Evidence map›Paper›PMID 36561171›Full record

ArticlemedRxiv : the preprint server for health sciences2022

Local-Scale phylodynamics reveal differential community impact of SARS-CoV-2 in metropolitan US county.

Miguel I Paredes, Amanda C Perofsky, Lauren Frisbie, Louise H Moncla, Pavitra Roychoudhury, Hong Xie, Shah A Mohamed Bakhash, Kevin Kong, Isabel Arnould, Tien V Nguyen and 21 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in medRxiv : the preprint server for health sciences, 2022. 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.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

31 authors.

Miguel I ParedesDepartment of Epidemiology, University of Washington, Seattle, WA, USA.
Amanda C PerofskyBrotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA USA.
Lauren FrisbieWashington State Department of Health, Shoreline, WA USA.
Louise H MonclaThe University of Pennsylvania, Department of Pathobiology, Philadelphia, PA.
Pavitra RoychoudhuryVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA.
Hong XieDepartment of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
Shah A Mohamed BakhashDepartment of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
Kevin KongDepartment of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
Isabel ArnouldDepartment of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
Tien V NguyenDepartment of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
Seffir T WendmDepartment of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
Pooneh HajianDepartment of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
Sean EllisDepartment of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
Patrick C MathiasDepartment of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
Alexander L GreningerVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA.
Lea M StaritaBrotman Baty Institute for Precision Medicine, 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.
Weizhi ZhongBrotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA USA.
Luis GamboaBrotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA USA.
Machiko ThrelkeldDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.
Jover LeeVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA.
Jeremy StoneBrotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA USA.
Evan McDermotBrotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA USA.
Melissa TruongDepartment of Genome Sciences, University of Washington, Seattle, WA, USA.
Jay ShendureBrotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA USA.
Hanna N OlteanWashington State Department of Health, Shoreline, WA USA.
Cécile ViboudFogarty International Center, National Institutes of Health, Bethesda, MD, USA.
Helen ChuDepartment of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA.
Nicola F MüllerVaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA.
Trevor BedfordDepartment of Epidemiology, University of Washington, 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
Quantifying the genetic and environmental factors driving avian influenza spilloverR00AI147029 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI MONCLA, LOUISE HILLIER · 2022 to 2023
$498k
NIAID NIH HHS R00 AI147029NIGMS NIH HHS R35 GM119774
6 · The paper itself

Abstract

SARS-CoV-2 transmission is largely driven by heterogeneous dynamics at a local scale, leaving local health departments to design interventions with limited information. We analyzed SARS-CoV-2 genomes sampled between February 2020 and March 2022 jointly with epidemiological and cell phone mobility data to investigate fine scale spatiotemporal SARS-CoV-2 transmission dynamics in King County, Washington, a diverse, metropolitan US county. We applied an approximate structured coalescent approach to model transmission within and between North King County and South King County alongside the rate of outside introductions into the county. Our phylodynamic analyses reveal that following stay-at-home orders, the epidemic trajectories of North and South King County began to diverge. We find that South King County consistently had more reported and estimated cases, COVID-19 hospitalizations, and longer persistence of local viral transmission when compared to North King County, where viral importations from outside drove a larger proportion of new cases. Using mobility and demographic data, we also find that South King County experienced a more modest and less sustained reduction in mobility following stay-at-home orders than North King County, while also bearing more socioeconomic inequities that might contribute to a disproportionate burden of SARS-CoV-2 transmission. Overall, our findings suggest a role for local-scale phylodynamics in understanding the heterogeneous transmission landscape.

Identifiers

PMID36561171
PMCPMC9774227

What OpenQuestion holds

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LicenceCC BY-NC-ND
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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.