HIV-1 Immune Escape Maps Figure 6. HLA-B*57-associated escape and covariation pathways in HIV-1 Gag. The 500 amino acids of consensus B Gag are drawn counterclockwise, with the N-terminus of Gag at the 3 o’clock position. All direct (covariation-corrected) and indirect (covariation uncorrected) B*57- associated polymorphisms at q#0.2 are identified at their respective positions along the circle’s circumference, while covarying amino acids (also q#0.2) are joined together by arcs within the circle. Note that this figure is limited to ‘‘one-hop’’ covarying amino acids only, meaning that only the codons directly associated with variation at a B*57-associated sites are shown. (Our analyses also identify, for example, codons associated with variation at the ‘‘one-hop’’ sites, and so on and so forth, but for simplicity we have limited the figure to the ‘‘one-hop’’ sites only. The strength of the association between two covarying codons (expressed in terms of q-value) is indicated by the color of the arc. The program used to construct these figures is available at http://research.microsoft.com/en-us/um/redmond/projects/MSCompBio/PhyloDViewer/ [27]. doi:10.1371/journal.pone.0006687.g006 Author Contributions Conceived and designed the experiments: ZLB MJ JMC DH SAM. Performed the experiments: ZLB MJ JMC CJB LS IT SS DH SAM. Analyzed the data: ZLB MJ JMC CJB PR JS CK DH SAM. Contributed References 1. Koup RA, Safrit JT, Cao Y, Andrews CA, McLeod G, et al. (1994) Temporal association of cellular immune responses with the initial control of viremia in primary human immunodeficiency virus type 1 syndrome. J Virol 68: 4650–4655. 2. Borrow P, Lewicki H, Hahn BH, Shaw GM, Oldstone MB (1994) Virus-specific CD8+ cytotoxic T-lymphocyte activity associated with control of viremia in primary human immunodeficiency virus type 1 infection. J Virol 68: 6103–6110. reagents/materials/analysis tools: JMC CJB DC MB CK NF CB DWH SR RH BDW PRH DH SAM. Wrote the paper: ZLB. Critical review of manuscript: MJ JMC CJB MB PR JS NF BDW PRH DH SAM. 3. Matano T, Shibata R, Siemon C, Connors M, Lane HC, et al. (1998) Administration of an anti-CD8 monoclonal antibody interferes with the clearance of chimeric simian/human immunodeficiency virus during primary infections of rhesus macaques. J Virol 72: 164–169. 4. Schmitz JE, Kuroda MJ, Santra S, Sasseville VG, Simon MA, et al. (1999) Control of viremia in simian immunodeficiency virus infection by CD8+ lymphocytes. Science 283: 857–860. PLoS ONE | www.plosone.org 10 August 2009 | Volume 4 | Issue 8 | e6687