Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States

Abstract

As of January of 2021, the highly transmissible B.1.1.7 variant of SARS-CoV-2, which was first identified in the United Kingdom (U.K.), has gained a strong foothold across the world. Because of the sudden and rapid rise of B.1.1.7, we investigated the prevalence and growth dynamics of this variant in the United States (U.S.), tracking it back to its early emergence and onward local transmission. We found that the RT-qPCR testing anomaly of S gene target failure (SGTF), first observed in the U.K., was a reliable proxy for B.1.1.7 detection. We sequenced 212 B.1.1.7 SARS-CoV-2 genomes collected from testing facilities in the U.S. from December 2020 to January 2021. We found that while the fraction of B.1.1.7 among SGTF samples varied by state, detection of the variant increased at a logistic rate similar to those observed elsewhere, with a doubling rate of a little over a week and an increased transmission rate of 35-45%. By performing time-aware Bayesian phylodynamic analyses, we revealed several independent introductions of B.1.1.7 into the U.S. as early as late November 2020, with onward community transmission enabling the variant to spread to at least 30 states as of January 2021. Our study shows that the U.S. is on a similar trajectory as other countries where B.1.1.7 rapidly became the dominant SARS-CoV-2 variant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality.

Figure 1. SGTF and B.1.1.7 in SARS-CoV-2 tests at Helix since December 15, 2020.

(A) Map of contiguous states in the USA with each bubble representing the number of positive 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 U.S., California and Florida from December 15th, 2020 to January 30th, 2021. The proportion of B.1.1.7 samples was estimated using: (Observed B.1.1.7 sequences/Sequenced SGTF samples) * (Positive tests with SGTF/Total positive tests). Due to the lag in sequencing, the average proportion of B.1.1.7 sequences in sequenced samples with SGTF from the last five days (January 13-18) was used to infer the proportion of B.1.1.7 cases in total positive tests for the January 19-30 time period between. The black line shows the 5-day rolling average of the estimated proportion of B.1.1.7 in total positives. (C) Logistic growth curves fit to the rolling average of the estimated proportion of B.1.1.7 in total positives for the U.S., Florida and California. The predicted time when the estimated proportion of B.1.1.7 cases crosses 0.5 is indicated in red.

Figure 2.. Phylogenetic analysis of B.1.1.7 lineage in the USA.

(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. Clades that consist primarily of sequences sampled in the U.S. supported by a basal node with posterior probability ≥0.98 are colored in blue. 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. States with no B.1.1.7 sequence sampling in the dataset are shown in white. (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 panel B.