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. 2021 Aug;27(8):2219-2221.
doi: 10.3201/eid2708.204875.

Whole-Genome Sequencing of SARS-CoV-2 from Quarantine Hotel Outbreak

Lex E X Leong, Julien Soubrier, Mark Turra, Emma Denehy, Luke Walters, Karin Kassahn, Geoff Higgins, Tom Dodd, Robert Hall, Katina D'Onise, Nicola Spurrier, Ivan Bastian, Chuan K Lim

Whole-Genome Sequencing of SARS-CoV-2 from Quarantine Hotel Outbreak

Lex E X Leong et al. Emerg Infect Dis. 2021 Aug.

Abstract

Hotel quarantine for international travelers has been used to prevent coronavirus disease spread into Australia. A quarantine hotel-associated community outbreak was detected in South Australia. Real-time genomic sequencing enabled rapid confirmation tracking the outbreak to a recently returned traveler and linked 2 cases of infection in travelers at the same facility.

Keywords: Australia; COVID-19; SARS-CoV-2; coronavirus disease; genome sequencing; hotel quarantine; respiratory infections; severe acute respiratory syndrome coronavirus 2; vaccines; viruses; zoonoses.

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Figures

Figure
Figure
Maximum-likelihood phylogenetic tree of severe acute respiratory syndrome coronavirus 2 genomes from a quarantine hotel–associated community outbreak of coronavirus disease in South Australia, Australia. A) Genomes from lineage B.1.36 (n = 3,038). B) Subtree of lineage B.1.36.1 focusing on the quarantine hotel clusters and a returned traveler from the United Kingdom; bold type indicates those strains. Consensus genomes were profile-aligned using COVID-Align (5), and phylogenetic trees were constructed using IQ-TREE with general time reversible plus invariate plus gamma 4 sites model (6). SH-like approximate likelihood ratio test score was 98.3%, ultrafast bootstrap approximation 99%. Scale bar indicates substitutions per site.
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