doi: https://doi.org/10.1101/2021.02.06.21251159
Nicole L. Washington
1Helix, San Mateo, CA
Karthik Gangavarapu
2Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
Mark Zeller
2Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
Alexandre Bolze
1Helix, San Mateo, CA
Elizabeth T. Cirulli
1Helix, San Mateo, CA
Kelly M. Schiabor Barrett
1Helix, San Mateo, CA
Brendan B. Larsen
3Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
Catelyn Anderson
2Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
Simon White
1Helix, San Mateo, CA
Tyler Cassens
1Helix, San Mateo, CA
Sharoni Jacobs
1Helix, San Mateo, CA
Geraint Levan
1Helix, San Mateo, CA
Jason Nguyen
1Helix, San Mateo, CA
Jimmy M. Ramirez III
1Helix, San Mateo, CA
Charlotte Rivera-Garcia
1Helix, San Mateo, CA
Efren Sandoval
1Helix, San Mateo, CA
Xueqing Wang
1Helix, San Mateo, CA
David Wong
1Helix, San Mateo, CA
Emily Spencer
2Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
Refugio Robles-Sikisaka
2Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
Ezra Kurzban
2Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
Laura D. Hughes
12Department of Integrative, Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
Xianding Deng
4Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
Candace Wang
4Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
Venice Servellita
4Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
Holly Valentine
5University of California, San Diego, CA
Peter De Hoff
5University of California, San Diego, CA
Phoebe Seaver
5University of California, San Diego, CA
Shashank Sathe
5University of California, San Diego, CA
Kimberly Gietzen
6Illumina, San Diego, CA
Brad Sickler
6Illumina, San Diego, CA
Jay Antico
6Illumina, San Diego, CA
Kelly Hoon
6Illumina, San Diego, CA
Jingtao Liu
6Illumina, San Diego, CA
Aaron Harding
7Sharp Healthcare, San Diego, CA
Omid Bakhtar
7Sharp Healthcare, San Diego, CA
Tracy Basler
8San Diego County Health and Human Services Agency, San Diego, CA
Brett Austin
8San Diego County Health and Human Services Agency, San Diego, CA
Magnus Isaksson
1Helix, San Mateo, CA
Phillip G. Febbo
6Illumina, San Diego, CA
David Becker
1Helix, San Mateo, CA
Marc Laurent
1Helix, San Mateo, CA
Eric McDonald
8San Diego County Health and Human Services Agency, San Diego, CA
Gene W. Yeo
5University of California, San Diego, CA
Rob Knight
5University of California, San Diego, CA
Louise C. Laurent
5University of California, San Diego, CA
Eileen de Feo
6Illumina, San Diego, CA
Michael Worobey
3Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
Charles Chiu
4Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA
9Innovative Genomics Institute, Berkeley, CA
Marc A. Suchard
10Department 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. Lu
1Helix, San Mateo, CA
William Lee
1Helix, San Mateo, CA
Kristian G. Andersen
2Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
11Scripps Research Translational Institute, La Jolla, CA
Summary
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.
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Competing Interest Statement
NLW, AB, ETC, KMSB, SW, CRG, ES, TC, XW, JN, JMR, GL, DW, DB, ML, MI, SJ, JTL, andWL are employees of Helix. KG, BS, JA, KH, JL, EdF, and PGF are employees of Illumina. JN,CRG, ML own stock in ILMN.
Funding Statement
This work has been funded by CDC BAA contracts 75D30121P10258 (Illumina, Helix) and 75D30120C09795 (GWY, RK, LCL, KGA), NIH NIAID 3U19AI135995-03S2 (MAS, KGA), U19AI135995 (MAS, KGA), U01AI151812 (KGA), NIH NCATS UL1TR002550(KGA), the Innovative Genomics Institute (CYC), and the New Frontiers in Research Fund provided by the Canadian Institutes of Health Research (CYC).
Author Declarations
I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.
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Yes
The details of the IRB/oversight body that provided approval or exemption for the research described are given below:
Helix data analyzed and presented here were obtained through IRB protocol WIRB#20203438,which grants a waiver of consent for a limited dataset for the purposes of public health undersection 164.512(b) of the Privacy Rule (45 CFR 164.512(b)). This work was also evaluated andapproved by the Institutional Review Board at The Scripps Research Institute under IRB protocol IRB-15-6664. The work was conducted under a waiver of consent and received a non-human subjects research designation (category 4 exemption) because this research was performed with remnant clinical diagnostic specimens. All samples were de-identified before receipt by the study investigators.
All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.
Yes
I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).
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Yes
I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.
Yes
Data Availability
Raw data and processing scripts are available at https://github.com/andersen-lab/paper_2021_early-b117-usa;Viral sequences have been deposited at GISAID, with accession numbers as listed in Supplemental Tables.;Additionally, continuing monitoring of the phenomena described in the manuscript can be found at https://www.helix.com/covid19db
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