RNA and DNA Sanger sequencing versus next-generation sequencing for HIV-1 drug resistance testing in treatment-naive patients
| Autor: | Didier Hober, Olivier Robineau, Enagnon Kazali Alidjinou, Philippe Choisy, C. Hallaert, J Deldalle, Faiza Ajana, Laurence Bocket |
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| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Microbiology (medical) Cancer genome sequencing Adult Male Sequence analysis Anti-HIV Agents 030106 microbiology HIV Infections Drug resistance HIV Integrase Microbial Sensitivity Tests Biology DNA sequencing 03 medical and health sciences symbols.namesake HIV Protease Drug Resistance Viral Humans Pharmacology (medical) Illumina dye sequencing Exome sequencing Pharmacology Genetics Sanger sequencing Sequence Analysis RNA High-Throughput Nucleotide Sequencing Sequence Analysis DNA Middle Aged Viral Load Virology Reverse transcriptase HIV Reverse Transcriptase 030104 developmental biology Infectious Diseases Treatment Outcome Mutation symbols HIV-1 RNA Viral Female |
| Zdroj: | The Journal of antimicrobial chemotherapy. 72(10) |
| ISSN: | 1460-2091 |
| Popis: | Background Sanger sequencing of plasma RNA is the standard method for HIV-1 drug resistance testing in treatment-naive patients, but is limited by the non-detection of resistance-associated mutations (RAMs) with prevalence below approximately 20%. Objectives We compared RNA and DNA Sanger sequencing (RSS and DSS) with RNA next-generation sequencing (NGS) for RAM detection in HIV-1 reverse transcriptase (RT), protease (PR) and integrase (IN) genes. Methods Sanger sequencing was performed on RNA and DNA, following the recommendations of the French Agency for AIDS Research (ANRS). NGS was performed on RNA using the HIV-1 Drug Resistance Assay, v. 3.0 (Roche) on the 454 GS Junior sequencer. The IAS-USA list was used to identify RAMs. ANRS, Rega and Stanford algorithms were used for drug resistance interpretation. Results The study included 48 ART-naive patients. The number of patients with at least one major RAM was 3, 3, 4 and 8 when using RSS, DSS, NGS 20% and NGS 5%, respectively. Numerous minor mutations were detected in patients, especially in the protease gene. None of the methods detected any major mutation in the integrase gene. Overall, the mutation detection rate was similar between RSS and DSS, and higher with NGS 20%. Differences in drug resistance interpretation were found between algorithms. No impact of the minority RAMs detected by NGS was found on the short-term treatment outcome. Conclusions DSS does not clearly improve the detection of RAMs in ART-naive patients, as compared with RSS. NGS allows detection of additional minority RAMs; however, their clinical relevance requires further investigation. |
| Databáze: | OpenAIRE |
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