  Recent studies have shown that single-stranded viral RNAs fold into more
compact structures than random RNA sequences with similar chemical composition
and identical length. Based on this comparison it has been suggested that
wild-type viral RNA may have evolved to be atypically compact so as to aid its
encapsidation and assist the viral assembly process. In order to further
explore the compactness selection hypothesis, we systematically compare the
predicted sizes of more than one hundred wild-type viral sequences with those
of their mutants, which are evolved in silico and subject to a number of known
evolutionary constraints. In particular, we enforce mutation synonynimity,
preserve the codon-bias, and leave untranslated regions intact. It is found
that progressive accumulation of these restricted mutations still suffices to
completely erase the characteristic compactness imprint of the viral RNA
genomes, making them in this respect physically indistinguishable from randomly
shuffled RNAs. This shows that maintaining the physical compactness of the
genome is indeed a primary factor among ssRNA viruses evolutionary constraints,
contributing also to the evidence that synonymous mutations in viral ssRNA
genomes are not strictly neutral.
