Evidence map›Paper›PMID 35891568›Full record

ArticleViruses2022

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

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Viruses, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.1field-weighted citation impact, top 61% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed, 3 citations in OpenAlex.

  1. Article
  2. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors at 4 institutions in 2 countries.

Paballo NkoneDepartment of Medical Virology, University of Pretoria, Tshwane 0031, South Africa.ORCID 0000-0002-1612-8979
Shayne LoubserNational Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa.
Thomas C QuinnDivision of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Andrew D ReddDivision of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Oliver LaeyendeckerDivision of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Caroline T TiemessenNational Institute for Communicable Diseases and Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa.ORCID 0000-0002-0991-1690
Simnikiwe H MayaphiDepartment of Medical Virology, University of Pretoria, Tshwane 0031, South Africa.ORCID 0000-0002-5453-4353
National Institutes of Health · USUniversity of the Witwatersrand · ZANational Health Laboratory Service · ZAUniversity of Pretoria · ZA

Funding

NIH HHS TCQ, ADR & OL
6 · The paper itself

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.

Indexed as

HIV-1HIV InfectionsHIV SeropositivityAmino AcidsGenes, polHumansAmino Acidschronic HIV-1 infectionfalse recency rateHIV-1 polymeraserecent HIV-1 infectionsanger sequencingsequence diversityShannon entropy

Identifiers

PMID35891568
PMCPMC9324365
OpenAlexW4286462509

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.