DINUCLEOTIDE AND STOP CODON FREQUENCIES IN SINGLE-STRANDED RNA VIRUSES

To identify potential selection pressures which lead to RNA sequence c onservation, we examined the occurrence rates of dinucleotides in 64 s ingle-stranded RNA virus genomes, These viruses may offer a particular insight into these pressures since their RNA-dependent RNA polymerase s lack proof-reading capability, This potentiates introduction of muta tions into their genomes, yet unidentified selection processes conserv e the genomes to a large degree. We report a strong inverse correlatio n between the C+G content and the occurrence of the CpG dinucleotide ( r=0.71) in the RNA virus genomes, in contrast to earlier reports (Karl in et al., 1994, Journal of Virology 68, 2889-2897), We also detected significant suppression of UpA, correlating inversely with genomic U+A content, These suppressions are coupled with over-representation of t he complementary pair of dinucleotides, CpA and UpG, In addition, we h ighlight the fact that odds ratios for dinucleotides are not independe nt variables, a situation apparently not widely appreciated in the lit erature, This led us to view the over-representation of CpA and UpG as a consequential outcome of UpA and CpG suppression in the virus genom es, Potential factors influencing these disturbances are discussed, In addition, higher than random incidence was observed for 'out-of-frame ' stop codons in the viral RNA genomes, with some preferences for indi vidual codons being exhibited by certain virus groups, The UAG codon a ppeared more common in the +1 frame, the UGA in the -1 frame.