Resistance Mutations in the Protease of drug-naive and drug-treated individuals.

<p>250 samples from 234 drug-naive patients and 115 samples from 78 treated A/AE patients were genotyped. 31 patients were sampled both prior to treatment and after treatment failure. PI mutations found in all A/AE naive patients were compared to those found in A/AE drug-treated ones and to samples from 254 drug naive and 60 drug treated B individuals diagnosed since 2001. The first available sample from each drug-naive individual was used for analysis. For mutation-frequency analysis of drug-treated patients each mutation was counted once. Only mutations showing statistically significant differences between drug-naive and drug-treated patients and/or between A/AE and B frequencies are included.</p><p>Mutations in the Protease: The PI mutations L23I, L24I, D30N, V32I, M46I/L, I47A, G48V, I50L/V, I54V, V82A/S, I84V/A/C, N88S/T and L90M were considered major mutations. Secondary PI mutations included L10V/I/F/M, K20R, L33F, M36I, F53L, A71V/I and G73S/T/C/A.</p><p>N – NRTIs; NN – NNRTIs; NNRTIs – Non-nucleosides reverse transcriptase inhibitors; NS – Not significant; NRTIs – Nucleosides reverse transcriptase inhibitors; PI – Protease inhibitors;</p>a<p>Subtyping was performed using the Stanford Database Rapid Subtyping Tool <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057789#pone.0057789-Rhee1" target="_blank">[23]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057789#pone.0057789-Rhee2" target="_blank">[24]</a>. According to that classification 192 patients had virus containing protease of subtype A and RT most similar to CRF01_AE; for 70 both the protease and the RT were CRF01_AE; 52 were of subtype A; and four had protease classified as CRF01_AE and RT classified as A. Other subtyping tools such as Geno2Pheno (<a href="http://www.geno2pheno.org/" target="_blank">http://www.geno2pheno.org/</a>) or the Rega Subtyping Tool (<a href="http://jose.med.kuleuven.be/subtypetool/html/" target="_blank">http://jose.med.kuleuven.be/subtypetool/html/</a>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057789#pone.0057789-deOliveira1" target="_blank">[57]</a> vary to some extent in the classification of variants.</p

First-administrated and actual drug regimens while failing treatment.

a<p>All except 5 received NRTIs as part of the first regimen. A few received mono- or duo-therapy or combinations of PIs and NNRTIs.</p>b<p>All 78 treatment-failing patients received NRTI backbone. Thirty-four received also PI and 39 NNRTI as additional drug.</p><p>3TC – lamivudine; EFV – efavirenz; FTC – emtricitabine; LPV/r – lopinavir/r; NNRTI – Non-Nucleoside Reverse Trancriptase Inhibitor; NRTI – Nucleoside Reverse Trancriptase Inhibitor; NVP – nevirapine; PI – Protease inhibitor; r – ritonavir; TDF – tenofovir; ZDV – zidovudine.</p

Mutations found in patients failing regiments containing LPV/r or NNRTIs.

<p>Mutations found in patients failing regiments containing LPV/r or NNRTIs.</p><p>The Table classifies patients failing on LPV/r or NNRTI containing regimens according to the number of mutations conferring resistance to the different drug classes. “+” indicates presence of mutations, but for some patients the actual mutations are listed. “–” indicates “no mutations” or also “no previous PI-containing regimens”.</p><p>EFV – efavirenz; IDV – indinavir; LPV/r – lopinovir/ritonavir; NFV – nelfinavir; NNRTIs – Non-nucleosides reverse transcriptase inhibitors; NRTIs – Nucleosides reverse transcriptase inhibitors; NVP – nevirapine; SQV – saquinavir; PIs – protease inhibitors.</p

Phylogenetic tree of Pr-RT sequences from A/AE-HIV samples.

