SARS-CoV-2 Variants Associated with Vaccine Breakthrough in the Delaware Valley through Summer 2021
Andrew D. Marques, Scott Sherrill-Mix, J.K. Everett, Shantan Reddy, Pascha Hokama, Aoife M. Roche, Young Sun Hwang, Abigail Glascock, Samantha A. Whiteside, Jevon Graham-Wooten, Layla A. Khatib, Ayannah S. Fitzgerald, Ahmed M. Moustafa, Colleen Bianco, Swetha Rajagopal, Jenna Helton, Regan Deming, Lidiya Denu, Azad Ahmed, Eimear Kitt, Susan Coffin, Claire Newbern, Josh Chang Mell, Paul J. Planet, Nitika Badjatia, Bonnie Richards, Zixuan Wang, Carolyn C. Cannuscio, Katherine M. Strelau, Anne Jaskowiak‐Barr, Leigh Cressman, Sean Loughrey, Arupa Ganguly, Michael D. Feldman, Ronald G. Collman, Kyle G. Rodino, Brendan J. Kelly, Frederic D. Bushman
Abstract
SARS-CoV-2 vaccination is highly effective at reducing viral infection, hospitalization and death. However, vaccine breakthrough infections have been widely observed, raising the question of whether particular viral variants or viral mutations are associated with breakthrough. Here, we report analysis of 2621 surveillance isolates from people diagnosed with COVID-19 in the Delaware Valley in southeastern Pennsylvania, allowing rigorous comparison to 159 vaccine breakthrough case specimens. Our best estimate is a 3-fold enrichment for some lineages of delta among breakthroughs, and enrichment of a notable spike substitution, N501Y. We introduce statistical methods that should be widely useful for evaluating vaccine breakthroughs and other viral phenotypes.