CDC reports on genomic surveillance for SARS-CoV-2 variants in the U.S.

June 14, 2021

To respond to emerging SARS-CoV-2 variants, the Centers for Disease Control and Prevention (CDC) rapidly expanded national genomic surveillance to monitor trends in circulating SARS-CoV-2 variants nationally and regionally, as reported in the agency’s Morbidity and Mortality Weekly Report.

Along with efforts to characterize the clinical and public health impact of variants, surveillance can help guide interventions to mitigate the COVID-19 pandemic in the United States by informing prevention strategies (e.g., enhanced vaccination coverage efforts) and clinical management decisions (e.g., monoclonal antibody distribution).

SARS-CoV-2 variants have the potential to affect transmission, disease severity, diagnostics, therapeutics, and natural and vaccine-induced immunity. Robust genomic surveillance can help guide prevention strategies (e.g., enhanced vaccination coverage efforts) and clinical management decisions (e.g., monoclonal antibody distribution) to control the COVID-19 pandemic in the U.S.

CDC’s genomic surveillance for SARS-CoV-2 variants generates population-based estimates of the proportions of variants among all SARS-CoV-2 infections in the U.S. During April 11 to 24, 2021, the B.1.1.7 and P.1 variants represented an estimated 66.0% and 5.0% of U.S. infections, respectively, demonstrating the potential for new variants to emerge and become predominant.

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 Dec. 20, 2020 to May 6, 2021, from 55 U.S. jurisdictions had been generated by or reported to CDC. These included 3,275 sequences for the two-week period ending Jan. 2, 2021, compared with 25,000 sequences for the two-week period ending April 24, 2021 (0.1% and 3.1% of reported positive SARS-CoV-2 tests, respectively).

In December 2020, CDC expanded the volume of SARS-CoV-2 sequencing through contracts with large commercial diagnostic laboratories, which were selected based on geographic coverage and specimen volume. Commercial laboratories submit random samples of geographically diverse sequences with limited demographic data to CDC weekly. Specimen sources for these laboratories include retail pharmacies, community testing sites, and inpatient and outpatient health care settings served by large commercial laboratories; any type of specimen tested for SARS-CoV-2 by reverse transcription–polymerase chain reaction (RT-PCR) may be submitted.

The distribution of circulating SARS-CoV-2 variants in the United States changed rapidly during December 2020 to May 2021. The expansion of the B.1.1.7 VOC to become the predominant variant in all U.S. regions within a four-month period, and the more recent emergence of the P.1 VOC in all regions, underscore the critical need for robust and timely genomic surveillance. These findings are consistent with reports of potential increased transmission of the B.1.1.7 and P.1 variants. In addition, there is evidence of potential impact of B.1.1.7 on diagnostics (i.e., SGTF in at least one RT-PCR–based diagnostic assay) and disease severity and potential impact of P.1 on therapeutics and immunity. Four additional VOIs or VOCs (B.1.526, B.1.526.1, B.1.429, and B.1.427) are estimated to each account for >1% of circulating infections domestically as of the two-week period ending April 24. Currently, there is no variant listed as a VOHC.

CDC has the report.

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