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Neufeld B, Munyuza C, Reimer A, Capiña R, Lee ER, Becker M, Sandstrom P, Ji H, Cholette F. A validated in-house assay for HIV drug resistance mutation surveillance from dried blood spot specimens. J Virol Methods 2024; 327:114939. [PMID: 38604585 DOI: 10.1016/j.jviromet.2024.114939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 03/28/2024] [Accepted: 04/05/2024] [Indexed: 04/13/2024]
Abstract
Despite increasing scale-up of antiretroviral therapy (ART) coverage, challenges related to adherence and HIV drug resistance (HIVDR) remain. The high cost of HIVDR surveillance is a persistent challenge with implementation in resource-constrained settings. Dried blood spot (DBS) specimens have been demonstrated to be a feasible alternative to plasma or serum for HIVDR genotyping and are more suitable for lower resource settings. There is a need for affordable HIVDR genotyping assays which can amplify HIV-1 sequences from DBS specimens, particularly those with low viral loads, at a low cost. Here, we present an in-house assay capable of reliably amplifying HIV-1 protease and partial reverse transcriptase genes from DBS specimens, which covers the complete World Health Organization 2009 list of drug resistance mutations under surveillance. DBS specimens were prepared using whole blood spiked with HIV-1 at concentrations of 10,000, 5000, 1000, and 500 copies/mL (n=30 for each concentration). Specimens were tested in triplicate. A two-step approach was used consisting of cDNA synthesis followed by nested PCR. The limit of detection of the assay was calculated to be approximately 5000 (95% CI: 3200-10,700) copies/mL for the protease gene and 3600 (95% CI: 2200-10,000) copies/mL for reverse transcriptase. The assay was observed to be most sensitive with higher viral load specimens (97.8% [95% CI: 92.2-99.7]) for both protease and reverse transcriptase at 10,000 copies/mL with performance decreasing with the use of specimens with lower viral loads (46.7% [36.1-57.5] and 60.0% [49.1-70.2] at 500 copies/mL for protease and reverse transcriptase, respectively). Ultimately, this assay presents a promising opportunity for use in resource-constrained settings. Future work should involve validation under field conditions including sub-optimal storage conditions and preparation of DBS with fingerprick blood in order to accurately reflect real-world collection scenarios.
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Affiliation(s)
- Bronwyn Neufeld
- National Sexually Transmitted and Blood-Borne Infections Laboratory, J.C. Wilt Infectious Diseases Research Centre at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada.
| | - Chantal Munyuza
- National Sexually Transmitted and Blood-Borne Infections Laboratory, J.C. Wilt Infectious Diseases Research Centre at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Alexandria Reimer
- National Sexually Transmitted and Blood-Borne Infections Laboratory, J.C. Wilt Infectious Diseases Research Centre at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Rupert Capiña
- National Sexually Transmitted and Blood-Borne Infections Laboratory, J.C. Wilt Infectious Diseases Research Centre at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Emma R Lee
- National Sexually Transmitted and Blood-Borne Infections Laboratory, J.C. Wilt Infectious Diseases Research Centre at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Marissa Becker
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada; Department of Community Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Paul Sandstrom
- National Sexually Transmitted and Blood-Borne Infections Laboratory, J.C. Wilt Infectious Diseases Research Centre at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Hezhao Ji
- National Sexually Transmitted and Blood-Borne Infections Laboratory, J.C. Wilt Infectious Diseases Research Centre at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada; Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
| | - François Cholette
- National Sexually Transmitted and Blood-Borne Infections Laboratory, J.C. Wilt Infectious Diseases Research Centre at the National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada; Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
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Neufeld B, Cholette F, Sandstrom P, Musyoki H, Ma H, Kaosa S, Kioko J, Isac S, Bhattacharjee P, Cheuk E, Pickles M, Mwatelah R, Capiña R, Daniuk C, Mckinnon LR, Blanchard J, Mishra S, Becker M. HIV acquisition prior to entry into formal sex work: inference from next-generation viral sequencing. AIDS 2023; 37:987-992. [PMID: 36727844 PMCID: PMC10090304 DOI: 10.1097/qad.0000000000003484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 12/15/2022] [Accepted: 01/04/2023] [Indexed: 02/03/2023]
Abstract
OBJECTIVE To infer the timing of HIV acquisition in relation to self-reported events in the sexual life course of adolescent girls and young women (AGYW) who self-identify as female sex workers (FSW) in Mombasa, Kenya. DESIGN Next-generation viral sequencing of samples of AGYW living with HIV in the Transitions study, a cross-sectional bio-behavioural survey of AGYW aged 14-24 years in Mombasa, Kenya. METHOD Dried blood spot specimens were collected from study participants ( n = 37, all FSW). A portion of the HIV pol gene was sequenced using an in-house next-generation sequencing assay for HIV drug resistance mutation genotyping. Estimated time since infection (ETI) was inferred using the HIV EVO web-based tool ( https://hiv.biozentrum.unibas.ch/ETI/ ), and data on self-reported events were obtained from the survey. RESULTS The median ETI among FSW was 3.4 (interquartile range = 1.7, 6.3) years, with a median ETI of 1.5 years prior to entry into formal sex work. We estimated that 74.1% (95% confidence interval = 53.7-88.9%) of participants living with HIV and who self-identified as FSW likely acquired HIV prior to self-identification as a sex worker. CONCLUSIONS Findings suggest a large fraction of prevalent HIV infection among AGYW engaged in sex work stems from acquisition prior to entry into formal sex work. Current HIV prevention programs tailored for sex workers may miss key opportunities for HIV prevention as they are designed to reach women after entry into formal sex work, signaling a need for tailored programs to reach high-risk AGYW earlier on in their sexual life course.
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Affiliation(s)
- Bronwyn Neufeld
- Institute for Global Public Health, Department of Community Health Sciences, Rady Faculty of Health Sciences, University of Manitoba
| | - François Cholette
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
| | - Paul Sandstrom
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
| | - Helgar Musyoki
- National AIDS and STI Control Programme, Ministry of Health, Nairobi, Kenya
| | - Huiting Ma
- MAP Centre for Urban Health Solutions, St. Michael's Hospital, Unity Health Toronto, Toronto, Canada
| | - Shem Kaosa
- Partners for Health and Development in Africa, Nairobi, Kenya
| | - Japheth Kioko
- Partners for Health and Development in Africa, Nairobi, Kenya
| | - Shajy Isac
- India Health Action Trust, New Delhi, India
| | - Parinita Bhattacharjee
- Institute for Global Public Health, Department of Community Health Sciences, Rady Faculty of Health Sciences, University of Manitoba
- Partners for Health and Development in Africa, Nairobi, Kenya
| | - Eve Cheuk
- Institute for Global Public Health, Department of Community Health Sciences, Rady Faculty of Health Sciences, University of Manitoba
| | - Michael Pickles
- Medical Research Council Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Ruth Mwatelah
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
| | - Rupert Capiña
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada
| | - Christina Daniuk
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at the JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada
| | - Lyle R. Mckinnon
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - James Blanchard
- Institute for Global Public Health, Department of Community Health Sciences, Rady Faculty of Health Sciences, University of Manitoba
| | - Sharmistha Mishra
- MAP Centre for Urban Health Solutions, St. Michael's Hospital, Unity Health Toronto, Toronto, Canada
- Department of Medicine
- Institute of Medical Sciences
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Canada
| | - Marissa Becker
- Institute for Global Public Health, Department of Community Health Sciences, Rady Faculty of Health Sciences, University of Manitoba
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Canada
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