Skip directly to site content Skip directly to page options Skip directly to A-Z link Skip directly to A-Z link Skip directly to A-Z link
Volume 27, Number 8—August 2021
Research

Transmission Dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 in High-Density Settings, Minnesota, USA, March–June 2020

Nicholas B. LehnertzComments to Author , Xiong Wang, Jacob Garfin, Joanne Taylor, Jennifer Zipprich, Brittany VonBank, Karen Martin, Dana Eikmeier, Carlota Medus, Brooke Wiedinmyer, Carmen Bernu, Matthew Plumb, Kelly Pung, Margaret A. Honein, Rosalind Carter, Duncan MacCannell, Kirk E. Smith, Kathryn Como-Sabetti, Kris Ehresmann, Richard Danila, and Ruth Lynfield
Author affiliations: Minnesota Department of Health, St. Paul, Minnesota, USA (N. Lehnertz, X. Wang, J. Garfin, J. Zipprich, B. VonBank, K. Martin, D. Eikmeier, C. Medus, B. Wiedinmyer, C. Bernu, M. Plumb, K. Pung, K.E. Smith, K. Como-Sabetti, K. Ehresmann, R. Danila, R. Lynfield); Centers for Disease Control and Prevention, Atlanta, Georgia, USA (J. Taylor, M.A. Honein, R. Carter, D. MacCannell)

Main Article

Figure 5

Phylogenetic tree of severe acute respiratory syndrome coronavirus 2 genome sequences associated with long-term care facility C and correctional facility B, Minnesota, US, April–June 2020. Filled circles represent sequences from samples from inmates or residents; open circles represent sequences from facility staff or healthcare workers. Sequences from long-term care facility C are shown on a white background; sequences from correctional facility B, on a gray background. Sequences from 2 household contacts are noted with stars. IQ-TREE (29) was used with the general time reversible substitution model for tree generation. Branch lengths were scaled to represent number of single-nucleotide mutations, as shown in the scale. MDH, Minnesota Department of Health.

Figure 5. Phylogenetic tree of severe acute respiratory syndrome coronavirus 2 genome sequences associated with long-term care facility C and correctional facility B, Minnesota, US, April–June 2020. Filled circles represent sequences from samples from inmates or residents; open circles represent sequences from facility staff or healthcare workers. Sequences from long-term care facility C are shown on a white background; sequences from correctional facility B, on a gray background. Sequences from 2 household contacts are noted with stars. IQ-TREE (29) was used with the general time reversible substitution model for tree generation. Branch lengths were scaled to represent number of single-nucleotide mutations, as shown in the scale. MDH, Minnesota Department of Health.

