Evidence map›Paper›PMID 25034127›Full record

Trial reportJournal of virological methods2014

Concordance between allele-specific PCR and ultra-deep pyrosequencing for the detection of HIV-1 non-nucleoside reverse transcriptase inhibitor resistance mutations.

Gillian M Hunt, Lynn Morris, Anitha Moorthy, Ashraf Coovadia, Elaine J Abrams, Renate Strehlau, Louise Kuhn, Deborah Persaud

Abstract readClinical TrialComparative StudyRandomized Controlled Trial
PubMed Full text at PMC Publisher
In one paragraph

Trial report in Journal of virological methods, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
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

1 citing paper in PubMed.

  1. Next generation sequencing improves detection of drug resistance mutations in infants after PMTCT failure.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2015
    Article
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

8 authors.

Gillian M HuntCentre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. Electronic address: gillianh@nicd.ac.za.
Lynn MorrisCentre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. Electronic address: lynnm@nicd.ac.za.
Anitha MoorthyJohns Hopkins University School of Medicine, Baltimore, MD, United States. Electronic address: akmoorthy@gmail.com.
Ashraf CoovadiaEmpilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. Electronic address: ashraf.coovadia@wits.ac.za.
Elaine J AbramsICAP, Columbia University Mailman School of Public Health, New York, NY, United States. Electronic address: eja1@cumb.columbia.edu.
Renate StrehlauEmpilweni Services and Research Unit, Rahima Moosa Mother and Child Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. Electronic address: renate.strehlau@wits.ac.za.
Louise KuhnGertrude H. Sergievsky Center, College of Physicians and Surgeons and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States. Electronic address: lk24@cumc.columbia.edu.
Deborah PersaudJohns Hopkins University School of Medicine, Baltimore, MD, United States. Electronic address: dpers@jhmi.edu.

Funding

Clinical Relevance of Transient Nevirapine ResistanceR01HD047177 · NICHD · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI KUHN, LOUISE · 2004 to 2008
$2.6M
HIV-1 chemoprophylaxis and archived drug resistance in infantsR01HD057784 · NICHD · JOHNS HOPKINS UNIVERSITY · PI PERSAUD, DEBORAH · 2007 to 2010
$2.3M
NICHD NIH HHS HD057784NICHD NIH HHS HD 47177NICHD NIH HHS R01 HD047177NICHD NIH HHS R01 HD057784
6 · The paper itself

Abstract

Recent advances in genotyping technologies have allowed for detection of HIV-1 drug resistance mutations present at low levels. The presence and percentage of Y181C and K103N drug-resistant variants in the blood of 105 subtype C HIV-infected infants who failed single-dose nevirapine prophylaxis for HIV transmission were compared using two highly sensitive genotyping methods, allele-specific PCR (AS-PCR) and ultra-deep pyrosequencing. Significant correlations in detection between both methods were found for both Y181C (correlation coefficients of 0.94 [95% CI 0.91-0.96]) and K103N (0.89 [95% CI 0.84-0.92]) mutations. The majority of discordant specimens (3/5 Y181C and 8/11 K103N) had wild-type variants when population sequencing was used, but mutant variants were detectable at very low levels (≤5%) with either assay. This difference is most likely due to stochastic variations in the appearance of mutant variants. Overall, both AS-PCR and ultra-deep pyrosequencing methods have proven to be sensitive and accurate, and may confidently be used where feasible.

Indexed as

Drug Resistance, ViralMutation, MissenseAllelesFemaleGenotyping TechniquesHIV-1HIV InfectionsHIV Reverse TranscriptaseHumansInfantInfant, NewbornMaleMicrobial Sensitivity TestsPolymerase Chain ReactionSequence Analysis, DNAHIV Reverse Transcriptasereverse transcriptase, Human immunodeficiency virus 1Allele-specific PCRHIV-1 drug resistanceLow-frequency NNRTI variantsUltra-deep sequencing

Identifiers

PMID25034127
PMCPMC4150030

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.