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Volume 27, Number 8—August 2021
Research Letter

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

Lex E.X. LeongComments to Author , Julien Soubrier, Mark Turra, Emma Denehy, Luke Walters, Karin Kassahn, Geoff Higgins, Tom Dodd, Robert Hall, Katina D’Onise, Nicola Spurrier, Ivan Bastian, and Chuan K. Lim
Author affiliations: University of South Australia, Adelaide, South Australia, Australia (L.E.X. Leong); South Australian Health and Medical Research Institute, Adelaide (L.E.X. Leong); SA Pathology, Adelaide (L.E.X. Leong, J. Soubrier, M. Turra, L. Walters, K. Kassahn, G. Higgins, T. Dodd, I. Bastian, C.K. Lim); University of Adelaide, Adelaide (J. Soubrier, G. Higgins, I. Bastian, C.K. Lim); Department for Health and Wellbeing, Adelaide (E. Denehy, R. Hall, K. D’Onise, N. Spurrier); Royal Adelaide Hospital, Adelaide (C.K. Lim)

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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.

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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