Evaluation of the HIV-1 Polymerase Gene Sequence Diversity for Prediction of Recent HIV-1 Infections Using Shannon Entropy Analysis

Paballo Nkone; Shayne Loubser; Thomas C. Quinn; Andrew D. Redd; Oliver Laeyendecker; Caroline T. Tiemessen; Simnikiwe H. Mayaphi

doi:10.3390/v14071587

Viruses (Jul 2022)

Evaluation of the HIV-1 Polymerase Gene Sequence Diversity for Prediction of Recent HIV-1 Infections Using Shannon Entropy Analysis

Paballo Nkone,
Shayne Loubser,
Thomas C. Quinn,
Andrew D. Redd,
Oliver Laeyendecker,
Caroline T. Tiemessen,
Simnikiwe H. Mayaphi

Affiliations

Paballo Nkone: Department of Medical Virology, University of Pretoria, Tshwane 0031, South Africa
Shayne Loubser: National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
Thomas C. Quinn: Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
Andrew D. Redd: Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
Oliver Laeyendecker: Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
Caroline T. Tiemessen: National Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
Simnikiwe H. Mayaphi: Department of Medical Virology, University of Pretoria, Tshwane 0031, South Africa

DOI: https://doi.org/10.3390/v14071587
Journal volume & issue: Vol. 14, no. 7
p. 1587

Abstract

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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 p-values ranging from 0.011 to 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.

Published in Viruses

ISSN: 1999-4915 (Online)
Publisher: MDPI AG
Country of publisher: Switzerland
LCC subjects: Science: Microbiology
Website: http://www.mdpi.com/journal/viruses

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