Evidence map›Paper›PMID 24842159›Full record

ArticlePloS one2014

HIV-1 quasispecies delineation by tag linkage deep sequencing.

Nicholas C Wu, Justin De La Cruz, Laith Q Al-Mawsawi, C Anders Olson, Hangfei Qi, Harding H Luan, Nguyen Nguyen, Yushen Du, Shuai Le, Ting-Ting Wu and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.

0numbers the graph read from it
0cells of the map it votes in
18citing 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

18 citing papers in PubMed.

  1. Article
  2. Article
  3. Low-level viraemia despite emergence of dolutegravir-resistant variants.Southern African journal of HIV medicine · 2022
    Article
  4. Article
  5. Article
  6. Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Article
  12. Rational Protein Engineering Guided by Deep Mutational Scanning.International journal of molecular sciences · 2015
    Review
  13. Article
  14. Article
  15. Review
  16. Article
  17. Article
  18. 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

14 authors.

Nicholas C WuDepartment of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America; Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America.
Justin De La CruzDepartment of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America.
Laith Q Al-MawsawiDepartment of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America.
C Anders OlsonDepartment of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America.
Hangfei QiDepartment of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America.
Harding H LuanDepartment of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America.
Nguyen NguyenDepartment of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America.
Yushen DuDepartment of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America.
Shuai LeDepartment of Microbiology, Third Military Medical University, Chongqing, China.
Ting-Ting WuDepartment of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America.
Xinmin LiDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America.
Martha J LewisDivision of Infectious Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America; AIDS Institute, University of California Los Angeles, Los Angeles, California, United States of America.
Otto O YangDepartment of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America; Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America; AIDS Institute, University of California Los Angeles, Los Angeles, California, United States of America; AIDS Healthcare Foundation, Los Angeles, California, United States of America.
Ren SunDepartment of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, United States of America; Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America; AIDS Institute, University of California Los Angeles, Los Angeles, California, United States of America.

Funding

Women's CancersP30CA016042 · NCI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI ARION Xenofon CHATZIIOANNOU · 1985 to 2026
$134.5M
HIV-1 Excape from Inhibiton by Cytotoxic T LymphocytesR01AI043203 · NIAID · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI YANG, OTTO O · 1998 to 2012
$4.6M
A Stanford - SJSU Postdoctoral Training Program to Enhance URM TeachingK12GM088033 · NIGMS · STANFORD UNIVERSITY · PI BOOTHROYD, JOHN C · 2010 to 2016
$4.1M
NCI NIH HHS P30 CA016042NIAID NIH HHS R01 AI043203NIGMS NIH HHS K12 GM088033
6 · The paper itself

Abstract

Trade-offs between throughput, read length, and error rates in high-throughput sequencing limit certain applications such as monitoring viral quasispecies. Here, we describe a molecular-based tag linkage method that allows assemblage of short sequence reads into long DNA fragments. It enables haplotype phasing with high accuracy and sensitivity to interrogate individual viral sequences in a quasispecies. This approach is demonstrated to deduce ∼ 2000 unique 1.3 kb viral sequences from HIV-1 quasispecies in vivo and after passaging ex vivo with a detection limit of ∼ 0.005% to ∼ 0.001%. Reproducibility of the method is validated quantitatively and qualitatively by a technical replicate. This approach can improve monitoring of the genetic architecture and evolution dynamics in any quasispecies population.

Indexed as

Genome, ViralHigh-Throughput Nucleotide SequencingHIV-1Reproducibility of Results

Identifiers

PMID24842159
PMCPMC4026136

What OpenQuestion holds

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Registered trials

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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.