Main Article

References
  1. Arons  MM, Hatfield  KM, Reddy  SC, Kimball  A, James  A, Jacobs  JR, et al.; Public Health–Seattle and King County and CDC COVID-19 Investigation Team. Presymptomatic SARS-CoV-2 infections and transmission in a skilled nursing facility. N Engl J Med. 2020;382:2081–90. DOIPubMedGoogle Scholar
  2. Kimball  A, Hatfield  KM, Arons  M, James  A, Taylor  J, Spicer  K, et al.; Public Health – Seattle & King County; CDC COVID-19 Investigation Team. Public Health–Seattle and King County and CDC COVID-19 Investigation Team. Asymptomatic and presymptomatic SARS-CoV-2 infections in residents of a long-term care skilled nursing facility—King County, Washington, March 2020. MMWR Morb Mortal Wkly Rep. 2020;69:377–81. DOIPubMedGoogle Scholar
  3. Taylor  J, Carter  RJ, Lehnertz  N, Kazazian  L, Sullivan  M, Wang  X, et al.; Minnesota Long-Term Care COVID-19 Response Group. Serial testing for SARS-CoV-2 and virus whole genome sequencing inform infection risk at two skilled nursing facilities with COVID-19 outbreaks—Minnesota, April–June 2020. MMWR Morb Mortal Wkly Rep. 2020;69:1288–95. DOIPubMedGoogle Scholar
  4. Dora  AV, Winnett  A, Jatt  LP, Davar  K, Watanabe  M, Sohn  L, et al. Universal and serial laboratory testing for SARS-CoV-2 at a long-term care skilled nursing facility for veterans–Los Angeles, California, 2020. MMWR Morb Mortal Wkly Rep. 2020;69:651–5. DOIPubMedGoogle Scholar
  5. Ladhani  SN, Chow  JY, Janarthanan  R, Fok  J, Crawley-Boevey  E, Vusirikala  A, et al.; London Care Home Investigation Team. Increased risk of SARS-CoV-2 infection in staff working across different care homes: enhanced CoVID-19 outbreak investigations in London care Homes. J Infect. 2020;81:621–4. DOIPubMedGoogle Scholar
  6. Wallace  M, Hagan  L, Curran  KG, Williams  SP, Handanagic  S, Bjork  A, et al. COVID-19 in correctional and detention facilities—United States, February–April 2020. MMWR Morb Mortal Wkly Rep. 2020;69:587–90. DOIPubMedGoogle Scholar
  7. Montoya-Barthelemy  AG, Lee  CD, Cundiff  DR, Smith  EB. COVID-19 and the correctional environment: the American prison as a focal point for public health. Am J Prev Med. 2020;58:888–91. DOIPubMedGoogle Scholar
  8. Watson  C, Warmbrod  L, Vahey  R, Cicero  A, Inglesby  T, Beyrer  C, et al. COVID-19 and the US criminal justice system: evidence for public health measures to reduce risk. Baltimore: Johns Hopkins Center for Health Security; 2020.
  9. Waltenburg  MA, Victoroff  T, Rose  CE, Butterfield  M, Jervis  RH, Fedak  KM, et al.; COVID-19 Response Team. Update: COVID-19 among workers in meat and poultry processing facilities—United States, April–May 2020. MMWR Morb Mortal Wkly Rep. 2020;69:887–92. DOIPubMedGoogle Scholar
  10. Steinberg  J, Kennedy  ED, Basler  C, Grant  MP, Jacobs  JR, Ortbahn  D, et al. COVID-19 outbreak among employees at a meat-processing facility—South Dakota, March–April 2020. MMWR Morb Mortal Wkly Rep. 2020;69:1015–9. DOIPubMedGoogle Scholar
  11. Waltenburg  MA, Rose  CE, Victoroff  T, Butterfield  M, Dillaha  JA, Heinzerling  A, et al.; CDC COVID-; Emergency Response Team. Coronavirus disease among workers in food processing, food manufacturing, and agriculture workplaces. Emerg Infect Dis. 2021;27:243–9. DOIPubMedGoogle Scholar
  12. Thielen  BK, Bye  E, Wang  X, Maroushek  S, Friedlander  H, Bistodeau  S, et al. Summer outbreak of severe RSV-B disease, Minnesota, 2017 associated with emergence of a genetically distinct viral lineage. J Infect Dis. 2020;222:288–97. DOIPubMedGoogle Scholar
  13. Longmire  AG, Sims  S, Rytsareva  I, Campo  DS, Skums  P, Dimitrova  Z, et al. GHOST: global hepatitis outbreak and surveillance technology. BMC Genomics. 2017;18(Suppl 10):916. DOIPubMedGoogle Scholar
