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Moore HP, Palumbo PJ, Notarte KI, Fogel JM, Cummings V, Gamble T, Del Rio C, Batey DS, Mayer KH, Farley JE, Remien RH, Beyrer C, Hudelson SE, Eshleman SH. Performance of the Applied Biosystems HIV-1 Genotyping Kit with Integrase. J Clin Microbiol 2024; 62:e0013624. [PMID: 38727213 PMCID: PMC11237527 DOI: 10.1128/jcm.00136-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 04/15/2024] [Indexed: 06/13/2024] Open
Abstract
HIV genotyping is used to assess HIV susceptibility to antiretroviral drugs. The Applied Biosystems HIV-1 Genotyping Kit with Integrase (AB kit, Thermo Fisher Scientific) detects resistance-associated mutations (RAMs) in HIV protease (PR), reverse transcriptase (RT), and integrase (IN). We compared results from the AB kit with results obtained previously with the ViroSeq HIV-1 Genotyping System. DNA amplicons from the AB kit were also analyzed using next-generation sequencing (NGS). HIV RNA was extracted using the MagNA Pure 24 instrument (Roche Diagnostics; 96 plasma samples, HIV subtype B, viral load range: 530-737,741 copies/mL). FASTA files were generated from AB kit data using Exatype (Hyrax Biosciences). DNA amplicons from the AB kit were also analyzed by NGS using the Nextera XT kit (Illumina). Drug resistance was predicted using the Stanford HIV Drug Resistance Database. The mean genetic distance for sequences from ViroSeq and the AB kit was 0.02% for PR/RT and 0.04% for IN; 103 major RAMs were detected by both methods. Four additional major RAMs were detected by the AB kit only. These four major RAMs were also detected by NGS (detected in 18.1%-38.2% of NGS reads). NGS detected 27 major RAMs that were not detected with either of the Sanger sequencing-based kits. All major RAMs detected with ViroSeq were detected with the AB kit; additional RAMs were detected with the AB kit only. DNA amplicons from the AB kit can be used for NGS for more sensitive detection of RAMs.
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Affiliation(s)
- Hannah P Moore
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Philip J Palumbo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kin Israel Notarte
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jessica M Fogel
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Vanessa Cummings
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Carlos Del Rio
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - D Scott Batey
- School of Social Work, Tulane Universtiy, New Orleans, Louisiana, USA
| | - Kenneth H Mayer
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Fenway Institute, Boston, Massachusetts, USA
| | - Jason E Farley
- The Center for Infectious Disease and Nursing Innovation, Johns Hopkins University School of Nursing, Baltimore, Maryland, USA
| | - Robert H Remien
- HIV Center for Clinical and Behavioral Studies, New York State Psychiatric Institute, New York, New York, USA
- Department of Psychiatry, Columbia University, New York, New York, USA
| | - Chris Beyrer
- Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Sarah E Hudelson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Susan H Eshleman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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2
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Park SY, Faraci G, Ganesh K, Dubé MP, Lee HY. Portable Nanopore sequencing solution for next-generation HIV drug resistance testing. J Clin Virol 2024; 171:105639. [PMID: 38219684 PMCID: PMC10947882 DOI: 10.1016/j.jcv.2024.105639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/06/2023] [Accepted: 01/07/2024] [Indexed: 01/16/2024]
Abstract
BACKGROUND Tackling HIV drug resistance is one of major challenges for ending AIDS epidemic, but the elevated expense of cutting-edge genomics hampers the advancement of HIV genotype testing for clinical care. METHODS We developed a HIV genotype testing pipeline that centers on a cost-efficient portable Nanopore sequencer. Accuracy verification was conducted through comparison with parallel data obtained via fixed-site Pacbio sequencing. Our complete pol-gene sequencing strategy coupled with portable high-throughput sequencing was applied to identify drug resistance mutations across 58 samples sourced from the ART-treated Los Angeles General Medical Center Rand Schrader Clinic (LARSC) cohort (7 samples from 7 individuals) and the ART-naïve Center for HIV/AIDS Vaccine Immunology (CHAVI) cohort (51 samples from 38 individuals). RESULTS A total of 472 HIV consensus sequences, each tagged with a unique molecular identifier, were produced from over 1.4 million bases acquired through portable Nanopore sequencing, which matched those obtained independently via Pacbio sequencing. With this desirable accuracy, we first documented the linkage of multidrug cross-resistance mutations across Integrase Strand Transfer inhibitors (INSTIs) and Non-Nucleoside Reverse Transcriptase Inhibitors (NNRTIs) from an individual failing a second-generation INSTI regimen. By producing more than 500 full-length HIV pol gene sequences in a single portable sequencing run, we detected Protease Inhibitor (PI), Nucleoside Reverse Transcriptase Inhibitor (NRTI), NNRTI and INSTI resistance mutations. All drug resistance mutations identified through portable sequencing were cross-validated using fixed-site Pacbio sequencing. CONCLUSIONS Our accurate and affordable HIV drug resistance testing solution is adaptable for both individual patient care and large-scale surveillance initiatives.
