Genetic diversity and characterization of cucumber mosaic virus infecting chilli in Zone II and Zone IIIB of Bihar, India

Objective Chilli ( Capsicum annuum L.) is an economically important spice and vegetable crop widely cultivated in Bihar; however, its productivity is severely affected by viral diseases, particularly cucumber mosaic virus (CMV). The present study was undertaken to investigate the occurrence, molecular characterization, and genetic diversity of CMV infecting chilli in Zone II and Zone IIIB of Bihar. Extensive field surveys conducted during 2019–2020 in major chilli-growing districts, including Kishanganj, Purnia, and Bhagalpur, revealed characteristic symptoms such as mosaic, mottling, chlorosis, leaf deformation, vein clearing, shoestring leaves, and stunted growth. A total of 355 symptomatic samples were collected and screened through Direct Antigen Coating Enzyme-Linked Immunosorbent Assay (DAC-ELISA), among which 115 samples tested positive for CMV infection. Methods Representative isolates from different locations were biologically maintained through mechanical sap inoculation on indicator hosts. Total RNA extracted from infected plants was subjected to reverse transcription–polymerase chain reaction (RT-PCR) using coat protein (CP) gene-specific primers, which amplified the expected 657 bp fragment from six selected isolates, namely Sabour, Kahalgoan, Purnia, Kasba, Belwa, and Kharkhari. The amplified products were cloned, sequenced, and submitted to GenBank. Comparative nucleotide and deduced amino acid sequence analyses revealed a high degree of sequence conservation among the Bihar isolates, with only minor nucleotide polymorphisms and limited amino acid substitutions. Results Phylogenetic analysis based on CP gene sequences grouped all six Bihar isolates within CMV subgroup IA, indicating close genetic relatedness with previously reported Indian CMV isolates. The Sabour and Kahalgoan isolates formed a closely related cluster, whereas the remaining isolates also grouped within the same lineage with minimal genetic divergence. The observed sequence conservation suggests that CMV populations infecting chilli in Bihar are genetically stable and may have originated from a common ancestral source followed by regional dissemination. Conclusion The present study provides a comprehensive molecular characterization and phylogenetic analysis of CMV infecting chilli in Zone II and Zone IIIB of Bihar. The findings highlight the importance of continuous surveillance, molecular diagnostics, and the development of resistant cultivars for effective management of CMV-associated diseases and sustainable chilli production.