Health AI Central
Peer-Reviewed Publication
Nature2026September 16, 2026Journal Article

Scalable near-real-time Bayesian phylogenetics for outbreaks with Delphy.

Patrick Varilly1, Mark Schifferli2, Katherine Yang2, Paul Cronan2, Ivan Specht3,4, Tim Burcham2, Olivia Glennon2, Olivia Jacks2, Ellory Laning2, Libby Marrs2, Kyle Oba2, Shannon Yeung2, Karlie Wenran Zhao2, Edyth Parker5, Ifeanyi Omah6,7, Jonathan E Pekar6, Laura Luebbert8,9,10, Kristian G Andersen11,12, Daniel J Park3, Stephen F Schaffner3,13, Bronwyn L MacInnis3,13,14, Christian Happi5,13,15, Jacob E Lemieux3,16, Al Ozonoff3,17, Michael Mitzenmacher18, Ben Fry2, Pardis C Sabeti19,20,21,22,23
1Broad Institute of Harvard and MIT, Cambridge, MA, USA. pvarilly@broadinstitute.org.
2Fathom Information Design, Boston, MA, USA.
3Broad Institute of Harvard and MIT, Cambridge, MA, USA.
4Institute for Computational and Mathematical Engineering, School of Engineering, Stanford University, Stanford, CA, USA.
5The Institute of Genomics and Global Health, Redeemer's University, Ede, Nigeria.
6Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK.
7Department of Parasitology and Entomology, Nnamdi Azikiwe University, Awka, Nigeria.
8Eric and Wendy Schmidt Center, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
9Department of Organismic and Evolutionary Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA.
10FutureHouse, San Francisco, CA, USA.
11Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
12Scripps Research Translational Institute, La Jolla, CA, USA.
13Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
14Massachusetts Consortium on Pathogen Readiness, Harvard Medical School, Harvard University, Boston, MA, USA.
15Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria.
16Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
17Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
18Department of Computer Science, School of Engineering and Applied Sciences, Harvard University, Boston, MA, USA.
19Broad Institute of Harvard and MIT, Cambridge, MA, USA. pardis@broadinstitute.org.
20Department of Organismic and Evolutionary Biology, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA. pardis@broadinstitute.org.
21Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA. pardis@broadinstitute.org.
22Massachusetts Consortium on Pathogen Readiness, Harvard Medical School, Harvard University, Boston, MA, USA. pardis@broadinstitute.org.
23Howard Hughes Medical Institute, Chevy Chase, MD, USA. pardis@broadinstitute.org.
PubMed DOI

Abstract

Pathogen genomic analysis is central to tracking, understanding and containing outbreaks1-13, but the complexity and cost of state-of-the-art phylogenetic tools limit global access and impact. Here we introduce Delphy, an exact reformulation of Bayesian phylogenetics14-17 designed to transform its speed, scalability and accessibility while retaining Bayesian state-of-the-art accuracy. Delphy's cen…

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