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Affiliation(s)
- Sung Yong Park
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Gina Faraci
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Kevin Ganesh
- Los Angeles General Medical Center, Los Angeles, CA, United States; Department of Medicine and Division of Infectious Diseases, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Michael P Dubé
- Department of Medicine and Division of Infectious Diseases, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Ha Youn Lee
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.
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Steegen K, van Zyl GU, Claassen M, Khan A, Pillay M, Govender S, Bester PA, van Straaten JM, Kana V, Cutler E, Kalimashe MN, Lebelo RL, Moloi MBH, Hans L. Advancing HIV Drug Resistance Technologies and Strategies: Insights from South Africa's Experience and Future Directions for Resource-Limited Settings. Diagnostics (Basel) 2023; 13:2209. [PMID: 37443603 DOI: 10.3390/diagnostics13132209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Monitoring of HIV drug resistance (HIVDR) remains critical for ensuring countries attain and sustain the global goals for ending HIV as a public health threat by 2030. On an individual patient level, drug resistance results assist in ensuring unnecessary treatment switches are avoided and subsequent regimens are tailored on a case-by-case basis, should resistance be detected. Although there is a disparity in access to HIVDR testing in high-income countries compared to low- and middle-income countries (LMICS), more LMICs have now included HIVDR testing for individual patient management in some groups of patients. In this review, we describe different strategies for surveillance as well as where HIVDR testing can be implemented for individual patient management. In addition, we briefly review available technologies for HIVDR testing in LMICs, including Sanger sequencing, next-generation sequencing, and some point-of-care options. Finally, we describe how South Africa has implemented HIVDR testing in the public sector.
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Affiliation(s)
- Kim Steegen
- Department of Molecular Medicine and Haematology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Hospital, Johannesburg 2193, South Africa
- Department of Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
- Wits Diagnostic Innovation Hub, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Gert U van Zyl
- Division of Medical Virology, Stellenbosh University, Stellenbosh 7602, South Africa
- Division of Medical Virology, Stellenbosh National Health Laboratory Service, Tygerberg Hospital, Tygerberg 7505, South Africa
| | - Mathilda Claassen
- Division of Medical Virology, Stellenbosh University, Stellenbosh 7602, South Africa
- Division of Medical Virology, Stellenbosh National Health Laboratory Service, Tygerberg Hospital, Tygerberg 7505, South Africa
| | - Aabida Khan
- Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
- Department of Virology, National Health Laboratory Service, Inkosi Albert Luthuli Central Hospital, Durban 4058, South Africa
| | - Melendhran Pillay
- Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
- Department of Virology, National Health Laboratory Service, Inkosi Albert Luthuli Central Hospital, Durban 4058, South Africa
| | - Subitha Govender
- Department of Virology, National Health Laboratory Service, Inkosi Albert Luthuli Central Hospital, Durban 4058, South Africa
| | - Phillip A Bester
- Department of Medical Microbiology and Virology, University of the Free State, Bloemfontein 9300, South Africa
- Department of Medical Microbiology and Virology, National Health Laboratory Service, Universitas Academic Hospital, Bloemfontein 9301, South Africa
| | - Johanna M van Straaten
- Department of Medical Microbiology and Virology, National Health Laboratory Service, Universitas Academic Hospital, Bloemfontein 9301, South Africa
| | - Vibha Kana
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg 2192, South Africa
| | - Ewaldé Cutler
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg 2192, South Africa
| | - Monalisa N Kalimashe
- Centre for HIV and STIs, National Institute for Communicable Diseases, Johannesburg 2192, South Africa
| | - Ramokone L Lebelo
- Department of Virological Pathology, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa
- Department of Virological Pathology, National Health Laboratory Service, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa
| | - Mokopi B H Moloi
- Department of Virological Pathology, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa
- Department of Virological Pathology, National Health Laboratory Service, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa
| | - Lucia Hans
- Department of Molecular Medicine and Haematology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Hospital, Johannesburg 2193, South Africa
- Department of Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
- Wits Diagnostic Innovation Hub, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
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Williams E, Moso M, Lim C, Chibo D, Nicholson S, Jackson K, Williamson DA. Laboratory diagnosis of HIV: a contemporary overview in the Australian context. Pathology 2023:S0031-3025(23)00125-3. [PMID: 37302942 DOI: 10.1016/j.pathol.2023.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 03/02/2023] [Accepted: 04/19/2023] [Indexed: 06/13/2023]
Abstract
Over the past decade there have been technical advances in human immunodeficiency virus (HIV) assays and updates to testing regulations that have substantially changed the landscape of laboratory testing for HIV. In addition, there have been significant changes in the epidemiology of HIV in Australia in the context of highly effective contemporary biomedical treatment and prevention strategies. Here, we provide an update on contemporary issues for the laboratory detection and confirmation of HIV in Australia. These include (1) the impact of early treatment and biological prevention strategies on the serological and virological detection of HIV; (2) the updated national HIV laboratory case definition and its interaction with testing regulations, public health and clinical guidelines; and (3) novel strategies for the laboratory detection of HIV, including the incorporation of HIV nucleic acid amplification tests (NAATs) into testing algorithms. These developments present an opportunity to develop a nationally consistent contemporary HIV testing algorithm that would result in optimisation and standardisation of HIV testing in Australia.
