1
|
HIV-1 Drug Resistance Assay Using Ion Torrent Next Generation Sequencing and On-Instrument End-to-End Analysis Software. J Clin Microbiol 2022; 60:e0025322. [PMID: 35699434 DOI: 10.1128/jcm.00253-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HIV-1 antiretroviral therapy management requires sequencing the protease, reverse transcriptase, and integrase portions of the HIV-1 pol gene. Most resistance testing is performed with Sanger sequencing, which has limited ability to detect minor variants. Next generation sequencing (NGS) platforms enable variant detection at frequencies as low as 1% allowing for earlier detection of resistance and modification of therapy. Implementation of NGS assays in the clinical laboratory is hindered by complicated assay design, cumbersome wet bench procedures, and the complexity of data analysis and bioinformatics. We developed a complete NGS protocol and companion analysis and reporting pipeline using AmpliSeq multiplex PCR, Ion Torrent S5 XL sequencing, and Stanford's HIVdb resistance algorithm. Implemented as a Torrent Suite software plugin, the pipeline runs automatically after sequencing. An optimum variant frequency threshold of 10% was determined by comparing Sanger sequences of archived samples from ViroSeq testing, resulting in a sensitivity of 98.2% and specificity of 99.0%. The majority (91%) of drug resistance mutations were detected by both Sanger and NGS, with 1.7% only by Sanger and 7.3% only by NGS. Variant calls were highly reproducible and there was no cross-reactivity to VZV, HBV, CMV, EBV, and HCV. The limit of detection was 500 copies/mL. The NGS assay performance was comparable to ViroSeq Sanger sequencing and has several advantages, including a publicly available end-to-end analysis and reporting plugin. The assay provides a straightforward path for implementation of NGS for HIV drug resistance testing in the laboratory setting without additional investment in bioinformatics infrastructure and resources.
Collapse
|
2
|
Gao P, Yu F, Yang X, Li D, Shi Y, Wang Y, Zhang F. Evaluation of a novel in-house HIV-1 genotype drug resistance assay using clinical samples in China. Curr HIV Res 2021; 20:32-41. [PMID: 34515004 PMCID: PMC9127726 DOI: 10.2174/1570162x19666210910144433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 07/08/2021] [Accepted: 08/04/2021] [Indexed: 11/22/2022]
Abstract
Background HIV drug resistance poses a major challenge for anti-retroviral treatment (ART) and the prevention and control of HIV epidemic. Objective The study aims to establish a novel in-house assay with high efficiency, named AP in- house method, that would be suitable for HIV-1 drug resistance detection in China. Methods An in-house HIV-1 genotyping method was used to sequence the partial pol gene from 60 clinical plasma samples; the results of our test were compared with a commercial ViroSeq HIV-1 genotyping system. Results Among sixty samples, 58(96.7%) were successfully amplified by AP in-house method, five of them harbored viral load below 1,000 copies/ml. The genotype distribution was 43.1% CRF07_BC (25/58), 39.7% CRF01_AE (23/58), 6.9% CRF55_01B (4/58), 5.2% subtype B (3/58) and 5.2% CRF08_BC (3/58). Compared with that of the ViroSeq system, the consistent rate of these nucleotides and amino acids obtained by AP in-house method was up to 99.5 ± 0.4% and 99.5 ± 0.4%, respectively. A total of 290 HIV-1 drug resistance mutations were identified by two methods, including 126 nucleoside reverse transcriptase inhibitors (NRTIs), 145 non-nucleoside reverse transcriptase inhibitors (NNRTIs) and 19 protease inhibitors (PIs) resistance mutations. Out of them, 94.1% (273/290) were completely concordant between the AP in-house method and the ViroSeq system. Conclusion Overall, the evaluation of AP in-house method provided comparable results to those of the ViroSeq system on diversified HIV-1 subtypes in China.
