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Mallela A, Chen Y, Lin YT, Miller EF, Neumann J, He Z, Nelson KE, Posner RG, Hlavacek WS. Impacts of Vaccination and Severe Acute Respiratory Syndrome Coronavirus 2 Variants Alpha and Delta on Coronavirus Disease 2019 Transmission Dynamics in Four Metropolitan Areas of the United States. Bull Math Biol 2024; 86:31. [PMID: 38353870 DOI: 10.1007/s11538-024-01258-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 01/08/2024] [Indexed: 02/16/2024]
Abstract
To characterize Coronavirus Disease 2019 (COVID-19) transmission dynamics in each of the metropolitan statistical areas (MSAs) surrounding Dallas, Houston, New York City, and Phoenix in 2020 and 2021, we extended a previously reported compartmental model accounting for effects of multiple distinct periods of non-pharmaceutical interventions by adding consideration of vaccination and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants Alpha (lineage B.1.1.7) and Delta (lineage B.1.617.2). For each MSA, we found region-specific parameterizations of the model using daily reports of new COVID-19 cases available from January 21, 2020 to October 31, 2021. In the process, we obtained estimates of the relative infectiousness of Alpha and Delta as well as their takeoff times in each MSA (the times at which sustained transmission began). The estimated infectiousness of Alpha ranged from 1.1x to 1.4x that of viral strains circulating in 2020 and early 2021. The estimated relative infectiousness of Delta was higher in all cases, ranging from 1.6x to 2.1x. The estimated Alpha takeoff times ranged from February 1 to February 28, 2021. The estimated Delta takeoff times ranged from June 2 to June 26, 2021. Estimated takeoff times are consistent with genomic surveillance data.
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Affiliation(s)
- Abhishek Mallela
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Ye Chen
- Department of Mathematics and Statistics, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Yen Ting Lin
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
- Information Sciences Group, Computer, Computational and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Ely F Miller
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Jacob Neumann
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Zhili He
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Kathryn E Nelson
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Richard G Posner
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - William S Hlavacek
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
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