Identification of a SARS-CoV-2 Lineage B1.1.7 Virus in New York following Return Travel from the United Kingdom

Abstract

Here, we report the identification and coding-complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strain (NYI.B1-7.01-21) obtained from a patient with symptoms of COVID-19 who had a recent travel history to the United Kingdom. The sample was tested by the Cayuga Health Systems laboratory as part of New York State's travel testing guidance and was sequenced at Cornell University after testing positive.

FIG 1

Phylogenetic tree of strain NYI.B1-7.01-21, highlighted in red in a clade with other B.1.1.7 sequences. Other samples from New York belonging to this lineage are shown in blue. A whole-genome nucleotide sequence alignment was performed with sequences retrieved from GISAID (https://www.gisaid.org) using MAFFT v7.450 (8) with the parameters Auto for algorithm, scoring matrix of 200PAM/k=2, gap open penalty of 1.53, and offset value of 0.123. The phylogenetic tree was constructed using 1,000 bootstrap replicates and the model TIM2+F, selected as the best-fit model by the IQ-TREE Web server (9).