Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States

Abstract

The highly transmissible B.1.1.7 variant of SARS-CoV-2, first identified in the United Kingdom, has gained a foothold across the world. Using S gene target failure (SGTF) and SARS-CoV-2 genomic sequencing, we investigated the prevalence and dynamics of this variant in the United States (US), tracking it back to its early emergence. We found that, while the fraction of B.1.1.7 varied by state, the variant increased at a logistic rate with a roughly weekly doubling rate and an increased transmission of 40%-50%. We revealed several independent introductions of B.1.1.7 into the US as early as late November 2020, with community transmission spreading it to most states within months. We show that the US is on a similar trajectory as other countries where B.1.1.7 became dominant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality.

Keywords: 501Y.V1; B.1.1.7; COVID-19; SARS-CoV-2; VOC-202012/01; genomic epidemiology; variant of concern.

Graphical abstract

Figure 1

Estimated proportion of B.1.1.7 in SARS-CoV-2 tests at Helix since December 15, 2020 (A) Map of contiguous states in the US with each bubble representing the number of positive Helix COVID-19 tests from each state. (B) Estimated proportion of B.1.1.7 in total number of positive tests with Cq(N gene) <27, in the US overall, California, Florida, and Georgia from December 15^th, 2020 to February 11^th, 2021. The proportion of B.1.1.7 samples was estimated using: $\frac{ObservedB.\mathrm{1.1.7}sequences}{SequencedSGTFsamples}\times \frac{PositivetestswithSGTF}{Totalpositivetests}$. There is an ∼2 week lag between sequence data and testing data. We had sequence data until February 2^nd, but we had testing data until February 19^th. To fully utilize the testing data, we used the average proportion of B.1.1.7 sequences in sequenced samples with SGTF from the last 5 days of available sequence data in each location to infer the proportion of B.1.1.7 cases in total positive tests for an additional 2 week period (February 3 to February 19). The black line shows the 5-day rolling average of the estimated proportion of B.1.1.7 in total positives. The inverted bar chart shows the temporal distribution of the B.1.1.7 genomes sequenced and the number of sequenced samples with SGTF. (C) Logistic growth curves fit to the rolling average of the estimated proportion of B.1.1.7 in total positives for the US, Florida, California, and Georgia. The shaded area represents the 95% CI for each fit. The inset shows the zoomed in view of the curve fit. The predicted time when the estimated proportion of B.1.1.7 cases crosses 0.5 is indicated in red. See also Data S1.

Figure 2

Phylogenetic analysis of B.1.1.7 lineage in the US (A) Maximum clade credibility (MCC) tree of the time resolved phylogenetic analysis of B.1.1.7 sequences in the US in the context of sequences sampled globally. The gradient represents uncertainty in the tree topology and is used to mask internal nodes with very low support (posterior probability ≪0.1). Clades that consist primarily of sequences sampled in the US supported by a basal node with posterior probability ≥0.98 are highlighted in the tree with the posterior probability annotated at the basal node. The closest ancestral node to each clade with a posterior probability ≥0.98 is highlighted in black. In this phylogeny, we only show clades with ≥20 sequences and independent introductions into Pennsylvania (PA) and Georgia (GA). Please see Figure S1 for a phylogeny with all the annotations of the MCC tree. (B) The color scheme of terminal nodes sampled in the MCC tree. Sequences sampled outside the US are colored in light gray. US states with no B.1.1.7 sequence sampling in the dataset are shown in light gray in the map. (C) The TMRCA of each clade highlighted in the MCC tree. (D) The proportion of the geographic sampling of sequences within each clade (singletons have been excluded, including those in Texas, Pennsylvania, and Massachusetts). The colors follow the same scheme as shown in (B). See also Figure S1.

Figure S1

Phylogenetic analysis of B.1.1.7 lineage in the US, related to Figure 2 (A) Maximum clade credibility (MCC) tree of the time resolved phylogenetic analysis of B.1.1.7 sequences in the U.S. in the context of sequences sampled globally. The gradient represents uncertainty in the tree topology and is used to mask internal nodes with very low support (posterior probability ≪ 0.1). Clades that consist primarily of sequences sampled in the U.S. supported by a basal node with posterior probability ≥ 0.98 are highlighted in the tree with the posterior probability annotated at the basal node. The closest ancestral node to each clade with a posterior probability ≥ 0.98 is highlighted in black. (B) The color scheme of terminal nodes sampled in the MCC tree. Sequences sampled outside the U.S. are colored in light gray. U.S. States with no B.1.1.7 sequence sampling in the dataset are shown in light-gray in the map. (C) The TMRCA of each clade highlighted in the MCC tree. (D) The proportion of the geographic sampling of sequences within each clade (singletons have been excluded, including those in Texas, Pennsylvania, and Massachusetts).