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Affiliation(s)
- Eloise Williams
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia.
| | - Michael Moso
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Microbiology, The Royal Melbourne Hospital, Melbourne, Vic, Australia
| | - Chuan Lim
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Doris Chibo
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Suellen Nicholson
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Kathy Jackson
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Deborah Anne Williamson
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
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Ssekagiri A, Jjingo D, Lujumba I, Bbosa N, Bugembe DL, Kateete DP, Jordan IK, Kaleebu P, Ssemwanga D. QuasiFlow: a Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data. BIOINFORMATICS ADVANCES 2022; 2:vbac089. [PMID: 36699347 PMCID: PMC9722223 DOI: 10.1093/bioadv/vbac089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/10/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022]
Abstract
Summary Next-generation sequencing (NGS) enables reliable detection of resistance mutations in minority variants of human immunodeficiency virus type 1 (HIV-1). There is paucity of evidence for the association of minority resistance to treatment failure, and this requires evaluation. However, the tools for analyzing HIV-1 drug resistance (HIVDR) testing data are mostly web-based which requires uploading data to webservers. This is a challenge for laboratories with internet connectivity issues and instances with restricted data transfer across networks. We present QuasiFlow, a pipeline for reproducible analysis of NGS-based HIVDR testing data across different computing environments. Since QuasiFlow entirely depends on command-line tools and a local copy of the reference database, it eliminates challenges associated with uploading HIV-1 NGS data onto webservers. The pipeline takes raw sequence reads in FASTQ format as input and generates a user-friendly report in PDF/HTML format. The drug resistance scores obtained using QuasiFlow were 100% and 99.12% identical to those obtained using web-based HIVdb program and HyDRA web respectively at a mutation detection threshold of 20%. Availability and implementation QuasiFlow and corresponding documentation are publicly available at https://github.com/AlfredUg/QuasiFlow. The pipeline is implemented in Nextflow and requires regular updating of the Stanford HIV drug resistance interpretation algorithm. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
| | - Daudi Jjingo
- Department of Computer Science, Makerere University, Kampala 10207, Uganda,African Center of Excellence in Bioinformatics and Data Intensive Sciences, Makerere University, Kampala 10207, Uganda
| | - Ibra Lujumba
- Department of Immunology and Molecular Biology, Makerere University, Kampala 10206, Uganda
| | - Nicholas Bbosa
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 31405, Uganda
| | - Daniel L Bugembe
- Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 31405, Uganda
| | - David P Kateete
- Department of Immunology and Molecular Biology, Makerere University, Kampala 10206, Uganda
| | - I King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Pontiano Kaleebu
- Department of General Virology, Uganda Virus Research Institute, Entebbe 31405, Uganda,Medical Research Council (MRC)/Uganda Virus Research Institute (UVRI) and London School of Hygiene and Tropical Medicine (LSHTM) Uganda Research Unit, Entebbe 31405, Uganda
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6
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MILNE RS, BECK IA, LEVINE M, SO I, ANDERSEN N, DENG W, PANPRADIST N, KINGOO J, KIPTINNESS C, YATICH N, KIARIE JN, SAKR SR, CHUNG MH, FRENKEL LM. Low-frequency pre-treatment HIV drug resistance: effects on 2-year outcome of first-line efavirenz-based antiretroviral therapy. AIDS 2022; 36:1949-1958. [PMID: 36305180 PMCID: PMC9623471 DOI: 10.1097/qad.0000000000003361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Assess the impact of pre-treatment high-frequency and low-frequency drug-resistant HIV variants on long-term outcomes of first-line efavirenz-based antiretroviral therapy (ART). DESIGN Prospective observational study. METHODS Participants' pre-treatment plasma RNA had two sections of HIV pol encoding reverse transcriptase sequenced (Illumina, MiSeq) using unique molecular identifiers to detect wild-type (pre-treatment drug-resistant variants less than 1% of viral quasispecies), low-frequency (1-9%) or high-frequency drug-resistant variants (10-100%). Associations between pre-treatment drug resistance and virologic outcomes over 24 months of efavirenz-based ART were assessed for the number and frequency of mutations by drug class and other resistance parameters. RESULTS Virologic failure was detected in 30 of 352 (9%) and pre-treatment drug-resistant variants were detected in the viral quasispecies of 31 of 352 (9%) participants prescribed efavirenz-based ART. Survival analyses revealed statistically significant associations between pre-treatment drug resistance at low (P < 0.0001) and high (P < 0.001) frequencies, at oligonucleotide ligation assay (OLA) (P < 0.00001) and non-OLA (P < 0.01) codons, to a single-antiretroviral class (P < 0.00001), and a shorter time to virologic failure of efavirenz-based ART. Regression analyses detected independent effects across resistance categories, including both low-frequency (P < 0.01) and high-frequency (P < 0.001) drug-resistant variants. CONCLUSION We observed that pre-treatment HIV drug resistance detected at low frequencies increased the risk of virologic failure over 24 months of efavirenz-based ART, but that most failures, regardless of drug-resistant variants' frequencies, were detected within a year of ART initiation. These observations suggest that when efavirenz-based ART is prescribed, screening for pre-treatment drug resistance by an assay capable of detecting low-frequency variants, including OLA, may guide clinicians to prescribe more effective ART.
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Affiliation(s)
- Ross S. MILNE
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Ingrid A. BECK
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Molly LEVINE
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Isaac SO
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Nina ANDERSEN
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Wenjie DENG
- University of Washington, Seattle, Washington, USA
| | | | - James KINGOO
- University of Washington, Seattle, Washington, USA
- Coptic Hospital, Nairobi, Kenya
| | | | - Nelly YATICH
- University of Washington, Seattle, Washington, USA
| | | | | | | | - Lisa M. FRENKEL
- Seattle Children’s Research Institute, Seattle, Washington, USA
- University of Washington, Seattle, Washington, USA
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7
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Current Research on HIV Drug Resistance—A Topical Collection with “Pathogens”. Pathogens 2022; 11:pathogens11090966. [PMID: 36145398 PMCID: PMC9504728 DOI: 10.3390/pathogens11090966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
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Li Y, Han L, Wang Y, Wang X, Jia L, Li J, Han J, Zhao J, Li H, Li L. Establishment and application of a method of tagged-amplicon deep sequencing for low-abundance drug resistance in HIV-1. Front Microbiol 2022; 13:895227. [PMID: 36071961 PMCID: PMC9444182 DOI: 10.3389/fmicb.2022.895227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
In the latest HIV-1 global drug resistance report released by WHO, countries are advised to strengthen pre-treatment monitoring of drug resistance in AIDS patients. In this study, we established an NGS-based segmented amplification HIV-1 drug resistance mutation detection method. The pol region of HIV-1 was divided into three short fragments for NGS. The entire amplification and sequencing panel were more cost-effective and batched by using the barcode sequence corresponding to the sample. Each parameter was evaluated using samples with known resistance variants frequencies. The nucleotide sequence error rate, amino acid error rate, and noise value of the NGS-based segmented amplification method were both less than 1%. When the threshold was 2%, the consensus sequences of the HIV-1 NL4-3 strain were completely consistent with the Sanger sequences. This method can detect the minimum viral load of the sample at 102 copies/ml, and the input frequency and detection frequency of HIV-1 resistance mutations within the range of 1%–100% had good conformity (R2 = 0.9963; R2 = 0.9955). This method had no non-specific amplification for Hepatitis B and C. Under the 2% threshold, the incidence of surveillance drug resistance mutations in ART-naive HIV-infected patients was 20.69%, among which NRTIs class resistance mutations were mainly.
