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. 2015 Jun 25;18(1):20035. doi: 10.7448/IAS.18.1.20035

Figure 2.

Figure 2

Phylogenetic and variability analysis of sequenced Swedish HIV-1 strains. (a) Maximum likelihood phylogenetic tree with reference HIV-1 sequences downloaded from Los Alamos Database. Four subtypes are indicated: HIV-1B (dark blue), HIV-1C (orange), CRF01_AG (green) and CRF02_AG (purple). The Swedish strains are indicated with filled circle with a respective colour. (b) Genetic diversity of HIV-1 subtypes: all the 24 HIV-1 genomes were aligned with reference to HXB2 [GenBank:K03455]. For each sequence, every nucleotide differing from the reference HXB2 strain (mutation) is shown as a green line, an insertion is shown in orange, and a deletion is shown in purple. The top panel shows the open-reading frame of HIV-1 genes: gag (violet), pol (lemon green), vif (pink), vpr (light red), tat exon 1 and 2 (black), rev exon 1 and 2 (grey), vpu (cyan), env (light yellow) and nef (green).