Vaccines (May 2024)
Antigenic Characterization of Circulating and Emerging SARS-CoV-2 Variants in the U.S. throughout the Delta to Omicron Waves
- Han Di,
- Elizabeth A. Pusch,
- Joyce Jones,
- Nicholas A. Kovacs,
- Norman Hassell,
- Mili Sheth,
- Kelly Sabrina Lynn,
- Matthew W. Keller,
- Malania M. Wilson,
- Lisa M. Keong,
- Dan Cui,
- So Hee Park,
- Reina Chau,
- Kristine A. Lacek,
- Jimma D. Liddell,
- Marie K. Kirby,
- Genyan Yang,
- Monique Johnson,
- Sharmi Thor,
- Natosha Zanders,
- Chenchen Feng,
- Diya Surie,
- Jennifer DeCuir,
- Sandra N. Lester,
- Lydia Atherton,
- Heather Hicks,
- Azaibi Tamin,
- Jennifer L. Harcourt,
- Melissa M. Coughlin,
- Wesley H. Self,
- Jillian P. Rhoads,
- Kevin W. Gibbs,
- David N. Hager,
- Nathan I. Shapiro,
- Matthew C. Exline,
- Adam S. Lauring,
- Benjamin Rambo-Martin,
- Clinton R. Paden,
- Rebecca J. Kondor,
- Justin S. Lee,
- John R. Barnes,
- Natalie J. Thornburg,
- Bin Zhou,
- David E. Wentworth,
- Charles Todd Davis
Affiliations
- Han Di
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Elizabeth A. Pusch
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Joyce Jones
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Nicholas A. Kovacs
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Norman Hassell
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Mili Sheth
- Division of Core Laboratory Services and Response, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Kelly Sabrina Lynn
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Matthew W. Keller
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Malania M. Wilson
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Lisa M. Keong
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Dan Cui
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- So Hee Park
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Reina Chau
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Kristine A. Lacek
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Jimma D. Liddell
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Marie K. Kirby
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Genyan Yang
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Monique Johnson
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Sharmi Thor
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Natosha Zanders
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Chenchen Feng
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Diya Surie
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Jennifer DeCuir
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Sandra N. Lester
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Lydia Atherton
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Heather Hicks
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Azaibi Tamin
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Jennifer L. Harcourt
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Melissa M. Coughlin
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Wesley H. Self
- Vanderbilt Institute for Clinical & Translational Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Jillian P. Rhoads
- Vanderbilt Institute for Clinical & Translational Research, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Kevin W. Gibbs
- Department of Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
- David N. Hager
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Nathan I. Shapiro
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
- Matthew C. Exline
- Department of Medicine, The Ohio State University, Columbus, OH 43210, USA
- Adam S. Lauring
- Departments of Internal Medicine and Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
- Benjamin Rambo-Martin
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Clinton R. Paden
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Rebecca J. Kondor
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Justin S. Lee
- Division of Core Laboratory Services and Response, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- John R. Barnes
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Natalie J. Thornburg
- Coronavirus and Other Respiratory Viruses Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Bin Zhou
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- David E. Wentworth
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- Charles Todd Davis
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
- DOI
- https://doi.org/10.3390/vaccines12050505
- Journal volume & issue
-
Vol. 12,
no. 5
p. 505
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into numerous lineages with unique spike mutations and caused multiple epidemics domestically and globally. Although COVID-19 vaccines are available, new variants with the capacity for immune evasion continue to emerge. To understand and characterize the evolution of circulating SARS-CoV-2 variants in the U.S., the Centers for Disease Control and Prevention (CDC) initiated the National SARS-CoV-2 Strain Surveillance (NS3) program and has received thousands of SARS-CoV-2 clinical specimens from across the nation as part of a genotype to phenotype characterization process. Focus reduction neutralization with various antisera was used to antigenically characterize 143 SARS-CoV-2 Delta, Mu and Omicron subvariants from selected clinical specimens received between May 2021 and February 2023, representing a total of 59 unique spike protein sequences. BA.4/5 subvariants BU.1, BQ.1.1, CR.1.1, CQ.2 and BA.4/5 + D420N + K444T; BA.2.75 subvariants BM.4.1.1, BA.2.75.2, CV.1; and recombinant Omicron variants XBF, XBB.1, XBB.1.5 showed the greatest escape from neutralizing antibodies when analyzed against post third-dose original monovalent vaccinee sera. Post fourth-dose bivalent vaccinee sera provided better protection against those subvariants, but substantial reductions in neutralization titers were still observed, especially among BA.4/5 subvariants with both an N-terminal domain (NTD) deletion and receptor binding domain (RBD) substitutions K444M + N460K and recombinant Omicron variants. This analysis demonstrated a framework for long-term systematic genotype to antigenic characterization of circulating and emerging SARS-CoV-2 variants in the U.S., which is critical to assessing their potential impact on the effectiveness of current vaccines and antigen recommendations for future updates.
Keywords
- SARS-CoV-2
- COVID-19 vaccine
- Delta variant
- Omicron variant
- antigenic characterization
- neutralizing antibody