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Affiliation(s)
- Yang Li
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Leilei Han
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- School of Public Health, North China University of Science and Technology, Tangshan, Hebei, China
| | - Yanglan Wang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xiaolin Wang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lei Jia
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingwan Han
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jin Zhao
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Hanping Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- *Correspondence: Hanping Li,
| | - Lin Li
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Lin Li,
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9
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Climaco-Arvizu S, Flores-López V, González-Torres C, Gaytán-Cervantes FJ, Hernández-García MC, Zárate-Segura PB, Chávez-Torres M, Tesoro-Cruz E, Pinto-Cardoso SM, Bekker-Méndez VC. Protease and gag diversity and drug resistance mutations among treatment-naive Mexican people living with HIV. BMC Infect Dis 2022; 22:447. [PMID: 35538426 PMCID: PMC9088029 DOI: 10.1186/s12879-022-07446-8] [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: 03/03/2022] [Accepted: 04/29/2022] [Indexed: 08/30/2023] Open
Abstract
Introduction In Mexico, HIV genotyping is performed in people living with HIV (PLWH) failing their first-line antiretroviral (ARV) regimen; it is not routinely done for all treatment-naive PLWH before ARV initiation. The first nationally representative survey published in 2016 reported that the prevalence of pretreatment drug mutations in treatment-naive Mexican PLWH was 15.5% to any antiretroviral drug and 10.6% to non-nucleoside reverse transcriptase inhibitors (NNRTIs) using conventional Sanger sequencing. Most reports in Mexico focus on HIV pol gene and nucleoside and non-nucleoside reverse transcriptase inhibitor (NRTI and NNRTI) drug resistance mutations (DRMs) prevalence, using Sanger sequencing, next-generation sequencing (NGS) or both. To our knowledge, NGS has not be used to detect pretreatment drug resistance mutations (DRMs) in the HIV protease (PR) gene and its substrate the Gag polyprotein. Methods Treatment-naive adult Mexican PLWH were recruited between 2016 and 2019. HIV Gag and protease sequences were obtained by NGS and DRMs were identified using the WHO surveillance drug resistance mutation (SDRM) list. Results One hundred PLWH attending a public national reference hospital were included. The median age was 28 years-old, and most were male. The median HIV viral load was 4.99 [4.39–5.40] log copies/mL and median CD4 cell count was 150 [68.0–355.78] cells/mm3. As expected, most sequences clustered with HIV-1 subtype B (97.9%). Major PI resistance mutations were detected: 8 (8.3%) of 96 patients at a detection threshold of 1% and 3 (3.1%) at a detection threshold of 20%. A total of 1184 mutations in Gag were detected, of which 51 have been associated with resistance to PI, most of them were detected at a threshold of 20%. Follow-up clinical data was available for 79 PLWH at 6 months post-ART initiation, seven PLWH failed their first ART regimen; however no major PI mutations were identified in these individuals at baseline. Conclusions The frequency of DRM in the HIV protease was 7.3% at a detection threshold of 1% and 3.1% at a detection threshold of 20%. NGS-based HIV drug resistance genotyping provide improved detection of DRMs. Viral load was used to monitor ARV response and treatment failure was 8.9%. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07446-8.
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Affiliation(s)
- Samantha Climaco-Arvizu
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología "Dr Daniel Méndez Hernández", Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social (IMSS), Ciudad de México, C.P. 02990, México.,Laboratorio de Medicina Traslacional, Instituto Politécnico Nacional, Ciudad de México, México
| | | | - Carolina González-Torres
- División de Desarrollo de La Investigación, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | | | - María Concepción Hernández-García
- Instituto Mexicano del Seguro Social (IMSS), Hospital de Infectología "Dr Daniel Méndez Hernández", Centro Médico Nacional (CMN), La Raza", Ciudad de México, México
| | | | - Monserrat Chávez-Torres
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, C.P. 14080, México
| | - Emiliano Tesoro-Cruz
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología "Dr Daniel Méndez Hernández", Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social (IMSS), Ciudad de México, C.P. 02990, México
| | - Sandra María Pinto-Cardoso
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México, C.P. 14080, México.
| | - Vilma Carolina Bekker-Méndez
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología "Dr Daniel Méndez Hernández", Centro Médico Nacional "La Raza", Instituto Mexicano del Seguro Social (IMSS), Ciudad de México, C.P. 02990, México.
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10
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Analytical Assessment of the Vela Diagnostics NGS Assay for HIV Genotyping and Resistance Testing: The Apulian Experience. Int J Mol Sci 2022; 23:ijms23052727. [PMID: 35269868 PMCID: PMC8911269 DOI: 10.3390/ijms23052727] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 01/22/2023] Open
Abstract
Drug-resistance monitoring is one of the hardest challenges in HIV management. Next-generation sequencing (NGS) technologies speed up the detection of drug resistance, allowing the adjustment of antiretroviral therapy and enhancing the quality of life of people living with HIV. Recently, the NGS Sentosa® SQ HIV Genotyping Assay (Vela Diagnostics) received approval for in vitro diagnostics use. This work is the first Italian evaluation of the performance of the Vela Diagnostics NGS platform, assessed with 420 HIV-1 clinical samples. A comparison with Sanger sequencing performance is also reported, highlighting the advantages and disadvantages of the Sentosa® NGS assay. The precision of the technology was studied with reference specimens, while intra- and inter-assay reproducibility were evaluated for selected clinical samples. Vela Diagnostics’ NGS assay reached an 87% success rate through 30 runs of analysis in a real-world clinical context. The concordance with Sanger sequencing outcomes was equal to 97.2%. Several detected mismatches were due to NGS’s superior sensitivity to low-frequency variants. A high accuracy was observed in testing reference samples. Repeatability and reproducibility assays highlighted the good performance of the NGS platform. Beyond a few technical issues that call for further optimization, the key improvement will be a better balance between costs and processing speed. Once these issues have been solved, the Sentosa® SQ HIV Genotyping Assay will be the way forward for HIV resistance testing.
