NYU Data Catalog

NYU Dataset

Dataset and Code to Model Dispersal Dynamics of SARS-CoV-2 Lineages During the First Epidemic Wave in New York City

UID: 10441
Author(s): Simon Dellicour, Samuel L. Hong, Bram Vrancken, Antoine Chaillon, Mandev S. Gill...
* Corresponding Author
Description
To construct a fixed time-scaled phylogenetic tree, the investigators combined 828 viral genome sequences obtained from COVID-19 patients at NYU Langone Health between March and May 2020 with 1,899 background sequences that were contributed to the Nextstrain repository. A total of 2,727 SARS-CoV-2 genomic sequences are available in the dataset. The supporting R code included with the dataset will produce phylogenetic trees through discrete and continuous Bayesian phylogeographic methods.
Timeframe
2020
Geographic Coverage
New York (State) - New York City
Subject of Study
Homo sapiens
Subject Domain
COVID-19
Genomics
Infectious Disease
Keywords
Coronavirus
COVID-19
Epidemiology
Genetic Data
Genomics
Infectious Diseases
Medical Geography
Mutation
New York City
Pandemics
Phylogeny
RNA
RNA Sequencing
SARS-CoV-2
Viral Genome
Viruses

Access

Restrictions
Free to All
Instructions
R code and datasets are available publicly using the Access Link to the Github repository.
Access via Github

Datasets and code

Associated Publications
Dellicour S, Hong SL, Vrancken B, Chaillon A, Gill MS, Maurano MT, Ramaswami S, Zappile P, Marier C, Harkins GW, Baele G, Duerr R, Heguy A. Dispersal dynamics of SARS-CoV-2 lineages during the first epidemic wave in New York City. PLoS Pathog. 2021 May 20;17(5):e1009571. doi: 10.1371/journal.ppat.1009571.
Data Type
Genomic
Geospatial
Study Type
Observational
Grant Support
P30 CA016087/NCI NIH
R35 GM119703/NIGMS NIH
U01 AI152151/NIAID NIH
R01 AI122953/NIAID NIH
12U7121N/Research Foundation - Flanders
G0D5117N/Research Foundation - Flanders
K24 AI100665/NIAID NIH
G0E1420N/Research Foundation - Flanders
G098321N/Research Foundation - Flanders
C14/18/094/Internal Funds KU Leuven
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