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Fig. 3 | Retrovirology

Fig. 3

From: Utilization of HIV-1 envelope V3 to identify X4- and R5-specific Tat and LTR sequence signatures

Fig. 3

HIV-1 gp120 demonstrates high Jensen–Shannon divergence in regions with high genetic diversity. HIV-1 gp120 sequences were classified as CCR5 (R5) (n = 1681) or CXCR4 (X4) (n = 52) according to the predicted co-receptor usage of the V3 domain Web-PSSM score [17]. a The diversity index at a Hill number of 1 was calculated for each position for both R5 (red) and X4 (blue) gp120 amino acid sequence populations. Diversity values range from 1 to greater than 10, with the variable domains of gp120 displaying the greatest diversity. b The Jensen–Shannon divergence between R5 and X4 gp120 sequence populations was computed for each amino acid position and plotted with a diamond. Statistically divergent positions (P < 0.01) were plotted in red. A Monte Carlo permutation test was performed to iteratively group gp120 sequences into random groups and calculate a distribution of expected Jensen–Shannon divergence values. The full range of this distribution was plotted in light blue with the interquartile range plotted in dark blue. The full range of divergence for randomly generated groups is in close agreement with the combined diversity of the R5 and X4 populations

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