Evidence map›Paper›PMID 41929033›Full record

ArticlebioRxiv : the preprint server for biology2026

Nextstrain automates real-time phylodynamic analysis of open data for endemic and emerging pathogens.

Kimberly R Andrews, Jennifer Chang, Cornelius Roemer, James Hadfield, Victor Lin, Anderson F Brito, Richard Olumide Daodu, Isabel A Joia, Kathryn Kistler, Allison Li and 14 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. 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

24 authors.

Kimberly R AndrewsVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.ORCID 0000-0003-4721-1924
Jennifer ChangVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.ORCID 0000-0002-8381-3765
Cornelius RoemerBiozentrum, University of Basel, Basel, Switzerland.ORCID 0000-0002-6138-6539
James HadfieldVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.ORCID 0000-0002-4118-6468
Victor LinVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.ORCID 0000-0002-8670-3377
Anderson F BritoInstituto Todos pela Saúde, São Paulo, SP, Brazil.ORCID 0000-0001-5785-7222
Richard Olumide DaoduCenter for Artificial Intelligence in Public Health Research, Robert Koch Institute, Berlin, Germany.ORCID 0009-0008-9568-4455
Isabel A JoiaBiozentrum, University of Basel, Basel, Switzerland.ORCID 0009-0000-6241-7467
Kathryn KistlerVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.ORCID 0000-0002-3216-0020
Allison LiVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.ORCID 0009-0003-4751-0016
Louise H MonclaDepartment of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.ORCID 0000-0001-5722-1988
Miguel I ParedesVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.ORCID 0000-0002-9712-1663
Denise KühnertCenter for Artificial Intelligence in Public Health Research, Robert Koch Institute, Berlin, Germany.ORCID 0000-0002-5657-018X
Laura Marcela TorresWashington Department of Health, Shoreline, WA, USA.ORCID 0000-0001-9496-0595
Laura VoitlBiozentrum, University of Basel, Basel, Switzerland.ORCID 0009-0002-7987-1185
Ivan AksamentovBiozentrum, University of Basel, Basel, Switzerland.ORCID 0000-0002-7557-9673
Emma B HodcroftSwiss Institute of Bioinformatics, Lausanne, Switzerland.ORCID 0000-0002-0078-2212
John HuddlestonVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.ORCID 0000-0002-4250-2063
John T McCroneVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.ORCID 0000-0002-9846-8917
John S J AndersonVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
Thomas R SibleyVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.ORCID 0000-0001-5269-2297
Jover LeeVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.ORCID 0000-0002-2391-0512
Richard A NeherBiozentrum, University of Basel, Basel, Switzerland.ORCID 0000-0003-2525-1407
Trevor BedfordVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.ORCID 0000-0002-4039-5794

Funding

NIAID Centers of Excellence for Influenza Research and Response: Universal Influenza Vaccine Research Activities75N93021C00016 · NIAID · ST. JUDE CHILDREN'S RESEARCH HOSPITAL · PI WEBBY, RICHARD · 2021 to 2025
$91.4M
Real-time tracking of virus evolution for vaccine strain selection and epidemiological investigationR35GM119774 · NIGMS · FRED HUTCHINSON CANCER RESEARCH CENTER · PI BEDFORD, TREVOR BC · 2016 to 2025
$4.1M
Bill & Melinda Gates Foundation INV-018979NCEZID CDC HHS U01 CK000630NIGMS NIH HHS R35 GM119774NIH HHS 75N93021C00016
6 · The paper itself

Abstract

Motivation: Genome sequencing provides an exceptional window into the evolutionary and epidemiological dynamics of endemic and emerging pathogens, and thus allows for better, more targeted, public health interventions. Online genomic surveillance platforms can provide near real-time insight into these dynamics. Results: Nextstrain provides continually updated real-time genomic surveillance for 21 viruses and the bacterial pathogen Availability and Implementation: All source code is available at https://github.com/nextstrain. Phylodynamic results can be visualized and downloaded at https://nextstrain.org/pathogens, and open sequence data and curated metadata are available at https://nextstrain.org/pathogens/files.

Identifiers

PMID41929033
PMCPMC13041781

What Socratic holds

Textmetadata
LicenceCC BY
Read underepoch 390

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 Socratic graph.