Evidence map›Paper›PMID 33564780›Full record

ArticlemedRxiv : the preprint server for health sciences2021

Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States.

Nicole L Washington, Karthik Gangavarapu, Mark Zeller, Alexandre Bolze, Elizabeth T Cirulli, Kelly M Schiabor Barrett, Brendan B Larsen, Catelyn Anderson, Simon White, Tyler Cassens and 43 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in medRxiv : the preprint server for health sciences, 2021. 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

53 authors.

Nicole L WashingtonHelix, San Mateo, CA.
Karthik GangavarapuDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA.
Mark ZellerDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA.
Alexandre BolzeHelix, San Mateo, CA.
Elizabeth T CirulliHelix, San Mateo, CA.
Kelly M Schiabor BarrettHelix, San Mateo, CA.
Brendan B LarsenDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ.
Catelyn AndersonDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA.
Simon WhiteHelix, San Mateo, CA.
Tyler CassensHelix, San Mateo, CA.
Sharoni JacobsHelix, San Mateo, CA.
Geraint LevanHelix, San Mateo, CA.
Jason NguyenHelix, San Mateo, CA.
Jimmy M RamirezHelix, San Mateo, CA.
Charlotte Rivera-GarciaHelix, San Mateo, CA.
Efren SandovalHelix, San Mateo, CA.
Xueqing WangHelix, San Mateo, CA.
David WongHelix, San Mateo, CA.
Emily SpencerDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA.
Refugio Robles-SikisakaDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA.
Ezra KurzbanDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA.
Laura D HughesDepartment of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Xianding DengDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA.
Candace WangDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA.
Venice ServellitaDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA.
Holly ValentineUniversity of California, San Diego, CA.
Peter De HoffUniversity of California, San Diego, CA.
Phoebe SeaverUniversity of California, San Diego, CA.
Shashank SatheUniversity of California, San Diego, CA.
Kimberly GietzenIllumina, San Diego, CA.
Brad SicklerIllumina, San Diego, CA.
Jay AnticoIllumina, San Diego, CA.
Kelly HoonIllumina, San Diego, CA.
Jingtao LiuIllumina, San Diego, CA.
Aaron HardingSharp Healthcare, San Diego, CA.
Omid BakhtarSharp Healthcare, San Diego, CA.
Tracy BaslerSan Diego County Health and Human Services Agency, San Diego, CA.
Brett AustinSan Diego County Health and Human Services Agency, San Diego, CA.
Magnus IsakssonHelix, San Mateo, CA.
Phillip G FebboIllumina, San Diego, CA.
David BeckerHelix, San Mateo, CA.
Marc LaurentHelix, San Mateo, CA.
Eric McDonaldSan Diego County Health and Human Services Agency, San Diego, CA.
Gene W YeoUniversity of California, San Diego, CA.
Rob KnightUniversity of California, San Diego, CA.
Louise C LaurentUniversity of California, San Diego, CA.
Eileen de FeoIllumina, San Diego, CA.
Michael WorobeyDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ.
Charles ChiuDepartment of Laboratory Medicine, University of California San Francisco, San Francisco, CA.
Marc A SuchardDepartment of Biostatistics, Fielding School of Public Health, and Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA.
James T LuHelix, San Mateo, CA.
William LeeHelix, San Mateo, CA.
Kristian G AndersenDepartment of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA.

Funding

Technology CoreU19AI135995 · NIAID · SCRIPPS RESEARCH INSTITUTE, THE · PI Kristian Graugaard Andersen · 2018 to 2026
$32.0M
Scripps Translational Science InstituteUL1TR002550 · NCATS · SCRIPPS RESEARCH INSTITUTE, THE · PI TOPOL, ERIC JEFFREY · 2018 to 2022
$28.9M
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
NCATS NIH HHS UL1 TR002550NIAID NIH HHS U01 AI151812NIAID NIH HHS U19 AI135995
6 · The paper itself

Abstract

As of January of 2021, the highly transmissible B.1.1.7 variant of SARS-CoV-2, which was first identified in the United Kingdom (U.K.), has gained a strong foothold across the world. Because of the sudden and rapid rise of B.1.1.7, we investigated the prevalence and growth dynamics of this variant in the United States (U.S.), tracking it back to its early emergence and onward local transmission. We found that the RT-qPCR testing anomaly of S gene target failure (SGTF), first observed in the U.K., was a reliable proxy for B.1.1.7 detection. We sequenced 212 B.1.1.7 SARS-CoV-2 genomes collected from testing facilities in the U.S. from December 2020 to January 2021. We found that while the fraction of B.1.1.7 among SGTF samples varied by state, detection of the variant increased at a logistic rate similar to those observed elsewhere, with a doubling rate of a little over a week and an increased transmission rate of 35-45%. By performing time-aware Bayesian phylodynamic analyses, we revealed several independent introductions of B.1.1.7 into the U.S. as early as late November 2020, with onward community transmission enabling the variant to spread to at least 30 states as of January 2021. Our study shows that the U.S. is on a similar trajectory as other countries where B.1.1.7 rapidly became the dominant SARS-CoV-2 variant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality.

Identifiers

PMID33564780
PMCPMC7872373

What OpenQuestion holds

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LicenceCC BY-NC
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.