Evidence map›Paper›PMID 37745602›Full record

ArticlebioRxiv : the preprint server for biology2023

Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.

Alexander Crits-Christoph, Joshua I Levy, Jonathan E Pekar, Stephen A Goldstein, Reema Singh, Zach Hensel, Karthik Gangavarapu, Matthew B Rogers, Niema Moshiri, Robert F Garry and 12 more

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed, 13 citations in OpenAlex.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

22 authors at 15 institutions in 8 countries.

Alexander Crits-ChristophIndependent researcher.
Joshua I LevyDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Jonathan E PekarDepartment of Biomedical Informatics, University of California San Diego, La Jolla, CA, USA.
Stephen A GoldsteinDepartment of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA.
Reema SinghVaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.ORCID 0000-0001-7049-5473
Zach HenselITQB NOVA, Universidade NOVA de Lisboa, Lisbon, Av. da Republica, 2780-157, Oeiras, Portugal.
Karthik GangavarapuDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90024, USA.
Matthew B RogersVaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.
Niema MoshiriDepartment of Computer Science & Engineering, University of California San Diego, La Jolla, CA, USA.
Robert F GarryTulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, LA 70112, USA; Zalgen Labs, Frederick, MD 21703, USA; Global Virus Network (GVN), Baltimore, MD 21201, USA.
Edward C HolmesSydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
Marion P G KoopmansDepartment of Viroscience, and Pandemic and Disaster Preparedness Centre., Erasmus Medical Centre, Rotterdam, The Netherlands.ORCID 0000-0002-5204-2312
Philippe LemeyDepartment of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
Saskia PopescuUniversity of Maryland, School of Medicine, Department of Epidemiology & Public Health, Baltimore, MD 21201, USA.
Andrew RambautInstitute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK.
David L RobertsonMRC-University of Glasgow Center for Virus Research, Glasgow, G61 1QH, UK.ORCID 0000-0001-6338-0221
Marc A SuchardDepartment of Biostatistics, University of California, Los Angeles, Los Angeles, CA 90024, USA.
Joel O WertheimDepartment of Medicine, University of California San Diego, La Jolla, CA, USA.
Angela L RasmussenVaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.ORCID 0000-0001-9462-3169
Kristian G AndersenDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Michael WorobeyDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
Florence DébarreInstitut d'Écologie et des Sciences de l'Environnement (IEES-Paris, UMR 7618), CNRS, Sorbonne Université, UPEC, IRD, INRAE, Paris, France.ORCID 0000-0003-2497-833X
University of California San Diego · USUniversity of Saskatchewan · CAScripps Research Institute · USUniversity of California, Los Angeles · USCentre National de la Recherche Scientifique · FRErasmus University Rotterdam · NLMRC University of Glasgow Centre for Virus Research · GBRega Institute for Medical Research · BEThe University of Sydney · AUTulane University · USUniversidade Nova de Lisboa · PTUniversity of Arizona · USUniversity of Edinburgh · GBUniversity of Maryland, Baltimore · USUniversity of Utah · US

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 Robert F Garry · 2018 to 2026
$32.0M
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
San Diego Biomedical Informatics Education & Research (SABER)T15LM011271 · NLM · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SHAMIM NEMATI · 2012 to 2026
$9.7M
PATHOGENESIS AND IMMUNOLOGY OF DISEASET32AI007244 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI NEMAZEE, DAVID · 1985 to 2022
$8.8M
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 T32 AI007244NIAID NIH HHS U01 AI151812NIAID NIH HHS U19 AI135995NLM NIH HHS T15 LM011271Wellcome Trust
6 · The paper itself

Abstract

Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Wholesale Seafood Market, the site with the most reported wildlife vendors in the city of Wuhan, China. Here, we analyze publicly available qPCR and sequencing data from environmental samples collected in the Huanan market in early 2020. We demonstrate that the SARS-CoV-2 genetic diversity linked to this market is consistent with market emergence, and find increased SARS-CoV-2 positivity near and within a particular wildlife stall. We identify wildlife DNA in all SARS-CoV-2 positive samples from this stall. This includes species such as civets, bamboo rats, porcupines, hedgehogs, and one species, raccoon dogs, known to be capable of SARS-CoV-2 transmission. We also detect other animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them to those from other markets. This analysis provides the genetic basis for a short list of potential intermediate hosts of SARS-CoV-2 to prioritize for retrospective serological testing and viral sampling.

Identifiers

PMID37745602
PMCPMC10515900
OpenAlexW4386791185

What OpenQuestion 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 OpenQuestion graph.