Low-Abundance Drug-Resistant Viral Variants in Chronically HIV-Infected, Antiretroviral Treatment–Naive Patients Significantly Impact Treatment Outcomes
BackgroundMinor (i.e., <20% prevalence) drug-resistant human immunodeficiency virus (HIV) variants may go undetected, yet be clinically important ObjectivesTo compare the prevalence of drug-resistant variants detected with standard and ultra-deep sequencing (detection down to 1% prevalence) and t...
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| Published in | The Journal of infectious diseases Vol. 199; no. 5; pp. 693 - 701 |
|---|---|
| Main Authors | , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Oxford
The University of Chicago Press
01.03.2009
University of Chicago Press Oxford University Press |
| Subjects | |
| Online Access | Get full text |
| ISSN | 0022-1899 1537-6613 |
| DOI | 10.1086/596736 |
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| Abstract | BackgroundMinor (i.e., <20% prevalence) drug-resistant human immunodeficiency virus (HIV) variants may go undetected, yet be clinically important ObjectivesTo compare the prevalence of drug-resistant variants detected with standard and ultra-deep sequencing (detection down to 1% prevalence) and to determine the impact of minor resistant variants on virologic failure (VF) MethodsThe Flexible Initial Retrovirus Suppressive Therapies (FIRST) Study (N = 1397) compared 3 initial antiretroviral therapy (ART) strategies. A random subset (n = 491) had baseline testing for drug-resistance mutations performed by use of standard sequencing methods. Ultra-deep sequencing was performed on samples that had sufficient viral content (N = 264). Proportional hazards models were used to compare rates of VF for those who did and did not have mutations identified ResultsMutations were detected by standard and ultra-deep sequencing (in 14% and 28% of participants, respectively; P<.001). Among individuals who initiated treatment with an ART regimen that combined nucleoside and nonnucleoside reverse-transcriptase inhibitors (hereafter, “NNRTI strategy”), all individuals who had an NNRTI-resistance mutation identified by ultra-deep sequencing experienced VF. When these individuals were compared with individuals who initiated treatment with the NNRTI strategy but who had no NNRTI-resistance mutations, the risk of VF was higher for those who had an NNRTI-resistance mutation detected by both methods (hazard ratio [HR], 12.40 [95% confidence interval {CI}, 3.41–45.10]) and those who had mutation(s) detected only with ultra-deep sequencing (HR, 2.50 [95% CI, 1.17–5.36]) ConclusionsUltra-deep sequencing identified a significantly larger proportion of HIV-infected, treatment-naive persons as harboring drug-resistant viral variants. Among participants who initiated treatment with the NNRTI strategy, the risk of VF was significantly greater for participants who had low- and high-prevalence NNRTI-resistant variants |
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| AbstractList | BackgroundMinor (i.e., <20% prevalence) drug-resistant human immunodeficiency virus (HIV) variants may go undetected, yet be clinically important ObjectivesTo compare the prevalence of drug-resistant variants detected with standard and ultra-deep sequencing (detection down to 1% prevalence) and to determine the impact of minor resistant variants on virologic failure (VF) MethodsThe Flexible Initial Retrovirus Suppressive Therapies (FIRST) Study (N = 1397) compared 3 initial antiretroviral therapy (ART) strategies. A random subset (n = 491) had baseline testing for drug-resistance mutations performed by use of standard sequencing methods. Ultra-deep sequencing was performed on samples that had sufficient viral content (N = 264). Proportional hazards models were used to compare rates of VF for those who did and did not have mutations identified ResultsMutations were detected by standard and ultra-deep sequencing (in 14% and 28% of participants, respectively; P<.001). Among individuals who initiated treatment with an ART regimen that combined