Early introductions and transmission of SARS-CoV-2 variant B.1.1.7 in the United States

Tara Alpert; Anderson F Brito; Erica Lasek-Nesselquist; Jessica Rothman; Andrew L Valesano; Matthew J MacKay; Mary E Petrone; Mallery I Breban; Anne E Watkins; Chantal B F Vogels; Chaney C Kalinich; Simon Dellicour; Alexis Russell; John P Kelly; Matthew Shudt; Jonathan Plitnick; Erasmus Schneider; William J Fitzsimmons; Gaurav Khullar; Jessica Metti; Joel T Dudley; Megan Nash; Nike Beaubier; Jianhui Wang; Chen Liu; Pei Hui; Anthony Muyombwe; Randy Downing; Jafar Razeq; Stephen M Bart; Ardath Grills; Stephanie M Morrison; Steven Murphy; Caleb Neal; Eva Laszlo; Hanna Rennert; Melissa Cushing; Lars Westblade; Priya Velu; Arryn Craney; Lin Cong; David R Peaper; Marie L Landry; Peter W Cook; Joseph R Fauver; Christopher E Mason; Adam S Lauring; Kirsten St George; Duncan R MacCannell; Nathan D Grubaugh

doi:10.1016/j.cell.2021.03.061

Early introductions and transmission of SARS-CoV-2 variant B.1.1.7 in the United States

Cell. 2021 May 13;184(10):2595-2604.e13. doi: 10.1016/j.cell.2021.03.061. Epub 2021 Apr 3.

Authors

Tara Alpert¹, Anderson F Brito¹, Erica Lasek-Nesselquist², Jessica Rothman¹, Andrew L Valesano³, Matthew J MacKay⁴, Mary E Petrone¹, Mallery I Breban¹, Anne E Watkins¹, Chantal B F Vogels¹, Chaney C Kalinich¹, Simon Dellicour⁵, Alexis Russell⁶, John P Kelly⁶, Matthew Shudt², Jonathan Plitnick², Erasmus Schneider², William J Fitzsimmons³, Gaurav Khullar⁴, Jessica Metti⁴, Joel T Dudley⁴, Megan Nash⁴, Nike Beaubier⁴, Jianhui Wang⁷, Chen Liu⁷, Pei Hui⁷, Anthony Muyombwe⁸, Randy Downing⁸, Jafar Razeq⁸, Stephen M Bart⁹, Ardath Grills¹⁰, Stephanie M Morrison¹⁰, Steven Murphy¹¹, Caleb Neal¹¹, Eva Laszlo¹¹, Hanna Rennert¹², Melissa Cushing¹², Lars Westblade¹², Priya Velu¹², Arryn Craney¹², Lin Cong¹², David R Peaper¹³, Marie L Landry¹³, Peter W Cook¹⁰, Joseph R Fauver¹, Christopher E Mason¹⁴, Adam S Lauring³, Kirsten St George¹⁵, Duncan R MacCannell¹⁶, Nathan D Grubaugh¹⁷

Affiliations

¹ Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA.
² Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA; Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA.
³ Department of Internal Medicine, Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA.
⁴ Tempus Labs, Chicago, IL 60654, USA.
⁵ Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Bruxelles, Belgium; Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
⁶ Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA.
⁷ Department of Pathology, Yale University School of Medicine, New Haven, CT 06510, USA.
⁸ Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA.
⁹ Connecticut State Department of Public Health, Rocky Hill, CT 06067, USA; Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.
¹⁰ Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.
¹¹ Murphy Medical Associates, Greenwich, CT 06830, USA.
¹² Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA.
¹³ Departments of Laboratory Medicine and of Medicine, Yale School of Medicine, New Haven, CT 06510, USA.
¹⁴ Tempus Labs, Chicago, IL 60654, USA; Department of Pathology and Laboratory Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY 10021, USA.
¹⁵ Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA; Department of Biomedical Sciences, University at Albany, SUNY, Albany, NY 12222, USA. Electronic address: [email protected].
¹⁶ Centers for Disease Control and Prevention, Atlanta, GA 30329, USA. Electronic address: [email protected].
¹⁷ Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06510, USA. Electronic address: [email protected].

Abstract

The emergence and spread of SARS-CoV-2 lineage B.1.1.7, first detected in the United Kingdom, has become a global public health concern because of its increased transmissibility. Over 2,500 COVID-19 cases associated with this variant have been detected in the United States (US) since December 2020, but the extent of establishment is relatively unknown. Using travel, genomic, and diagnostic data, we highlight that the primary ports of entry for B.1.1.7 in the US were in New York, California, and Florida. Furthermore, we found evidence for many independent B.1.1.7 establishments starting in early December 2020, followed by interstate spread by the end of the month. Finally, we project that B.1.1.7 will be the dominant lineage in many states by mid- to late March. Thus, genomic surveillance for B.1.1.7 and other variants urgently needs to be enhanced to better inform the public health response.

Keywords: B.1.1.7; SARS-CoV-2; community transmission; epidemiology; flight volumes; genomic surveillance; introductions; lineage; phylogenetics; variant.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

COVID-19 Testing*
COVID-19* / genetics
COVID-19* / mortality
COVID-19* / transmission
Female
Humans
Male
Models, Biological*
SARS-CoV-2* / genetics
SARS-CoV-2* / metabolism
SARS-CoV-2* / pathogenicity
United States / epidemiology

Abstract

Publication types

MeSH terms

Grants and funding