Genomic Surveillance for SARS-CoV-2 Variants: Predominance of the Delta (B.1.617.2) and Omicron (B.1.1.529) Variants — United States, June 2021–January 2022

Lambrou, Anastasia S.; Shirk, Philip; Steele, Molly; Paul, Prabasaj; Paden, Clinton R.; Cadwell, Betsy L.; Reese, Heather; Aoki, Yutaka; Hassell, Norman; Zheng, Xiao-yu; Talarico, Sarah; Chen, Jessica C.; Oberste, M. Steven; Batra, Dhwani; McMullan, Laura K.; Halpin, Alison Laufer; Galloway, Summer E.; MacCannell, Duncan; Kondor, Rebecca; Barnes, John; MacNeil, Adam; Silk, Benjamin J.; Dugan, Vivien G.; Scobie, Heather M.; Wentworth, David E.

doi:10.15585/mmwr.mm7106a4

Cited by 151 publications

(134 citation statements)

References 6 publications

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“…On November 24, 2021, the World Health Organization was first notified of the new SARS-CoV-2 B.1.1.529 Variant (Omicron). In the USA, by the end of January, over 90% of Covid cases were related to this variant, which has rapidly become the dominant circulating variant of concern [ 9 ] . The Omicron variant harbors a remarkable 59–amino acid substitution throughout its genome relative to the ancestral Wuhan-hu-1 SARS-CoV-2 virus, where almost 37 of these nonsynonymous mutations are located within the spike protein, the target of neutralizing antibodies against SARS-CoV-2 [ 10 ].…”

Section: Introductionmentioning

confidence: 99%

Breakthrough infections after COVID-19 vaccination: Insights, perspectives and challenges

et al. 2022

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Section: Introductionmentioning

confidence: 99%

Breakthrough infections after COVID-19 vaccination: Insights, perspectives and challenges

et al. 2022

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“…The constant need to rapidly identify new and emerging SC-2 variants for clinical, epidemiological and research purposes necessitates vigilant and continuous development of new tools. Since the onset of the SC-2 pandemic, the increased infectivity of the SC-2 variants compared with the initial strain, led to their unprecedented spread in the entire globe, within a matter of a few months (Volz et al 2021, Chakraborty et al 2021, Lambrou et al 2022. Due to their increased infectivity and pathogenicity, the effect of the spreading of different SC-2 variants on public health can be significant and so is the demand for adequate diagnostic tools.…”

Section: Discussionmentioning

confidence: 99%

NOVEL RT-qPCR ASSAYS ENABLE RAPID DETECTION AND DIFFERENTIATION BETWEEN SARS-COV-2 OMICRON (BA.1) AND BA.2 VARIANTS

Erster

Kabat

Asraf

et al. 2022

Preprint

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In this report, we describe the development and initial validation of novel SARS-COV-2 Omicron-specific reactions that enable the identification of Omicron (BA.1) and BA.2 variants. Mutations that are either shared by both BA.1 and BA.2, or are exclusive for BA.1 or for BA.2 were identified by bioinformatic analysis, and corresponding probe-based quantitative PCR reactions were developed to identify them. We show that multiplex combinations of these reactions provide a single-reaction identification of the sample as BA.1, BA.2, or as non-Omicron SARS-COV-2. All four reactions described herein have a sensitivity of less than ten copies per reaction, and are amendable for multiplexing. The results of this study suggest that the new assays may be useful for testing both clinical and environmental samples to differentiate between these two variants.

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“…We observe two peaks that are present in all states at the same time. The first peak occurs between June and August 2021 (light-yellow window) and corresponds to the wave of the Delta (B.1.617.2) variant [38,39]. The second peak occurs between November 2021 and January 2022 (light-purple window) and corresponds to the wave of the Omicron (B.1.1.529) variant [38].…”

Section: Covid-19 Transmission In the Us Statesmentioning

confidence: 99%

“…The first peak occurs between June and August 2021 (light-yellow window) and corresponds to the wave of the Delta (B.1.617.2) variant [38,39]. The second peak occurs between November 2021 and January 2022 (light-purple window) and corresponds to the wave of the Omicron (B.1.1.529) variant [38]. There are other bumps in the reproduction numbers occurring at the same time in several states for which we have not identified the causes.…”

Section: Covid-19 Transmission In the Us Statesmentioning

confidence: 99%

Nonparametric inference for the reproductive rate in generalized compartmental models

Trejo

Lin

Patrick

et al. 2022

Preprint

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We develop a tractable non-parametric model for the time-varying reproductive rate of infectious diseases that combines the structure of a deterministic compartmental model and a stochastic model for incidence data. We use Bayesian inference to estimate, with uncertainty, the reproductive rate of the Coronavirus 2019 outbreak in the U.S. states of California, Florida, Michigan, New Mexico, New York, and Texas from January 2020 to March 2022. We use the inferred reproductive rates to estimate the posterior distribution of the time-varying reproduction numbers for each state. Compering the time-varying reproduction numbers across the states, we identify some epidemic waves, potentially driven from changes in human behavior and virus mutations.

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Genomic Surveillance for SARS-CoV-2 Variants: Predominance of the Delta (B.1.617.2) and Omicron (B.1.1.529) Variants — United States, June 2021–January 2022

Cited by 151 publications

References 6 publications

Breakthrough infections after COVID-19 vaccination: Insights, perspectives and challenges

Breakthrough infections after COVID-19 vaccination: Insights, perspectives and challenges

NOVEL RT-qPCR ASSAYS ENABLE RAPID DETECTION AND DIFFERENTIATION BETWEEN SARS-COV-2 OMICRON (BA.1) AND BA.2 VARIANTS

Nonparametric inference for the reproductive rate in generalized compartmental models

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