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Low-abundance HIV drug-resistant viral variants in treatment-experienced persons correlate with historical antiretroviral use.

Le T, Chiarella J, Simen BB, Hanczaruk B, Egholm M, Landry ML, Dieckhaus K, Rosen MI, Kozal MJ - PLoS ONE (2009)

Bottom Line: Low-abundance HIV drug-resistant mutations in antiretroviral-experienced subjects at time of virologic failure can increase a subject's overall burden of resistance, yet commonly go unrecognized by conventional genotyping.The majority of unrecognized resistant mutations correlate with historical antiretroviral use.Ultra-deep sequencing can provide important historical resistance information for clinicians when planning subsequent antiretroviral regimens for highly treatment-experienced patients, particularly when their prior treatment histories and longitudinal genotypes are not available.

View Article: PubMed Central - PubMed

Affiliation: Yale University School of Medicine, New Haven, CT, USA. Thuy.Le@yale.edu

ABSTRACT

Background: It is largely unknown how frequently low-abundance HIV drug-resistant variants at levels under limit of detection of conventional genotyping (<20% of quasi-species) are present in antiretroviral-experienced persons experiencing virologic failure. Further, the clinical implications of low-abundance drug-resistant variants at time of virologic failure are unknown.

Methodology/principal findings: Plasma samples from 22 antiretroviral-experienced subjects collected at time of virologic failure (viral load 1380 to 304,000 copies/mL) were obtained from a specimen bank (from 2004-2007). The prevalence and profile of drug-resistant mutations were determined using Sanger sequencing and ultra-deep pyrosequencing. Genotypes were interpreted using Stanford HIV database algorithm. Antiretroviral treatment histories were obtained by chart review and correlated with drug-resistant mutations. Low-abundance drug-resistant mutations were detected in all 22 subjects by deep sequencing and only in 3 subjects by Sanger sequencing. In total they accounted for 90 of 247 mutations (36%) detected by deep sequencing; the majority of these (95%) were not detected by standard genotyping. A mean of 4 additional mutations per subject were detected by deep sequencing (p<0.0001, 95%CI: 2.85-5.53). The additional low-abundance drug-resistant mutations increased a subject's genotypic resistance to one or more antiretrovirals in 17 of 22 subjects (77%). When correlated with subjects' antiretroviral treatment histories, the additional low-abundance drug-resistant mutations correlated with the failing antiretroviral drugs in 21% subjects and correlated with historical antiretroviral use in 79% subjects (OR, 13.73; 95% CI, 2.5-74.3, p = 0.0016).

Conclusions/significance: Low-abundance HIV drug-resistant mutations in antiretroviral-experienced subjects at time of virologic failure can increase a subject's overall burden of resistance, yet commonly go unrecognized by conventional genotyping. The majority of unrecognized resistant mutations correlate with historical antiretroviral use. Ultra-deep sequencing can provide important historical resistance information for clinicians when planning subsequent antiretroviral regimens for highly treatment-experienced patients, particularly when their prior treatment histories and longitudinal genotypes are not available.

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Mutation detection by standard versus ultra-deep sequencing according to mutation classes.A mean of 4 additional mutations per subject were detected by ultra-deep sequencing. The difference in the number of mutations detected by the two methods were statistically significant for NRTI (nucleotide/nucleoside reverse transcriptase inhibitor), NNRTI (non-nucleotide reverse transcriptase inhibitor), and PI (protease inhibitor) mutations. Two-tailed p values and 95% confidence intervals were calculated from the paired Student T test.
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pone-0006079-g001: Mutation detection by standard versus ultra-deep sequencing according to mutation classes.A mean of 4 additional mutations per subject were detected by ultra-deep sequencing. The difference in the number of mutations detected by the two methods were statistically significant for NRTI (nucleotide/nucleoside reverse transcriptase inhibitor), NNRTI (non-nucleotide reverse transcriptase inhibitor), and PI (protease inhibitor) mutations. Two-tailed p values and 95% confidence intervals were calculated from the paired Student T test.

Mentions: Paired Student T test was used to compare the mean number of DRMs detected by ultra-deep versus standard sequencing in 22 samples for all mutations, nucleoside reverse transcriptase inhibitor (NRTI) mutations, NNRTI mutations and protease inhibitor (PI) mutations, respectively. All p values presented were two tailed, and 95% confidence intervals were calculated and reported in figure 1. Odds ratios were used to describe the association of low-abundance DRMs and subjects' current failing antiretroviral versus historical antiretroviral drugs. Fisher exact test was used to determine the statistical significance of the association.


