key: cord-0917002-ag5845qy
authors: Vanmechelen, Bert; Logist, Anne-Sophie; Wawina-Bokalanga, Tony; Verlinden, Jens; Martí-Carreras, Joan; Geenen, Caspar; Slechten, Bram; Cuypers, Lize; André, Emmanuel; Baele, Guy; Maes, Piet
title: Identification of the First SARS-CoV-2 Lineage B.1.1.529 Virus Detected in Europe
date: 2022-02-03
journal: Microbiology resource announcements
DOI: 10.1128/mra.01161-21
sha: 10ab598d4e597abf22892cb444178b0ceaf93518
doc_id: 917002
cord_uid: ag5845qy

We 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.

are not present in this sequence. Nextclade v1.10.0 was used for comparison with the RefSeq sequence (7). This genome contains 54 mutations and 39 indels (Table 1) , compared to the RefSeq sequence, highlighting the strong divergence of this novel variant. A phylogenetic analysis was performed using all available B.1.1.529 genomes in GISAID on 27 November 2021, along with a few representative genomes of the different VOCs (to root the phylogeny). MAFFT v7.475 was used to align the genome sequences, and the initial tree was generated using IQ-TREE v2.1.3 with automated model selection (8, 9) . 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) . The resulting tree was visualized using FigTree v1.4.4 (Fig. 1 ). The phylogenetic analysis shows that the sequence reported here, hCoV-19/Belgium/rega-20174/2021, clusters as part of a larger clade with South African cases, the two previously confirmed cases from Hong Kong, and the one confirmed case from Israel.

Data availability. This sequence has been deposited in GISAID (accession number EPI_ISL_6794907) and GenBank (accession number OL672836). The accession numbers for the raw sequencing reads in the NCBI Sequence Read Archive (SRA) are PRJNA784547 and SRR17066006.

This work and the sequencing capacity were supported in part by a COVID19 research grant from the Research Foundation Flanders (grant G0H4420N) and by an Internal Funds KU Leuven grant awarded to P.M. (grant 3M170314). G.B. acknowledges support from

The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

China Novel Coronavirus Investigating and Research Team. 2020. A novel coronavirus from patients with pneumonia in China

World Health Organization. 2021. Tracking SARS-CoV-2 variants

Classification of Omicron (B.1.1.529): SARS-CoV-2 variant of concern

2020. nCoV-2019 novel coronavirus bioinformatics protocol

Nextstrain: real-time tracking of pathogen evolution

IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies

MAFFT multiple sequence alignment software version 7: improvements in performance and usability

TreeTime: maximum-likelihood phylodynamic analysis

Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)

Internal Funds KU Leuven (grant C14/18/094) and the Research Foundation Flanders (grants G0E1420N and G098321N ). UZ Leuven, as a national reference center for respiratory pathogens, is supported by Sciensano, which is gratefully acknowledged.