Pathogenic and genetic diversity of chilli veinal mottle virus associated with U-morok (Capsicum chinense) decline in Manipur state of North East India

• Published in: Indian phytopathology Vol. 75; no. 4; pp. 1221 - 1229
• Main Authors: Devi, Huirem Chandrajini, Sharma, Susheel Kumar, Devi, Konjengbam Sarda, Devi, Oinam Priyoda, Roy, Subhra Saikat, Devi, Ph. Sobita
• Format: Journal Article
• Language: English
• Published: New Delhi Springer India 01.12.2022
• Subjects: Biomedical and Life Sciences; Life Sciences; Plant Pathology; Short Communication; Mechanical inoculation; Symptom diversity; Phylogeny; Reverse transcription-polymerase chain reaction
• ISSN: 0367-973X; 2248-9800
• DOI: 10.1007/s42360-022-00566-w

Chilli veinal mottle virus (ChiVMV), a potyvirus has emerged as the most devastating threat to chilli cultivation in North East Region (NER) of India. Its wide prevalence and higher rate of transmission led to crippling of chilli groves, especially of landrace U-morok ( C. chinense ) in NER of India. Current study elucidates widespread occurrence of ChiVMV, its association with varied symptoms of U-morok and the genetic diversity from Manipur state of NER India. A total of 1241 chilli leaf samples were collected during 2019–2021 from the 42 major U-morok groves exhibiting diverse symptoms of mild to severe decline. Molecular detection using standard reverse transcription polymerase chain reaction (RT-PCR) by employing the ChiVMV specific primers targeting coat protein (CP) and 3′-UTR (3′-untranslated region) genomic region of ChiVMV genome showed that out of a total of 1241 U-morok samples, 788 samples (63.50%) were positive for ChiVMV. Six representative ChiVMV isolates (ChiVMV-MNP1, ChiVMV-MNP2, ChiVMV-MNP3, ChiVMV-MNP4, ChiVMV-MNP5 and ChiVMV-MNP10) sampled from different locations of Manipur upon mechanical inoculation showed diverse and distinct symptoms, indicating significant pathogenic diversity among them. Nucleotide sequences of CP gene along with 3′-UTR of 11 ChiVMV isolates showed 87.57 to 92.84% nucleotide sequence identity with ChiVMV sequences available in the GenBank. Analysis of partial coat protein sequence and 3′-UTR of 11 ChiVMV isolates sampled from different locations of Manipur showed homologous sequences among them, but were distinct in comparison to the earlier reported ChiVMV isolates from India and other parts of the world. Phylogenetic analysis of ChiVMV isolates characterized in present study revealed that the virus might have spread across the geographical borders.