A Biogeographic Analysis of SARS-CoV-2 Variants of Concern in Hawai‘i
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2022
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Abstract
In late 2020 and into 2021, the World Health Organization (WHO) began labeling emerging SARS-CoV-2 strains with increased transmissibility and/or virulence as variants of concern (VOCs). Communities, including Hawai‘i, that have limited ICU resources and are geographically isolated and experience frequent international and domestic travel, were very concerned about the potential for these variants to enter through domestic or international travel and implemented strict travel restrictions to reduce the likelihood of introductions. In this study, the dynamics of importation and spread in Hawaiʻi of the Alpha, Gamma Mu, Delta, and Omicron VOCs were investigated. A phylogeographic analysis of these VOCs was conducted using a time-calibrated phylogenetic reconstruction through maximum likelihood and Bayesian methods, followed by a biogeographic analysis using Dispersal-Extinction-Cladogenesis evolutionary models to describe the pattern of spread between counties in the state. This study recovered 1,268 independent introductions into Hawai‘i from international and domestic sources, with only ~30% of those introductions resulting in subsequent community transmission. Nine hundred thirty interisland movements were identified, with ~50% as imports/exports from Honolulu County. It appears that the non-pharmaceutical interventions implemented in Hawai‘i, primarily the pre-travel testing, played a large role in reducing the number of imports, especially early in the pandemic before widespread vaccination of the population. The effect of travel restrictions was confirmed by comparing introductions and community spread before and after the relaxation of these guidelines. Evidence indicates that these policies allowed Hawai‘i’s medical infrastructure to manage severe cases of COVID-19 without being overrun, a particular concern for a geographically isolated population like that in Hawai‘i. More generally, the comparison of sequenced viral genomes with geographic data can reveal movement of the virus between communities at fine spatial and temporal scales, and may be useful for informing public health decisions in future pandemics.
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Microbiology, Biogeography, Phylogenetics, Phylogeography, SARS-CoV-2
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41 pages
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