Evidence map›Paper›PMID 40196005›Full record

ArticleResearch square2025

JUNIPER: Reconstructing Transmission Events from Next-Generation Sequencing Data at Scale.

Ivan Specht, Gage K Moreno, Taylor Brock-Fisher, Lydia A Krasilnikova, Brittany A Petros, Jonathan E Pekar, Mark Schifferli, Ben Fry, Catherine M Brown, Lawrence C Madoff and 8 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in Research square, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

18 authors.

Ivan SpechtThe Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Gage K MorenoThe Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Taylor Brock-FisherThe Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Lydia A KrasilnikovaThe Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Brittany A PetrosThe Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.ORCID 0000-0003-2110-7475
Jonathan E PekarThe Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Mark SchifferliFathom Information Design, Boston, MA 02114, USA.
Ben FryFathom Information Design, Boston, MA 02114, USA.ORCID 0000-0002-6414-5570
Catherine M BrownMassachusetts Department of Public Health, Boston, MA 02108, USA.
Lawrence C MadoffMassachusetts Department of Public Health, Boston, MA 02108, USA.ORCID 0000-0003-2589-7777
Meagan BurnsMassachusetts Department of Public Health, Boston, MA 02108, USA.ORCID 0000-0001-7802-4721
Stephen F SchaffnerThe Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.ORCID 0000-0001-6699-3568
Daniel J ParkThe Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.ORCID 0000-0001-7226-7781
Bronwyn L MacInnisThe Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.ORCID 0000-0003-0082-968X
Al OzonoffThe Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.ORCID 0000-0003-4233-5899
Patrick VarillyThe Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Michael D MitzenmacherDepartment of Computer Science, School of Engineering and Applied Sciences, Harvard University, Boston, MA 02134, USA.
Pardis C SabetiThe Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.ORCID 0000-0002-9843-1890

Funding

Viral Genomics: evolution, spread, and host interactionsU19AI110818 · NIAID · BROAD INSTITUTE, INC. · PI NEAFSEY, DANIEL E · 2014 to 2024
$66.5M
Medical Scientist Training ProgramT32GM007753 · NIGMS · HARVARD UNIVERSITY (MEDICAL SCHOOL) · PI WALENSKY, LOREN DAVID · 1985 to 2021
$50.0M
Medical Scientist Training ProgramT32GM144273 · NIGMS · HARVARD MEDICAL SCHOOL · PI David Shumway Jones, Jacqueline A. Lees · 2022 to 2026
$14.7M
West African Emerging Infectious Disease Research Center (WA-EIDRC)U01AI151812 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI ANDERSEN, KRISTIAN GRAUGAARD, GARRY, ROBERT F · 2020 to 2024
$13.2M
Partners Healthcare Training Program in Precision and Genomic MedicineT32HG010464 · NHGRI · MASSACHUSETTS GENERAL HOSPITAL · PI HEIDI L REHM, JORDAN W SMOLLER · 2019 to 2026
$3.1M
NHGRI NIH HHS T32 HG010464NIAID NIH HHS U01 AI151812NIAID NIH HHS U19 AI110818NIGMS NIH HHS T32 GM007753NIGMS NIH HHS T32 GM144273
6 · The paper itself

Abstract

Transmission reconstruction-the inference of who infects whom in disease outbreaks-offers critical insights into how pathogens spread and provides opportunities for targeted control measures. We developed JUNIPER (Joint Underlying Network Inference for Phylogenetic and Epidemiological Reconstructions), a highly-scalable pathogen outbreak reconstruction tool that incorporates intrahost variation, incomplete sampling, and algorithmic parallelization. Central to JUNIPER is a statistical model for within-host variant frequencies observed by next generation sequencing, which we validated on a dataset of over 160,000 deep-sequenced SARS-CoV-2 genomes. Combining this within-host variation model with population-level evolutionary and transmission models, we developed a method for inferring phylogenies and transmission trees simultaneously. We benchmarked JUNIPER on computer-generated and real outbreaks in which transmission links were known or epidemiologically confirmed. We demonstrated JUNIPER's real-world utility on two large-scale datasets: over 1,500 bovine H5N1 cases and over 13,000 human COVID-19 cases. Based on these analyses, we quantified the elevated H5N1 transmission rates in California and identified high-confidence transmission events, and demonstrated the efficacy of vaccination for reducing SARS-CoV-2 transmission. By overcoming computational and methodological limitations in existing outbreak reconstruction tools, JUNIPER provides a robust framework for studying pathogen spread at scale.

Identifiers

PMID40196005
PMCPMC11975037

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.