SARS-CoV-2 variant Delta rapidly displaced variant Alpha in the United States and led to higher viral loads

Alexandre Bolze; Shishi Luo; Simon White; Elizabeth T. Cirulli; Dana Wyman; Andrew Dei Rossi; Henrique Machado; Tyler Cassens; Sharoni Jacobs; Kelly M. Schiabor Barrett; Francisco Tanudjaja; Kevin Tsan; Jason Nguyen; Jimmy M. Ramirez; Efren Sandoval; Xueqing Wang; David Wong; David Becker; Marc Laurent; James T. Lu; Magnus Isaksson; Nicole L. Washington; William Lee

doi:10.1016/j.xcrm.2022.100564

SARS-CoV-2 variant Delta rapidly displaced variant Alpha in the United States and led to higher viral loads

Alexandre Bolze, Shishi Luo, Simon White, Elizabeth T. Cirulli, Dana Wyman, Andrew Dei Rossi, Henrique Machado, Tyler Cassens, Sharoni Jacobs, Kelly M. Schiabor Barrett, Francisco Tanudjaja, Kevin Tsan, Jason Nguyen, Jimmy M. Ramirez, Efren Sandoval, Xueqing Wang, David Wong, David Becker, Marc Laurent, James T. LuMagnus Isaksson, Nicole L. Washington, William Lee

Research output: Contribution to journal › Article › peer-review

52 Scopus citations

Abstract

We report on the sequencing of 74,348 SARS-CoV-2 positive samples collected across the United States and show that the Delta variant, first detected in the United States in March 2021, made up the majority of SARS-CoV-2 infections by July 1, 2021 and accounted for >99.9% of the infections by September 2021. Not only did Delta displace variant Alpha, which was the dominant variant at the time, it also displaced the Gamma, Iota, and Mu variants. Through an analysis of quantification cycle (Cq) values, we demonstrate that Delta infections tend to have a 1.7× higher viral load compared to Alpha infections (a decrease of 0.8 Cq) on average. Our results are consistent with the hypothesis that the increased transmissibility of the Delta variant could be due to the ability of the Delta variant to establish a higher viral load earlier in the infection as compared to the Alpha variant.

Original language	English
Article number	100564
Journal	Cell Reports Medicine
Volume	3
Issue number	3
DOIs	https://doi.org/10.1016/j.xcrm.2022.100564
State	Published - 15 Mar 2022
Externally published	Yes

Keywords

Alpha
COVID-19
Delta
Gamma
Iota
Mu
SARS-CoV-2
surveillance
transmissibility
viral load

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10.1016/j.xcrm.2022.100564

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Bolze, A., Luo, S., White, S., Cirulli, E. T., Wyman, D., Dei Rossi, A., Machado, H., Cassens, T., Jacobs, S., Schiabor Barrett, K. M., Tanudjaja, F., Tsan, K., Nguyen, J., Ramirez, J. M., Sandoval, E., Wang, X., Wong, D., Becker, D., Laurent, M., ... Lee, W. (2022). SARS-CoV-2 variant Delta rapidly displaced variant Alpha in the United States and led to higher viral loads. Cell Reports Medicine, 3(3), Article 100564. https://doi.org/10.1016/j.xcrm.2022.100564

@article{947b1af0b92f42979cca14a491a90801,

title = "SARS-CoV-2 variant Delta rapidly displaced variant Alpha in the United States and led to higher viral loads",

abstract = "We report on the sequencing of 74,348 SARS-CoV-2 positive samples collected across the United States and show that the Delta variant, first detected in the United States in March 2021, made up the majority of SARS-CoV-2 infections by July 1, 2021 and accounted for >99.9% of the infections by September 2021. Not only did Delta displace variant Alpha, which was the dominant variant at the time, it also displaced the Gamma, Iota, and Mu variants. Through an analysis of quantification cycle (Cq) values, we demonstrate that Delta infections tend to have a 1.7× higher viral load compared to Alpha infections (a decrease of 0.8 Cq) on average. Our results are consistent with the hypothesis that the increased transmissibility of the Delta variant could be due to the ability of the Delta variant to establish a higher viral load earlier in the infection as compared to the Alpha variant.",

keywords = "Alpha, COVID-19, Delta, Gamma, Iota, Mu, SARS-CoV-2, surveillance, transmissibility, viral load",

