Evidence map›Paper›PMID 29856864›Full record

ArticlePloS one2018

Evaluation of different analysis pipelines for the detection of HIV-1 minority resistant variants.

Marine Perrier, Nathalie Désiré, Alexandre Storto, Eve Todesco, Christophe Rodriguez, Mélanie Bertine, Quentin Le Hingrat, Benoit Visseaux, Vincent Calvez, Diane Descamps and 2 more

Open access · goldAbstract read

PubMed Full text at PMC Publisher

In one paragraph

Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it

0cells of the map it votes in

8citing papers in PubMed

1.1field-weighted citation impact, top 26% 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

8 citing papers in PubMed, 11 citations in OpenAlex.

Ion Torrent Genexus as a Fast and Reliable Solution for HIV-1 Drug Resistance Testing: Comparison with the GeneStudio S5 Workflow.International journal of molecular sciences · 2026
Article
HIV-1 Evolutionary Dynamics under Nonsuppressive Antiretroviral Therapy.mBio · 2022
Article
A Systematic Evaluation of High-Throughput Sequencing Approaches to Identify Low-Frequency Single Nucleotide Variants in Viral Populations.Viruses · 2020
Article
Near point-of-care, point-mutation test to detect drug resistance in HIV-1: a validation study in a Mexican cohort.AIDS (London, England) · 2020
Article
Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses.Viruses · 2020
Article
Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based HIV Drug Resistance Testing.Viruses · 2020
Article
High prevalence of integrase mutation L74I in West African HIV-1 subtypes prior to integrase inhibitor treatment.The Journal of antimicrobial chemotherapy · 2020
Article
Validation of publicly-available software used in analyzing NGS data for HIV-1 drug resistance mutations and transmission networks in a Washington, DC, Cohort.PloS one · 2019
Observational

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

12 authors at 2 institutions in 1 country.

Marine PerrierIAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France.

Nathalie DésiréSorbonne University, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France.

Alexandre StortoIAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France.

Eve TodescoSorbonne University, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France.

Christophe RodriguezDépartement de Microbiologie, Next-Generation Sequencing Platform pACT, IMRB Créteil, Créteil, France.

Mélanie BertineIAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France.

Quentin Le HingratIAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France.

Benoit VisseauxIAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France.

Vincent CalvezSorbonne University, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France.

Diane DescampsIAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France.

Anne-Geneviève MarcelinSorbonne University, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), Paris, France.

Charlotte CharpentierIAME, UMR 1137, INSERM, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Laboratoire de Virologie, Hôpital Bichat, AP-HP, Paris, France.ORCID 0000-0002-6441-7054

Inserm · FRInstitut Mondor de Recherche Biomédicale · FR

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

objectiveReliable detection of HIV minority resistant variants (MRVs) requires bioinformatics analysis with specific algorithms to obtain good quality alignments. The aim of this study was to analyze ultra-deep sequencing (UDS) data using different analysis pipelines.

methodsHIV-1 protease, reverse transcriptase (RT) and integrase sequences from antiretroviral-naïve patients were obtained using GS-Junior® (Roche) and MiSeq® (Illumina) platforms. MRVs were defined as variants harbouring resistance-mutation present at a frequency of 1%-20%. Reads were analyzed using different alignment algorithms: Amplicon Variant Analyzer®, Geneious® compared to SmartGene® NGS HIV-1 module.

results101 protease and 51 RT MRVs identified in 139 protease and 124 RT sequences generated with a GS-Junior® platform were analyzed using AVA® and SmartGene® software. The correlation coefficients for the MRVs were R2 = 0.974 for protease and R2 = 0.972 for RT. Discordances (n = 13 in protease and n = 15 in RT) mainly concerned low-level MRVs (i.e., with frequencies of 1%-2%, n = 18/28) and they were located in homopolymeric regions (n = 10/15). Geneious® and SmartGene® software were used to analyze 143 protease, 45 RT and 26 integrase MRVs identified in 172 protease, 69 RT, and 72 integrase sequences generated with a MiSeq® platform. The correlation coefficients for the MRVs were R2 = 0.987 for protease, R2 = 0.995 for RT and R2 = 0.993 for integrase. Discordances (n = 9 in protease, n = 3 in RT, and n = 3 in integrase) mainly concerned low-level MRVs (n = 13/15).

conclusionWe found an excellent correlation between the various UDS analysis pipelines that we tested. However, our results indicate that specific attention should be paid to low-level MRVs, for which the use of two different analysis pipelines and visual inspection of sequences alignments might be beneficial. Thus, our results argue for use of a 2% threshold for MRV detection, rather than the 1% threshold, to minimize misalignments and time-consuming sight reading steps essential to ensure accurate results for MRV frequencies below 2%.

Indexed as

MutationAnti-HIV AgentsDNA Mutational AnalysisDrug Resistance, ViralGene FrequencyHigh-Throughput Nucleotide SequencingHIV-1HIV InfectionsHIV IntegraseHIV ProteaseHIV Reverse TranscriptaseHumansMicrobial Sensitivity TestsSequence AlignmentAnti-HIV AgentsHIV IntegraseHIV ProteaseHIV Reverse Transcriptasep16 protease, Human immunodeficiency virus 1

Identifiers

PMID29856864

DOI10.1371/journal.pone.0198334

PMCPMC5983569

OpenAlexW2806889329

What OpenQuestion holds

Textmetadata

LicenceCC BY

Read underepoch 390

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.