Fig. 1: Alpha and Iota dominated the circulating SARS-CoV-2 populations in Connecticut and New York City in early 2021.

a Trends in COVID-19 incidence were consistent across northeastern states throughout the pandemic. (map) Connecticut (teal) is bordered by New York, Rhode Island, and Massachusetts. New York City is less than 50 miles from Fairfield County. Weekly COVID-19 incidence was tabulated according to the Johns Hopkins COVID-19 portal (https://github.com/CSSEGISandData/COVID-19). Shapefile source: United States Census Bureau. b New Haven County led the state in the percentage of COVID-19 cases sequenced between November 30, 2020 and May 9, 2021 (3.33%). During this period, 0.51% of COVID-19 cases in New York City were sequenced. Genomes that were collected through targeted variant screening (e.g., spike-gene target failure) were excluded from this analysis. Shapefile source: the Connecticut Department of Energy & Environmental Protection (DEEP) Geographic Information Systems Open Data Website. c Together, Alpha and Iota variants displaced nearly all other SARS-CoV-2 lineages in New Haven County (n = 2086), Fairfield County (n = 612), and New York City (n = 4528). The lineages of sequenced viruses were assigned using pangolin v.2.4.2. The lineages B.1.526, B.1.526.1, and B.1.526.2 were assigned to the general lineage category ‘Iota’. We calculated a 7-day rolling average for the proportion of Alpha, Iota, and ‘other’ SARS-CoV-2 lineages sequenced in our dataset. d Daily variant incidence estimated by fitting a logistic growth model to the daily sequenced variant frequencies shown in c. This analysis was completed using Rv.4.0.1. Line colors correspond to the legend in c. e Daily growth rates of variants estimated using the logistic growth model shown in d. Bar colors correspond to the legend in c.