Phage-encoded contingency loci enable bet-hedging against host defence mechanisms

Bacteriophages are the most diverse biological entities on Earth, but the processes influencing the evolution of genomic diversity in phages are poorly understood. Here, we show that phage genomes contain contingency loci, hypermutable DNA regions that promote reversible frameshift mutations through DNA polymerase slippage on simple sequence repeats. Contingency loci have been extensively described in bacteria, archaea and eukaryotes, yet are understudied in phages. We use experimental evolution and genome sequencing to demonstrate that contingency loci in E. coli phages T2 and T4 reversibly generate genomic and phenotypic heterogeneity in progeny that allow them to hedge their bets against host defences. We find that simple sequence repeats are widespread in diverse E. coli phages and vary in abundance across genes with different functions. Collectively, our study describes a previously unappreciated facet of phage replication in which mutagenic simple sequence repeats drive genetic diversification and population heterogeneity, allowing phages to exploit hosts despite varying defence mechanisms.