Evidence map›Paper›PMID 38826243›Full record

ArticlemedRxiv : the preprint server for health sciences2024

Fine-scale spatial and social patterns of SARS-CoV-2 transmission from identical pathogen sequences.

Cécile Tran-Kiem, Miguel I Paredes, Amanda C Perofsky, Lauren A Frisbie, Hong Xie, Kevin Kong, Amelia Weixler, Alexander L Greninger, Pavitra Roychoudhury, JohnAric M Peterson and 16 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in medRxiv : the preprint server for health sciences, 2024. 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

5 · Who and what money

Authors and funding

26 authors.

Cécile Tran-KiemVaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.ORCID 0000-0003-0563-8428
Miguel I ParedesVaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
Amanda C PerofskyBrotman Baty Institute, University of Washington, Seattle, WA, USA.
Lauren A FrisbieWashington State Department of Health, Shoreline, WA, USA.
Hong XieDepartment of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
Kevin KongDepartment of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
Amelia WeixlerDepartment of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
Alexander L GreningerVaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
Pavitra RoychoudhuryVaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
JohnAric M PetersonWashington State Department of Health, Shoreline, WA, USA.
Andrew DelgadoWashington State Department of Health, Shoreline, WA, USA.
Holly HalsteadWashington State Department of Health, Shoreline, WA, USA.
Drew MacKellarWashington State Department of Health, Shoreline, WA, USA.
Philip DykemaWashington State Department of Health, Shoreline, WA, USA.
Luis GamboaBrotman Baty Institute, University of Washington, Seattle, WA, USA.
Chris D FrazarDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.
Erica RykeDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.
Jeremy StoneBrotman Baty Institute, University of Washington, Seattle, WA, USA.
David ReinhartBrotman Baty Institute, University of Washington, Seattle, WA, USA.
Lea StaritaBrotman Baty Institute, University of Washington, Seattle, WA, USA.
Allison ThibodeauWashington State Department of Health, Shoreline, WA, USA.
Cory YunWashington State Department of Health, Shoreline, WA, USA.
Frank AragonaWashington State Department of Health, Shoreline, WA, USA.
Allison BlackWashington State Department of Health, Shoreline, WA, USA.
Cécile ViboudFogarty International Center, National Institutes of Health, Bethesda, MD, USA.
Trevor BedfordVaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.

Funding

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
High-Performance Compute Cluster for Comprehensive Cancer and Infectious Diseases ResearchS10OD028685 · OD · FRED HUTCHINSON CANCER RESEARCH CENTER · PI BRADLEY, PHILIP · 2020 to 2020
$2.0M
FHCRC High-Performance Computing ClusterS10OD020069 · OD · FRED HUTCHINSON CANCER RESEARCH CENTER · PI KOOPERBERG, CHARLES L · 2015 to 2015
$600k
NCEZID CDC HHS U01 CK000630NIGMS NIH HHS R35 GM119774NIH HHS S10 OD020069NIH HHS S10 OD028685
6 · The paper itself

Abstract

Pathogen genomics can provide insights into underlying infectious disease transmission patterns, but new methods are needed to handle modern large-scale pathogen genome datasets and realize this full potential. In particular, genetically proximal viruses should be highly informative about transmission events as genetic proximity indicates epidemiological linkage. Here, we leverage pairs of identical sequences to characterise fine-scale transmission patterns using 114,298 SARS-CoV-2 genomes collected through Washington State (USA) genomic sentinel surveillance with associated age and residence location information between March 2021 and December 2022. This corresponds to 59,660 sequences with another identical sequence in the dataset. We find that the location of pairs of identical sequences is highly consistent with expectations from mobility and social contact data. Outliers in the relationship between genetic and mobility data can be explained by SARS-CoV-2 transmission between postal codes with male prisons, consistent with transmission between prison facilities. We find that transmission patterns between age groups vary across spatial scales. Finally, we use the timing of sequence collection to understand the age groups driving transmission. Overall, this work improves our ability to leverage large pathogen genome datasets to understand the determinants of infectious disease spread.

Identifiers

PMID38826243
PMCPMC11142302

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.