SARS-CoV-2 variant Delta rapidly displaced variant Alpha in the United States and led to higher viral loads
Open accessPreprint — published as 10.1016/j.xcrm.2022.100564
Abstract
This study reports on the displacement of Alpha (B.1.1.7) by Delta (B.1.617.2 and its substrains AY.1, AY.2, and AY.3) in the United States. By analyzing RT-qPCR testing results and viral sequencing results of samples collected across the United States, we show that the percentage of SARS-CoV-2 positive cases caused by Alpha dropped from 67% in May 2021 to less than 3.0% in just 10 weeks. We also show that the Delta variant has outcompeted the Iota (B.1.526) variant of interest and Gamma (P.1) variant of concern. An analysis of the mean quantification cycles (Cq) values in positive tests over time also reveal that Delta infections lead to a higher viral load on average compared to Alpha infections, but this increase is only 2 to 3x on average for our study design. Our results are consistent with the hypothesis that the Delta variant is more transmissible than the Alpha variant, and that this could be due to the Delta variant's ability to establish a higher viral load earlier in the infection compared to the Alpha variant.
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By June 2021, the Gamma variant accounted for a high proportion of infections in several South American and Caribbean countries and 10% of US infections.
“By June 2021, the Gamma variant accounted for a high proportion of infections in several South American and Caribbean countries 196 and 10% of US infections 33 .”
From The biological and clinical significance of emerging SARS-CoV-2 variants (2021) · cites this paper as [33]
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BackgroundKhamis, F., Awaidy, S. A., Ba'Omar, M., Osman, W., Chhetri, S., Ambusaid, Z., Fahdi, Z. A., Al-Lawati, J., Sulaimi, K. A., Bulushi, S. A., et al. (2022) · Diseases · doi:10.3390/diseases10040100 · Cited by 4 · see citing works
Lai, E., Becker, D., Brzoska, P., Cassens, T., Davis-Turak, J., Diamond, E., Furtado, M., Gandhi, M., Gort, D., Greninger, A. L., et al. (2022) · medRxiv · doi:10.1101/2022.01.08.22268865 · Cited by 4
Self-citationMutnal, M. B., Johnson, S., Mohamed, N., Abddelgader, R., Morales, L., Volz, M., Walker, K., Arroliga, A. C., & Rao, A. (2021) · Journal of Medical Virology · doi:10.1002/jmv.27373 · Cited by 7 · see citing works
“(12, 13) By 223 July 3, 2021, the delta (B.”
BackgroundBlanchard, A. C., Desforges, M., Labbé, A., Nguyen, C. T., Petit, Y., Besner, D., Zinszer, K., Séguin, O., Laghdir, Z., Adams, K., et al. (2021) · medRxiv · doi:10.1101/2021.10.13.21264960 · Cited by 5 · see citing works
Zhang, Q., Qiao, R., Niu, J., Xiong, X., Wang, N., Zhang, R., Luo, S., Guo, Y.-W., Liu, Z., Peng, L., et al. (2023) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2023.1180297 · Cited by 2 · see citing works
“The Delta variant was first found in India in late 2020 and displaced Alpha as the dominant variant in mid-2021, leading to a resurgence of COVID-19 cases in many countries (Centers for Disease Control and Prevention, 2021; Bolze et al., 2022).”
BackgroundSelf-citationJumamil, R. B., & Rutherford, G. W. (2023) · AJPM Focus · doi:10.1016/j.focus.2023.100075 · Cited by 2
“S.(1) During this time, the Centers for Disease Control and Prevention recognized the San Francisco Bay Area as a hot spot on”
BackgroundArantes, I., Bello, G., do Nascimento, V. A., de Souza, V. C., da Silva, A., Silva, D., Nascimento, F., Mejía, M., Brandão, M. J., Gonçalves, L. M. F., et al. (2022) · medRxiv · doi:10.1101/2022.09.21.22280193 · Cited by 2 · see citing works
“This pattern contrasts with the exponential surge of SARS-CoV-2 cases due to the spread of Delta in Europe, North America, Africa, and Asia (Kupferschmidt & Wadman, 2021; Elliott et al., 2021; Dhar et al., 2021; Cherian et al., 2021; Bolze et al., 2022; Yang & Shaman, 2022; Wadman, 2021).”
ResultHernandez, M., Banu, R., Gonzalez-Reiche, A., Gray, B., Shrestha, P., Cao, L., Chen, F., Shi, H.-Z., Hanna, A., Ramírez, J., et al. (2021) · medRxiv · doi:10.1016/j.jmoldx.2022.04.003 · Cited by 2 · see citing works
Ma, Y., Hu, Y., Xia, B., Du, P., Wu, L., Liang, M., Chen, Q., Yan, H., Gao, G. F., Wang, Q., et al. (2021) · China CDC Weekly · doi:10.46234/ccdcw2021.235 · Cited by 2 · see citing works
Laing, E., Weiss, C., Samuels, E., et al. (2021) · medRxiv · doi:10.1101/2021.10.16.21265087 · Cited by 2
Ayass, M. A., Zhang, J., Zhu, K. J., et al. (2021) · medRxiv · doi:10.1101/2021.09.21.21263898 · Cited by 2 · see citing works
“2, a viral lineage first identified in India was seen as the “greatest threat” in the world’s effort to contain COVID-19 (Bolze et al., 2021).”