nucleoside and nonnucleoside reverse-transcriptase inhibitors (hereafter, “NNRTI strategy”), all individuals who had an NNRTI-resistance mutation identified by ultra-deep sequencing experienced VF. When these individuals were compared with individuals who initiated treatment with the NNRTI strategy but who had no NNRTI-resistance mutations, the risk of VF was higher for those who had an NNRTI-resistance mutation detected by both methods (hazard ratio [HR], 12.40 [95% confidence interval {CI}, 3.41–45.10]) and those who had mutation(s) detected only with ultra-deep sequencing (HR, 2.50 [95% CI, 1.17–5.36]) ConclusionsUltra-deep sequencing identified a significantly larger proportion of HIV-infected, treatment-naive persons as harboring drug-resistant viral variants. Among participants who initiated treatment with the NNRTI strategy, the risk of VF was significantly greater for participants who had low- and high-prevalence NNRTI-resistant variants Minor (i.e., <20% prevalence) drug-resistant human immunodeficiency virus (HIV) variants may go undetected, yet be clinically important. To compare the prevalence of drug-resistant variants detected with standard and ultra-deep sequencing (detection down to 1% prevalence) and to determine the impact of minor resistant variants on virologic failure (VF). The Flexible Initial Retrovirus Suppressive Therapies (FIRST) Study (N = 1397) compared 3 initial antiretroviral therapy (ART) strategies. A random subset (n = 491) had baseline testing for drug-resistance mutations performed by use of standard sequencing methods. Ultra-deep sequencing was performed on samples that had sufficient viral content (N = 264). Proportional hazards models were used to compare rates of VF for those who did and did not have mutations identified. Mutations were detected by standard and ultra-deep sequencing (in 14% and 28% of participants, respectively; P < .001). Among individuals who initiated treatment with an ART regimen that combined nucleoside and nonnucleoside reverse-transcriptase inhibitors (hereafter, "NNRTI strategy"), all individuals who had an NNRTI-resistance mutation identified by ultra-deep sequencing experienced VF. When these individuals were compared with individuals who initiated treatment with the NNRTI strategy but who had no NNRTI-resistance mutations, the risk of VF was higher for those who had an NNRTI-resistance mutation detected by both methods (hazard ratio [HR], 12.40 [95% confidence interval {CI}, 3.41-45.10]) and those who had mutation(s) detected only with ultra-deep sequencing (HR, 2.50 [95% CI, 1.17-5.36]). Ultra-deep sequencing identified a significantly larger proportion of HIV-infected, treatment-naive persons as harboring drug-resistant viral variants. Among participants who initiated treatment with the NNRTI strategy, the risk of VF was significantly greater for participants who had low- and high-prevalence NNRTI-resistant variants. Minor (i.e., <20% prevalence) drug-resistant human immunodeficiency virus (HIV) variants may go undetected, yet be clinically important.BACKGROUNDMinor (i.e., <20% prevalence) drug-resistant human immunodeficiency virus (HIV) variants may go undetected, yet be clinically important.To compare the prevalence of drug-resistant variants detected with standard and ultra-deep sequencing (detection down to 1% prevalence) and to determine the impact of minor resistant variants on virologic failure (VF).OBJECTIVESTo compare the prevalence of drug-resistant variants detected with standard and ultra-deep sequencing (detection down to 1% prevalence) and to determine the impact of minor resistant variants on virologic failure (VF).The Flexible Initial Retrovirus Suppressive Therapies (FIRST) Study (N = 1397) compared 3 initial antiretroviral therapy (ART) strategies. A random subset (n = 491) had baseline testing for drug-resistance mutations performed by use of standard sequencing methods. Ultra-deep sequencing was performed on samples that had sufficient viral content (N = 264). Proportional hazards models were used to compare rates of VF for those