@article{99173e0a9f2a487f9c9effdb2bbceed2,
title = "Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons",
abstract = "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).",
keywords = "COVID-19 vaccines, Delta, Omicron, SARS-CoV-2, Translation to population health, epidemiology, genomic surveillance",
author = "Chrispin Chaguza and Andreas Coppi and Rebecca Earnest and David Ferguson and Nicholas Kerantzas and Frederick Warner and Young, {H. Patrick} and Breban, {Mallery I.} and Kendall Billig and Koch, {Robert Tobias} and Kien Pham and Kalinich, {Chaney C.} and Ott, {Isabel M.} and Fauver, {Joseph R.} and Hahn, {Anne M.} and Tikhonova, {Irina R.} and Christopher Castaldi and {De Kumar}, Bony and Pettker, {Christian M.} and Warren, {Joshua L.} and Weinberger, {Daniel M.} and Landry, {Marie L.} and Peaper, {David R.} and Wade Schulz and Vogels, {Chantal B.F.} and Grubaugh, {Nathan D.}",
note = "Funding Information: We would like to thank the Yale New Haven Health COVID-19 testing enterprise for collecting and testing samples and all of the health care workers supporting patients during the “Omicron surge.” This work was supported by CTSA Grant Number TL1 TR001864 (R.E.), Fast Grant from Emergent Ventures at the Mercatus Center at George Mason University (N.D.G.), and the Centers for Disease Control and Prevention (CDC) Broad Agency Announcement # 75D30120C09570 (N.D.G.). Funding Information: We would like to thank the Yale New Haven Health COVID-19 testing enterprise for collecting and testing samples and all of the health care workers supporting patients during the “Omicron surge.” This work was supported by CTSA Grant Number TL1 TR001864 (R.E.), Fast Grant from Emergent Ventures at the Mercatus Center at George Mason University (N.D.G.), and the Centers for Disease Control and Prevention (CDC) Broad Agency Announcement # 75D30120C09570 (N.D.G.). C.C. J.L.W. D.M.W. W.S. C.B.F.V. and N.D.G. conceived the study; A.C. R.E. D.F. N.K. F.H. H.P.Y. W.S. and N.D.G. collected the data and/or samples; C.M.P. M.L.L. and D.R.P. supervised the testing labs; M.I.B. K.B. R.T.K. K.P. I.M.O. J.R.F. I.R.T. C.C. B.D.K. C.B.F.V. and N.D.G. performed the sequencing and analysis; C.C. A.C. R.E. J.L.W. and D.M.W. designed the analysis methods and/or analyzed the data; C.C.K. and N.D.G. wrote the IRB protocol; C.C. R.E. A.M.H. C.B.F.V. and N.D.G. drafted the manuscript; All authors reviewed and approved the manuscript; N.D.G. secured funds for the project; W.S. C.B.F.V. and N.D.G. supervised the project. N.D.G. is a consultant for Tempus Labs and the National Basketball Association for work related to COVID-19 but is outside the submitted work. All other authors declare no competing interests. Publisher Copyright: {\textcopyright} 2022 Elsevier Inc.",
year = "2022",
month = may,
day = "13",
doi = "10.1016/j.medj.2022.03.010",
language = "English (US)",
volume = "3",
pages = "325--334.e4",
journal = "Med",
issn = "2666-6359",
publisher = "Cell Press",
number = "5",
}