Collapse
Affiliation(s)
- Peijie Gao
- Beijing Anapure Bioscitific Co. Ltd. Beijing. China
| | - Fengting Yu
- Clinical and Research Center of Infectious Diseases, Beijing Ditan Hospital. China
| | | | - Dan Li
- Beijing Anapure Bioscitific Co. Ltd. Beijing. China
| | - Yalun Shi
- Beijing Anapure Bioscitific Co. Ltd. Beijing. China
| | - Yan Wang
- Clinical and Research Center of Infectious Diseases, Beijing Ditan Hospital. China
| | - Fujie Zhang
- Clinical and Research Center of Infectious Diseases, Beijing Ditan Hospital. China
| |
Collapse
|
3
|
Nucleic acid testing and molecular characterization of HIV infections. Eur J Clin Microbiol Infect Dis 2019; 38:829-842. [PMID: 30798399 DOI: 10.1007/s10096-019-03515-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 02/14/2019] [Indexed: 01/21/2023]
Abstract
Significant advances have been made in the molecular assays used for the detection of human immunodeficiency virus (HIV), which are crucial in preventing HIV transmission and monitoring disease progression. Molecular assays for HIV diagnosis have now reached a high degree of specificity, sensitivity and reproducibility, and have less operator involvement to minimize risk of contamination. Furthermore, analyses have been developed for the characterization of host gene polymorphisms and host responses to better identify and monitor HIV-1 infections in the clinic. Currently, molecular technologies including HIV quantitative and qualitative assays are mainly based on the polymerase chain reaction (PCR), transcription-mediated amplification (TMA), nucleic acid sequence-based amplification (NASBA), and branched chain (b) DNA methods and widely used for HIV detection and characterization, such as blood screening, point-of-care testing (POCT), pediatric diagnosis, acute HIV infection (AHI), HIV drug resistance testing, antiretroviral (AR) susceptibility testing, host genome polymorphism testing, and host response analysis. This review summarizes the development and the potential utility of molecular assays used to detect and characterize HIV infections.
Collapse
|
4
|
Diphoko T, Gaseitsiwe S, Kasvosve I, Moyo S, Okatch H, Musonda R, Wainberg M, Makhema J, Marlink R, Novitsky V, Essex M. Prevalence of Rilpivirine and Etravirine Resistance Mutations in HIV-1 Subtype C-Infected Patients Failing Nevirapine or Efavirenz-Based Combination Antiretroviral Therapy in Botswana. AIDS Res Hum Retroviruses 2018; 34:667-671. [PMID: 29732907 PMCID: PMC6079649 DOI: 10.1089/aid.2017.0135] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Rilpivirine (RPV) and Etravirine (ETR) are approved second-generation non-nucleoside reverse transcriptase inhibitors (NNRTIs) for HIV treatment. There is a cross-resistance HIV mutation profile between first- and second-generation NNRTI drugs. We determined the prevalence of HIV-1 drug resistance mutations (DRMs) to RPV and ETR in Botswana. A total of 168 HIV-1 polymerase gene sequences from participants failing nevirapine (NVP)- or efavirenz (EFV)-containing regimens were analyzed for DRMs using the Stanford University HIV drug resistance database. Forty-one sequences were from an adult antiretroviral therapy (ART) study, the Tshepo study, and 127 from a prevention of mother-to-child transmission (PMTCT) study, the Mashi study, all conducted in Botswana. Prevalence of RPV and ETR highest DRM in the adult ART study (n = 41) were K101E (26.2%), E138A (23.8%), and Y181C (26.2%). The PMTCT cohort's (n = 127) high prevalence mutations were Y181C (15.7%), E138A (15%), and K101E (11%). A total of 42.9% and 3.2% of patients in the adult ART study and PMTCT study, respectively, had three or more NNRTI mutations at virologic failure. We identified HIV-1 mutations conferring resistance to RPV and ETR even though they have not been used in Botswana. Of concern was the high proportion of sequences from the adult ART study that displayed multiple DRMs; as the number of NNRTI mutations increases, the level of cross-resistance increases. It is plausible that patients displaying such profiles maybe at increased risk of failing second-generation NNRTI drugs, hence, calls for genotyping in patients with prior NVP or efavirenz exposure before prescription of RPV- or ETR-containing cART.
Collapse
Affiliation(s)
- Thabo Diphoko
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, Massachusetts
| | - Ishmael Kasvosve
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, Massachusetts
| | - Harriet Okatch
- Centre for Public Health Initiatives, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Rosemary Musonda
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, Massachusetts
| | - Mark Wainberg
- Lady Davis Institute for Medical Research, McGill University, Montreal, Canada
| | - Joseph Makhema
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, Massachusetts
| | - Richard Marlink
- Rutgers Global Health Institute, Rutgers Biomedical and Health Sciences, Rutgers University, New Brunswick, New Jersey
| | - Vladimir Novitsky
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, Massachusetts
| | - Max Essex
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Department of Immunology and Infectious Diseases, Boston, Massachusetts
| |
Collapse
|
5
|
Parikh UM, McCormick K, van Zyl G, Mellors JW. Future technologies for monitoring HIV drug resistance and cure. Curr Opin HIV AIDS 2017; 12:182-189. [PMID: 28059958 PMCID: PMC6738332 DOI: 10.1097/coh.0000000000000344] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
PURPOSE OF REVIEW Sensitive, scalable and affordable assays are critically needed for monitoring the success of interventions for preventing, treating and attempting to cure HIV infection. This review evaluates current and emerging technologies that are applicable for both surveillance of HIV drug resistance (HIVDR) and characterization of HIV reservoirs that persist despite antiretroviral therapy and are obstacles to curing HIV infection. RECENT FINDINGS Next-generation sequencing (NGS) has the potential to be adapted into high-throughput, cost-efficient approaches for HIVDR surveillance and monitoring during continued scale-up of antiretroviral therapy and rollout of preexposure prophylaxis. Similarly, improvements in PCR and NGS are resulting in higher throughput single genome sequencing to detect intact proviruses and to characterize HIV integration sites and clonal expansions of infected cells. SUMMARY Current population genotyping methods for resistance monitoring are high cost and low throughput. NGS, combined with simpler sample collection and storage matrices (e.g. dried blood spots), has considerable potential to broaden global surveillance and patient monitoring for HIVDR. Recent adaptions of NGS to identify integration sites of HIV in the human genome and to characterize the integrated HIV proviruses are likely to facilitate investigations of the impact of experimental 'curative' interventions on HIV reservoirs.
