Genomic Epidemiology of SARS-CoV-2 Infection During the Initial Pandemic Wave and Association With Disease Severity

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Abstract
As of February 2021, there have been more 27 million confirmed SARS-CoV-2 infections in the US occurring in 3 waves.1 Before governmental policies aimed at infection containment were enacted, initial wave infections were travel related, most of which originated from Europe and were associated with high hospitalization and mortality rates in certain at-risk groups.2,3 Over time, disease associated with infection demonstrated decreasing length of stay and reduced case fatality ratios despite elevated numbers of hospitalizations.4 Although the development of antiviral medications and improved clinical care protocols have had substantial effects, the contribution of virus evolution on changes in clinical outcomes remains understudied.5,6

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