Mean number of partners of various types per 3 months since HIV diagnosis among HIV-positive MSM in San Francisco, 2009–2010.

<p>An immediate drop in the total number of male partners in the first year of infection was followed by increases in number of partners over the following 3–4 years. The trend was similar for potentially serodiscordand partners (PDPs) although they comprised only 1/3 to 1/2 of total partnerships. However, unprotected anal intercourse (UAI) with PDPs occurred in far fewer partnerships throughout the follow-up period. Partnerships in which the HIV-positive participant was the insertive partner during unprotected anal intercourse (uIAI) accounted for fewer than 10% of all partnerships and in very few of those partnerships did the participant have sufficient plasma viral load (VL >500 copies/ml) to present a significant transmission risk.</p

Estimated mean number of sexual partners per prior 3-month period and 95% confidence intervals [CI] for each sexual behavior variable of interest among MSM in Options/San Francisco, 2009–2010.

∧<p>Number of participants who contribute to each time point varies because this was not a strictly longitudinal cohort study. All participants started contributing data in 2009, and were at various times since diagnosis when they completed their ACASIs.</p>∧∧<p>PDP = potentially discordant partners (HIV-negative or unknown-status partners).</p>*<p>UAI = unprotected anal intercourse.</p>**<p>uIAI = unprotected insertive anal intercourse.</p>***<p>For participants with plasma viral load <500 copies/ml, number of PDP with whom uIAI occurred was set to 0.</p

Characteristics of HIV-positive men who have sex with men (MSM) in San Francisco in the Options cohort at the time of first ACASI, 2009–2010.

<p>Characteristics of HIV-positive men who have sex with men (MSM) in San Francisco in the Options cohort at the time of first ACASI, 2009–2010.</p

HIV-1 mean nonsynonymous and synonymous substitution rates for internal branches in HLA-B*5701 subjects.

<p>Subject- specific estimates were based on 200 randomly sampled trees from the posterior distribution obtained with a Bayesian coalescent framework enforcing a relaxed molecular clock. HRPs (P1-P3) and LRPs (P4-P6) are shown in orange and purple, respectively. The <i>p</i>-value is marked in bold when there is a significant difference between the two groups of patients. Along the y-axis, internal refers to all internal branches; backbone refers to rates averaged along all the possible backbone paths.</p

HIV-1 <i>gag</i> p24 genealogies for all six HLA-B*5701 subjects displaying different branch sets.

<p>Internal and external branches are shown for each subject (P1-P6), colored in purple and black, respectively. Orange branches indicate one of the possible backbone paths in the genealogy (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003830#s4" target="_blank">Methods</a>). Specific estimates were based on 200 randomly sampled trees from the posterior distribution obtained with a Bayesian coalescent framework enforcing a relaxed molecular clock. Branch lengths are drawn proportional to the time scale (in days) at the bottom of each tree.</p

Replication capacity in six HLA-B*5701 subjects.

1<p>Replication capacity (RC) was determined by using PhenoSense Gag-Pro assay, and expressed as a percentage of viral infectivity (luciferase activity) relative to NL4-3 reference control.</p><p>Replication capacity in six HLA-B*5701 subjects.</p

HIV-1 mean nonsynonymous and synonymous divergence for internal branches over time in HLA-B*5701 subjects.

<p>Subject- specific estimates were based on 200 randomly sampled trees from the posterior distribution obtained with a Bayesian coalescent framework enforcing a relaxed molecular clock. HRPs (P1-P3) and LRPs (P4-P6) are shown in orange and purple, respectively. Along the y-axis, internal refers to all internal branches; backbone refers to rates averaged along all the possible backbone paths.</p

HIV-1 mean synonymous substitution rates along backbone paths <i>vs</i>. CD4⁺ T cell count at baseline for each subject.

<p>HIV-1 synonymous rates (dS) in <i>gag</i> p24 within each HLA-B*5701 subject (y-axis) were plotted against baseline CD4⁺ T cell counts (10–11 wpi). The squared correlation coefficient (r²) is given in the graph and resulted highly significant (<i>p</i> = 0.002).</p

HIV-1 mean nucleotide substitution rate for different branches for all six HLA-B*5701 subjects.

<p>Estimates along internal branches (purple), backbone paths (orange) and external branches (black) are shown for the HRPs (P1-P3) and the LRPs (P4-P6).</p

Annual prevalence of transmitted HIV-1 drug resistance in 372 patients with acute/early HIV, 2002-2009.

<p>Prevalence (dot) and 95% confidence interval (vertical line) of overall transmitted drug resistance <i>(A),</i> NRTI resistance <i>(B),</i> NNRTI resistance <i>(C),</i> and PI resistance <i>(D).</i> TDR, transmitted drug resistance; NRTI, nucleoside reverse transcriptase inhibitor; NNRTI, non-nucleoside reverse transcriptase inhibitor; PI, protease inhibitor.</p