrations, and subjected to virome profiling. rRNA-depleted RNA was used to prepare mRNA and sRNA libraries, which were sequenced on the Illumina NovaSeq 6000 platform. Bioinformatics tools were used to analyze the sequencing data and identify plant viruses.
Results: Viral disease incidences varied from 26.6 to 47.5% in the farmer fields surveyed. Virome analyses revealed complete/ near-complete genomes of six different viruses: chilli leaf curl virus (ChiLCV), cucumber mosaic virus (CMV), groundnut bud necrosis orthotospovirus (GBNV), pepper cryptic virus-2 (PCV-2), pepper vein yellows virus (PeVYV) and bell pepper alphaendornavirus (BPEV). The viral copy number of ChiLCV was found to be the highest (45.36%) and had the least mutational frequency (SNPs) and was also associated with five satellites. Recombination breakpoints were observed in ChiLCV (coat protein and AC4 regions), CMV RNA2 (2a protein) and PeVYV (P0, P3 and P5 proteins), indicating their origins from intra- and interspecific recombination events. Identified viruses in the pooled RNA sample were confirmed by PCR. Further, novel loop-mediated isothermal amplification (LAMP) diagnostic assays were developed for diagnosing the identified viruses for future use. Among the six viruses identified in chilli, PeVYV and BPEV are the first reports from India.

Item Type:	Article
Additional Information:	University of Agricultural Sciences funded the publication charges. - MP
Uncontrolled Keywords:	chilli viruses, high-throughput sequencing (HTS), virome analysis, PeVYV, BPEV, LAMP
Subjects:	Q Science > Q Science (General) Q Science > QR Microbiology Q Science > QR Microbiology > QR355 Virology
Faculty / School / Research Centre / Research Group:	Faculty of Engineering & Science Faculty of Engineering & Science > Natural Resources Institute Faculty of Engineering & Science > Natural Resources Institute > Centre for Sustainable Agriculture 4 One Health Faculty of Engineering & Science > Natural Resources Institute > Centre for Sustainable Agriculture 4 One Health > Plant Disease & Vectors
Last Modified:	05 Nov 2025 08:55
URI:	https://gala.gre.ac.uk/id/eprint/51463

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