Cryptic transmission of SARS-CoV-2 in Washington state

  1. Trevor Bedford
  2. Alexander L. Greninger
  3. Pavitra Roychoudhury
  4. Lea M. Starita
  5. Michael Famulare
  6. Meei-Li Huang
  7. Arun Nalla
  8. Gregory Pepper
  9. Adam Reinhardt
  10. Hong Xie
  11. Lasata Shrestha
  12. Truong N. Nguyen
  13. Amanda Adler
  14. Elisabeth Brandstetter
  15. Shari Cho
  16. Danielle Giroux
  17. Peter D. Han
  18. Kairsten Fay
  19. Chris D. Frazar
  20. Misja Ilcisin
  21. Kirsten Lacombe
  22. Jover Lee
  23. Anahita Kiavand
  24. Matthew Richardson
  25. Thomas R. Sibley
  26. Melissa Truong
  27. Caitlin R. Wolf
  28. Deborah A. Nickerson
  29. Mark J. Rieder
  30. Janet A. Englund
  31. The Seattle Flu Study Investigators
  32. James Hadfield
  33. Emma B. Hodcroft
  34. John Huddleston
  35. Louise H. Moncla
  36. Nicola F. Müller
  37. Richard A. Neher
  38. Xianding Deng
  39. Wei Gu
  40. Scot Federman
  41. Charles Chiu
  42. Jeffrey S. Duchin
  43. Romesh Gautom
  44. Geoff Melly
  45. Brian Hiatt
  46. Philip Dykema
  47. Scott Lindquist
  48. Krista Queen
  49. Ying Tao
  50. Anna Uehara
  51. Suxiang Tong
  52. Duncan MacCannell
  53. Gregory L. Armstrong
  54. Geoffrey S. Baird
  55. Helen Y. Chu
  56. Jay Shendure
  57. Keith R. Jerome
  58. Helen Y. Chu
  59. Michael Boeckh
  60. Janet A. Englund
  61. Michael Famulare
  62. Barry R. Lutz
  63. Deborah A. Nickerson
  64. Mark J. Rieder
  65. Lea M. Starita
  66. Matthew Thompson
  67. Jay Shendure
  68. Trevor Bedford
  69. Amanda Adler
  70. Elisabeth Brandstetter
  71. Shari Cho
  72. Chris D. Frazar
  73. Danielle Giroux
  74. Peter D. Han
  75. James Hadfield
  76. Shichu Huang
  77. Michael L. Jackson
  78. Anahita Kiavand
  79. Louise E. Kimball
  80. Kirsten Lacombe
  81. Jennifer Logue
  82. Victoria Lyon
  83. Kira L. Newman
  84. Matthew Richardson
  85. Thomas R. Sibley
  86. Monica L. Zigman Suchsland
  87. Melissa Truong
  88. Caitlin R. Wolf

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Abstract

The history of how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread around the planet has been far from clear. Several narratives have been propagated by social media and, in some cases, national policies were forged in response. Now that many thousands of virus sequences are available, two studies analyzed some of the key early events in the spread of SARS-CoV-2. Bedford et al. found that the virus arrived in Washington state in late January or early February. The viral genome from the first case detected had mutations similar to those found in Chinese samples and rapidly spread and dominated subsequent undetected community transmission. The other viruses detected had origins in Europe. Worobey et al. found that early introductions into Germany and the west coast of the United States were extinguished by vigorous public health efforts, but these successes were largely unrecognized. Unfortunately, several major travel events occurred in February, including repatriations from China, with lax public health follow-up. Serial, independent introductions triggered the major outbreaks in the United States and Europe that still hold us in the grip of control measures.

Science , this issue p. 571 , p. 564

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  1. Version published to 10.1126/science.abc0523
  2. ScreenIT

    SciScore for 10.1101/2020.04.02.20051417: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Filtered reads were de novo assembled using SPAdes (30) and contigs were ordered against the reference using BWA-MEM (31).
    SPAdes
    suggested: (SPAdes, RRID:SCR_000131)
    BWA-MEM
    suggested: (Sniffles, RRID:SCR_017619)
    Consensus sequences were annotated using Prokka (32) and deposited to Genbank (accessions pending)
    Prokka
    suggested: (Prokka, RRID:SCR_014732)
    ) bioinformatics pipeline Augur to align genomes via MAFFT v7.4 (33), build maximum likelihood phylogeny via IQTREE v1.6 (34) and reconstruct nucleotide and amino acid changes on the ML tree.
    MAFFT
    suggested: (MAFFT, RRID:SCR_011811)
    Additionally, 293 SARS-CoV-2 aligned genomes from the WA1 outbreak clade were analyzed in BEAST (35) to estimate time of common ancestor and rate of epidemic growth.
    BEAST
    suggested: (BEAST, RRID:SCR_010228)

    Results from OddPub: Thank you for sharing your code and data.

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

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  3. Version published to 10.1101/2020.04.02.20051417v2 on medRxiv
  4. Version published to 10.1101/2020.04.02.20051417v1 on medRxiv