The emergence and spread of SARS-CoV-2 lineage B.1.1.7, first detected in the United Kingdom, has become a global public health concern because of its increased transmissibility. Over 2500 COVID-19 cases associated with this variant have been detected in the US since December 2020, but the extent of establishment is relatively unknown. Using travel, genomic, and diagnostic data, we highlight the primary ports of entry for B.1.1.7 in the US and locations of possible underreporting of B.1.1.7 cases. Furthermore, we found evidence for many independent B.1.1.7 establishments starting in early December 2020, followed by interstate spread by the end of the month. Finally, we project that B.1.1.7 will be the dominant lineage in many states by mid to late March. Thus, genomic surveillance for B.1.1.7 and other variants urgently needs to be enhanced to better inform the public health response.

/pdf/early-introductions-and-community-transmission-of-sars-cov-2-2gful9x3qo.pdf

Early introductions and community transmission of SARS-CoV-2 variant B.1.1.7 in the United States

Following the COVID-19 pandemic, safe and effective vaccines were developed and authorized for use in the general population. Studying factors that encourage community acceptance of these vaccines is needed to prevent proliferation of SARS-CoV-2 variants, to safely relax local restrictions, and to return to pre-pandemic living conditions. To our knowledge, United States (US) county-level disparities in vaccination are yet to be investigated. Our data span February - May 2021 across 3138 US counties. We consider percentage of residents with at least one dose of an authorized COVID vaccine as the outcome. Spatio-temporal models were used to determine associations of vaccination rates with time-fixed and time-varying covariates. Spatial variability was modelled via Conditional Auto-regressive models; county trajectories over time were specified using random slopes. Greater vaccination rates occur in counties with older residents, high educational attainment, and high proportion of minority residents. Vaccination rates change with COVID risk metrics, suggesting continued slowing of vaccine uptake due to decreasing incidence and infection rates. County effects reveal strong regional patterns in average vaccination rates and trajectories. Although local herd immunity can be expected in August 2021 for counties with typical uptake rates, these counties are clustered in relatively few areas of the country.

/pdf/covid-19-vaccine-uptake-in-united-states-counties-geospatial-2iloz37o0x.pdf

COVID-19 vaccine uptake in United States counties: geospatial vaccination patterns and trajectories towards herd immunity

NSCLC patient "migration" for treatment: A retrospective analysis of patient characteristics, travel patterns, and survival differences.

Simplify the Creation of Choropleth Maps in R [R package choroplethr version 3.7.0]

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Simplify the Creation of Choropleth Maps in R [R package choroplethr version 3.7.0]