Figure 2

HIV-2 has a lower mutation frequency and distinct mutation spectrum relative to HIV-1. a Mutation frequency analysis. Mutation frequencies were calculated by dividing the number of mutations by the number of reference bases (mutations + wild-type bases) and are expressed as mutations/bp, or m/bp. Mutation frequencies were determined for HIV-1 and HIV-2, as well as for plasmid controls to assess background error levels. b Transition frequency analysis. Transition frequencies were compared across the five different amplicons subjected to Illumina DNA sequencing. c Mutation spectra analysis. Mutation spectra were determined by dividing the frequency of each type of mutation by the total mutation frequency, with the results expressed as a percentage of total mutations. Data in all panels represent the mean of three experimental replicates, with error bars indicating the standard deviation. Asterisks denote statistically significant differences between HIV-1 and 2 (*p < 0.05, ***p < 0.001, N.S. not significant). The actual numbers of read pairs, mutations, and reference bases are listed in Additional file 3: Dataset S1.