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. 2021 Jun 11;70(23):846-850.
doi: 10.15585/mmwr.mm7023a3.

Genomic Surveillance for SARS-CoV-2 Variants Circulating in the United States, December 2020-May 2021

Prabasaj Paul, Anne Marie France, Yutaka Aoki, Dhwani Batra, Matthew Biggerstaff, Vivien Dugan, Summer Galloway, Aron J Hall, Michael A Johansson, Rebecca J Kondor, Alison Laufer Halpin, Brian Lee, Justin S Lee, Brandi Limbago, Adam MacNeil, Duncan MacCannell, Clinton R Paden, Krista Queen, Heather E Reese, Adam C Retchless, Rachel B Slayton, Molly Steele, Suxiang Tong, Maroya S Walters, David E Wentworth, Benjamin J Silk

Genomic Surveillance for SARS-CoV-2 Variants Circulating in the United States, December 2020-May 2021

Prabasaj Paul et al. MMWR Morb Mortal Wkly Rep. .

Abstract

SARS-CoV-2, the virus that causes COVID-19, is constantly mutating, leading to new variants (1). Variants have the potential to affect transmission, disease severity, diagnostics, therapeutics, and natural and vaccine-induced immunity. In November 2020, CDC established national surveillance for SARS-CoV-2 variants using genomic sequencing. As of May 6, 2021, sequences from 177,044 SARS-CoV-2-positive specimens collected during December 20, 2020-May 6, 2021, from 55 U.S. jurisdictions had been generated by or reported to CDC. These included 3,275 sequences for the 2-week period ending January 2, 2021, compared with 25,000 sequences for the 2-week period ending April 24, 2021 (0.1% and 3.1% of reported positive SARS-CoV-2 tests, respectively). Because sequences might be generated by multiple laboratories and sequence availability varies both geographically and over time, CDC developed statistical weighting and variance estimation methods to generate population-based estimates of the proportions of identified variants among SARS-CoV-2 infections circulating nationwide and in each of the 10 U.S. Department of Health and Human Services (HHS) geographic regions.* During the 2-week period ending April 24, 2021, the B.1.1.7 and P.1 variants represented an estimated 66.0% and 5.0% of U.S. SARS-CoV-2 infections, respectively, demonstrating the rise to predominance of the B.1.1.7 variant of concern† (VOC) and emergence of the P.1 VOC in the United States. Using SARS-CoV-2 genomic surveillance methods to analyze surveillance data produces timely population-based estimates of the proportions of variants circulating nationally and regionally. Surveillance findings demonstrate the potential for new variants to emerge and become predominant, and the importance of robust genomic surveillance. Along with efforts to characterize the clinical and public health impact of SARS-CoV-2 variants, surveillance can help guide interventions to control the COVID-19 pandemic in the United States.

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Conflict of interest statement

All authors have completed and submitted the International Committee of Medical Journal Editors form for disclosure of potential conflicts of interest. No potential conflicts of interest were disclosed.

Figures

FIGURE
FIGURE
Number of SARS-CoV-2 genomic sequences generated by National SARS-CoV-2 Strain Surveillance or reported to CDC by commercial laboratories for specimens collected December 20, 2020—May 6, 2021, by laboratory source — United States, May 6, 2021 Abbreviation: NS3 = National SARS-CoV-2 Strain Surveillance * Sequences generated by or reported to CDC through NS3 and contract laboratories do not include the >5,000 sequences per week produced by public health laboratories and other U.S. institutions, which are not currently integrated into CDC’s surveillance for SARS-CoV-2 variants using genomic sequencing. https://covid.cdc.gov/covid-data-tracker/#published-covid-sequences
See this image and copyright information in PMC

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