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SARS-CoV-2 Variant Delta Rapidly Displaced Variant Alpha in the United States and Led to Higher Viral Loads

17 Pages Posted: 28 Oct 2021 Publication Status: Published

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Abstract

The sequencing of 74,348 SARS-CoV-2 positive samples collected across the United States showed that the Delta variant was responsible for the majority of SARS-CoV-2 infections by July 1, 2021, and that Delta variant infections accounted for >99.9% of positive tests in the United States in September 2021. Delta displaced variant Alpha, which was the dominant variant at the time. Delta also directly outcompeted the Gamma variant of concern as well as the Iota and Mu variants of interest. An analysis of the mean quantification cycles (Cq) values in positive tests revealed that Delta infections lead to a higher viral load on average compared to Alpha infections, but this increase was only ~1.7x (equivalent to a decrease of 0.8 Cq) on average in our study design. Our results are consistent with the hypothesis that the increased transmissibility of the Delta variant could be due to the Delta variant’s ability to establish a higher viral load earlier in the infection compared to the Alpha variant.

Funding: This work has been funded in part by CDC BAA contract 75D30121P10258 (Illumina, Helix).

Declaration of Interests: A.B., S.L., E.T.C., S.W., D.W., A.D.R., H.M., T.C., S.J., K.M.S.B., F.T., K.T., J.N., J.M.R., E.S., X.W., D.W., D.B., M.L., J.T.L., M.I., N.L.W. and W.L. are employees of Helix.

Ethics Approval Statement: The Helix data analyzed and presented here were obtained through IRB protocol WIRB#20203438, which grants a waiver of consent for a limited dataset for the purposes of public health under section 164.512(b) of the Privacy Rule (45 CFR § 164.512(b)).

Keywords: SARS-CoV-2, Delta, Alpha, Gamma, Mu, Variant of Concern, Genomic surveillance, Higher transmissibility, RT-qPCR, viral load

Suggested Citation

Bolze, Alexandre and Luo, Shishi and White, Simon and Cirulli, Elizabeth T. and Wyman, Dana and Dei Rossi, Andrew and Machado, Henrique and Cassens, Tyler and Jacobs, Sharoni and Schiabor Barrett, Kelly M. and Tanudjaja, Francisco and Tsan, Kevin and Nguyen, Jason and Ramirez III, Jimmy M. and Sandoval, Efren and Wang, Xueqing and Wong, David and Becker, David and Laurent, Marc and Lu, James T. and Isaksson, Magnus and Washington, Nicole L. and Lee, William, SARS-CoV-2 Variant Delta Rapidly Displaced Variant Alpha in the United States and Led to Higher Viral Loads. Available at SSRN: https://ssrn.com/abstract=3952083 or http://dx.doi.org/10.2139/ssrn.3952083
This version of the paper has not been formally peer reviewed.

Alexandre Bolze (Contact Author)

Helix ( email )

San Mateo, CA
United States

Shishi Luo

Helix ( email )

San Mateo, CA
United States

Simon White

Helix ( email )

San Mateo, CA
United States

Elizabeth T. Cirulli

Helix ( email )

San Mateo, CA
United States

Dana Wyman

Helix ( email )

San Mateo, CA
United States

Andrew Dei Rossi

Helix ( email )

San Mateo, CA
United States

Henrique Machado

Helix ( email )

San Mateo, CA
United States

Tyler Cassens

Helix ( email )

San Mateo, CA
United States

Sharoni Jacobs

Helix ( email )

San Mateo, CA
United States

Kelly M. Schiabor Barrett

Helix ( email )

San Mateo, CA
United States

Francisco Tanudjaja

Helix ( email )

San Mateo, CA
United States

Kevin Tsan

Helix ( email )

San Mateo, CA
United States

Jason Nguyen

Helix ( email )

San Mateo, CA
United States

Jimmy M. Ramirez III

Helix ( email )

San Mateo, CA
United States

Efren Sandoval

Helix ( email )

San Mateo, CA
United States

Xueqing Wang

Helix ( email )

San Mateo, CA
United States

David Wong

Helix ( email )

San Mateo, CA
United States

David Becker

Helix ( email )

San Mateo, CA
United States

Marc Laurent

Helix ( email )

San Mateo, CA
United States

James T. Lu

Helix ( email )

San Mateo, CA
United States

Magnus Isaksson

Helix ( email )

San Mateo, CA
United States

Nicole L. Washington

Helix ( email )

San Mateo, CA
United States

William Lee

Helix ( email )

San Mateo, CA
United States

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