Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons

Chrispin Chaguza, Andreas Coppi, Rebecca Earnest, David Ferguson, Nicholas Kerantzas, Frederick Warner, H. Patrick Young, Mallery I. Breban, Kendall Billig, Robert Tobias Koch, Kien Pham, Chaney C. Kalinich, Isabel M. Ott, Joseph R. Fauver, Anne M. Hahn, Irina R. Tikhonova, Christopher Castaldi, Bony De Kumar, Christian M. Pettker, Joshua L. WarrenDaniel M. Weinberger, Marie L. Landry, David R. Peaper, Wade Schulz, Chantal B.F. Vogels, Nathan D. Grubaugh

Research output: Contribution to journalArticlepeer-review

48 Scopus citations


Background: The SARS-CoV-2 Omicron variant became a global concern due to its rapid spread and displacement of the dominant Delta variant. We hypothesized that part of Omicron's rapid rise was based on its increased ability to cause infections in persons that are vaccinated compared to Delta. Methods: We analyzed nasal swab PCR tests for samples collected between December 12 and 16, 2021, in Connecticut when the proportion of Delta and Omicron variants was relatively equal. We used the spike gene target failure (SGTF) to classify probable Delta and Omicron infections. We fitted an exponential curve to the estimated infections to determine the doubling times for each variant. We compared the test positivity rates for each variant by vaccination status, number of doses, and vaccine manufacturer. Generalized linear models were used to assess factors associated with odds of infection with each variant among persons testing positive for SARS-CoV-2. Findings: For infections with high virus copies (Ct < 30) among vaccinated persons, we found higher odds that they were infected with Omicron compared to Delta, and that the odds increased with increased number of vaccine doses. Compared to unvaccinated persons, we found significant reduction in Delta positivity rates after two (43.4%–49.1%) and three vaccine doses (81.1%), while we only found a significant reduction in Omicron positivity rates after three doses (62.3%). Conclusion: The rapid rise in Omicron infections was likely driven by Omicron's escape from vaccine-induced immunity. Funding: This work was supported by the Centers for Disease Control and Prevention (CDC).

Original languageEnglish (US)
Pages (from-to)325-334.e4
Issue number5
StatePublished - May 13 2022


  • COVID-19 vaccines
  • Delta
  • Omicron
  • SARS-CoV-2
  • Translation to population health
  • epidemiology
  • genomic surveillance

ASJC Scopus subject areas

  • General Medicine


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