The 3′ non-coding regions (NCR) of RNA1 and RNA2 of blueberry leaf mottle nepovirus (BBLMV) are nearly identical with differences occurring at only four positions. The presence of this 1·4 kb duplication indicates that recombination has occurred at least once in the evolutionary history of BBLMV. Since high mutation rates are common in RNA viruses, strong selection pressure and/or high frequency of recombination must be operating in order to maintain identity in this duplicated region. The possible involvement of high frequency RNA recombination in maintaining identity was investigated. The four conserved differences between the 3′ NCR of RNA1 and RNA2 were used as markers to detect recombinants in a viral population. Nucleotide sequences of BBLMV cDNA clones were compared to the 3′ consensus sequence and deviations were examined to determine whether they were due to single base mutations or recombinational events. No evidence of recombination was found in any of the cDNA clones sequenced and all differences were attributed to mutations. If recombination occurred in the 3′ NCR of BBLMV, the frequency was below 1·1% between markers. The data indicate that identity in the 3′ NCR of RNA1 and RNA2 of BBLMV was maintained without high levels of recombination. The high number of mutations observed in a BBLMV population and lack of observable recombination indicate that other mechanisms, such as selection, play an important role in the conservation of identity in the 3′ NCR.


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