Crimean-Congo hemorrhagic fever virus (CCHFV) genomic characteristics. A, Treatment regimen of the second patient with Crimean-Congo hemorrhagic fever, where days are numbered according to length of time after the initiation of ribavirin treatment on day 1. B, CCHFV load (right y-axis), measured on the basis of CCHFV RNA detection by reverse transcription–polymerase chain reaction, decreased during ribavirin treatment (x-axis). Viral populations were enriched by RNA Access, using CCHFV-specific oligomeric probes; sequenced on an Illumina MiSeq; and aligned to the consensus sequence of the day 1 sample. The percentage coverage of sequenced segments (S, M, and L; left y-axis) varied with the viral load. C, Paired-end FASTQ reads from each sample that aligned to the CCHFV consensus sequence were segregated on the basis of the strandedness of the input sample RNA. Values are percentages of reads that are negative stranded (left y-axis). D, Subclonal diversity (left y-axis), measured on the basis of the number of base changes per site per genome, in CCHFV populations increased during ribavirin treatment. Values are measured with respect to day 1 and were derived from base changes with a frequency ≥2% at each site. Subclonal diversity was significantly different across sample days (P = .0336, by 2-way analysis of variance). Closed circles indicate samples collected during ribavirin treatment. Open circles indicate samples collected after the cessation of ribavirin treatment.