Introductions and early spread of SARS-CoV-2 in the New York City area

  1. Ana S. Gonzalez-Reiche
  2. Matthew M. Hernandez
  3. Mitchell J. Sullivan
  4. Brianne Ciferri
  5. Hala Alshammary
  6. Ajay Obla
  7. Shelcie Fabre
  8. Giulio Kleiner
  9. Jose Polanco
  10. Zenab Khan
  11. Bremy Alburquerque
  12. Adriana van de Guchte
  13. Jayeeta Dutta
  14. Nancy Francoeur
  15. Betsaida Salom Melo
  16. Irina Oussenko
  17. Gintaras Deikus
  18. Juan Soto
  19. Shwetha Hara Sridhar
  20. Ying-Chih Wang
  21. Kathryn Twyman
  22. Andrew Kasarskis
  23. Deena R. Altman
  24. Melissa Smith
  25. Robert Sebra
  26. Judith Aberg
  27. Florian Krammer
  28. Adolfo García-Sastre
  29. Marta Luksza
  30. Gopi Patel
  31. Alberto Paniz-Mondolfi
  32. Melissa Gitman
  33. Emilia Mia Sordillo
  34. Viviana Simon
  35. Harm van Bakel

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Abstract

Deaths caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in New York City (NYC) during the spring of 2020 have vastly exceeded those reported in China and many other countries. What were the early events that led to such a severe outbreak? Gonzalez-Reiche et al. sampled some of the early patients seeking assistance in February and March of 2020 at the Mount Sinai Health System. Phylogenetic analysis of virus sequences in these people, who were drawn from across NYC, showed that the virus had been independently introduced many times from Europe and elsewhere in the United States. Subsequent clusters of community transmission occurred. The focus of infection in NYC is a marker of the role this city plays as a two-way hub for human movement.

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  1. Version published to 10.1126/science.abc1917
  2. ScreenIT

    SciScore for 10.1101/2020.04.08.20056929: (What is this?)

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

    Table 1: Rigor

    Institutional Review Board StatementIRB: Ethics statement: This study was reviewed and approved by the Institutional Review Board of the Icahn School of Medicine at Mount Sinai.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.
    Sex as a biological variablenot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    Additionally, a conserved region in the E-gene was chosen for pan-Sarbecovirus detection including SARS-CoV-2.
    SARS-CoV-2
    suggested: (Active Motif Cat# 91351, RRID:AB_2847848)
    For genomes sequenced on the PacBio Sequel II platform, high-quality (>Q20) circular consensus sequence (CCS) reads were first generated from raw subreads, using the SMRTLink analysis suite, v8.0 with a minimum of 3 passes.
    SMRTLink
    suggested: None
    Trimmed reads were aligned to SARS-CoV-2 genome MN908947.3 using minimap2 version 2.17-r941 (Li 2018), and consensus sequence was called using Pilon v1.23 (Walker et al. 2014), allowing for all variant types (single nucleotide variants, small insertions/deletions, large insertions/deletions or block substitution events, and local misassemblies).
    Pilon
    suggested: (Pilon , RRID:SCR_014731)
    The ML tree was inspected in TempEst for outliers that deviated from a temporal root-to-tip divergence (Andrew Rambaut et al. 2016).
    TempEst
    suggested: (TempEst, RRID:SCR_017304)
    Tree visualization and annotations were done in FigTree v1.4.4 (A.
    FigTree
    suggested: (FigTree, RRID:SCR_008515)
    Maps were created in ArcGIS Desktop using the ArcMap v10.6 application available through the Environmental Systems Research Institute (ESRI).
    ArcMap
    suggested: None

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    A limitation of our analysis is the relatively small number of isolates from cases identified in the first week of March 2020 which means that our model relies on inferences based on sequences deposited in the GISAID database. Since sequencing efforts vary by country, the fraction of sequences available by region/country is not necessarily representative of the number of cases reported for each of these regions. Thus, some of these inferences may change as more complete and representative SARS-CoV-2 sequences become available. Taken together, we provide a first analysis of the SARS-CoV-2 viral genotypes collected from patients seeking medical care. We find that New York City, as an international hub, provides not only a snapshot of the diversity of disease-causing SARS-CoV-2 at the global level but also informs on the dynamics of the pandemic at the local level. Future studies are needed to define viral phenotypes and explore the impact of the public health measures such as closing of educational facilities (March 18, 2020), closing of non-essential services (March 20, 2020) and stay at home orders (March 22, 2020) on community transmission.

    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.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2020.04.08.20056929v2 on medRxiv
  4. Version published to 10.1101/2020.04.08.20056929v1 on medRxiv