Low-Abundance Drug-Resistant Viral Variants in Chronically HIV-Infected, Antiretroviral Treatment-Naive Patients Significantly Impact Treatment Outcomes

454 Life Sciences, a Roche Company, Branford, Connecticut, USA.
The Journal of Infectious Diseases (Impact Factor: 6). 03/2009; 199(5):693-701. DOI: 10.1086/596736
Source: PubMed

ABSTRACT 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.

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    • "The new technologies of next-generation sequencing can detect and quantify minority HIV-1 drug resistance mutations. Reports of feasibility and clinical relevance have been presented for HIV-1 drug resistance testing (Codoner et al., 2011; Hoffmann et al., 2007; Lataillade et al., 2010; Le et al., 2009; Simen et al., 2009; Wang et al., 2007) and reviewed in (Beerenwinkel et al., 2012) and for analyzing HIV-1 tropism and coreceptor usage (Abbate et al., 2011; D ¨ aumer et al., 2011; Swenson et al., 2011; Tsibris et al., 2009). Prior to incorporating next-generation sequencing into daily routine diagnoses, proper validation based on consensus criteria is a prerequisite. "
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    Journal of virological methods 04/2014; 204. DOI:10.1016/j.jviromet.2014.04.007 · 1.78 Impact Factor
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    • "The impact of minor variants on disease progression and HIV evolution is controversial. In drug resistance studies, some have reported an association between minor variants and poor clinical outcome [35-40], while others have found no such association [41-44]. Another important application of MPS is for the detection of minor variants in acute HIV infection, and possibility of early evolution resulting from immune selection pressure as detectable viremia emerges [27]. "
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    PLoS ONE 10/2013; 8(10):e76502. DOI:10.1371/journal.pone.0076502 · 3.23 Impact Factor
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    • "Massively parallel sequencing (MPS) technologies, such as 454 pyrosequencing (Margulies et al., 2005), are becoming common to rapidly and cost-effectively detect and quantitate rare sequence variants. Pyrosequencing generates up to millions of reads that can include rare variants to detect low frequency drug resistance and immune escape variants in viral (Human immunodeficiency virus [HIV] and Simian immunodeficiency virus [SIV]) populations (Bimber et al., 2009, 2010; Burwitz et al., 2011; Fischer et al., 2010; Hedskog et al., 2010; Henn et al., 2012; Love et al., 2010; O&apos;Connor et al., 2012; Poon et al., 2010; Simen et al., 2009; Tsibris et al., 2009; Wang et al., 2007). However, the PCR required before pyrosequencing of HIV/SIV populations introduces misincorporation errors, and the pyrosequencing process introduces a significant number of indels and carryforward errors (Margulies et al., 2005). "
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