Clinical outcome of LPV/r treatment of patients stratified according to different VL and CD4 levels at baseline.

<p>Patients were stratified according to VL: above 100,000 cp/ml; between 10 and 100 thousands cp/ml and below 10,000 cp/ml when starting LPV/r. Each group was further divided according to baseline CD4 count: below 200 cells/µl; between 200 and 500 cells/µl and above 500 cell/µl, creating altogether 9 groups. Group 9 (VL below 10,000 cp/ml and CD4 counts more than 500 cell/µl) was significantly different from the other groups in two parameters: shorter time on LPV/r treatment and lower percent of patients receiving LPV/r as first PI. As the median VL of this group was initially below detection level and baseline CD4 count above 700, no further decline in viral load could be observed and the lack of further increase in CD4 was also expected.</p><p>cp/ml – copies/ml; Gr – group; VL –Viral Load.</p

Resistance status of patients failing LPV/r.

<p>Clinical resistance status of 237 patients failing cART including LPV/r was determined according to the True-gene™ software (version 10). The last available sample under LPV/r from each patient was used.</p

Side effects and other reasons for stopping LPV/r treatment.

<p>(A) Reasons for stopping LPV/r treatment as reported by physicians. Although samples from 31 patients were resistant to LPV/r, only for 14 it was the only reason for stopping the treatment. Technical reasons include refrigeration problems, inability to increase volume of syrup, travel, unavailability for follow-up, <i>etc.</i> (B). Side effects reported by physicians.</p><p>Abbreviations: CNS –Central Nervous System; ND – no data; PMTCT – treatment during pregnancy only, to Prevent Mother to Child Transmission.</p

Patient classification.

<p>FSU – Former Soviet Union; IVDU – Intravenous drug users; MSM – Men who have sex with men; SEM – standard error of mean.</p

Viral load and CD4 counts at the beginning and the end of the study.

<p>Patients were grouped as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086239#pone-0086239-t003" target="_blank">Table 3</a>. The median of the individual CD4 changes, ΔCD4, was calculated for each group (rather than the difference between the medians of CD4 counts). Selected <i>p</i>-values between relevant groups are shown. Significant differences between groups in other parameters were not found.</p><p>Abbreviations: 1st_PI – patients receiving LPV/r as first PI; 2nd _PI – patients receiving LPV/r as second or higher-order PI; B – patients with HIV subtype B; C – patients with HIV subtype C; C_M – male patients with subtype C; F –female; F-UP – follow up, time from diagnosis to start of the study, in years; M– male; MSM – men who have sex with Men; non-BC- patients with HIV subtype other than subtype B or C; PI – protease inhibitor; VL – viral load; a</p><p><i>p</i> values were calculated between groups in the box. The C or non-BC groups were compared to the B group.</p>b<p>the median values of the individual ΔCD4 values of patients.</p

Partition of the viral-loads of treatment-failing patients into “high” and “low” categories.

<p>Shown are box-plots indicating partition of the viral-load distributions at treatment failure for those who failed either with or without mutations. Each plot shows median, quartiles and range. Viral load is expressed in copies/ml plasma. Dashed line – viral load cutoff, at 6,000 copies/ml. Mut – resistance conferring mutations; n – number; No-mut – No resistance conferring mutations; PI – Protease Inhibitor.</p

Mutation patterns in LPV/r failing C patients from Israel and South Africa.

<p>The table lists all mutation patterns that appeared more than once in the combined dataset of 101 samples, 55 from South Africa (van Zyl <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086239#pone.0086239-VanZyl1" target="_blank">[33]</a>) and 46 from Israel (this study). Fifty nine samples (58% of total) included 16 patterns. The actual frequency (number of times a pattern appeared in the dataset) and the calculated frequency (based on the overall frequencies of each mutation included in that pattern, assuming independence) for the most prevalent patterns are compared. <i>p</i>-values were calculated using Fisher's two- tailed Exact Test. IL – Israel; SA – South Africa.</p