Fig. 2

Alignments and entropy plots in Env sequences from the database for the C2 region. a Sequence alignment of the region C2 for the four wild type Env proteins used in this study. Color code: orange hydrophilic, green hydrophobic, red acidic, light blue weak basic, blue basic, violet aromatic, light violet histidine, yellow sulphur-containing, white glycine, gray alanine, pink proline. The three variable sub-regions we defined are highlighted by squares: R1 in blue, R2 in green and R3 in red. b–e Shannon entropy plots. Data were obtained from 201 isolates for subtype A1 (b), 1719 isolates for subtype B (c), 1361 isolates for subtype C (d), and 63 isolates for subtype G (e). The three variable sub-regions are delimited using the same color code as in a. The limits taken to define the borders of the C2, R1, R2, and R3 regions in the different isolates are the following, according to HxB2 numbering: 197–296 (included) for C2, 197–202 for R1, 208–240 for R2, 268–296 for R3. The slightly different sizes of the regions in the different subtypes are due to the presence of insertions and deletions in the multiple sequence alignments in the data from the database