Fig. 1.

Summary of phylogenetic tree construction from 144 women who each provided duplicate samples (anal + vaginal swabs). The L1 region of HPV was sequenced using next generation sequencing on the Illumina MiSeq platform. The sequence pairs generated were filtered, clustered and aligned to produce 35 phylogenetic trees. HPV 16, 18 and 52 were further analysed for in-depth statistical description of the distribution of clades by site of HPV infection, cervical cytology result and HIV statuses of the women.