Figure 1.

Experimental system and potential sources of error. Experimentally-induced recombination or mutation may arise at any point from plasmid production to sequencing. To control for this and to assess the contribution of different stages of processing to the observed rates, we analysed a variety of controls. All controls included underlying sequencing error, and in addition (A) DNA PCR control measures PCR induced recombination and mutation (B) Intervirion control measures PCR and homozygous infection induced recombination, and total mutation mutation rate due to transfection, infection and sequencing. (C) Transfection induced recombination control measures mutation and recombination rates due to transfection of CEM cells, reverse transcription of virus and PCR amplification. (D) Our experimental samples—heterozygous infection—allows us estimate the rate of infection-associated mutation and recombination.