Transmission of HIV‐1 Drug‐Resistant Variants: Prevalence and Effect on Treatment Outcome

Jakobsen, Martin R.; Tolstrup, Martin; Søgaard, Ole Schmeltz; Jørgensen, Lars; Gorry, Paul R; Laursen, Alex Lund; Østergaard, Lars

doi:10.1086/650001

Cited by 61 publications

(76 citation statements)

References 32 publications

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“…Using ultrasensitive genotypic assays, many research groups have reported high proportions of transmitted DRM among ART-naïve individuals (15,30,32,37,48,58,65), but these findings are not consistent with the descriptions of mono-or oligoclonal transmission in the env coding region by SGS and UDS (1,19,25,33). The primary goal of this analysis was to investigate whether detected minority viral variants in the earliest part of HIV-1 infection were (i) truly transmitted, (ii) a consequence of viral evolution and selection early after transmission, (iii) technical errors in highly sensitive detection methods, or (iii) de novo mutations resulting as a consequence of the high error rate of HIV-1 replication.…”

Section: Discussionmentioning

confidence: 99%

“…It appears, however, to be increasing in these settings as well (2,14,51). Using more-sensitive genotypic assays, different research groups (15,30,32,37,48,58,65) have reported higher proportions of transmitted DRM in ART-naive individuals. The clinical importance of these low-level DRM remains unclear, as they have been associated with clinical consequences in some (21,24,32,36,37,40,46,54,55,63,66,71) but not all (30,47,58) studies.…”

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confidence: 99%

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Detection of Minority Resistance during Early HIV-1 Infection: Natural Variation and Spurious Detection rather than Transmission and Evolution of Multiple Viral Variants

Gianella

Delport

Pacold

et al. 2011

J Virol

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Reports of a high frequency of the transmission of minority viral populations with drug-resistant mutations (DRM) are inconsistent with evidence that HIV-1 infections usually arise from mono-or oligoclonal transmission. We performed ultradeep sequencing (UDS) of partial HIV-1 gag, pol, and env genes from 32 recently infected individuals. We then evaluated overall and per-site diversity levels, selective pressure, sequence reproducibility, and presence of DRM and accessory mutations (AM). To differentiate biologically meaningful mutations from those caused by methodological errors, we obtained multinomial confidence intervals (CI) for the proportion of DRM at each site and fitted a binomial mixture model to determine background error rates for each sample. We then examined the association between detected minority DRM and the virologic failure of first-line antiretroviral therapy (ART). Similar to other studies, we observed increased detection of DRM at low frequencies (average, 0.56%; 95% CI, 0.43 to 0.69; expected UDS error, 0.21 ؎ 0.08% mutations/site). For 8 duplicate runs, there was variability in the proportions of minority DRM. There was no indication of increased diversity or selection at DRM sites compared to other sites and no association between minority DRM and AM. There was no correlation between detected minority DRM and clinical failure of first-line ART. It is unlikely that minority viral variants harboring DRM are transmitted and maintained in the recipient host. The majority of low-frequency DRM detected using UDS are likely errors inherent to UDS methodology or a consequence of error-prone HIV-1 replication.Using standard population-based genotypic assays of HIV from individuals not yet treated with antiretroviral drugs, several studies (43,64,69,76) have estimated the rate of transmitted drug resistance to be between 8 and 27% in countries with the highest rates of antiretroviral therapy (ART) use. In resource-limited settings, in which the introduction of ART has been more recent, the estimated frequency of transmitted drug resistance mutations (DRM) is substantially lower (41). It appears, however, to be increasing in these settings as well (2,14,51). Using more-sensitive genotypic assays, different research groups (15,30,32,37,48,58,65) have reported higher proportions of transmitted DRM in ART-naive individuals. The clinical importance of these low-level DRM remains unclear, as they have been associated with clinical consequences in some (21,24,32,36,37,40,46,54,55,63,66,71) but not all (30, 47, 58) studies.Highly sensitive assays for detecting low-frequency DRM include point mutation assays and high-resolution sequencing techniques. Point mutation assays, such as allele-specific PCR, can detect DRM at frequencies as low as 0.01% of the sampled viral population (31,45,53,54), but they do not provide information about the sequence context surrounding a given DRM and may be prone to false positives at the lower level of detection (22). High-resolution sequencing techniques, such as single ge...

