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Evaluation of the HIV-1 Polymerase Gene Sequence Diversity for Prediction of Recent HIV-1 Infections Using Shannon Entropy Analysis. Viruses 2022; 14:v14071587. [PMID: 35891568 PMCID: PMC9324365 DOI: 10.3390/v14071587] [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: 06/24/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 02/04/2023] Open
Abstract
HIV-1 incidence is an important parameter for assessing the impact of HIV-1 interventions. The aim of this study was to evaluate HIV-1 polymerase (pol) gene sequence diversity for the prediction of recent HIV-1 infections. Complete pol Sanger sequences obtained from 45 participants confirmed to have recent or chronic HIV-1 infection were used. Shannon entropy was calculated for amino acid (aa) sequences for the entire pol and for sliding windows consisting of 50 aa each. Entropy scores for the complete HIV-1 pol were significantly higher in chronic compared to recent HIV-1 infections (p < 0.0001) and the same pattern was observed for some sliding windows (p-values ranging from 0.011 to <0.001), leading to the identification of some aa mutations that could discriminate between recent and chronic infection. Different aa mutation groups were assessed for predicting recent infection and their performance ranged from 64.3% to 100% but had a high false recency rate (FRR), which was decreased to 19.4% when another amino acid mutation (M456) was included in the analysis. The pol-based molecular method identified in this study would not be ideal for use on its own due to high FRR; however, this method could be considered for complementing existing serological assays to further reduce FRR.
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Stoner MCD, Edwards JK, Westreich D, Kilburn K, Ahern J, Lippman SA, Gómez-Olivé FX, Kahn K, Pettifor A. Modeling Cash Plus Other Psychosocial and Structural Interventions to Prevent HIV Among Adolescent Girls and Young Women in South Africa (HPTN 068). AIDS Behav 2021; 25:133-143. [PMID: 33475905 PMCID: PMC8292433 DOI: 10.1007/s10461-021-03158-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2021] [Indexed: 11/25/2022]
Abstract
Poverty alleviation programs can reduce HIV incidence but may have greater impacts when combined with other psychosocial interventions. We modeled the change in HIV incidence among South African adolescent girls and young women (AGYW) associated with combining a cash transfer (the South African Child Support Grant (CSG)) with other structural and behavioral interventions. We modeled observational data from the HPTN 068 study where 2328 HIV negative AGYW (13–20 years) were followed for 4 years. In a Monte Carlo simulation based on this cohort (N = 10,000), CSG receipt was not independently associated with HIV incidence. Providing the CSG combined with increasing caregiver care and reducing adolescent depression had the largest reduction in HIV incidence with the fewest number of combined interventions (RD − 3.0%; (95% CI − 5.1%, − 0.9%). Combining a monthly grant with interventions to increase caregiver care and reduce adolescent depression could substantially reduce HIV incidence above the provision of cash alone.
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Affiliation(s)
- Marie C D Stoner
- Women's Global Health Imperative, RTI International, Berkeley, CA, USA.
- Carolina Population Center, University of North Carolina, Chapel Hill, NC, USA.
| | - Jessie K Edwards
- Department of Epidemiology, University of North Carolina, Chapel Hill, NY, USA
| | - Daniel Westreich
- Department of Epidemiology, University of North Carolina, Chapel Hill, NY, USA
| | - Kelly Kilburn
- Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Jennifer Ahern
- Division of Epidemiology & Biostatistics, School of Public Health, University of California, Berkeley, USA
| | - Sheri A Lippman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Medicine, University of California, San Francisco, USA
| | - F Xavier Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- INDEPTH Network, Accra, Ghana
| | - Kathleen Kahn
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- INDEPTH Network, Accra, Ghana
- Epidemiology and Global Health Unit, Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Audrey Pettifor
- Carolina Population Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Epidemiology, University of North Carolina, Chapel Hill, NY, USA
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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