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

  • Author(s): Washington, Nicole L;
  • Gangavarapu, Karthik;
  • Zeller, Mark;
  • Bolze, Alexandre;
  • Cirulli, Elizabeth T;
  • Schiabor Barrett, Kelly M;
  • Larsen, Brendan B;
  • Anderson, Catelyn;
  • White, Simon;
  • Cassens, Tyler;
  • Jacobs, Sharoni;
  • Levan, Geraint;
  • Nguyen, Jason;
  • Ramirez, Jimmy M;
  • Rivera-Garcia, Charlotte;
  • Sandoval, Efren;
  • Wang, Xueqing;
  • Wong, David;
  • Spencer, Emily;
  • Robles-Sikisaka, Refugio;
  • Kurzban, Ezra;
  • Hughes, Laura D;
  • Deng, Xianding;
  • Wang, Candace;
  • Servellita, Venice;
  • Valentine, Holly;
  • De Hoff, Peter;
  • Seaver, Phoebe;
  • Sathe, Shashank;
  • Gietzen, Kimberly;
  • Sickler, Brad;
  • Antico, Jay;
  • Hoon, Kelly;
  • Liu, Jingtao;
  • Harding, Aaron;
  • Bakhtar, Omid;
  • Basler, Tracy;
  • Austin, Brett;
  • Isaksson, Magnus;
  • Febbo, Phil;
  • Becker, David;
  • Laurent, Marc;
  • McDonald, Eric;
  • Yeo, Gene W;
  • Knight, Rob;
  • Laurent, Louise C;
  • de Feo, Eileen;
  • Worobey, Michael;
  • Chiu, Charles;
  • Suchard, Marc A;
  • Lu, James T;
  • Lee, William;
  • Andersen, Kristian G
  • et al.
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.

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