Evidence map›Paper›PMID 33517458›Full record

ArticleThe Journal of infectious diseases2021

Microdrop Human Immunodeficiency Virus Sequencing for Incidence and Drug Resistance Surveillance.

Sung Yong Park, Gina Faraci, Gary Murphy, Christopher Pilcher, Michael P Busch, Ha Youn Lee

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in The Journal of infectious diseases, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing 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

6 citing papers in PubMed.

  1. Article
  2. Portable Nanopore sequencing solution for next-generation HIV drug resistance testing.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2024
    Article
  3. Full-spectrum HIV drug resistance mutation detection by high-resolution complete pol gene sequencing.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2023
    Article
  4. Review
  5. Article
  6. 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

6 authors.

Sung Yong ParkDepartment of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.
Gina FaraciDepartment of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.
Gary MurphyPublic Health England, London, United Kingdom.
Christopher PilcherDepartment of Medicine, University of California, San Francisco, California, USA.
Michael P BuschResearch and Scientific Programs, Vitalant Research Institute, San Francisco, California, USA.
Ha Youn LeeDepartment of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.

Funding

HIV Incidence Assay via Deep Sequencing and Statistical TestsR01AI095066 · NIAID · UNIVERSITY OF SOUTHERN CALIFORNIA · PI LEE, HA YOUN · 2011 to 2025
$8.4M
NIAID NIH HHS R01 AI095066
6 · The paper itself

Abstract

backgroundPrecise and cost-efficient human immunodeficiency virus (HIV) incidence and drug resistance surveillances are in high demand for the advancement of the 90-90-90 "treatment for all" target.

methodsWe developed microdrop HIV sequencing for the HIV incidence and drug resistance assay (HIDA), a single-blood-draw surveillance tool for incidence and drug resistance mutation (DRM) detection. We amplified full-length HIV envelope and pol gene sequences within microdroplets, and this compartmental amplification with long-read high-throughput sequencing enabled us to recover multiple unique sequences.

resultsWe achieved greater precision in determining the stage of infection than current incidence assays, with a 1.2% false recency rate (proportion of misclassified chronic infections) and a 262-day mean duration of recent infection (average time span of recent infection classification) from 83 recently infected and 81 chronically infected individuals. Microdrop HIV sequencing demonstrated an increased capacity to detect minority variants and linked DRMs. By screening all 93 World Health Organization surveillance DRMs, we detected 6 pretreatment drug resistance mutations with 2.6%-13.2% prevalence and cross-linked mutations.

conclusionsHIDA with microdrop HIV sequencing may promote global HIV real-time surveillance by serving as a precise and high-throughput cross-sectional survey tool that can be generalized for surveillance of other pathogens.

Indexed as

Anti-HIV AgentsCross-Sectional StudiesDrug Resistance, ViralGenotypeHIV-1HIV InfectionsHumansIncidenceMutationpol Gene Products, Human Immunodeficiency VirusRNA, ViralAnti-HIV Agentspol Gene Products, Human Immunodeficiency VirusRNA, ViralDrug resistance mutationsGenomic surveillanceHIVIncidence

Identifiers

PMID33517458
PMCPMC8448441

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.