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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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Filippone P, Serrano S, Gwadz M, Cleland CM, Freeman R, Linnemayr S, Cluesman SR, Campos S, Rosmarin-DeStefano C, Amos B, Israel K. A virtual pilot optimization trial for African American/Black and Latino persons with non-suppressed HIV viral load grounded in motivational interviewing and behavioral economics. Front Public Health 2023; 11:1167104. [PMID: 37234760 PMCID: PMC10205984 DOI: 10.3389/fpubh.2023.1167104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/18/2023] [Indexed: 05/28/2023] Open
Abstract
Introduction Virtual and low-touch behavioral interventions are needed for African American/Black and Latino persons living with HIV (PLWH) with barriers to HIV viral suppression, particularly during COVID-19. Guided by the multiphase optimization strategy, we explored three components for PLWH without viral suppression, grounded in motivational interviewing and behavioral economics: (1) motivational interviewing counseling, (2) 21-weeks of automated text messages and quiz questions about HIV management, and (3) financial rewards for viral suppression (lottery prize vs. fixed compensation). Methods This pilot optimization trial used sequential explanatory mixed methods to explore the components' feasibility, acceptability, and preliminary evidence of effects using an efficient factorial design. The primary outcome was viral suppression. Participants engaged in baseline and two structured follow-up assessments over an 8-month period, and provided laboratory reports to document HIV viral load. A subset engaged in qualitative interviews. We carried out descriptive quantitative analyses. Then, qualitative data were analyzed using directed content analysis. Data integration used the joint display method. Results Participants (N = 80) were 49 years old, on average (SD = 9), and 75% were assigned male sex at birth. Most (79%) were African American/Black, and the remainder were Latino. Participants were diagnosed with HIV 20 years previously on average (SD = 9). Overall, components were feasible (>80% attended) and acceptability was satisfactory. A total of 39% (26/66) who provided laboratory reports at follow-up evidenced viral suppression. Findings suggested no components were entirely unsuccessful. The lottery prize compared to fixed compensation was the most promising component level. In qualitative analyses, all components were seen as beneficial to individual wellbeing. The lottery prize appeared more interesting and engaging than fixed compensation. However, structural barriers including financial hardship interfered with abilities to reach viral suppression. The integrated analyses yielded areas of convergence and discrepancy and qualitative findings added depth and context to the quantitative results. Conclusions The virtual and/or low-touch behavioral intervention components tested are acceptable and feasible and show enough potential to warrant refinement and testing in future research, particularly the lottery prize. Results must be interpreted in the context of the COVID-19 pandemic. Trial registration NCT04518241 (https://clinicaltrials.gov/ct2/show/NCT04518241).
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Affiliation(s)
- Prema Filippone
- Intervention Innovations Team Lab (IIT-Lab), New York University Silver School of Social Work, New York, NY, United States
- Center for Drug Use and HIV Research, School of Global Public Health, New York University, New York, NY, United States
| | - Samantha Serrano
- Intervention Innovations Team Lab (IIT-Lab), New York University Silver School of Social Work, New York, NY, United States
| | - Marya Gwadz
- Intervention Innovations Team Lab (IIT-Lab), New York University Silver School of Social Work, New York, NY, United States
- Center for Drug Use and HIV Research, School of Global Public Health, New York University, New York, NY, United States
| | - Charles M. Cleland
- Center for Drug Use and HIV Research, School of Global Public Health, New York University, New York, NY, United States
- Division of Biostatistics, Department of Population Health, New York University School of Medicine, New York, NY, United States
| | | | | | - Sabrina R. Cluesman
- Intervention Innovations Team Lab (IIT-Lab), New York University Silver School of Social Work, New York, NY, United States
| | | | | | - Brianna Amos
- Intervention Innovations Team Lab (IIT-Lab), New York University Silver School of Social Work, New York, NY, United States
| | - Khadija Israel
- Intervention Innovations Team Lab (IIT-Lab), New York University Silver School of Social Work, New York, NY, United States
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