Serological and Molecular Identification of CMV Subgroup IA Infecting Bhut Jolokia (Capsicum chinense Jacq.) in Assam, India

Abstract

Bhut Jolokia (Capsicum chinense), a high-value chili pepper indigenous to Northeast India, faces significant yield constraints due to viral diseases. Extensive field surveys conducted during 2020-2021 in the major Bhut Jolokia growing districts of Assam (Jorhat, Golaghat, Lakhimpur, and Dhemaji) revealed a high incidence of virus-like symptoms, including mosaic, mottling, leaf distortion, and stunting. Serological detection using Double Antibody Sandwich Enzyme-Linked Immunosorbent Assay (DAS-ELISA) confirmed the widespread presence of Cucumber mosaic virus (CMV), with disease incidence ranging from 30% to 80%. Molecular analysis further validated these findings. Reverse Transcription-Polymerase Chain Reaction (RT-PCR) using specific primers amplified fragments of the replicase (1052 bp) and coat protein (1130 bp) genes. Nucleotide sequencing of these amplicons revealed 98-100% identity among the Assam isolates. Phylogenetic analysis based on both genes unequivocally clustered the Assam CMV isolates within the subgroup IA, showing closest homology with other Indian isolates from chili. This study provides conclusive evidence of CMV as a predominant viral pathogen infecting Bhut Jolokia in Assam and offers essential genetic information for developing effective management strategies.