BackgroundInfluentialTo Test or Not to Test: COVID-19 Prevention Strategies to Keep Large Gatherings Safe
Estelle, C., & Perl, T. (2021) · Annals of Internal Medicine · doi:10.7326/m21-2976 · Cited by 2
An update on vaccine status and the role of nanomedicine against SARS‐CoV‐2: A narrative review
Tajnur, R., Rezwan, R., Aziz, A., & Islam, M. S. (2023) · Health Science Reports · doi:10.1002/hsr2.1377 · Cited by 1 · see citing works
“While the Delta variant has higher transmissibility, it is not due to vaccine inefficiency but a higher viral load.(101,102) The”
BackgroundErgören, M. Ç., Akan, G., Volkan, E., Kandemiş, E., Evren, E. Ü., Evren, H., Volkan, E., Tuncel, G., Süer, K., & Şanlıdağ, T. (2022) · Journal of Medical Virology · doi:10.1002/jmv.28309 · Cited by 1 · see citing works
“Previous studies showed that infection with the Delta variant was associated with higher infectious virus loads, which enabled it to displace the Alpha variant rapidly.(27,28) Furthermore, shorter presentation of symptoms in Omicron‐infected cases was highlighted as a factor leading to lower infectivity.”
BackgroundRamos, E. M., Rúa, K. A. P., Ayala, C. A., García-Correa, J. F., & Zuluaga, A. F. (2022) · Enfermedades infecciosas y microbiologia clinica (English ed ) · doi:10.1016/j.eimce.2022.10.003 · Cited by 1 · see citing works
Yeung, P.-S., Wang, H., Sibai, M., Solis, D., Yamamoto, F., Iwai, N., Jiang, B., Hammond, N., Truong, B., Bihon, S., et al. (2022) · medRxiv · doi:10.1101/2022.02.07.22270629 · Cited by 1
“46 Importantly, these VOCs differ in their clinical prognosis, transmissibility, antibody susceptibility, and 47 response to vaccination (1-21).”
BackgroundDelta variant of SARS-CoV-2: characteristics and implications for public health in Colombia
Yomayusa, N., Vega, R., Restrepo, A., Morón, L., Vaca, C., & Oñate, J. (2021) · Revista de la Facultad de Medicina · doi:10.15446/revfacmed.v70n1.97460 · Cited by 29 · see citing works
Jiang, M., Akers, N. K., Gill, D. B., Eckhert, B., Svejnoha, E., & Robins, H. S. (2022) · medRxiv · doi:10.1101/2022.07.01.22277108
“Timing of test orders among survey respondents was generally consistent with that of the testing population, with a peak in August and September of 2021 corresponding to the SARS-CoV-2 Delta wave in the US [33,34] (Figure 1A).”
ResultLazović, M., Bojat, V., Vuković, V., Smiljanic, N., Milić, M., Velicki, R., Nikolić, N., Pustahija, T., & Ristić, M. (2022) · Facta Universitatis Series Medicine and Biology · doi:10.22190/fumb220507001l
“In addition, new variants of SARS-CoV-2 are emerging, which are more contagious than the previous ones and against which somewhat lower effectiveness of several vaccines has been observed [9,10,16,17].”
BackgroundPetersen, J. D., Lu, J., Fitzgerald, W., Zhou, F., Blank, P. S., Matthies, D., & Zimmerberg, J. J. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.04.07.487415
“This phenotype is similar to real-world reports of faster initial infection by Delta SARS-CoV-2 [37].”
BackgroundResultSelf-citationEarly emergence phase of SARS-CoV-2 Delta variant in Florida
Cella, E., Ali, S., Schmedes, S., et al. (2022) · medRxiv · doi:10.1101/2022.02.18.22271195
Discovery of nanobodies against SARS-CoV-2 and an uncommon neutralizing mechanismPreprint
Li, T., Zhou, B., Luo, Z., Lai, Y., Huang, S., Zhou, Y., Gautam, A., Bourgeau, S., Wang, S., Bao, J., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.20.453054
- Authors
- Bolze, A., Cirulli, E. T., Luo, S., White, S., Wyman, D., Dei Rossi, A., Machado, H., Cassens, T., Jacobs, S., Schiabor Barrett, K. M., Tsan, K., Nguyen, J., Ramirez, J. M., Sandoval, E., Wang, X., Wong, D., Becker, D., Laurent, M., Lu, J., Isaksson, M., Washington, N. L., & Lee, W.
- Affiliations
- Helix (United States) (US)
- Corresponding author
- Bolze, Alexandre
- Lee, William
- ORCID
- Venue
- Cell Reports Medicine
- Publisher
- openRxiv
- Published
- 2021-06-21
- Volume
- 3
- Issue
- 3
- Pages
- 100564-100564
- ISSN
- 2666-3791 (ISSN-L)
- PMC
- PMC8922438
- OpenAlex
- W4220894005
- Cited by
- 116
- References
- 6
- Citations by year
- 2026: 6 · 2025: 9 · 2024: 15 · 2023: 23 · 2022: 40 · 2021: 22 · 2020: 1
- FWCI
- 7.92
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by-nc-nd
- Locations
- Cell Reports Medicine (publishedVersion, cc-by-nc-nd)
- SSRN Electronic Journal (publishedVersion)
- medRxiv (acceptedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Funders
- Public Health England
- Centers for Disease Control and Prevention
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Physical Sciences › Mathematics › Modeling and Simulation › COVID-19 epidemiological studies
- Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
- Keywords
- SARS-CoV-2, Alpha variant, viral load, transmissibility, COVID-19 pandemic, United States
- MeSH terms
- COVID-19, SARS-CoV-2, Humans, United States, Viral Load
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