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Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Detection of Minority Resistance during Early HIV-1 Infection: Natural Variation and Spurious Detection rather than Transmission and Evolution of Multiple Viral Variants

Gianella

Delport

Pacold

et al. 2011

J Virol

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“…11 The utility of pretherapy testing may be limited by minority HIV-1 variants present in < 20% of the viral population that are not reliably detected by standard sequencing, 12 and that may jeopardize virologic response. [13][14][15][16][17] The prevalence of minority pretherapy drug resistance mutations varies, with estimates based on highly sensitive research assays often double those reported using standard sequence analysis. [14][15][16][17][18][19] Some variation may be related to methods for measuring low abundance resistance mutations.…”

Section: Introductionmentioning

confidence: 99%

“…[13][14][15][16][17] The prevalence of minority pretherapy drug resistance mutations varies, with estimates based on highly sensitive research assays often double those reported using standard sequence analysis. [14][15][16][17][18][19] Some variation may be related to methods for measuring low abundance resistance mutations. For example, allele-specific polymerase chain reaction (PCR) detects mutations that make up ‡ 0.01% of the viral population, 15 which would require at least 30,000 input templates for reasonable sampling; however, prevalence estimates are based on a few, predetermined mutations, and estimates of resistance mutations in an individual may be biased by differential amplification.…”

Section: Introductionmentioning

confidence: 99%

Primer ID Informs Next-Generation Sequencing Platforms and Reveals Preexisting Drug Resistance Mutations in the HIV-1 Reverse Transcriptase Coding Domain

Keys

Zhou

Anderson

et al. 2015

AIDS Research and Human Retroviruses

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Sequencing of a bulk polymerase chain reaction (PCR) product to identify drug resistance mutations informs antiretroviral therapy selection but has limited sensitivity for minority variants. Alternatively, deep sequencing is capable of detecting minority variants but is subject to sequencing errors and PCR resampling due to low input templates. We screened for resistance mutations among 184 HIV-1-infected, therapy-naive subjects using the 454 sequencing platform to sequence two amplicons spanning HIV-1 reverse transcriptase codons 34-245. Samples from 19 subjects were also analyzed using the MiSeq sequencing platform for comparison. Errors and PCR resampling were addressed by tagging each HIV-1 RNA template copy (i.e., cDNA) with a unique sequence tag (Primer ID), allowing a consensus sequence to be constructed for each original template from resampled sequences. In control reactions, Primer ID reduced 454 and MiSeq errors from 71 to 2.6 and from 24 to 1.2 errors/10,000 nucleotides, respectively. MiSeq also allowed accurate sequencing of codon 65, an important drug resistance position embedded in a homopolymeric run that is poorly resolved by the 454 platform. Excluding homopolymeric positions, 14% of subjects had evidence of ‡ 1 resistance mutation among Primer ID consensus sequences, compared to 2.7% by bulk population sequencing. When calls were restricted to mutations that appeared twice among consensus sequence populations, 6% of subjects had detectable resistance mutations. The use of Primer ID revealed 5-15% template utilization on average, limiting the depth of deep sequencing sampling and revealing sampling variation due to low template utilization. Primer ID addresses important limitations of deep sequencing and produces less biased estimates of low-level resistance mutations in the viral population.

