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Diversity, mutation and recombination analysis of chilli infecting geminiviruses from the Indian Subcontinent

Research Paper | May 1, 2022

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Muhammad Atif, Uzma Bashir, Muhammad Tariq Manzoor, Nida Rafaqat, Muhammad Waqar Alam, Mubeen Sarwar, Sumreen Anjum, Talha Ali Chohan, and Ammarah Hasnain

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Int. J. Biosci.20( 5), 23-36, May 2022

DOI: http://dx.doi.org/10.12692/ijb/20.5.23-36


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The epidemic of the chilli leaf curl disease complex (ChiLCD) has been of great concern for about a few decades in the Indian subcontinent. A severe epidemic was observed in Jodhpur (India) in 2004. This virus is transmitted by whitefly (Bemisia tabaci). The huge population of virus vectors introduces this virus throughout the subcontinent. Analysis of different sequences reported from different parts of the subcontinent showed huge diversity of this Begomovirus. Phylogenetic analysis indicates that two sequences (KF312364, KR779820) are ancestors and others are descendants. These two sequences (KF312364, KR779820) evolve and different strains, variants come into being. Total 101 full-length sequences of this begomovirus have been analyzed in phylogenetic analysis. Recombination analysis showed that sequences having accession number (JX524173, JN135234) are fully recombinant. Sequence having accession number JX524173 is the only sequence having all positive results in all RDP tests. We determined different substitution rates for different isolates. Our results indicate that ChiLCV is a highly virulent strain and could be the most devastating for chilli crops in the Indian subcontinent.


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Diversity, mutation and recombination analysis of chilli infecting geminiviruses from the Indian Subcontinent

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