Differences in selective profiles among single or double stranded DNA or RNA viruses. Statistical detection of its double or single stranded condition

Abstract

ABSTRACTI developed a test to study the probability distribution of bases in dinucleotides separated by 0, 1, 2…K nucleotides sites. This analysis define selective profiles of dinucleotides by their sign and selection coefficients, their distance to neutrality measured by a chi-square value and the order of significance of their distance to randomness among the 16 possible values. In double stranded (ds) DNA or RNA an index (index = I, with 5’-3’ sense) dinucleotide participates in evolutionary processes together with three dinucleotides defined by base complementarity and 5’-3’ sense. The anti-sense dinucleotide in the same strand, the parallel (Par, with 3’-5’ sense) and anti-parallel (a-Par, with 5’-3’ sense) dinucleotides in the complementary strand. Single stranded (ss) RNA or DNA do not have these set of dinucleotides and would not present similarities or differences, among those four dinucleotides. I studied viromes taken from GenBank, with ds and ss RNA and DNA by this dinucleotide analysis. The core matrix has rows with Separations (Sep) of bases and columns with their selective profiles of the Index, Par and a-Par dinucleotides. Profiles distances I-Par and I-a-Par where compared. The ds RNA or DNA showed larger selective profiles differences between I-Par than I-a-Par. Ss RNA or DNA viruses showed non-significant differences between these comparisons. Those ss virus that exist as ds virus in their hosts, as Hindbis and HIV virus behaved similarly to ds viruses. Coli phage PhiX174 an ss DNA virus showed smaller I-Par than I-a-Par selective distances.IMPORTANCEI present a new method for the comparison of selective profiles that allows know whether a RNA or DNA behaves preferentially as ds or ss nucleic acid and gives information about their dynamic or evolutionary mechanisms of replication cycles. This changes our vision of viruses constituted in the virion as ds or ss viruses towards a functional evolutionary vision where viruses are ds and ss according to their behavior along with their life cycle. This evolutionary vision may be crucial in epidemiology.