who did and did not have mutations identified.METHODSThe Flexible Initial Retrovirus Suppressive Therapies (FIRST) Study (N = 1397) compared 3 initial antiretroviral therapy (ART) strategies. A random subset (n = 491) had baseline testing for drug-resistance mutations performed by use of standard sequencing methods. Ultra-deep sequencing was performed on samples that had sufficient viral content (N = 264). Proportional hazards models were used to compare rates of VF for those who did and did not have mutations identified.Mutations were detected by standard and ultra-deep sequencing (in 14% and 28% of participants, respectively; P < .001). Among individuals who initiated treatment with an ART regimen that combined nucleoside and nonnucleoside reverse-transcriptase inhibitors (hereafter, "NNRTI strategy"), all individuals who had an NNRTI-resistance mutation identified by ultra-deep sequencing experienced VF. When these individuals were compared with individuals who initiated treatment with the NNRTI strategy but who had no NNRTI-resistance mutations, the risk of VF was higher for those who had an NNRTI-resistance mutation detected by both methods (hazard ratio [HR], 12.40 [95% confidence interval {CI}, 3.41-45.10]) and those who had mutation(s) detected only with ultra-deep sequencing (HR, 2.50 [95% CI, 1.17-5.36]).RESULTSMutations were detected by standard and ultra-deep sequencing (in 14% and 28% of participants, respectively; P < .001). Among individuals who initiated treatment with an ART regimen that combined nucleoside and nonnucleoside reverse-transcriptase inhibitors (hereafter, "NNRTI strategy"), all individuals who had an NNRTI-resistance mutation identified by ultra-deep sequencing experienced VF. When these individuals were compared with individuals who initiated treatment with the NNRTI strategy but who had no NNRTI-resistance mutations, the risk of VF was higher for those who had an NNRTI-resistance mutation detected by both methods (hazard ratio [HR], 12.40 [95% confidence interval {CI}, 3.41-45.10]) and those who had mutation(s) detected only with ultra-deep sequencing (HR, 2.50 [95% CI, 1.17-5.36]).Ultra-deep sequencing identified a significantly larger proportion of HIV-infected, treatment-naive persons as harboring drug-resistant viral variants. Among participants who initiated treatment with the NNRTI strategy, the risk of VF was significantly greater for participants who had low- and high-prevalence NNRTI-resistant variants.CONCLUSIONSUltra-deep sequencing identified a significantly larger proportion of HIV-infected, treatment-naive persons as harboring drug-resistant viral variants. Among participants who initiated treatment with the NNRTI strategy, the risk of VF was significantly greater for participants who had low- and high-prevalence NNRTI-resistant variants. Minor (i.e., <20% prevalence) drug-resistant human immunodeficiency virus (HIV) variants may go undetected, yet be clinically important. Objectives. To compare the prevalence of drug-resistant variants detected with standard and ultra-deep sequencing (detection down to 1% prevalence) and to determine the impact of minor resistant variants on virologic failure (VF). Methods. The Flexible Initial Retrovirus Suppressive Therapies (FIRST) Study (N = 1397) compared 3 initial antiretroviral therapy (ART) strategies. A random subset (n = 491) had baseline testing for drug-resistance mutations performed by use of standard sequencing methods. Ultra-deep sequencing was performed on samples that had sufficient viral content (N = 264). Proportional hazards models were used to compare rates of VF for those who did and did not have mutations identified. Results. Mutations were detected by standard and ultra- deep sequencing (in 14% and 28% of participants, respectively). Among individuals who initiated treatment with an ART regimen that combined nucleoside and nonnucleoside reverse-transcriptase inhibitors (hereafter, "NNRTI strategy"), all individuals who had an NNRTI-resistance mutation identified by ultra-deep sequencing experienced VF. When these