Technical characteristic of EU-approved HIV screening rapid tests for use on whole blood and/or oral fluid.

<p>Technical characteristic of EU-approved HIV screening rapid tests for use on whole blood and/or oral fluid.</p

Sensitivity of rapid test detection according to the HIV genotype.

<p>*Failure from PCR, serotyping insufficient volume in one sample;</p><p>**HIV-1 Subtype non B: A (3); D (2); F (2); J (1); O (1); CRF01 (3); CRF02 (17); CRF06 (1); CRF19 (1); Recombinant B/CRF02 (1); Complex recombinant (2); Serotyped as non B (24). Fischer exact test, p>0.25.</p

Sensitivity of five rapid HIV tests in 200 HIV-infected patients, combining the results for finger-stick whole blood and, when the latter was negative, for serum.

<p>Differences in sensitivity between whole blood and serum were analyzed with the Mc Nemar test for paired samples.</p

Comparison of patient characteristics according to HIV screening rapid tests results on whole blood and/or oral fluid results.

<p>Comparison of patient characteristics according to HIV screening rapid tests results on whole blood and/or oral fluid results.</p

Dynamics of group O populations over time and contemporaneous contextual elements in Cameroon.

<p><b>a)</b> Bayesian Skyline Plot (BSP) inferred from the 154 concatenated group O sequences for which the three genome regions were obtained from a single time-point sample. <b>b)</b> BSP inferred from a subset of these sequences (N = 137), including the H strains (N = 124) and clusters T1 (N = 6) and T2 (N = 7) from the T strains. <b>c)</b> Periods of high viral growth rates for HIV-1 group M CRF02_AG [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005029#ppat.1005029.ref022" target="_blank">22</a>] (dark gray box), HIV-1 group O (grey boxes), HCV-1 [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005029#ppat.1005029.ref023" target="_blank">23</a>] (dark pink box), HCV-2 [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005029#ppat.1005029.ref023" target="_blank">23</a>] (pink box) and HCV-4 [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005029#ppat.1005029.ref023" target="_blank">23</a>] (brown box) in Cameroon; cohort with high HCV seroprevalence in Cameroon [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005029#ppat.1005029.ref024" target="_blank">24</a>] (orange box); population-scaled risk factors for iatrogenic transmission during trypanosomiaisis control campaigns in rural Cameroon [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005029#ppat.1005029.ref025" target="_blank">25</a>] (peak period: dark blue box), pentamidine prophylaxis campaigns in rural Cameroon [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005029#ppat.1005029.ref025" target="_blank">25</a>,<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005029#ppat.1005029.ref026" target="_blank">26</a>] (blue box) and intra-venous treatment for yaws and syphilis in Cameroon [<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1005029#ppat.1005029.ref025" target="_blank">25</a>] (peak period: light blue box).</p

Phylogenetic analysis of HIV-1 sequences.

<p><b>a)</b> Maximum likelihood tree inferred from the 190 concatenated group O sequences, with white diamonds at nodes with bootstrap values >70 and colours highlighting the nature of the residue at position 181 in the Reverse Transcriptase: Pink = C (N = 116); Green = Y (N = 71); Blue = mixed Y and C (N = 3); Grey = sequences from patients non NNRTI-naïve or with no data about NNRTI treatment. <b>b)</b> Maximum likelihood tree inferred from the 190 concatenated group M sequences.</p

Comparison of rate and ratio estimates between H and T subgroups.

<p>* the mean value for evolutionary and growth rates were estimated using BEAST, under the best fitting model (GTR+Γ+I and exponential growth); the mean values for the Non Synonymous (dN) versus synonymous (dS) mutation ratios were estimated using HyPhy under the GTR model.</p><p>^$ the 95% Higher Posterior Densities (HPD) upper and lower bound for evolutionary and growth rates were estimated using BEAST, under the best fitting model (GTR+Γ+I and exponential growth).</p><p>^£ the 95% confidence intervals (CI) for the Non Synonymous (dN) versus synonymous (dS) mutation ratios were estimated using HyPhy under the GTR model.</p><p>^# the p-value for the difference between two means was calculated using student T test; the Likelihood Ratio Test p-value against the hypothesis of a single rate was estimated using HyPhy under the GTR model.</p><p>Comparison of rate and ratio estimates between H and T subgroups.</p

Demographic characteristics of participants according to initial HIV status based on national HIV testing algorithms in West Africa.

Demographic characteristics of participants according to initial HIV status based on national HIV testing algorithms in West Africa.</p

HIV serological and molecular testing for dually HIV-1 and HIV-2 diagnosis in West Africa.

HIV serological and molecular testing for dually HIV-1 and HIV-2 diagnosis in West Africa.</p

Weekly distribution of the three main detected viruses.

<p>Weekly distribution of the three main detected viruses.</p