Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Feb;192(2):320-331.
doi: 10.1016/j.ajpath.2021.10.019. Epub 2021 Nov 11.

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

Paul A Christensen  1 , Randall J Olsen  1 , S Wesley Long  1 , Sishir Subedi  2 , James J Davis  3 , Parsa Hodjat  2 , Debbie R Walley  2 , Jacob C Kinskey  2 , Matthew Ojeda Saavedra  2 , Layne Pruitt  2 , Kristina Reppond  2 , Madison N Shyer  2 , Jessica Cambric  2 , Ryan Gadd  2 , Rashi M Thakur  2 , Akanksha Batajoo  2 , Regan Mangham  2 , Sindy Pena  2 , Trina Trinh  2 , Prasanti Yerramilli  2 , Marcus Nguyen  3 , Robert Olson  3 , Richard Snehal  2 , Jimmy Gollihar  4 , James M Musser  5
Affiliations

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

Paul A Christensen et al. Am J Pathol. 2022 Feb.

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.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Epidemiologic curve showing four coronavirus disease 2019 (COVID-19) waves in Houston Methodist patients. Number of new COVID-19 cases (y axis) totals are shown as a ±3-day moving average. Each of the four waves is shown in a different color simply as a stylistic device. The first and second waves were composed of a heterogeneous array of severe acute respiratory syndrome coronavirus 2 genotypes. The Alpha variant shown in the third wave and the Delta variant shown in the fourth wave indicate their numeric prominence in those waves and should not be interpreted to mean that all cases in the third and fourth waves were caused by Alpha and Delta variants of concern, respectively. The fourth wave shown includes data through September 20, 2021. The figure was generated with Tableau version 2020.3.4 (Tableau Software, LLC). The curve mirrors that of disease activity in metropolitan Houston, Texas.
Figure 2
Figure 2
Increase in Delta frequency over time and distribution in metropolitan Houston. The study time frame was March 15, 2021, through September 20, 2021. A: Cumulative increase in Delta during the study period; y axis is the cumulative number of new coronavirus disease 2019 cases. At the end of the study period, Delta continuously caused 99.9% of all cases of coronavirus disease 2019. B–E: Geospatial distribution of Delta based on home address zip code for each patient. B: April 15 to May 15. C: April 15 to June 15. D: April 15 to July 15. E: April 15 to August 15. F: April 15 to September 20. Note differences in heat map scale for each panel. Figures were generated by using Tableau version 2020.3.4.
Figure 3
Figure 3
Structural changes present in spike protein of the seven most abundant Delta subvariants identified in the study. The numbers denote the number of patients with each subvariant identified in this study. These seven subvariants represent 73% of the 13,043 Delta samples identified in the study. The figure includes all subvariants represented by at least 100 samples. Data presented in this image build on information that has been previously published., S1, S1 domain; S2, S2 domain; S1-NTD, S1 domain-aminoterminal domain; S1-RBD, S1 domain-receptor binding domain.
Figure 4
Figure 4
Lambda and Mu variants identified in metropolitan Houston in our patient population. A: Cumulative increase in the cases caused by Lambda variants identified in the study. B: Geospatial distribution of these Lambda variants based on the home address zip code for each patient. C: Cumulative increase in cases caused by the Mu variants identified in the study. D: Geospatial distribution of the Mu variants based on the home address zip code for each patient. Figures were generated by using Tableau version 2020.3.4.
See this image and copyright information in PMC

References

    1. Dhar M.S., Marwal R., Radhakrishnan V., Ponnusamy K., Jolly B., Bhoyar R.C., et al. Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India. medRxiv. 2021 doi: 10.1101/2021.06.02.21258076. [Preprint] doi: - DOI - PMC - PubMed
    1. Hacisuleyman E., Hale C., Saito Y., Blachere N.E., Bergh M., Conlon E.G., Schaefer-Babajew D.J., DaSilva J., Muecksch F., Gaebler C., Lifton R., Nussenzweig M.C., Hatziioannou T., Bieniasz P.D., Darnell R.B. Vaccine breakthrough infections with SARS-CoV-2 variants. N Engl J Med. 2021;384:2212–2218. - PMC - PubMed
    1. Brosh-Nissimov T., Orenbuch-Harroch E., Chowers M., Elbaz M., Nesher L., Stein M., Maor Y., Cohen R., Hussein K., Weinberger M., Zimhony O., Chazan B., Najjar R., Zayyad H., Rahav G., Wiener-Well Y. BNT162b2 vaccine breakthrough: clinical characteristics of 152 fully-vaccinated hospitalized COVID-19 patients in Israel. Clin Microbiol Infect. 2021;27:1652–1657. - PMC - PubMed
    1. CDC COVID-19 Vaccine Breakthrough Case Investigations Team. Birhane M., Bressler, et al. COVID-19 vaccine breakthrough infections reported to CDC—United States, January 1-April 30, 2021. MMWR Morb Mortal Wkly Rep. 2021;70:792–793. - PMC - PubMed
    1. Kustin T., Harel N., Finkel U., Perchik S., Harari S., Tahor M., Caspi I., Levy R., Leshchinsky M., Dror S.K., Bergerzon G., Gadban H., Gadban F., Eliassian E., Shimron O., Saleh L., Ben-Zvi H., Taraday E.K., Amichay D., Ben-Dor A., Sagas D., Strauss M., Shemer Avni Y., Huppert A., Kepten E., Balicer R.D., Netzer D., Ben-Shachar S., Stern A. Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2-mRNA-vaccinated individuals. Nat Med. 2021;27:1379–1384. - PMC - PubMed

Publication types

Substances

Supplementary concepts