individuals were compared with individuals who initiated treatment with the NNRTI strategy but who had no NNRTI-resistance mutations, the risk of VF was higher for those who had an NNRTI-resistance mutation detected by both methods (hazard ratio [HR], 12.40 [95% confidence interval {CI}, 3.41-45.10]) and those who had mutation(s) detected only with ultra-deep sequencing (HR, 2.50 [95% CI, 1.17-5.36]). Conclusions. Ultra-deep sequencing identified a significantly larger proportion of HIV-infected, treatment-naive persons as harboring drug-resistant viral variants. Among participants who initiated treatment with the NNRTI strategy, the risk of VF was significantly greater for participants who had low- and high-prevalence NNRTI-resistant variants. Background. Minor (i.e., <20% prevalence) drug-resistant human immunodeficiency virus (HIV) variants may go undetected, yet be clinically important. Objectives. To compare the prevalence of drug-resistant variants detected with standard and ultra- deep sequencing (detection down to 1% prevalence) and to determine the impact of minor resistant variants on virologic failure (VF). Methods. The Flexible Initial Retrovirus Suppressive Therapies (FIRST) Study (N = 1397) compared 3 initial antiretroviral therapy (ART) strategies. A random subset (n = 491) had baseline testing for drug-resistance mutations performed by use of standard sequencing methods. Ultra-deep sequencing was performed on samples that had sufficient viral content (N = 264). Proportional hazards models were used to compare rates of VF for those who did and did not have mutations identified Results. Mutations were detected by standard and ultra-deep sequencing (in 14% and 28% of participants, respectively, P < .001). Among individuals who initiated treatment with an ART regimen that combined nudeoside and nonnudeoside reverse-transcriptase inhibitors (hereafter, "NNRTI strategy"), all individuals who had an NNRTI-resistance mutation identified by ultra-deep sequencing experienced VF. When these individuals were compared with individuals who initiated treatment with the NNRTI strategy but who had no NNRTI-resistance mutations, the risk of VF was higher for those who had an NNRTI-resistance mutation detected by both methods (hazard ratio [HR], 12.40 [95% confidence interval {CI}, 3.41–45.10]) and those who had mutation(s) detected only with ultra-deep sequencing (HR, 2.50 [95% CI, 1.17–5.36]). Conclusions. Ultra-deep sequencing identified a significantly larger proportion of HIV-infected, treatment-naive persons as harboring drug-resistant viral variants. Among participants who initiated treatment with the NNRTI strategy, the risk of VF was significantly greater for participants who had low- and high-prevalence NNRTI-resistant variants. |
| Author | Novak, Richard M. Turenchalk, Gregory S. Simen, Birgitte B. Braverman, Michael S. Hullsiek, Katherine Huppler Rothberg, Jonathan M. Simons, Jan Fredrik Lubeski, Christine Egholm, Michael Huang, Chunli Desany, Brian MacArthur, Rodger D. Baxter, John D. |
| Author_xml | – sequence: 1 givenname: Birgitte B. surname: Simen fullname: Simen, Birgitte B. organization: 454 Life Sciences, a Roche Company, Branford, and – sequence: 2 givenname: Jan Fredrik surname: Simons fullname: Simons, Jan Fredrik organization: 454 Life Sciences, a Roche Company, Branford, and – sequence: 3 givenname: Katherine Huppler surname: Hullsiek fullname: Hullsiek, Katherine Huppler organization: Division of Biostatistics, University of Minnesota, Minneapolis, Minnesota – sequence: 4 givenname: Richard M. surname: Novak fullname: Novak, Richard M. organization: University of Illinois College of Medicine at Chicago, Department of Medicine, Chicago, Illinois – sequence: 5 givenname: Rodger D. surname: MacArthur fullname: MacArthur, Rodger D. organization: Wayne State University School of Medicine, Department of Medicine, Detroit, Michigan – sequence: 6 givenname: John D. surname: Baxter fullname: Baxter, John D. organization: Cooper University Hospital, University of Medicine and Dentistry, New Jersey–Robert