Virological failure and antiretroviral resistance among HIV-infected children after five years follow-up in the ANRS 12225-PEDIACAM cohort in Cameroon

Objective In the present study, we aimed to evaluate the virological failure (VF) and drug resistance among treated HIV-infected children after five years follow-up in the ANRS-Pediacam cohort in Cameroon. Methods From November 2007 to October 2011, HIV-infected children born to HIV-infected mothers were included in the ANRS-PEDIACAM study and followed-up for more than 5 years. Plasma viral load (VL) was measured at each visit (every three months until month 24 and every 6 months thereafter). VF was the main outcome and HIV drug resistance test was performed using the ANRS procedures and algorithm. Results Data from 155 children were analyzed. The median age at combination antiretroviral therapy (cART) initiation was 4.2 months (interquartile range (IQR): 3.2–5.8), with 103 (66.5%) children taking LPV/r-containing regimen and 51 (32.9%) children taking NVP. After five years follow-up, 63 (40.6%; CI: 32.9–48.8) children experienced VF. The median duration between cART initiation and VF was 22.1 months (IQR: 11.9–37.1) with a median VL of 4.8 log10 (IQR: 4.0–5.5). Among the 57 children with HIV drug resistance results, 40 (70.2%) had at least one drug resistance mutation. The highest resistance rates (30.4–66.1%) were obtained with Lamivudine; Efavirenz; Nevirapine and Rilpivirine. Conclusions These results show high resistance to NNRTI and emphasize the need of VL and resistance tests for optimal follow-up of HIV-infected people especially children.

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Shall I trust the report? Variable performance of Sanger sequencing revealed by deep sequencing on HIV drug resistance mutation detection

International Journal of Infectious Diseases ◽

10.1016/j.ijid.2020.02.004 ◽

2020 ◽

Vol 93 ◽

pp. 182-191 ◽

Cited By ~ 2

Author(s):

Nan-Yu Chen ◽

Shu-Wei Kao ◽

Zhuo-Hao Liu ◽

Ting-Shu Wu ◽

Chia-Lung Tsai ◽

...

Keyword(s):

Drug Resistance ◽

Deep Sequencing ◽

Sanger Sequencing ◽

Mutation Detection ◽

Resistance Mutation ◽

Drug Resistance Mutation ◽

Hiv Drug Resistance ◽

Variable Performance

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A23 Identification of HIV drug resistance mutation patterns using illumina MiSeq next generation sequencing in patients failing second-line boosted protease inhibitor therapy in Nigeria

Virus Evolution ◽

10.1093/ve/vew036.022 ◽

2017 ◽

Vol 3 (suppl_1) ◽

Author(s):

Onyemata E. James ◽

Ledwaba Johanna ◽

Datir Rawlings ◽

M. Babajehson ◽

Ismail Ashrad ◽

...

Keyword(s):

Drug Resistance ◽

Next Generation Sequencing ◽

Protease Inhibitor ◽

Resistance Mutation ◽

Illumina Miseq ◽

Drug Resistance Mutation ◽

Second Line ◽

Protease Inhibitor Therapy ◽

Hiv Drug Resistance ◽

Generation Sequencing

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Limited marginal utility of deep sequencing for HIV drug resistance testing in the age of integrase inhibitors

10.1101/414995 ◽

2018 ◽

Author(s):

Ronit Dalmat ◽

Negar Makhsous ◽

Gregory Pepper ◽

Amalia Magaret ◽

Keith R. Jerome ◽

...

Keyword(s):

