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The capsid protein gene of three Egyptian CTV isolates from two locations was amplified by immunocapture RT-PCR and analysed by single stranded conformation polymorphism and sequencing. The CTV isolates studied did not differ significantly in sequence composition and each isolate consisted of very similar haplotypes. Comparison with reference sequences from isolates elsewhere in the world showed that these haplotypes clustered very close to the severe strain T3 from Florida causing quick decline and stem pitting. Analysis of the deduced amino acid sequence showed the epitope characteristic of reactivity with the MCA13 antibody. Sequence comparison with the sequence of an Egyptian isolate (Qaha) available in the Genbank showed a distance of about 8%, suggesting that it had a different origin.