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Volume 28, Number 6—June 2022
Research Letter

Multistate Outbreak of Infection with SARS-CoV-2 Omicron Variant after Event in Chicago, Illinois, USA, 2021

Hillary SpencerComments to Author , Richard A. Teran, Hannah J. Barbian, Sarah Love, Rachel Berg, Stephanie R. Black, Isaac Ghinai1, and Janna L. Kerins1
Author affiliations: Centers for Disease Control and Prevention, Atlanta, Georgia, USA (H. Spencer, R.A. Teran); Chicago Department of Public Health, Chicago, Illinois, USA (H. Spencer, R.A. Teran, S. Love, R. Berg, S.R. Black, I. Ghinai, J.L. Kerins); Rush University, Chicago (H.J. Barbian)

Main Article

Figure

Cases in multistate (Colorado, Illinois, Louisiana, Missouri, Michigan) outbreak of infection with severe acute respiratory syndrome 2 Omicron variant after event in Chicago, Illinois, USA, November–December 2021. A) Cases over time. Sequencing results are shown, if available. B) Genetic relatedness of viruses isolated. Maximum-likelihood phylogeny of 7 sequenced Omicron samples in bar-associated outbreak (green and yellow) with 50 contextual sequences (black). Contextual sequences are a random sample of Omicron BA.1 and BA.1.1 sequences selected from all Omicron sequences in GISAID (https://www.gisaid.org) that were collected in the United States or before December 11, 2021, and had >90% genome coverage. Random selection was performed by using CLC Genomics Workbench (QIAGEN, https://www.qiagen.com). No contextual sequences were from Illinois. GISAID accession numbers for all included sequences are listed in the Appendix. One outbreak-associated specimen was sequenced by a private laboratory and not uploaded to GISAID. Full-genome sequences were used for PhyML phylogenetic analysis (4), excluding 250 bp from genome ends and an error-prone region (reference positions 21492–21935). Outbreak sequences were identical to each other or contained a single-nucleotide substitution (T12000C, T22813G, T25414C) and clustered (with 3 contextual sequences) in a clade diverged by 2 nts from the closest other sequences. The 2 nt substitutions that defined the outbreak branch (C11950T, C28472T) were present in just 5.2% of contemporaneous Omicron sequences from the United States available on GISAID, indicating that all available outbreak sequences were closely genetically related.

Figure. Cases in multistate (Colorado, Illinois, Louisiana, Missouri, Michigan) outbreak of infection with severe acute respiratory syndrome 2 Omicron variant after event in Chicago, Illinois, USA, November–December 2021. A) Cases over time. Sequencing results are shown, if available. B) Genetic relatedness of viruses isolated. Maximum-likelihood phylogeny of 7 sequenced Omicron samples in bar-associated outbreak (green and yellow) with 50 contextual sequences (black). Contextual sequences are a random sample of Omicron BA.1 and BA.1.1 sequences selected from all Omicron sequences in GISAID (https://www.gisaid.org) that were collected in the United States or before December 11, 2021, and had >90% genome coverage. Random selection was performed by using CLC Genomics Workbench (QIAGEN, https://www.qiagen.com). No contextual sequences were from Illinois. GISAID accession numbers for all included sequences are listed in the Appendix. One outbreak-associated specimen was sequenced by a private laboratory and not uploaded to GISAID. Full-genome sequences were used for PhyML phylogenetic analysis (4), excluding 250 bp from genome ends and an error-prone region (reference positions 21492–21935). Outbreak sequences were identical to each other or contained a single-nucleotide substitution (T12000C, T22813G, T25414C) and clustered (with 3 contextual sequences) in a clade diverged by 2 nts from the closest other sequences. The 2 nt substitutions that defined the outbreak branch (C11950T, C28472T) were present in just 5.2% of contemporaneous Omicron sequences from the United States available on GISAID, indicating that all available outbreak sequences were closely genetically related.

Main Article

References
  1. Fisher  KA, Tenforde  MW, Feldstein  LR, Lindsell  CJ, Shapiro  NI, Files  DC, et al.; IVY Network Investigators; CDC COVID-19 Response Team. CDC COVID-19 Response Team. Community and close contact exposures associated with COVID-19 among symptomatic adults ≥18 years in 11 outpatient health care facilities—United States, July 2020. MMWR Morb Mortal Wkly Rep. 2020;69:1258–64. DOIPubMedGoogle Scholar
  2. Sami  S, Turbyfill  CR, Daniel-Wayman  S, Shonkwiler  S, Fisher  KA, Kuhring  M, et al. Community transmission of SARS-CoV-2 associated with a local bar opening event—Illinois, February 2021. MMWR Morb Mortal Wkly Rep. 2021;70:528–32. DOIPubMedGoogle Scholar
  3. Majra  D, Benson  J, Pitts  J, Stebbing  J. SARS-CoV-2 (COVID-19) superspreader events. J Infect. 2021;82:36–40. DOIPubMedGoogle Scholar
  4. Guindon  S, Dufayard  JF, Lefort  V, Anisimova  M, Hordijk  W, Gascuel  O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59:307–21. DOIPubMedGoogle Scholar

Main Article

1These authors are co-senior authors.

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