Collapse
Affiliation(s)
- Urvi M Parikh
- aDivision of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA bDivision of Medical Virology, Stellenbosch University and NHLS Tygerberg, Cape Town, South Africa
| | | | | | | |
Collapse
|
6
|
Jenabian MA, Talla F, Talla P, Mbopi-Kéou FX, Charpentier C, Kane CT, Bélec L. Pitfalls of antiretroviral drug resistance genotyping of HIV-1 Group M and Group N from Cameroon by sequenced-based assays. Niger Med J 2016; 56:420-4. [PMID: 26903701 PMCID: PMC4743293 DOI: 10.4103/0300-1652.171613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background: HIV-1 genotyping for antiretroviral drug resistance mutations (DRMs) were developed based basically on subtype B HIV-1 Group M, which represents only 10% of HIV strains worldwide. In sub-Saharan Africa, non-B subtypes HIV-1 largely predominate and HIV-1 genetic diversity could affect the performance of drug resistance genotyping assays. We compared prospectively the performance of the ViroSeq® and Trugene® genotyping assays to detect DRM in HIV-1-infected adult patients living in Douala, Cameroun. Materials and Methods: DRM in protease (P) and reverse transcriptase (RT) genes were assessed in parallel using both ViroSeq® and Trugene® assays in plasma samples from 45 first-line antiretroviral treatment-experienced patients in Douala, Cameroon. Results: Trugene HIV-1 Genotyping Assay® (Siemens Health Care Diagnostics, NY, USA) and ViroSeq HIV-1 Genotyping System®(Celera Diagnostics, CA, USA) assessed equivalently antiretroviral DRMs in P and RT genes from non-B HIV-1 Group M in 44 Cameroonian adults in virological failure; Trugene® was slightly more sensitive than ViroSeq® (100% vs. 91%). One patient infected by HIV-1 Group N was successfully amplified only by the Trugene HIV-1 Genotyping assay®, while ViroSeq HIV-1 Genotyping System v2.0® assay could not. Conclusion: Results showed the higher performance of the Trugene® system to detected and amplify P and RT genes targeting DRM to the principal antiretroviral drugs used in sub-Saharan Africa. Discrepancies between the results of HIV viral load assays and molecular tests should alert clinicians and virologists to the possibility of infection by an atypical variant virus, especially in Central Africa where very broad HIV-1 genetic diversity exists.
Collapse
Affiliation(s)
- Mohammad-Ali Jenabian
- Department of Biological Science and Bio Med Research Centre, University of Quebec at Montreal (UQAM), Montreal, QC, Canada
| | - Frédéric Talla
- Laboratory of Bio-Medical Analysis Litto-Labo, Douala, Cameroon
| | - Perrine Talla
- Laboratory of Bio-Medical Analysis Litto-Labo, Douala, Cameroon
| | - François-Xavier Mbopi-Kéou
- Department of Laboratories and Blood Safety, Ministry of Public Health and University of Yaounde I, Yaounde, Cameroon
| | - Charlotte Charpentier
- IAME, UMR 1137, University of Paris Diderot, Sorbonne Paris Cité, and Bichat-Claude Bernard Hospital, Virology Laboratory, Paris, France
| | - Coumba Toure Kane
- Bacteriology and Virology Laboratory, CHU Aristide Le Dantec, Dakar, Senegal
| | - Laurent Bélec
- Faculty of Medicine, Paris Descartes University Paris Descartes (Paris V), Sorbonne Paris Cité, Paris and Georges Pompidou European Hospital, Paris, France
| |
Collapse
|