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11
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van Zyl GU. New Technological Developments in Identification and Monitoring of New and Emerging Infections. ENCYCLOPEDIA OF INFECTION AND IMMUNITY 2022. [PMCID: PMC8291697 DOI: 10.1016/b978-0-12-818731-9.00094-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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12
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Forde BM, De Oliveira DMP, Falconer C, Graves B, Harris PNA. Strengths and caveats of identifying resistance genes from whole genome sequencing data. Expert Rev Anti Infect Ther 2021; 20:533-547. [PMID: 34852720 DOI: 10.1080/14787210.2022.2013806] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Antimicrobial resistance (AMR) continues to present major challenges to modern healthcare. Recent advances in whole-genome sequencing (WGS) have made the rapid molecular characterization of AMR a realistic possibility for diagnostic laboratories; yet major barriers to clinical implementation exist. AREAS COVERED We describe and compare short- and long-read sequencing platforms, typical components of bioinformatics pipelines, tools for AMR gene detection and the relative merits of read- or assembly-based approaches. The challenges of characterizing mobile genetic elements from genomic data are outlined, as well as the complexities inherent to the prediction of phenotypic resistance from WGS. Practical obstacles to implementation in diagnostic laboratories, the critical role of quality control and external quality assurance, as well as standardized reporting standards are also discussed. Future directions, such as the application of machine-learning and artificial intelligence algorithms, linked to clinically meaningful outcomes, may offer a new paradigm for the clinical application of AMR prediction. EXPERT OPINION AMR prediction from WGS data presents an exciting opportunity to advance our capacity to comprehensively characterize infectious pathogens in a rapid manner, ultimately aiming to improve patient outcomes. Collaborative efforts between clinicians, scientists, regulatory bodies and healthcare administrators will be critical to achieve the full promise of this approach.
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Affiliation(s)
- Brian M Forde
- University of Queensland, Faculty of Medicine, Uq Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Australia
| | - David M P De Oliveira
- University of Queensland, Faculty of Science, School of Chemistry and Molecular Biosciences, St Lucia, Australia
| | - Caitlin Falconer
- University of Queensland, Faculty of Medicine, Uq Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Australia
| | - Bianca Graves
- Herston Infectious Disease Institute, Royal Brisbane & Women's Hospital, Herston, Australia
| | - Patrick N A Harris
- University of Queensland, Faculty of Medicine, Uq Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Australia.,Herston Infectious Disease Institute, Royal Brisbane & Women's Hospital, Herston, Australia.,Central Microbiology, Pathology Queensland, Royal Brisbane & Women's Hospital, Herston, Australia
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13
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Armenia D, Santoro MM, Bellocchi MC, Carioti L, Galli L, Galli A, Scutari R, Salsi E, Mussini C, Sterrantino G, Calza L, Rossetti B, Zazzi M, Castagna A. Viral resistance burden and APOBEC editing correlate with virological response in heavily treatment-experienced people living with multi-drug resistant HIV. Int J Antimicrob Agents 2021; 59:106492. [PMID: 34871747 DOI: 10.1016/j.ijantimicag.2021.106492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 09/15/2021] [Accepted: 11/24/2021] [Indexed: 12/31/2022]
Abstract
BACKGROUND The impact of drug resistance mutational load and APOBEC editing in heavily treatment-experienced (HTE) people living with multidrug-resistant HIV has not been investigated. MATERIAL AND METHODS This study explored the HIV-DNA and HIV-RNA mutational load of drug resistance and APOBEC-related mutations through next-generation sequencing (NGS, Illumina MiSeq) in 20 failing HTE participants enrolled in the PRESTIGIO registry. RESULTS The patients showed high levels of both HIV-DNA (4.5 [4.0-5.2] log10 copies/106 T-CD4+ cell) and HIV-RNA (4.5 [4.1-5.0] log10 copies/mL) with complex resistance patterns in both compartments. Among the 255 drug-resistant mutations found, 66.3% were concordantly detected in both HIV-DNA and HIV-RNA; 71.3% of mutations were already present in historical Sanger genotypes. At an intra-patient frequency > 5%, a considerable proportion of mutations detected through DNA-NGS were found in historical genotypes but not through RNA-NGS, and few patients had APOBEC-related mutations. Of 14 patients who switched therapy, the five who failed treatment had DNA resistance with higher intra-patient frequency and higher DNA/RNA mutational load in a context of tendentially less pronounced APOBEC editing compared with those who responded. CONCLUSIONS Using NGS in HIV-DNA and HIV-RNA together with APOBEC editing evaluation might help to identify HTE individuals with MDR who are more prone to experience virological failure.
