Changes (95% CI) in CD4 cell count at viral set-point (cells/mm³) using different models.

a<p>Homogeneous patient group: MSM from W-Europe/N-America. Patients with non-B subtype infection excluded.</p>b<p>Adjusted for gender, region of origin, subtype, age at seroconversion, HIV transmission group, interval between seroconversion and viral set-point, and presence of a resistance mutation.</p

Baseline characteristics.

<p>Baseline characteristics.</p

CD4 cell count at viral set-point and mean CD4 cell count at each time period.

<p>In MSM from W-Europe/N-America with a proven or likely subtype B infection: a) first CD4 cell count between 9 and 27 months after seroconversion (n = 578), b) at 12 months (n = 555), c) 18 months (n = 439), and d) 24 months (n = 347). The solid black line shows the mean CD4 cell count for patients with an estimated date of seroconversion from 1984 through 1995, 1996 through 2002, and 2003 through 2007 (as shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007365#pone-0007365-t002" target="_blank">Table 2</a>). The dashed black lines were obtained using linear models assuming a constant decrease between 1984 and 2007.</p

Mean (95% CI) differences in HIV-1 RNA concentration at viral set-point (log₁₀ copies/ml) according to time of seroconversion.

a<p>Homogeneous patient group: MSM from W-Europe/N-America. Patients with non-B subtype infection excluded.</p>b<p>Adjusted for gender, region of origin, subtype, age at seroconversion, HIV transmission group, interval between seroconversion and viral set-point, and presence of a resistance mutation.</p>c<p>Adjusted for availability of subtype data.</p

Hypothetical scenarios for the potential development of the HIV epidemic in Switzerland.

<p>Annual HIV incidence: A) without intervention and under various ‘Mission Possible’ scenarios with 10%, 50%, or 100% of MSM having safe sex for 3 months each year starting in 2011, followed by an HIV test; B) without intervention, under a ‘test and treat’ strategy (assuming that the average time between infection and diagnosis is reduced to 1 year and treatment is started immediately), or assuming that the net transmission rate falls to the levels attained in 1984–1994 or 1995–1999.</p

Model structure.

<p>Flow diagram of the mathematical model for HIV transmission amongst men who have sex with men (MSM) in Switzerland (adapted from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044819#pone.0044819-Bezemer2" target="_blank">[20]</a>). The model describes progression through different stages of untreated and treated HIV infection. Arrows represent the flow between compartments at rates denoted by Greek letters. Parameter values are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044819#pone.0044819.s001" target="_blank">Table S1</a>.</p

Estimated rates (per year) of viral suppression and viral rebound and fraction experiencing rebound in SHCS participants (n = 1729).

<p>Estimated rates (per year) of viral suppression and viral rebound and fraction experiencing rebound in SHCS participants (n = 1729).</p

Model fits and estimates.

<p>Model fits to reported HIV and AIDS cases. Panel A) annual HIV diagnoses separated into infections acquired in Switzerland (black filled squares, dashed line) and abroad (black filled circles, solid line); B) annual number of new AIDS cases (black filled circles, solid line) and concurrent HIV and AIDS diagnoses (squares, black dashed line). Model estimates: C) annual number of new infections in Switzerland, D) number of men who have sex in Switzerland living with HIV. Continuous lines show model fit; dashed lines in panels C and D are 95% confidence intervals. Solid shapes show reported data; black shapes are data points used for fitting, grey shapes are not used for fitting. Grey lines show results of multivariate sensitivity analyses.</p

Model estimates for unknown parameters.

<p>A) percentage of infected patients remaining undiagnosed (solid line, dashed lines show 95% confidence interval) and percentage of new infections transmitted by those remaining undiagnosed (dotted line, dashed lines show 95% confidence interval); B) net transmission rate relative to the period 1980–1983 (dotted line, dashed lines show 95% confidence interval); C) average time from HIV infection to diagnosis in years (dotted line, dashed lines show 95% confidence interval); D) reproduction number (dotted line, dashed lines show 95% confidence interval). Grey lines show results of multivariate sensitivity analyses.</p

Estimated case reproduction number over time for all MSM-majority transmission clusters of ≥10 cases.

<p>The solid lines show the mean <i>R</i>_<i>t</i> estimate for each transmission cluster. The bold black line is the mean <i>R</i>_<i>t</i> of all clusters, with the 95% confidence interval shown by the dotted lines. The shaded areas show the 95% confidence intervals for each transmission cluster: darker areas indicate overlapping intervals across different transmission clusters. Transmission clusters are shown in red if their first sequence appeared before 1991, in blue if their first sequence appeared between 1991 and 2000, and in green if their first diagnosed case appeared after 2000. The black horizontal dotted line represents the threshold value <i>R</i>_<i>t</i> = 1. (A) Main analysis. (B) Sensitivity analysis for a looser cluster definition. (C) Sensitivity analysis for a more stringent cluster definition. (D) Sensitivity analysis for the clusters defined under a single linkage branch length threshold.</p