Delta Variants of SARS-CoV-2 Cause Significantly Increased Vaccine Breakthrough COVID-19 Cases in Houston, Texas

Paul A. 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 N. Shyer, Jessica Cambric, Ryan Gadd, Rashi M. Thakur, Akanksha Batajoo, Regan Mangham, Sindy Pena, Trina Trinh, Prasanti YerramilliMarcus Nguyen, Robert Olson, Richard Snehal, Jimmy Gollihar, James M. Musser

Research output: Contribution to journalArticlepeer-review

65 Scopus citations


Genetic variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have repeatedly altered the course of the coronavirus disease 2019 (COVID-19) pandemic. Delta variants are now the focus of intense international attention because they are causing widespread COVID-19 globally and are associated with vaccine breakthrough cases. We sequenced 16,965 SARS-CoV-2 genomes 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 with all other variants combined, Delta caused a significantly higher rate of vaccine breakthrough cases (23.7% for Delta compared with 6.6% for all other variants combined). Importantly, significantly fewer fully vaccinated individuals required hospitalization. Vaccine breakthrough cases caused by Delta had a low median PCR cycle threshold value (a proxy for high virus load). This value was similar to the median cycle threshold 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. The integrated analysis indicates that vaccines used in the United States are highly effective in decreasing severe COVID-19, hospitalizations, and deaths.

Original languageEnglish (US)
Pages (from-to)320-331
Number of pages12
JournalAmerican Journal of Pathology
Issue number2
StatePublished - Feb 2022


  • Adult
  • COVID-19/virology
  • COVID-19 Vaccines
  • Female
  • Humans
  • Male
  • Middle Aged
  • SARS-CoV-2
  • Texas

ASJC Scopus subject areas

  • Pathology and Forensic Medicine


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