, Volume 29, Issue 1, pp 61–67 | Cite as

Rolling circle amplification-based analysis of Sri Lankan cassava mosaic virus isolates from Tamil Nadu, India, suggests a low level of genetic variability

  • Akhilesh Kumar Kushawaha
  • Ramalingam Rabindran
  • Indranil Dasgupta
Original Article


Cassava mosaic disease is a widespread disease of cassava in south Asia and the African continent. In India, CMD is known to be caused by two single-stranded DNA viruses (geminiviruses), Indian cassava mosaic virus (ICMV) and Sri Lankan cassava mosdaic virus (SLCMV). Previously, the diversity of ICMV and SLCMV in India has been studied using PCR, a sequence-dependent method. To have a more in-depth study of the variability of the above viruses and to detect any novel geminiviruses associated with CMD, sequence-independent amplification using rolling circle amplification (RCA)-based methods were used. CMD affected cassava plants were sampled across eighty locations in nine districts of the southern Indian state of Tamil Nadu. Twelve complete sequence of coat protein genes of the resident geminiviruses, comprising 256 amino acid residues were generated from the above samples, which indicated changes at only six positions. RCA followed by RFLP of the 80 samples indicated that most samples (47) contained only SLCMV, followed by 8, which were infected jointly with ICMV and SLCMV. In 11 samples, the pattern did not match the expected patterns from either of the two viruses and hence, were variants. Sequence analysis of an average of 700 nucleotides from 31 RCA-generated fragments of the variants indicated identities of 97–99% with the sequence of a previously reported infectious clone of SLCMV. The evidence suggests low levels of genetic variability in the begomoviruses infecting cassava, mainly in the form of scattered single nucleotide changes.


Cassava Begomovirus Rolling circle amplification RCA-RFLP Genetic diversity 



AKK gratefully acknowledges fellowships from University of Delhi and Department of Biotechnology, Government of India. This work was funded by the Grant Number BT/PR/13094/PBD/16/866/2005 by Department of Biotechnology, Government of India to ID.

Supplementary material

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Copyright information

© Indian Virological Society 2018

Authors and Affiliations

  1. 1.Department of Plant Molecular BiologyUniversity of DelhiNew DelhiIndia
  2. 2.Center for Plant Breeding and GeneticsTamil Nadu Agricultural UniversityCoimbatoreIndia

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