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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.

Main Article

References
  1. Miller  IF, Becker  AD, Grenfell  BT, Metcalf  CJE. Disease and healthcare burden of COVID-19 in the United States. Nat Med. 2020;26:1212–7. DOIPubMedGoogle Scholar
  2. Speake  H, Phillips  A, Chong  T, Sikazwe  C, Levy  A, Lang  J, et al. Flight-associated transmission of severe acute respiratory syndrome coronavirus 2 corroborated by whole-genome sequencing. Emerg Infect Dis. 2020;26:2872–80. DOIPubMedGoogle Scholar
  3. Zhou  F, Li  J, Lu  M, Ma  L, Pan  Y, Liu  X, et al. Tracing asymptomatic SARS-CoV-2 carriers among 3674 hospital staff:a cross-sectional survey. EClinicalMedicine. 2020;26:100510. DOIPubMedGoogle Scholar
  4. Rambaut  A, Holmes  EC, O’Toole  Á, Hill  V, McCrone  JT, Ruis  C, et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020;5:1403–7. DOIPubMedGoogle Scholar
  5. Lemoine  F, Blassel  L, Voznica  J, Gascuel  O. COVID-Align: accurate online alignment of hCoV-19 genomes using a profile HMM. Bioinform. 2020;btaa871.
  6. Nguyen  LT, Schmidt  HA, von Haeseler  A, Minh  BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32:268–74. DOIPubMedGoogle Scholar
  7. Elbe  S, Buckland-Merrett  G. Data, disease and diplomacy: GISAID’s innovative contribution to global health. Glob Chall. 2017;1:33–46. DOIPubMedGoogle Scholar
  8. Endo  A, Abbott  S, Kucharski  AJ, Funk  S; Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group. Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China. Wellcome Open Res. 2020;5:67. DOIPubMedGoogle Scholar
  9. van Dorp  L, Richard  D, Tan  CCS, Shaw  LP, Acman  M, Balloux  F. No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2. Nat Commun. 2020;11:5986. DOIPubMedGoogle Scholar

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Page updated: July 19, 2021
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