Low-abundance HIV drug-resistant viral variants in treatment-experienced persons correlate with historical antiretroviral use.

Le T, Chiarella J, Simen BB, Hanczaruk B, Egholm M, Landry ML, Dieckhaus K, Rosen MI, Kozal MJ - PLoS ONE (2009)

Mutation detection by standard versus ultra-deep sequencing according to mutation classes.A mean of 4 additional mutations per subject were detected by ultra-deep sequencing. The difference in the number of mutations detected by the two methods were statistically significant for NRTI (nucleotide/nucleoside reverse transcriptase inhibitor), NNRTI (non-nucleotide reverse transcriptase inhibitor), and PI (protease inhibitor) mutations. Two-tailed p values and 95% confidence intervals were calculated from the paired Student T test.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2698118&req=5

pone-0006079-g001: Mutation detection by standard versus ultra-deep sequencing according to mutation classes.A mean of 4 additional mutations per subject were detected by ultra-deep sequencing. The difference in the number of mutations detected by the two methods were statistically significant for NRTI (nucleotide/nucleoside reverse transcriptase inhibitor), NNRTI (non-nucleotide reverse transcriptase inhibitor), and PI (protease inhibitor) mutations. Two-tailed p values and 95% confidence intervals were calculated from the paired Student T test.
Mentions: Paired Student T test was used to compare the mean number of DRMs detected by ultra-deep versus standard sequencing in 22 samples for all mutations, nucleoside reverse transcriptase inhibitor (NRTI) mutations, NNRTI mutations and protease inhibitor (PI) mutations, respectively. All p values presented were two tailed, and 95% confidence intervals were calculated and reported in figure 1. Odds ratios were used to describe the association of low-abundance DRMs and subjects' current failing antiretroviral versus historical antiretroviral drugs. Fisher exact test was used to determine the statistical significance of the association.

Bottom Line: Low-abundance HIV drug-resistant mutations in antiretroviral-experienced subjects at time of virologic failure can increase a subject's overall burden of resistance, yet commonly go unrecognized by conventional genotyping.The majority of unrecognized resistant mutations correlate with historical antiretroviral use.Ultra-deep sequencing can provide important historical resistance information for clinicians when planning subsequent antiretroviral regimens for highly treatment-experienced patients, particularly when their prior treatment histories and longitudinal genotypes are not available.

View Article: PubMed Central - PubMed

Affiliation: Yale University School of Medicine, New Haven, CT, USA. Thuy.Le@yale.edu

ABSTRACT

Background: It is largely unknown how frequently low-abundance HIV drug-resistant variants at levels under limit of detection of conventional genotyping (<20% of quasi-species) are present in antiretroviral-experienced persons experiencing virologic failure. Further, the clinical implications of low-abundance drug-resistant variants at time of virologic failure are unknown.

Methodology/principal findings: Plasma samples from 22 antiretroviral-experienced subjects collected at time of virologic failure (viral load 1380 to 304,000 copies/mL) were obtained from a specimen bank (from 2004-2007). The prevalence and profile of drug-resistant mutations were determined using Sanger sequencing and ultra-deep pyrosequencing. Genotypes were interpreted using Stanford HIV database algorithm. Antiretroviral treatment histories were obtained by chart review and correlated with drug-resistant mutations. Low-abundance drug-resistant mutations were detected in all 22 subjects by deep sequencing and only in 3 subjects by Sanger sequencing. In total they accounted for 90 of 247 mutations (36%) detected by deep sequencing; the majority of these (95%) were not detected by standard genotyping. A mean of 4 additional mutations per subject were detected by deep sequencing (p<0.0001, 95%CI: 2.85-5.53). The additional low-abundance drug-resistant mutations increased a subject's genotypic resistance to one or more antiretrovirals in 17 of 22 subjects (77%). When correlated with subjects' antiretroviral treatment histories, the additional low-abundance drug-resistant mutations correlated with the failing antiretroviral drugs in 21% subjects and correlated with historical antiretroviral use in 79% subjects (OR, 13.73; 95% CI, 2.5-74.3, p = 0.0016).

Conclusions/significance: Low-abundance HIV drug-resistant mutations in antiretroviral-experienced subjects at time of virologic failure can increase a subject's overall burden of resistance, yet commonly go unrecognized by conventional genotyping. The majority of unrecognized resistant mutations correlate with historical antiretroviral use. Ultra-deep sequencing can provide important historical resistance information for clinicians when planning subsequent antiretroviral regimens for highly treatment-experienced patients, particularly when their prior treatment histories and longitudinal genotypes are not available.

Show MeSH