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Affiliation(s)
- Daniele Armenia
- Saint Camillus International University of Health Sciences, Rome, Italy; Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | | | | | - Luca Carioti
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Laura Galli
- Clinic of Infectious Diseases, Istituto Scientifico San Raffaele, Milano, Italy
| | - Andrea Galli
- Clinic of Infectious Diseases, Istituto Scientifico San Raffaele, Milano, Italy
| | - Rossana Scutari
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | | | | | - Gaetana Sterrantino
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | | | | | | | - Antonella Castagna
- Clinic of Infectious Diseases, Istituto Scientifico San Raffaele, Milano, Italy; Clinic of Infectious Diseases, Vita-Salute San Raffaele University, Milan, Italy
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14
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Khairunisa SQ, Indriati DW, Tumewu L, Widyawaruyanti A, Nasronudin N. Screening of anti-HIV activities in ethanol extract and fractions from Ficus fistulosa leaves. J Basic Clin Physiol Pharmacol 2021; 32:737-742. [PMID: 34214379 DOI: 10.1515/jbcpp-2020-0413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/08/2021] [Indexed: 02/07/2023]
Abstract
OBJECTIVES Human immunodeficiency virus (HIV) infection is considered as a major immunosuppressive disease linked to malignancies and other opportunistic infections. Recently, the high prevalence of HIV drug-resistant strains required a high demand for novel antiviral drug development, especially in herbal medicine approaches. The objective of this study was to evaluate the possibility of Ficus fistulosa leaves can inhibit HIV replication in ethanol extract form as well as its fractions using chloroform, ethyl acetate, and butanol solvents. METHODS F. fistulosa leaves were extracted using ethanol as a solvent and further gradually fractionated in chloroform, ethyl acetate, and butanol solvents. The targeted persistently infected virus (MT4/HIV) cell lines were cocultured with ethanol extract and fractions at different time points. The syncytium formation and cytotoxicity assays were performed to evaluate the potential antiviral activity of F. fistulosa leaves. RESULTS One of the four tested extract/fractions showed antiviral activity against HIV. The ethanol extract showed weak inhibition with a high level of toxicity (IC50 = 8.96 μg/mL, CC50 ≥50 μg/mL, and SI = 5.58). Meanwhile, chloroform fraction effectively inhibited the MT4/HIV cell proliferation while keeping the toxicity to a minimal level (IC50 = 3.27 μg/mL, CC50 = 29.30 μg/mL, and SI = 8.96). In contrast of ethyl acetate fraction and butanol fraction showed no anti HIV activity with a high level of toxicity (CC50 ≥50 μg/mL) and low SI value (>2.17 μg/mL and >0.97 μg/mL). CONCLUSIONS Chloroform fraction of F. fistulosa leaves showed effectively as anti-viral activity against MT4/HIV cells.
