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. 2022 Mar 15;3(3):100564.
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  1 , Shishi Luo  1 , Simon White  1 , Elizabeth T Cirulli  1 , Dana Wyman  1 , Andrew Dei Rossi  1 , Henrique Machado  1 , Tyler Cassens  1 , Sharoni Jacobs  1 , Kelly M Schiabor Barrett  1 , Francisco Tanudjaja  1 , Kevin Tsan  1 , Jason Nguyen  1 , Jimmy M Ramirez 3rd  1 , Efren Sandoval  1 , Xueqing Wang  1 , David Wong  1 , David Becker  1 , Marc Laurent  1 , James T Lu  1 , Magnus Isaksson  1 , Nicole L Washington  1 , William Lee  1
Affiliations

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

Alexandre Bolze et al. Cell Rep Med. .

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.

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Conflict of interest statement

A.B., S.L., E.T.C., S.W., D. Wyman, 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. Wong, D.B., M.L., J.T.L., M.I., N.L.W., and W.L. are employees of Helix.

Figures

None
Graphical abstract
Figure 1
Figure 1
Delta displaced Alpha and all other variants in the United States in the summer of 2021 For each variant of concern or of interest, the fraction of the total sequences each variant represented at a given time is plotted. There is 1 point per week starting from February 5 and ending September 30, 2021. (A) Sequences from samples collected in Florida. (B) Sequences from samples collected in California. (C) Sequences from samples collected in the rest of the United States. Each variant is represented by 1 line with a unique color. Alpha: dark blue; Beta: black; Gamma: light orange; Delta: purple; Epsilon: dark orange; Iota: pink; Lambda: dark gray; Mu: light blue; and all of the other variants by light gray. See also Table S1.
Figure 2
Figure 2
Higher viral loads in Delta infections compared to Alpha infections (all dates are in 2021) (A) Mean CqAlpha minus mean CqDelta levels over time in 2021. Each dot corresponds to a value of this difference for 1 day. Sequences from samples collected from all over the United States were used. (B) Epidemic phases in Florida. Chart downloaded from https://covid.cdc.gov/covid-data-tracker/#trends_dailycases after restricting the sample to cases in Florida. The blue bars show daily cases. The red line is the 7-day moving average of cases. (C) Mean CqAlpha and CqDelta by phase of the epidemic in Florida. The left 2 columns are while the epidemic was growing. The right 2 columns are while the epidemic was declining. Dark blue: Alpha; purple: Delta. The error bars represent the 95% confidence interval (CI). (D) Mean CqAlpha and CqDelta by phase of the epidemic in the United States, except Florida. The left 2 columns are while the epidemic was growing. The right 2 columns are while the epidemic was declining. Dark blue: Alpha; purple: Delta. The error bars represent the 95% CI. Mann-Whitney U tests were performed. ∗∗∗p < 0.001, ∗∗∗∗p < 0.0001. See also Figure S1 and Table S2.
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