Combining genomic data and infection estimates to characterize the complex dynamics of SARS-CoV-2 Omicron variants in the US

Lopes, Rafael; Pham, Kien; Klaassen, Fayette; Chitwood, Melanie H.; Hahn, Anne M.; Redmond, Seth; Swartwood, Nicole A.; Salomon, Joshua A.; Menzies, Nicolas A.; Cohen, Ted; Grubaugh, Nathan D.

doi:10.1016/j.celrep.2024.114451

Cited by 2 publications

References 32 publications

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Anomalies in regional and chronological distributions of Omicron BA.1.1 lineage in the United States

Kakeya

2024

Preprint

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This study compares the collection dates and locations of the Omicron BA.1 lineage and other major SARS-CoV-2 mutants registered in NCBI GenBank and provides a detailed analysis of the emergence patterns of pure reverse mutants, which contain only reverse mutations and no other mutations in the surface glycoprotein. The results indicate that Omicron BA.1.1 and its pure reverse mutants were widely distributed throughout the United States from the early days of their emergence, showing a statistically significant difference compared to other major variants, which spread from a small number of sources. The peak emergence of BA.1.1 and BA.1.1.18 pure reverse mutants occurred a few weeks before the peak of all collected samples, whereas the peak of pure reverse mutants in major BA.1 variants and BA.2 coincides with the overall sampling peak. Although the peaks of BA.1.x collections are not all synchronous, the peaks of pure reverse mutants in the BA.1 lineage completely overlap, with the number of such mutants declining abruptly after the peak. These regional and temporal anomalies in the Omicron BA.1 lineage, especially in the BA.1.1 lineage, are virtually impossible to explain by current theories of natural mutation and spread by human-to-human infection.

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Anomalies in regional and chronological distributions of Omicron BA.1.1 lineage in the United States

Kakeya

2024

Preprint

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From Emergence to Evolution: Dynamics of the SARS-CoV-2 Omicron Variant in Florida

Ali,

Giovanetti,

Johnston

et al. 2024

Pathogens

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The continual evolution of SARS-CoV-2 has significantly influenced the global response to the COVID-19 pandemic, with the emergence of highly transmissible and immune-evasive variants posing persistent challenges. The Omicron variant, first identified in November 2021, rapidly replaced the Delta variant, becoming the predominant strain worldwide. In Florida, Omicron was first detected in December 2021, leading to an unprecedented surge in cases that surpassed all prior waves, despite extensive vaccination efforts. This study investigates the molecular evolution and transmission dynamics of the Omicron lineages during Florida’s Omicron waves, supported by a robust dataset of over 1000 sequenced genomes. Through phylogenetic and phylodynamic analyses, we capture the rapid diversification of the Omicron lineages, identifying significant importation events, predominantly from California, Texas, and New York, and exportation to North America, Europe, and South America. Variants such as BA.1, BA.2, BA.4, and BA.5 exhibited distinct transmission patterns, with BA.2 showing the ability to reinfect individuals previously infected with BA.1. Despite the high transmissibility and immune evasion of the Omicron sub-lineages, the plateauing of cases by late 2022 suggests increasing population immunity from prior infection and vaccination. Our findings underscore the importance of continuous genomic surveillance in identifying variant introductions, mapping transmission pathways, and guiding public health interventions to mitigate current and future pandemic risks.

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Combining genomic data and infection estimates to characterize the complex dynamics of SARS-CoV-2 Omicron variants in the US

Cited by 2 publications

References 32 publications

Anomalies in regional and chronological distributions of Omicron BA.1.1 lineage in the United States

Anomalies in regional and chronological distributions of Omicron BA.1.1 lineage in the United States

From Emergence to Evolution: Dynamics of the SARS-CoV-2 Omicron Variant in Florida

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