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

Abstract

New York City (NYC) has emerged as one of the epicenters of the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. To identify the early transmission events underlying the rapid spread of the virus in the NYC metropolitan area, we sequenced the virus that causes coronavirus disease 2019 (COVID-19) in patients seeking care at the Mount Sinai Health System. Phylogenetic analysis of 84 distinct SARS-CoV-2 genomes indicates multiple, independent, but isolated introductions mainly from Europe and other parts of the United States. Moreover, we found evidence for community transmission of SARS-CoV-2 as suggested by clusters of related viruses found in patients living in different neighborhoods of the city.

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.”