Top 5 Takeaways

1. Expansion of Genomic Surveillance: CDC expanded its genomic surveillance to include data from public repositories and produce weighted estimates of variant proportions at the jurisdiction level.
2. Delta Variant Predominance: The Delta variant rose to predominance in late June 2021, accounting for over 50% of circulating viral lineages within 8 weeks.
3. Rapid Rise of Omicron: The Omicron variant rapidly increased from 1% to over 50% of circulating viral lineages in just 2 weeks in December 2021.
4. Omicron’s Dominance: By the week ending January 22, 2022, Omicron accounted for 99.2% of SARS-CoV-2 infections nationwide.
5. Importance of Genomic Surveillance: The dynamic landscape of SARS-CoV-2 variants underscores the need for robust genomic surveillance to inform public health planning and practice.

Original Article Author and Citation

Corresponding Author

Anastasia S. Lambrou, rix6@cdc.gov

Suggested Citation

Lambrou AS, Shirk P, Steele MK, et al. Genomic Surveillance for SARS-CoV-2 Variants: Predominance of the Delta (B.1.617.2) and Omicron (B.1.1.529) Variants — United States, June 2021–January 2022. MMWR Morb Mortal Wkly Rep 2022;71:206–211. DOI: http://dx.doi.org/10.15585/mmwr.mm7106a4

Summary

CDC expanded its genomic surveillance for SARS-CoV-2 to include data from public repositories, producing weighted estimates of variant proportions at the jurisdiction level. The Delta variant became predominant in late June 2021, followed by the rapid rise of the Omicron variant in December 2021. By January 2022, Omicron accounted for 99.2% of SARS-CoV-2 infections nationwide. These findings highlight the importance of robust genomic surveillance to inform public health planning and practice.

Methods

CDC’s genomic surveillance program integrates data from the National SARS-CoV-2 Strain Surveillance (NS3) program, CDC-contracted commercial sequencing data, and sequences from public health, academic, and clinical laboratories. The data are combined, assessed for quality, deduplicated, and analyzed to estimate variant proportions at national, regional, and jurisdictional levels. Weighted estimates correct potential biases, and multinomial regression models are used to nowcast variant proportions.

Discussion

The report highlights the changing landscape of SARS-CoV-2 variants in 2021, with Delta and Omicron driving major surges in COVID-19 cases. The rapid rise of Omicron, driven by increased transmissibility and immune escape, underscores the need for ongoing genomic surveillance to monitor emerging variants and inform public health responses.

Conclusion

CDC’s expanded genomic surveillance has improved the timeliness and accuracy of variant proportion estimates, enhancing public health planning and practice. Continued surveillance is essential to monitor emerging variants and promptly inform public health interventions.

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