Wood Johnson Medical School, Camden, New Jersey – sequence: 7 givenname: Chunli surname: Huang fullname: Huang, Chunli organization: 454 Life Sciences, a Roche Company, Branford, and – sequence: 8 givenname: Christine surname: Lubeski fullname: Lubeski, Christine organization: 454 Life Sciences, a Roche Company, Branford, and – sequence: 9 givenname: Gregory S. surname: Turenchalk fullname: Turenchalk, Gregory S. organization: 454 Life Sciences, a Roche Company, Branford, and – sequence: 10 givenname: Michael S. surname: Braverman fullname: Braverman, Michael S. organization: 454 Life Sciences, a Roche Company, Branford, and – sequence: 11 givenname: Brian surname: Desany fullname: Desany, Brian organization: 454 Life Sciences, a Roche Company, Branford, and – sequence: 12 givenname: Jonathan M. surname: Rothberg fullname: Rothberg, Jonathan M. organization: 454 Life Sciences, a Roche Company, Branford, and – sequence: 13 givenname: Michael surname: Egholm fullname: Egholm, Michael organization: 454 Life Sciences, a Roche Company, Branford, and |
| BackLink | http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=21182516$$DView record in Pascal Francis https://www.ncbi.nlm.nih.gov/pubmed/19210162$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.2144/03341dd05 10.1038/nature03959 10.1371/journal.pmed.0050158 10.1016/S0140-6736(06)69861-9 10.1310/hct0806-357 10.1097/QAI.0b013e31814258c0 10.1093/nar/gkm435 10.1097/QCO.0b013e3280109ff1 10.1038/nm1437 10.1111/j.1468-1293.2004.00244.x 10.1073/pnas.74.12.5463 10.1086/427212 10.1086/528802 10.1097/01.aids.0000216370.69066.7f 10.1371/journal.pmed.0030356 10.1016/S1871-0069(06)02005-2 10.1093/nar/gkg100 10.1097/01.aids.0000174455.01369.ad 10.1101/gr.6468307 |
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| Notes | Reprints or correspondence: Michael J Kozal, MD, Yale University School of Medicine, 135 College Street, Suite 323, New Haven, CT 06510 (michael.kozal@yale.edu); or Michael Egholm, PhD, 454 Life Sciences, a Roche Company, 20 Commercial Street, Branford, CT 06405 (michael.egholm@roche.com) ark:/67375/HXZ-NL33NB35-S istex:30ED83A84C84CA2F15DF9E536675E542218DE970 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 ObjectType-Undefined-3 |
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| Snippet | BackgroundMinor (i.e., <20% prevalence) drug-resistant human immunodeficiency virus (HIV) variants may go undetected, yet be clinically important ObjectivesTo... Background. Minor (i.e., <20% prevalence) drug-resistant human immunodeficiency virus (HIV) variants may go undetected, yet be clinically important.... Minor (i.e., <20% prevalence) drug-resistant human immunodeficiency virus (HIV) variants may go undetected, yet be clinically important. To compare the... Minor (i.e., <20% prevalence) drug-resistant human immunodeficiency virus (HIV) variants may go undetected, yet be clinically important. Objectives. To compare... Minor (i.e., <20% prevalence) drug-resistant human immunodeficiency virus (HIV) variants may go undetected, yet be clinically important.BACKGROUNDMinor (i.e.,... |
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| SubjectTerms | Adult AIDS Anti-HIV Agents - therapeutic use Antiretrovirals Biological and medical sciences Chronic Disease Disease Progression DNA, Complementary - chemistry Drug resistance Drug Resistance, Viral Female Fundamental and applied biological sciences. Psychology Genetic mutation Genetic Variation HIV HIV Infections - drug therapy HIV Infections - virology HIV-1 - drug effects HIV-1 - genetics HIV/AIDS Human immunodeficiency virus Human viral diseases Humans Infectious diseases Male Medical sciences Memory interference Microbiology Mutation Reverse transcriptase inhibitors RNA RNA, Viral - genetics Sequencing Viral diseases Viral diseases of the lymphoid tissue and the blood. Aids Virology |
| Title | Low-Abundance Drug-Resistant Viral Variants in Chronically HIV-Infected, Antiretroviral Treatment–Naive Patients Significantly Impact Treatment Outcomes |
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