author = "Alexandre Bolze and Shishi Luo and Simon White and Cirulli, {Elizabeth T.} and Dana Wyman and {Dei Rossi}, Andrew and Henrique Machado and Tyler Cassens and Sharoni Jacobs and {Schiabor Barrett}, {Kelly M.} and Francisco Tanudjaja and Kevin Tsan and Jason Nguyen and Ramirez, {Jimmy M.} and Efren Sandoval and Xueqing Wang and David Wong and David Becker and Marc Laurent and Lu, {James T.} and Magnus Isaksson and Washington, {Nicole L.} and William Lee",

note = "Publisher Copyright: {\textcopyright} 2022 The Author(s)",

year = "2022",

month = mar,

day = "15",

doi = "10.1016/j.xcrm.2022.100564",

language = "English",

volume = "3",

journal = "Cell Reports Medicine",

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Bolze, A, Luo, S, White, S, Cirulli, ET, Wyman, D, Dei Rossi, A, Machado, H, Cassens, T, Jacobs, S, Schiabor Barrett, KM, Tanudjaja, F, Tsan, K, Nguyen, J, Ramirez, JM, Sandoval, E, Wang, X, Wong, D, Becker, D, Laurent, M, Lu, JT, Isaksson, M, Washington, NL & Lee, W 2022, 'SARS-CoV-2 variant Delta rapidly displaced variant Alpha in the United States and led to higher viral loads', Cell Reports Medicine, vol. 3, no. 3, 100564. https://doi.org/10.1016/j.xcrm.2022.100564

TY - JOUR

T1 - SARS-CoV-2 variant Delta rapidly displaced variant Alpha in the United States and led to higher viral loads

AU - Bolze, Alexandre

AU - Luo, Shishi

AU - White, Simon

AU - Cirulli, Elizabeth T.

AU - Wyman, Dana

AU - Dei Rossi, Andrew

AU - Machado, Henrique

AU - Cassens, Tyler

AU - Jacobs, Sharoni

AU - Schiabor Barrett, Kelly M.

AU - Tanudjaja, Francisco

AU - Tsan, Kevin

AU - Nguyen, Jason

AU - Ramirez, Jimmy M.

AU - Sandoval, Efren

AU - Wang, Xueqing

AU - Wong, David

AU - Becker, David

AU - Laurent, Marc

AU - Lu, James T.

AU - Isaksson, Magnus

AU - Washington, Nicole L.

AU - Lee, William

PY - 2022/3/15

Y1 - 2022/3/15

N2 - We report on the sequencing of 74,348 SARS-CoV-2 positive samples collected across the United States and show that the Delta variant, first detected in the United States in March 2021, made up the majority of SARS-CoV-2 infections by July 1, 2021 and accounted for >99.9% of the infections by September 2021. Not only did Delta displace variant Alpha, which was the dominant variant at the time, it also displaced the Gamma, Iota, and Mu variants. Through an analysis of quantification cycle (Cq) values, we demonstrate that Delta infections tend to have a 1.7× higher viral load compared to Alpha infections (a decrease of 0.8 Cq) on average. Our results are consistent with the hypothesis that the increased transmissibility of the Delta variant could be due to the ability of the Delta variant to establish a higher viral load earlier in the infection as compared to the Alpha variant.

AB - We report on the sequencing of 74,348 SARS-CoV-2 positive samples collected across the United States and show that the Delta variant, first detected in the United States in March 2021, made up the majority of SARS-CoV-2 infections by July 1, 2021 and accounted for >99.9% of the infections by September 2021. Not only did Delta displace variant Alpha, which was the dominant variant at the time, it also displaced the Gamma, Iota, and Mu variants. Through an analysis of quantification cycle (Cq) values, we demonstrate that Delta infections tend to have a 1.7× higher viral load compared to Alpha infections (a decrease of 0.8 Cq) on average. Our results are consistent with the hypothesis that the increased transmissibility of the Delta variant could be due to the ability of the Delta variant to establish a higher viral load earlier in the infection as compared to the Alpha variant.

KW - Alpha

KW - COVID-19

KW - Delta

KW - Gamma

KW - Iota

KW - Mu

KW - SARS-CoV-2

KW - surveillance

KW - transmissibility

KW - viral load

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DO - 10.1016/j.xcrm.2022.100564

M3 - Article

C2 - 35474739

AN - SCOPUS:85126325604

SN - 2666-3791

VL - 3

JO - Cell Reports Medicine

JF - Cell Reports Medicine

IS - 3

M1 - 100564

ER -

SARS-CoV-2 variant Delta rapidly displaced variant Alpha in the United States and led to higher viral loads

Abstract

Keywords

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