Evidence map›Paper›PMID 40339581›Full record

ArticleCell2025

The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2.

Jonathan E Pekar, Spyros Lytras, Mahan Ghafari, Andrew F Magee, Edyth Parker, Yu Wang, Xiang Ji, Jennifer L Havens, Aris Katzourakis, Tetyana I Vasylyeva and 9 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.

0numbers the graph read from it
0cells of the map it votes in
15citing 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

15 citing papers in PubMed.

  1. Review
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  11. Comparative performance of viral landscape phylogeography approaches.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  12. Review
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

19 authors.

Jonathan E PekarInstitute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA; Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA 92093, USA; Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: jpekar@ed.ac.uk.
Spyros LytrasDivision of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow, UK. Electronic address: spyros@g.ecc.u-tokyo.ac.jp.
Mahan GhafariDepartment of Biology, University of Oxford, Oxford, UK.
Andrew F MageeDepartment of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Edyth ParkerDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Institute of Genomics and Global Health, Redeemer's University, Ede, Osun State, Nigeria.
Yu WangDepartment of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093, USA.
Xiang JiDepartment of Mathematics, School of Science and Engineering, Tulane University, New Orleans, LA, USA.
Jennifer L HavensBioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.
Aris KatzourakisDepartment of Biology, University of Oxford, Oxford, UK.
Tetyana I VasylyevaDepartment of Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Population Health and Disease Prevention, University of California, Irvine, Irvine, CA 92617, USA.
Marc A SuchardDepartment of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Alice C HughesSchool of Biological Sciences, University of Hong Kong, Hong Kong, Hong Kong; China Biodiversity Green Development Foundation, Beijing, China.
Joseph HughesMedical Research Council, University of Glasgow Centre for Virus Research, Glasgow, UK.
Andrew RambautInstitute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK.
David L RobertsonMedical Research Council, University of Glasgow Centre for Virus Research, Glasgow, UK.
Simon DellicourSpatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP160/12, 50 av. FD Roosevelt, 1050 Bruxelles, Belgium; Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium. Electronic address: simon.dellicour@ulb.be.
Michael WorobeyDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA. Electronic address: worobey@arizona.edu.
Joel O WertheimDepartment of Medicine, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: jwertheim@health.ucsd.edu.
Philippe LemeyDepartment of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium. Electronic address: philippe.lemey@kuleuven.be.

Funding

NIAID Centers of Excellence for Influenza Research and Response: Universal Influenza Vaccine Research Activities75N93021C00015 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI HENSLEY, SCOTT · 2021 to 2025
$50.7M
Technology CoreU19AI135995 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI Laura D. Hughes · 2018 to 2026
$32.0M
San Diego Biomedical Informatics Education & Research (SABER)T15LM011271 · NLM · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SHAMIM NEMATI · 2012 to 2026
$9.7M
Fast and flexible Bayesian phylogenetics via modern machine learningR01AI162611 · NIAID · FRED HUTCHINSON CANCER RESEARCH CENTER · PI MATSEN, FREDERICK ALBERT · 2021 to 2025
$3.8M
Automation and Evaluation of Real-Time Transmission Network-Based HIV Prevention Services in New York CityR01AI135992 · NIAID · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI WERTHEIM, JOEL OKRENT · 2018 to 2022
$3.6M
Statistical Innovation to Integrate Sequences and Phenotypes for Scalable Phylodynamic InferenceR01AI153044 · NIAID · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Marc A. Suchard · 2021 to 2026
$2.4M
NIAID NIH HHS 75N93021C00015NIAID NIH HHS R01 AI135992NIAID NIH HHS R01 AI153044NIAID NIH HHS R01 AI162611NIAID NIH HHS U19 AI135995NLM NIH HHS T15 LM011271Wellcome Trust
6 · The paper itself

Abstract

The emergence of SARS-CoV in 2002 and SARS-CoV-2 in 2019 led to increased sampling of sarbecoviruses circulating in horseshoe bats. Employing phylogenetic inference while accounting for recombination of bat sarbecoviruses, we find that the closest-inferred bat virus ancestors of SARS-CoV and SARS-CoV-2 existed less than a decade prior to their emergence in humans. Phylogeographic analyses show bat sarbecoviruses traveled at rates approximating their horseshoe bat hosts and circulated in Asia for millennia. We find that the direct ancestors of SARS-CoV and SARS-CoV-2 are unlikely to have reached their respective sites of emergence via dispersal in the bat reservoir alone, supporting interactions with intermediate hosts through wildlife trade playing a role in zoonotic spillover. These results can guide future sampling efforts and demonstrate that viral genomic regions extremely closely related to SARS-CoV and SARS-CoV-2 were circulating in horseshoe bats, confirming their importance as the reservoir species for SARS viruses.

Indexed as

ChiropteraSevere acute respiratory syndrome-related coronavirusAnimalsCOVID-19Disease ReservoirsEvolution, MolecularGenome, ViralHumansPhylogenyPhylogeographySARS-CoV-2molecular epidemiologyphylogeographysarbecovirusesvirus evolution

Identifiers

PMID40339581
PMCPMC12230244

What OpenQuestion holds

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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 OpenQuestion graph.