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

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Science  17 Jul 2020:
Vol. 369, Issue 6501, pp. 297-301
DOI: 10.1126/science.abc1917
  • Fig. 1 SARS-CoV-2 confirmed cases.

    Number of patients with positive molecular tests for SARS-CoV-2 up to 31 March 2020, compared with the daily number of patients with influenza A and B tests in the 2019–2020 season. The shaded area indicates the period in which the samples sequenced in this study were obtained (29 February to 18 March). The number of positive tests per virus was not normalized for the number of tested samples.

  • Fig. 2 Phylogenetic relationships of SARS-CoV-2 from New York and other global strains.

    (A) ML phylodynamic inference of 84 SARS-CoV-2 sequences from New York from this study in a global background of 2363 sequences available in the GISAID EpiCoV database as of 1 April 2020. Branches are colored according to the region of origin. Tip circles (red) indicate the position of the 84 New York sequences. Clades that contain New York sequences are highlighted, with names shown on the right; the local transmission clusters are indicated by the arrow. The node positions for the transmission events listed in Table 1 are marked by the numbers in white circles. The displayed time tree was inferred under a strict clock model with a fixed substitution rate of 0.8 × 10–3. (B) Stacked barplot showing the fraction of sequences per region by clade. (C) Local transmission clusters on the ML tree showing the source of cases by county. Bootstrap support values ≥70% are shown; sibling clusters are collapsed for easier visualization. The mutation identified specific to the community transmission cluster is indicated. The scale bar at the bottom indicates the number of nucleotide substitutions per site.

  • Fig. 3 Distribution of the geographic location of the patients with COVID-19 from which viral isolates were sequenced.

    (A) Distribution of 74 sequenced cases with available ZIP code information across NYC boroughs and neighborhoods. Neighborhoods are shaded according to the number of cases that were sampled. (B) Breakdown of sequenced cases according to phylogenetic clades across NYC boroughs and Westchester County. Cases without available ZIP code information are indicated as “Unknown.”

  • Table 1 Inferred SARS-CoV-2 virus transmission events related to NYC.

    CladeFirst NYC sequenceMutationsNodeCasesEvent typeInferred sourcetMRCA 95% HPD*
    A1a4 MarchORF3a:G251V, C14805T15Putative introductionEurope25 January to 6 February
    A2a11 MarchS:D624G, ORF1b:P314L24Untracked transmissionN/A5 January to 29 January
    S:D624G, ORF1b:P314L,OFR3a:Q57H35Putative introductionEurope/North America31 January to 11 February
    S:D624G, ORF1b:P314L,OFR3a:Q57H, ORF1a:T265I464Putative introductionEurope/North America15 February to 19 February
    A329 FebruaryORF1a:V378I51Travel
    exposure
    Middle East (epi link)29 February
    (Test date)
    B4 MarchORF8:L84S61Travel
    exposure
    Europe (epi link)4 March
    (Test date)
    71Putative introductionEurope/Asia2 February to 22 February
    81Putative introductionNorth America/Domestic28 January to 24 February
    B117 MarchC18060T, ORFb:P1427L91Putative introductionDomestic26 January to 7 February
    B414 MarchN:S202N, ORF14:V94I101Putative introductionAsia/Oceania31 January to 25 February

    *Inferred 95% High Posterior Density (HPD) interval for the mean time of tMRCA from the root of the node containing New York–origin strains with ≥70% bootstrap support value in the ML tree and ≥0.9 posterior probability in the maximum clade credibility (MCC) trees inferred for major clades. The 95% HPD intervals shown correspond to the MCC trees inferred by using a strict clock model. Travel exposures and putative introductions are shown for the cases described in this study.

    Supplementary Materials

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

      Ana S. Gonzalez-Reiche, Matthew M. Hernandez, Mitchell J. Sullivan, Brianne Ciferri, Hala Alshammary, Ajay Obla, Shelcie Fabre, Giulio Kleiner, Jose Polanco, Zenab Khan, Bremy Alburquerque, Adriana van de Guchte, Jayeeta Dutta, Nancy Francoeur, Betsaida Salom Melo, Irina Oussenko, Gintaras Deikus, Juan Soto, Shwetha Hara Sridhar, Ying-Chih Wang, Kathryn Twyman, Andrew Kasarskis, Deena R. Altman, Melissa Smith, Robert Sebra, Judith Aberg, Florian Krammer, Adolfo García-Sastre, Marta Luksza, Gopi Patel, Alberto Paniz-Mondolfi, Melissa Gitman, Emilia Mia Sordillo, Viviana Simon, Harm van Bakel

      Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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      • Materials and Methods
      • Figs. S1 to S3
      • Tables S1 and S2
      • References
      MDAR Reproducibility Checklist
      Data File S1
      Data File S2

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