Identification of the First SARS-CoV-2 Lineage B.1.1.529 Virus Detected in Europe.

Bert Vanmechelen,Joan Martí-Carreras,Anne-Sophie Logist,Emmanuel André,Caspar Geenen,Guy Baele,Tony Wawina-Bokalanga,Jens Verlinden,Piet Maes,Lize Cuypers,Bram Slechten,Simon Roux

doi:10.1128/mra.01161-21

Bert Vanmechelen, Joan Martí-Carreras + Show 10 more

Open Access

https://doi.org/10.1128/mra.01161-21

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Abstract

ABSTRACTWe report the complete genome sequence of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant (lineage B.1.1.529) from a Belgian patient with a history of recent travel to Egypt. At the time of writing, this genome constituted the first confirmed case of an infection with the Omicron variant in Europe.

Highlights

In December 2019, a novel betacoronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified in Wuhan, China [1, 2]
Nextclade v1.10.0 was used for comparison with the RefSeq sequence [7]
Following inspection of the resulting phylogeny using TempEst v1.5.3, nine outliers were removed to allow the subsequent estimation of a time-calibrated phylogeny using TreeTime v0.8.1 [10, 11]

Summary

Introduction

In December 2019, a novel betacoronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (genus Betacoronavirus, subfamily Orthocoronavirinae, family Coronaviridae), was identified in Wuhan, China [1, 2]. Coding sequence codon position(s)b — 856 — — 2083 2710 3255 3395 3674–3676 3758 — 314 — 1566 — 69–70 95 142–144 211 339 371 373 375 417 440 446 477 478 484 493 496 498 501 505 547 614 655 679 681 764 796 856 954 969 981 — — 9 3 19 63 — — — 13 31–33 27–29 203–204 B—, no amino acid or codon change occurred, and no nucleotide change occurred when a deletion was detected.

Results

Conclusion