Complete nucleotide sequence of an Indian isolate of Carnation etched ring virus and its homology with other caulimoviruses.

Carnation etched ring virus (CERV) is a member of Caulimovirus with double stranded DNA genome of approx. 8 kb. CERV has been previously characterized from Holland and the present article is an effort to completely characterize the Asian isolate of CERV. Primers were designed for amplification of all genes encoded by the CERV, viz. movement protein, aphid transmission factor, DNA binding protein, coat protein, poly protein and inclusion body matrix genes, including the complete genome. The CERV genome was sequenced by amplifying the complete genome of CERV using primers from 5¢- and 3¢-end and with internal primers that amplify individual genes and parts of the genes. The genome was found to comprise of 7924 bp, with GC content of 37%. The different genes encoded by CERV were compared with other known CERV isolates and caulimoviruses. They were found most conserved with respect to poly protein region (37–65% amino acid similarity), while least with respect to inclusion body matrix protein (5–37% amino acid similarity). CERV isolates from India and Holland when compared for different genes, showed 96–99% homology between different genes at the amino acid level. Multiplex PCR protocols were standardized to amplify different genes of the CERV genome in one reaction. Phylogenetic analysis based on different genes indicated that CERV has independently evolved among caulimoviruses, but is closely related to Cauliflower mosaic virus