Limits of variation, specific infectivity, and genome packaging of massively recoded poliovirus genomes

Abstract

Significance We constructed viable poliovirus (PV) variants carrying up to 2,104 synonymous mutations in the ORF. We studied proliferation phenotypes, particularly the specific infectivity ( si ) that defines the probability of a single virion to initiate a single cell infection. A recent hypothesis proposes that dozens of loosely conserved hairpins, formed within the viral genome, determine assembly specificity of +ssRNA viruses. Our analysis of recoded PVs does not support this hypothesis. We propose that the progression of +ssRNA virus assembly follows two steps. ( i ) Specificity: recognition between either ( a ) replication protein and capsid precursor or ( b ) single RNA packaging signal and cognate capsid precursor. ( ii ) Cocondensation, occurring between single genome/single capsid precursor complex and multiple cognate capsids aided by multiple genome-specific hairpins.