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“…This inroduction is frequently observed at position 215 of the reverse transcriptase (RT) and can result in the presence of several different amino acids at that position (T215D/E/I/S/V/N/A/L) (3, 14). Once formed, overgrowth of the fitter back-mutated variant may reduce the originally infecting variant to a level that is no longer detectable by population sequencing but that may be picked up by more-sensitive techniques, such as deep sequencing or allele-specific PCR, because these methods permit reliable detection of variants occupying 1% or less of the viral population (15)(16)(17)(18)(19)(20)(21)(22)(23)(24).It has been shown that resistant virus acquired at the time of primary infection massively fuels the cellular reservoir and persists there for a very long time (25). Sequencing of proviral DNA, therefore, seems to be an attractive substitute for RNA sequencing because it may increase the chance to identify the originally infecting virus.…”

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confidence: 99%

Deep Sequencing of HIV-1 RNA and DNA in Newly Diagnosed Patients with Baseline Drug Resistance Showed No Indications for Hidden Resistance and Is Biased by Strong Interference of Hypermutation

et al. 2016

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Deep sequencing of plasma RNA or proviral DNA may be an interesting alternative to population sequencing for the detection of baseline transmitted HIV-1 drug resistance. Using a Roche 454 GS Junior HIV-1 prototype kit, we performed deep sequencing of the HIV-1 protease and reverse transcriptase genes on paired plasma and buffy coat samples from newly diagnosed HIV-1-positive individuals. Selection was based on the outcome of population sequencing and included 12 patients with either a revertant amino acid at codon 215 of the reverse transcriptase or a singleton resistance mutation, 4 patients with multiple resistance mutations, and 4 patients with wild-type virus. Deep sequencing of RNA and DNA detected 6 and 43 mutations, respectively, that were not identified by population sequencing. A subsequently performed hypermutation analysis, however, revealed hypermutation in 61.19% of 3,188 DNA reads with a resistance mutation. The removal of hypermutated reads dropped the number of additional mutations in DNA from 43 to 17. No hypermutation evidence was found in the RNA reads. Five of the 6 additional RNA mutations and all additional DNA mutations, after full exclusion of hypermutation bias, were observed in the 3 individuals with multiple resistance mutations detected by population sequencing. Despite focused selection of patients with T215 revertants or singleton mutations, deep sequencing failed to identify the resistant T215Y/F or M184V or any other resistance mutation, indicating that in most of these cases there is no hidden resistance and that the virus detected at diagnosis by population sequencing is the original infecting variant.A nalyzing the presence of transmitted drug resistance mutations (TDRMs) after diagnosis of HIV-1 infection is the standard of care in most developed countries (1). Information on TDRMs allows clinicians to initiate the first-line regimen with the highest likelihood of virological response. Surveys revealed TDRM prevalences of approximately 10% in Europe, a number that has remained relatively stable over the last few years, although some shifts in affected drug classes have been reported (2). The most commonly observed TDRMs in Europe and North America are associated with resistance to nucleoside reverse transcriptase (RT) inhibitors (NRTIs) or nonnucleoside RT inhibitors (NNRTIs). Baseline resistance to protease inhibitors (PIs) is less prevalent (2, 3). Standard baseline resistance testing is still mainly performed using Sanger-based population sequencing. This method generally fails to detect mutants representing less than 20% of the viral population (4, 5).Resistant viruses that initially caused the infection may be overgrown, with time and in the absence of drugs, by fitter variants that lack all or part of the resistance mutations as a result of back mutation (6-11). The highest rates of disappearance have been recorded for the NRTI mutation M184V/I (11-13) and for the thymidine analogue-associated mutations K70R and T215Y (11). Back mutation may result in replacement of the...

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Transmission of HIV‐1 Drug‐Resistant Variants: Prevalence and Effect on Treatment Outcome

Cited by 61 publications

References 32 publications

Detection of Minority Resistance during Early HIV-1 Infection: Natural Variation and Spurious Detection rather than Transmission and Evolution of Multiple Viral Variants

Detection of Minority Resistance during Early HIV-1 Infection: Natural Variation and Spurious Detection rather than Transmission and Evolution of Multiple Viral Variants

Primer ID Informs Next-Generation Sequencing Platforms and Reveals Preexisting Drug Resistance Mutations in the HIV-1 Reverse Transcriptase Coding Domain

Deep Sequencing of HIV-1 RNA and DNA in Newly Diagnosed Patients with Baseline Drug Resistance Showed No Indications for Hidden Resistance and Is Biased by Strong Interference of Hypermutation

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