Figure 6
From: Molecular epidemiology and HIV-1 variant evolution in Poland between 2015 and 2019
Recombination pattern of the nine partial HIV-1 pol sequences from the identified A6B Cluster II. Analysed region include the protease with a fragment of the reverse transcriptase gene (2253–3554 bp) and the integrase gene (4230–5096 bp). In two cases (33-17L, 249-19WR) IN gene was not sequenced. Recombination breakpoints (according to HXB2 genome positions) were obtained using Simplot v3.5.1 software and jumping-profile hidden Markov model (jpHMM). The blue color stands for HIV-1 subtype B, red color stands for sub-subtype A6. Component subtype regions are labeled from 1 up to 3 on the genome map, corresponding with numbered on phylogenetic trees in Supplementary Figure S5. The mosaic map was generated using the Recombinant HIV-1 Drawing Tool (https://www.hiv.lanl.gov/content/sequence/DRAW_CRF/recom_mapper.html).
