We determined nucleotide sequences of the VP1 and 2AB genes and portions of the 2C and 3D genes of two evolving poliovirus lineages: circulating wild viruses of T geotype and Sabin vaccine-derived isolates from an immunodeficient patient. Different regions of the viral RNA were found to evolve nonsynchronously, and the rate of evolution of the 2AB region in the vaccine-derived population was not constant throughout its history. Synonymous replacements occurred not completely randomly, suggesting the need for conservation of certain rare codons (possibly to control translation elongation) and the existence of unidentified constraints in the viral RNA structure. Nevertheless the major contribution to the evolution of the two lineages came from linear accumulation of synonymous substitutions. Therefore, in agreement with current theories of viral evolution, we suggest that the majority of the mutations in both lineages were fixed as a result of successive sampling, from the heterogeneous populations, of random portions containing predominantly neutral and possibly adverse mutations. As a result of such a mode of evolution, the virus fitness may be maintained at a more or less constant level or may decrease unless more-fit variants are stochastically generated. The proposed unifying model of natural poliovirus evolution has important implications for the epidemiology of poliomyelitis.Analysis of polioviruses isolated either during a given outbreak of poliomyelitis (30,35,51) or from sequential fecal samples from infected individuals (29, 31, 34) has revealed rapid changes in the nucleotide sequence of the viral 7.5-kb RNA. Oligonucleotide fingerprinting (51) and genome sequencing (30, 34) suggested that, during the epidemic, the nucleotide substitutions ranged from 1 to 2% per year. The molecular basis of such genetic instability, common to all RNA viruses, resides in a high error rate of the viral RNA-dependent RNA polymerases, estimated to be, for poliovirus, on the order of 10 Ϫ4 to 10 Ϫ5 substitutions per base per replication (12,70,71), and the absence of proofreading mechanisms for the correction of the errors made. The combination of these properties results in a high heterogeneity (the "quasispecies" nature) of all populations of the virus (8,10,11,63).Less understood, however, are the rules governing the fixation of specific mutations upon passages of a viral population. Generally speaking, a mutation may decrease or increase the level of virus fitness for a particular ecological niche or leave it unchanged. Nucleotide substitutions associated with changes in the "sense" of codons (nonsynonymous mutations) are less likely to be neutral than substitutions resulting in no change of the codon meaning (synonymous mutations). Fixation of mutations conferring a selective advantage is readily understood in the framework of positive Darwinian selection. Adverse mutations may be eliminated by negative selection.The likelihood of fixation of a mutation depends not only on the associated changes in virus fitness but, ...