Evidence map›Paper›PMID 29401317›Full record

ArticleMolecular biology and evolution2018

HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens.

Sergei L Kosakovsky Pond, Steven Weaver, Andrew J Leigh Brown, Joel O Wertheim

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In one paragraph

Article in Molecular biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 190 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
190citing papers in PubMed, 2 pooled it
–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

190 citing papers in PubMed, 2 syntheses or guidelines pooled it.

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  14. Brief Report: National HIV Molecular Cluster Detection Supports Local Cluster Detection.Journal of acquired immune deficiency syndromes (1999) · 2026
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  15. HIV Transmission Dynamics in Greater Mexico City are Shaped by Dense Spatial Mixing.medRxiv : the preprint server for health sciences · 2026
    Article
  16. Article
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  18. Network Analysis in Microbiome Research: Methods, Tools, and Applications.Methods in molecular biology (Clifton, N.J.) · 2026
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  19. Review
  20. Article

130 more citing papers are in PubMed but not listed here.

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

4 authors.

Sergei L Kosakovsky PondInstitute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.
Steven WeaverInstitute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.
Andrew J Leigh BrownInstitute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.
Joel O WertheimDepartment of Medicine, University of California, San Diego, CA.

Funding

VirologyP30AI036214 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI David Mitchell Smith · 1994 to 2026
$78.4M
Turning big data analysis infrastructure for HIV researchR01AI134384 · NIAID · PENNSYLVANIA STATE UNIVERSITY, THE · PI NEKRUTENKO, ANTON, POND, SERGEI L KOSAKOVSKY · 2017 to 2021
$4.2M
Modeling Epidemic Infectious Diseases Using Sequence AnalysisU01GM110749 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI POND, SERGEI L KOSAKOVSKY · 2014 to 2018
$3.0M
HyPhy: Molecular Evolutionary AnalysesR01GM093939 · NIGMS · TEMPLE UNIV OF THE COMMONWEALTH · PI MUSE, SPENCER V., POND, SERGEI L KOSAKOVSKY · 2010 to 2018
$2.5M
Public Health Implications of HIV Transmission NetworksK01AI110181 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI WERTHEIM, JOEL OKRENT · 2014 to 2018
$668k
NIAID NIH HHS K01 AI110181NIAID NIH HHS P30 AI036214NIAID NIH HHS R01 AI134384NIGMS NIH HHS R01 GM093939NIGMS NIH HHS U01 GM110749
6 · The paper itself

Abstract

In modern applications of molecular epidemiology, genetic sequence data are routinely used to identify clusters of transmission in rapidly evolving pathogens, most notably HIV-1. Traditional 'shoe-leather' epidemiology infers transmission clusters by tracing chains of partners sharing epidemiological connections (e.g., sexual contact). Here, we present a computational tool for identifying a molecular transmission analog of such clusters: HIV-TRACE (TRAnsmission Cluster Engine). HIV-TRACE implements an approach inspired by traditional epidemiology, by identifying chains of partners whose viral genetic relatedness imply direct or indirect epidemiological connections. Molecular transmission clusters are constructed using codon-aware pairwise alignment to a reference sequence followed by pairwise genetic distance estimation among all sequences. This approach is computationally tractable and is capable of identifying HIV-1 transmission clusters in large surveillance databases comprising tens or hundreds of thousands of sequences in near real time, that is, on the order of minutes to hours. HIV-TRACE is available at www.hivtrace.org and from www.github.com/veg/hivtrace, along with the accompanying result visualization module from www.github.com/veg/hivtrace-viz. Importantly, the approach underlying HIV-TRACE is not limited to the study of HIV-1 and can be applied to study outbreaks and epidemics of other rapidly evolving pathogens.

Indexed as

Computational BiologyHIV-1HIV InfectionsHumansMolecular EpidemiologySoftware

Identifiers

PMID29401317
PMCPMC5995201

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.