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Delta variants of SARS-CoV-2 cause significantly increased vaccine breakthrough COVID-19 cases in Houston, Texas

2021; Cold Spring Harbor Laboratory; Linguagem: Inglês

10.1101/2021.07.19.21260808

Paul Christensen, Randall J. Olsen, S. Wesley Long, Sishir Subedi, James J. Davis, Parsa Hodjat, Debbie R. Walley, Jacob C. Kinskey, Matthew Ojeda Saavedra, Layne Pruitt, Kristina Reppond, Madison Shyer, Jessica Cambric, Ryan Gadd, Rashi M. Thakur, Akanksha Batajoo, Regan Mangham, Sindy Pena, Trina Trinh, Prasanti Yerramilli, Marcus Nguyen, Robert Olson, Richard Snehal, Jimmy Gollihar, James M. Musser,

vaccines and immunoinformatics approaches

Abstract Genetic variants of SARS-CoV-2 have repeatedly altered the course of the COVID-19 pandemic. Delta variants of concern are now the focus of intense international attention because they are causing widespread COVID-19 disease globally and are associated with vaccine breakthrough cases. We sequenced the genomes of 16,965 SARS-CoV-2 from samples acquired March 15, 2021 through September 20, 2021 in the Houston Methodist hospital system. This sample represents 91% of all Methodist system COVID-19 patients during the study period. Delta variants increased rapidly from late April onward to cause 99.9% of all COVID-19 cases and spread throughout the Houston metroplex. Compared to all other variants combined, Delta caused a significantly higher rate of vaccine breakthrough cases (23.7% for Delta compared to 6.6% for all other variants combined). Importantly, significantly fewer fully vaccinated individuals required hospitalization. Individuals with vaccine breakthrough cases caused by Delta had a low median PCR cycle threshold (Ct) value (a proxy for high virus load). This value was closely similar to the median Ct value for unvaccinated patients with COVID-19 caused by Delta variants, suggesting that fully vaccinated individuals can transmit SARS-CoV-2 to others. Patients infected with Alpha and Delta variants had several significant differences. Our integrated analysis emphasizes that vaccines used in the United States are highly effective in decreasing severe COVID-19 disease, hospitalizations, and deaths.