Publications by authors named "Marlin Figgins"

During the COVID-19 pandemic, SARS-CoV-2 variants drove large waves of infections, fueled by increased transmissibility and immune escape. Current models focus on changes in variant frequencies without linking them to underlying transmission mechanisms of intrinsic transmissibility and immune escape. We introduce a framework connecting variant dynamics to these mechanisms, showing how host population immunity interacts with viral transmissibility and immune escape to determine relative variant fitness.

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Genomic surveillance of pathogen evolution is essential for public health response, treatment strategies, and vaccine development. In the context of SARS-COV-2, multiple models have been developed including Multinomial Logistic Regression (MLR) describing variant frequency growth as well as Fixed Growth Advantage (FGA), Growth Advantage Random Walk (GARW) and Piantham parameterizations describing variant Rt. These models provide estimates of variant fitness and can be used to forecast changes in variant frequency.

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Article Synopsis
  • SARS-CoV-2 variants develop mutations in the spike protein that help the virus avoid the immune system and improve its ability to bind to the ACE2 receptor and enter cells.
  • Research involving over 9,000 mutations in the XBB.1.5 and BA.2 spike proteins revealed that changes occurring outside the receptor-binding domain (RBD) significantly impact ACE2 binding over the virus's evolution.
  • The study identifies key mutations that enable the virus to escape neutralization by antibodies in recently infected individuals, demonstrating varying effects on immunity and potential influences on the growth rates of different SARS-CoV-2 clades.
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Knockout of the ORF8 protein has repeatedly spread through the global viral population during SARS-CoV-2 evolution. Here we use both regional and global pathogen sequencing to explore the selection pressures underlying its loss. In Washington State, we identified transmission clusters with ORF8 knockout throughout SARS-CoV-2 evolution, not just on novel, high fitness viral backbones.

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The World Health Organization declared mpox a public health emergency of international concern in July 2022. To investigate global mpox transmission and population-level changes associated with controlling spread, we built phylogeographic and phylodynamic models to analyze MPXV genomes from five global regions together with air traffic and epidemiological data. Our models reveal community transmission prior to detection, changes in case reporting throughout the epidemic, and a large degree of transmission heterogeneity.

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Genomic surveillance of pathogen evolution is essential for public health response, treatment strategies, and vaccine development. In the context of SARS-COV-2, multiple models have been developed including Multinomial Logistic Regression (MLR) describing variant frequency growth as well as Fixed Growth Advantage (FGA), Growth Advantage Random Walk (GARW) and Piantham parameterizations describing variant . These models provide estimates of variant fitness and can be used to forecast changes in variant frequency.

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The World Health Organization declared mpox a public health emergency of international concern in July 2022. To investigate global mpox transmission and population-level changes associated with controlling spread, we built phylogeographic and phylodynamic models to analyze MPXV genomes from five global regions together with air traffic and epidemiological data. Our models reveal community transmission prior to detection, changes in case-reporting throughout the epidemic, and a large degree of transmission heterogeneity.

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Article Synopsis
  • Novel variants, especially Omicron, have emerged during the SARS-CoV-2 pandemic, prompting the need for effective genomic surveillance through university testing programs.* -
  • From September 2021 to February 2022, a study at a university identified 1,730 Omicron genomes out of nearly 3,000 positive cases, revealing Omicron's quicker transmission compared to Delta.* -
  • Even with high vaccination rates and strict health guidelines, Omicron outpaced Delta to become the dominant strain, resulting in a significant increase in COVID-19 cases within the university community.*
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