  14. Quick  J, Loman  NJ, Duraffour  S, Simpson  JT, Severi  E, Cowley  L, et al. Real-time, portable genome sequencing for Ebola surveillance. Nature. 2016;530:228–32. DOIPubMedGoogle Scholar
  15. Rounds  JM, Taylor  AJ, Eikmeier  D, Nichols  MM, Lappi  V, Wirth  SE, et al. Prospective Salmonella Enteritidis surveillance and outbreak detection using whole genome sequencing, Minnesota 2015-2017. Epidemiol Infect. 2020;148:e254. DOIPubMedGoogle Scholar
  16. To  KK, Hung  IF, Ip  JD, Chu  AW, Chan  WM, Tam  AR, et al. COVID-19 re-infection by a phylogenetically distinct SARS-coronavirus-2 strain confirmed by whole genome sequencing. Clin Infect Dis. 2020 Aug 25 [Epub ahead of print].
  17. Larson  D, Brodniak  SL, Voegtly  LJ, Cer  RZ, Glang  LA, Malagon  FJ, et al. A case of early re-infection with SARS-CoV-2. Clin Infect Dis. 2020 Sep 19 [Epub ahead of print].
  18. Van Elslande  J, Vermeersch  P, Vandervoort  K, Wawina-Bokalanga  T, Vanmechelen  B, Wollants  E, et al. Symptomatic SARS-CoV-2 reinfection by a phylogenetically distinct strain. Clin Infect Dis. 2020 Sep 5[Epub ahead of print].
  19. Gupta  V, Bhoyar  RC, Jain  A, Srivastava  S, Upadhayay  R, Imran  M, et al. Asymptomatic reinfection in two healthcare workers from India with genetically distinct SARS-CoV-2. Clin Infect Dis. 2020 Sep 23 [Epub ahead of print].
  20. Lucey  M, Macori  G, Mullane  N, Sutton-Fitzpatrick  U, Gonzalez  G, Coughlan  S, et al. Whole-genome sequencing to track SARS-CoV-2 transmission in nosocomial outbreaks. Clin Infect Dis. 2020 Jun 1 [Epub ahead of print].
  21. Oude Munnink  BB, Nieuwenhuijse  DF, Stein  M, O’Toole  Á, Haverkate  M, Mollers  M, et al.; Dutch-Covid-19 response team. Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands. Nat Med. 2020;26:1405–10. DOIPubMedGoogle Scholar
  22. Seemann  T, Lane  CR, Sherry  NL, Duchene  S, Gonçalves da Silva  A, Caly  L, et al. Tracking the COVID-19 pandemic in Australia using genomics. Nat Commun. 2020;11:4376. DOIPubMedGoogle Scholar
  23. Rockett  RJ, Arnott  A, Lam  C, Sadsad  R, Timms  V, Gray  KA, et al. Revealing COVID-19 transmission in Australia by SARS-CoV-2 genome sequencing and agent-based modeling. Nat Med. 2020;26:1398–404. DOIPubMedGoogle Scholar
  24. US Food and Drug Administration. CDC 2019-novel coronavirus (2019-nCoV) real-time RT-PCR diagnostic panel [cited 2020 Dec 10]. https://www.fda.gov/media/134922/download
  25. Quick  J. nCoV-2019 sequencing protocol V.1 [cited 2020 Dec 10].
  26. Sevinsky  J, Nassiri  A, Blankenship  H, Young  E, Libuit  K, Oakeson  K, et al. SARS-CoV-2 Sequencing on Illumina MiSeq using ARTIC protocol: part 2—Illumina DNA flex protocol V.1 [cited 2020 Dec 10].
  27. Hadfield  J, Megill  C, Bell  SM, Huddleston  J, Potter  B, Callender  C, et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics. 2018;34:4121–3. DOIPubMedGoogle Scholar
  28. Katoh  K, Standley  DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80. DOIPubMedGoogle Scholar
  29. 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
  30. Letunic  I, Bork  P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019;47(W1):W256–9. DOIPubMedGoogle Scholar
  31. Elbe  S, Buckland-Merrett  G. Data, disease and diplomacy: GISAID’s innovative contribution to global health. Glob Chall. 2017;1:33–46. DOIPubMedGoogle Scholar
  32. Gonzalez-Reiche  AS, Hernandez  MM, Sullivan  MJ, Ciferri  B, Alshammary  H, Obla  A, et al. Introductions and early spread of SARS-CoV-2 in the New York City area. Science. 2020;369:297–301. DOIPubMedGoogle Scholar
  33. Grabowski  DC, Mor  V. Nursing home care in crisis in the wake of COVID-19. JAMA. 2020;324:23–4. DOIPubMedGoogle Scholar

Main Article

Page created: May 19, 2021
Page updated: July 18, 2021
Page reviewed: July 18, 2021
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
file_external