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The American journal of pathology
02, 2022;192 (2): 320-331.

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 Yerramilli, Marcus Nguyen, Robert Olson, Richard Snehal, Jimmy Gollihar, James M Musser
Author Information
  1. Paul A Christensen: Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York.
  2. Randall J Olsen: Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York.
  3. S Wesley Long: Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York.
  4. Sishir Subedi: Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.
  5. James J Davis: Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois.
  6. Parsa Hodjat: Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.
  7. Debbie R Walley: Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.
  8. Jacob C Kinskey: Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.
  9. Matthew Ojeda Saavedra: Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.
  10. Layne Pruitt: Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.
  11. Kristina Reppond: Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.
  12. Madison N Shyer: Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.
  13. Jessica Cambric: Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.
  14. Ryan Gadd: Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.
  15. Rashi M Thakur: Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.
  16. Akanksha Batajoo: Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.
  17. Regan Mangham: Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.
  18. Sindy Pena: Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.
  19. Trina Trinh: Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.
  20. Prasanti Yerramilli: Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.
  21. Marcus Nguyen: Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois.
  22. Robert Olson: Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois; Computing, Environment and Life Sciences, Argonne National Laboratory, Lemont, Illinois.
  23. Richard Snehal: Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas.
  24. Jimmy Gollihar: Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; DEVCOM Army Research Laboratory-South, Austin, Texas.
  25. James M Musser: Laboratory of Human Molecular and Translational Human Infectious Diseases, Center for Infectious Diseases, Houston Methodist Research Institute and Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, Texas; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York. Electronic address: jmmusser@houstonmethodist.org.
PMID: 34774517 DOI: 10.1016/j.ajpath.2021.10.019

Abstract

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.

References

  1. Infect Genet Evol. 2021 Nov;95:105038 [PMID: 34403832]
  2. Lancet. 2021 Jan 9;397(10269):99-111 [PMID: 33306989]
  3. N Engl J Med. 2021 Jul 8;385(2):187-189 [PMID: 33951357]
  4. Am J Pathol. 2021 Jun;191(6):983-992 [PMID: 33741335]
  5. Microbiol Spectr. 2021 Oct 31;9(2):e0078921 [PMID: 34704780]
  6. N Engl J Med. 2021 Apr 15;384(15):1412-1423 [PMID: 33626250]
  7. Nature. 2021 Aug;596(7871):276-280 [PMID: 34237773]
  8. Clin Infect Dis. 2022 May 3;74(9):1515-1524 [PMID: 34358310]
  9. MMWR Morb Mortal Wkly Rep. 2021 Aug 06;70(31):1059-1062 [PMID: 34351882]
  10. Nature. 2021 Apr;592(7853):277-282 [PMID: 33545711]
  11. Science. 2021 Nov 19;374(6570):995-999 [PMID: 34648303]
  12. Lancet. 2021 Jun 26;397(10293):2461-2462 [PMID: 34139198]
  13. N Engl J Med. 2021 Dec 9;385(24):e85 [PMID: 34706170]
  14. Cell. 2021 May 13;184(10):2605-2617.e18 [PMID: 33831372]
  15. N Engl J Med. 2021 Jun 10;384(23):2212-2218 [PMID: 33882219]
  16. N Engl J Med. 2021 Dec 16;385(25):2397-2399 [PMID: 34731554]
  17. PLoS Pathog. 2022 Sep 30;18(9):e1010876 [PMID: 36178969]
  18. Clin Infect Dis. 2021 Aug 2;73(3):e815-e821 [PMID: 33507235]
  19. Clin Microbiol Infect. 2022 Apr;28(4):612.e1-612.e7 [PMID: 34826623]
  20. Nat Med. 2021 Aug;27(8):1379-1384 [PMID: 34127854]
  21. MMWR Morb Mortal Wkly Rep. 2021 May 28;70(21):792-793 [PMID: 34043615]
  22. N Engl J Med. 2021 Feb 4;384(5):403-416 [PMID: 33378609]
  23. J Infect Dis. 2022 Apr 1;225(7):1118-1123 [PMID: 34940844]
  24. J Med Virol. 2021 Dec;93(12):6845-6849 [PMID: 34370324]
  25. Microbiol Spectr. 2021 Dec 22;9(3):e0180321 [PMID: 34878296]
  26. Am J Pathol. 2021 Oct;191(10):1754-1773 [PMID: 34303698]
  27. Clin Microbiol Infect. 2021 Nov;27(11):1652-1657 [PMID: 34245907]
  28. N Engl J Med. 2021 Aug 12;385(7):585-594 [PMID: 34289274]
  29. J Infect Dis. 2021 Jan 4;223(1):23-27 [PMID: 33089317]
  30. N Engl J Med. 2021 Oct 14;385(16):1474-1484 [PMID: 34320281]
  31. N Engl J Med. 2020 Dec 3;383(23):2291-2293 [PMID: 33176080]
  32. N Engl J Med. 2020 Dec 31;383(27):2603-2615 [PMID: 33301246]

Grants

  1. 75N93019C00076/NIAID NIH HHS

MeSH Term

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

Chemicals

COVID-19 Vaccines
Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't
Article has an altmetric score of 25

Word Cloud

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