Drug Resistance ◽

Virological Failure ◽

Sanger Sequencing ◽

Low Frequency ◽

Resistance Testing ◽

Antiviral Resistance ◽

Resistance Mutations ◽

Hiv Drug Resistance ◽

Next Generation Sequencing Ngs

AbstractHIV drug resistance genotyping is a critical tool in the clinical management of HIV infections. Although resistance genotyping has traditionally been conducted using Sanger sequencing, next-generation sequencing (NGS) is emerging as a powerful tool due to its ability to detect lower frequency alleles. However, the value added from NGS approaches to antiviral resistance testing remains to be demonstrated. We compared the variant detection capacity of NGS versus Sanger sequencing methods for resistance genotyping of 144 drug resistance tests (105 protease-reverse transcriptase tests and 39 integrase tests) submitted to our clinical virology laboratory over a four-month period in 2016 for Sanger-based HIV drug resistance testing. NGS detected all true high frequency drug resistance mutations (>20% frequency) found by Sanger sequencing, with greater accuracy in one instance of a Sanger-detected false positive. Freely available online NGS variant callers Hydra and PASeq were superior to Sanger methods for interpretations of allele linkage and automated variant calling. NGS additionally detected low frequency mutations (1-20% frequency) associated with higher levels of drug resistance in 30/105 (29%) of protease-reverse transcriptase tests and 4/39 (10%) of integrase tests. Clinical follow-up of 69 individuals for a median of 674 days found no difference in rates of virological failure between individuals with and without low frequency mutations, although rates of virological failure were higher for individuals with drug-relevant low frequency mutations. However, all 27 individuals who experienced virological failure reported poor adherence to their drug regimen during preceding follow-up time, and all 19 who subsequently improved their adherence achieved viral suppression at later time points consistent with a lack of clinical resistance. In conclusion, in a population with low antiviral resistance emergence, NGS methods detected numerous instances of minor alleles that did not result in subsequent bona fide virological failure due to antiviral resistance.ImportanceGenotypic antiviral resistance testing for HIV is an essential component of the clinical microbiology and virology laboratory. Next-generation sequencing (NGS) has emerged as a powerful tool for the detection of low frequency sequence variants (allele frequencies <20%). Whether detecting these low frequency mutations in HIV contributes to improved patient health, however, remains unclear. We compared NGS to conventional Sanger sequencing for detecting resistance mutations for 144 HIV drug resistance tests submitted to our clinical virology laboratory and detected low frequency mutations in 24% of tests. Over approximately two years of follow-up for 69 patients for which we had access to electronic health records, no patients had virological failure due to antiviral resistance. Instead, virological failure was entirely explained by medication non-adherence. While larger studies are required, we suggest that detection of low frequency variants by NGS presents limited marginal clinical utility when compared to standard of care.

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Limited Marginal Utility of Deep Sequencing for HIV Drug Resistance Testing in the Age of Integrase Inhibitors

Journal of Clinical Microbiology ◽

10.1128/jcm.01443-18 ◽

2018 ◽

Vol 56 (12) ◽

Cited By ~ 12

Author(s):

Ronit R. Dalmat ◽

Negar Makhsous ◽

Gregory G. Pepper ◽

Amalia Magaret ◽

Keith R. Jerome ◽

...

Keyword(s):

Drug Resistance ◽

Reverse Transcriptase ◽

Virological Failure ◽

Sanger Sequencing ◽

Low Frequency ◽

Resistance Testing ◽

Antiviral Resistance ◽

Hiv Drug Resistance ◽

Drug Resistance Testing

ABSTRACTHIV drug resistance genotyping is a critical tool in the clinical management of HIV infections. Although resistance genotyping has traditionally been conducted using Sanger sequencing, next-generation sequencing (NGS) is emerging as a powerful tool due to its ability to detect low-frequency alleles. However, the clinical value added from NGS approaches to antiviral resistance testing remains to be demonstrated. We compared the variant detection capacity of NGS versus Sanger sequencing methods for resistance genotyping in 144 drug resistance tests (105 protease-reverse transcriptase tests and 39 integrase tests) submitted to our clinical virology laboratory over a four-month period in 2016 for Sanger-based HIV drug resistance testing. NGS detected all true high-frequency drug resistance mutations (>20% frequency) found by Sanger sequencing, with greater accuracy in one instance of a Sanger-detected false positive. Freely available online NGS variant callers HyDRA and PASeq were superior to Sanger methods for interpretations of allele linkage and automated variant calling. NGS additionally detected low-frequency mutations (1 to 20% frequency) associated with higher levels of drug resistance in 30/105 (29%) protease-reverse transcriptase tests and 4/39 (10%) integrase tests. In clinical follow-up of 69 individuals for a median of 674 days, we did not find a difference in rates of virological failure between individuals with and without low-frequency mutations, although rates of virological failure were higher for individuals with drug-relevant low-frequency mutations. However, all 27 individuals who experienced virological failure reported poor adherence to their drug regimen during the preceding follow-up time, and all 19 who subsequently improved their adherence achieved viral suppression at later time points, consistent with a lack of clinical resistance. In conclusion, in a population with low antiviral resistance emergence, NGS methods detected numerous instances of minor alleles that did not result in subsequent bona fide virological failure due to antiviral resistance.

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