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Affiliation(s)
| | - Dwi Wahyu Indriati
- HIV Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Departement of Health, Faculty of Vocational Studies, Universitas Airlangga, Surabaya, Indonesia
| | - Lidya Tumewu
- Natural Product Medicine Research and Development, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Aty Widyawaruyanti
- Natural Product Medicine Research and Development, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Faculty of Pharmacy, Universitas Airlangga, Surabaya, Indonesia
| | - Nasronudin Nasronudin
- HIV Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.,Department of Internal Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia.,Airlangga University Hospital, Universitas Airlangga, Surabaya, Indonesia
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15
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Manyana S, Gounder L, Pillay M, Manasa J, Naidoo K, Chimukangara B. HIV-1 Drug Resistance Genotyping in Resource Limited Settings: Current and Future Perspectives in Sequencing Technologies. Viruses 2021; 13:1125. [PMID: 34208165 PMCID: PMC8230827 DOI: 10.3390/v13061125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/27/2021] [Accepted: 05/31/2021] [Indexed: 12/14/2022] Open
Abstract
Affordable, sensitive, and scalable technologies are needed for monitoring antiretroviral treatment (ART) success with the goal of eradicating HIV-1 infection. This review discusses use of Sanger sequencing and next generation sequencing (NGS) methods for HIV-1 drug resistance (HIVDR) genotyping, focusing on their use in resource limited settings (RLS). Sanger sequencing remains the gold-standard method for detecting HIVDR mutations of clinical relevance but is mainly limited by high sequencing costs and low-throughput. NGS is becoming a more common sequencing method, with the ability to detect low-abundance drug-resistant variants and reduce per sample costs through sample pooling and massive parallel sequencing. However, use of NGS in RLS is mainly limited by infrastructure costs. Given these shortcomings, our review discusses sequencing technologies for HIVDR genotyping, focusing on common in-house and commercial assays, challenges with Sanger sequencing in keeping up with changes in HIV-1 treatment programs, as well as challenges with NGS that limit its implementation in RLS and in clinical diagnostics. We further discuss knowledge gaps and offer recommendations on how to overcome existing barriers for implementing HIVDR genotyping in RLS, to make informed clinical decisions that improve quality of life for people living with HIV.
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Affiliation(s)
- Sontaga Manyana
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
| | - Lilishia Gounder
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
| | - Melendhran Pillay
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
| | - Justen Manasa
- Department of Laboratory Medicine and Investigative Sciences, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe;
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa;
- South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban 4013, South Africa
| | - Benjamin Chimukangara
- National Health Laboratory Service, Department of Virology, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4058, South Africa; (L.G.); (M.P.); (B.C.)
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4013, South Africa;
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16
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Next Generation Sequencing for HIV-1 Drug Resistance Testing-A Special Issue Walkthrough. Viruses 2021; 13:v13020340. [PMID: 33671700 PMCID: PMC7926934 DOI: 10.3390/v13020340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 02/19/2021] [Indexed: 12/18/2022] Open
Abstract
Drug resistance remains a global challenge in the fight against the HIV pandemic [...].
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17
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Becker MG, Liang D, Cooper B, Le Y, Taylor T, Lee ER, Wu S, Sandstrom P, Ji H. Development and Application of Performance Assessment Criteria for Next-Generation Sequencing-Based HIV Drug Resistance Assays. Viruses 2020; 12:E627. [PMID: 32532083 PMCID: PMC7354553 DOI: 10.3390/v12060627] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/29/2020] [Accepted: 06/07/2020] [Indexed: 12/19/2022] Open
Abstract
Next-generation sequencing (NGS)-based HIV drug resistance (HIVDR) assays outperform conventional Sanger sequencing in scalability, sensitivity, and quantitative detection of minority resistance variants. Thus far, HIVDR assays have been applied primarily in research but rarely in clinical settings. One main obstacle is the lack of standardized validation and performance evaluation systems that allow regulatory agencies to benchmark and accredit new assays for clinical use. By revisiting the existing principles for molecular assay validation, here we propose a new validation and performance evaluation system that helps to both qualitatively and quantitatively assess the performance of an NGS-based HIVDR assay. To accomplish this, we constructed a 70-specimen proficiency test panel that includes plasmid mixtures at known ratios, viral RNA from infectious clones, and anonymized clinical specimens. We developed assessment criteria and benchmarks for NGS-based HIVDR assays and used these to assess data from five separate MiSeq runs performed in two experienced HIVDR laboratories. This proposed platform may help to pave the way for the standardization of NGS HIVDR assay validation and performance evaluation strategies for accreditation and quality assurance purposes in both research and clinical settings.
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Affiliation(s)
- Michael G. Becker
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.G.B.); (T.T.); (E.R.L.); (P.S.)
| | - Dun Liang
- ViroDx Clinical Diagnostics Laboratory, St. Louis, MO 63017, USA; (D.L.); (B.C.); (Y.L.)
| | - Breanna Cooper
- ViroDx Clinical Diagnostics Laboratory, St. Louis, MO 63017, USA; (D.L.); (B.C.); (Y.L.)
| | - Yan Le
- ViroDx Clinical Diagnostics Laboratory, St. Louis, MO 63017, USA; (D.L.); (B.C.); (Y.L.)
| | - Tracy Taylor
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.G.B.); (T.T.); (E.R.L.); (P.S.)
| | - Emma R. Lee
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.G.B.); (T.T.); (E.R.L.); (P.S.)
| | - Sutan Wu
- SutanStats, St. Louis, MO 63017, USA;
| | - Paul Sandstrom
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.G.B.); (T.T.); (E.R.L.); (P.S.)
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Hezhao Ji
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Center, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (M.G.B.); (T.T.); (E.R.L.); (P.S.)
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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