<p>Neighbor-joint analysis of A/AE protease and RT sequences, combined (918 nucleotides). The first available sequence from 216 drug-naive and 65 drug-treated individuals was used. Trees were colored according to: A. Birth place and infection site: red lines – born and infected in FSU; blue lines – born and infected in Israel; turquoise lines – born in FSU and infected in Israel; yellow lines – born in Israel and infected in Thailand; green lines – reference sequences. B. Transmission groups: red lines – IVDU; blue lines – MSM; turquoise lines – Hetero; green lines – reference sequences. Insert: red lines – posterior probability>0.95 of having a common ancestor. Major drug-resistance mutations in drug naive individuals: Red circles – K103N; Green triangle – M184V; orange rhombus – protease M46I. Reference sequences used in constructing the tree: Subtype-A/AE variants: subtype A – AF193275, subtype CRF01_AE – AF197340 and AF447851.1; subtype CRF03_AB – AF193276; subtype B – K03455, subtype C – AF286233 and AY585268; subtype D – AY322189; subtype F – AJ249238. Cl. – cluster. Clusters having more than 4 members with posterior probability>0.95 of having a common ancestor are marked with arrows.</p

Resistance Mutations in the reverse transcriptase of drug-naive and drug-treated individuals.

<p>250 samples from 234 drug-naive patients and 115 samples from 78 treated A/AE patients were genotyped. 31 patients were sampled both prior to treatment and after treatment failure. RT mutations found in all A/AE naive patients were compared to those found in A/AE drug-treated ones and to samples from 254 drug naive and 60 drug treated B individuals diagnosed since 2001. The first available sample from each drug-naive individual was used for analysis. For mutation-frequency analysis of drug-treated patients each mutation was counted once. Only mutations showing statistically significant differences between drug-naive and drug-treated patients and/or between A/AE and B frequencies are included.</p><p>Major NRTI related mutations included TAMs: M41L, D67N, K70R, L210W, T216Y/F and K219Q/E, as well as A62V, K65R, L74V/I, L77F, F116Y, Q151M and M184V/I. Major NNRTI mutations included A98G, L100I, K101E/P, K103N/S, V106A/M, V108I, Y181C, Y188C/H/I, G190A/S, P225H and K238T.</p><p>NNRTIs – Non-nucleosides reverse transcriptase inhibitors; NS – Not significant; NRTIs – Nucleosides reverse transcriptase inhibitors;</p>a<p>Subtyping was performed using the Stanford Database Rapid Subtyping Tool <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057789#pone.0057789-Rhee1" target="_blank">[23]</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057789#pone.0057789-Rhee2" target="_blank">[24]</a>. According to that classification 192 patients had virus containing protease of subtype A and RT most similar to CRF01_AE; for 70 both the protease and the RT were CRF01_AE; 52 were of subtype A; and four had protease classified as CRF01_AE and RT classified as A. Other subtyping tools such as Geno2Pheno (<a href="http://www.geno2pheno.org/" target="_blank">http://www.geno2pheno.org/</a>) or the Rega Subtyping Tool (<a href="http://jose.med.kuleuven.be/subtypetool/html/" target="_blank">http://jose.med.kuleuven.be/subtypetool/html/</a>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057789#pone.0057789-deOliveira1" target="_blank">[57]</a> vary to some extent in the classification of variants.</p

Propagation and incidence rates of A/AE-HIV in Israel.

<p>A. Birth sites of individuals diagnosed with A/AE by year of diagnosis. (FSU – red squares; Israel – blue triangles). B. Infection site of individuals diagnosed with A/AE by year of diagnosis. (FSU – red squares; Israel – blue triangles). C. Birth site and infection place of A/AE-patients of specified transmission groups, by year of diagnosis. Red solid line – IVDU born and infected in FSU; dashed brown line – IVDU born in FSU and infected in Israel; green solid line – heterosexuals (mostly females) born in FSU and infected in Israel; light blue solid line – heterosexsuals born and infected in Israel; blue solid line – MSM born and infected in Israel. D. Newly-diagnosed IVDU infected in Israel (blue triangles) or in FSU (red circles) per-year as a fraction of the total number of A/AE-infected IVDU in the same year. Also shown are the total numbers of immigrants from FSU to Israel per-year (dashed line). FSU – Former Soviet Union; IVDU – Intravenous drug users; Is – Israel; MSM – Men who have sex with men.</p

Co-infection with hepatitis and demographic data on patients stratified according to their hepatitis status.

<p>176 of the 318 A/AE-HIV carriers (55.3%) were co-infected with hepatitis: 148 had HCV, 11 HBV and 17 had both. 130 were not infected with hepatitis and for 12 there was no information.</p>a<p>For 8 IVDU, 2 MSM and 2 Others the status of hepatitis infection was unknown.</p>b<p>Other birth sites were in Africa, America, Asia, Europe, or unknown.</p><p>IVDU – Intravenous drug users; MSM – men who have sex with men; TG – Transmission group.</p