Data for the paper Dynamics of Eastern equine encephalitis virus during the 2019 outbreak in the Northeast United States https://www.medrxiv.org/content/10.1101/2023.03.06.23286851v1
- genomic_data: the alignment and associated metadata. This contains newly sequenced samples, and publicly available samples from genbank.
- phylogenetic_data: raw and processed output files from BEAST analyses, and XMLs. Also includes "recorded_outbreaks.csv", used to generate starting points for skygrid covariates prior to 2003
"combined_data_nomosquito" is all of the spatial level data combined but with mosquito specific data removed until approvals come through
"recorded_outbreaks.csv" is mostly from Tricia Corrin, Rachel Ackford, Mariola Mascarenhas, Judy Greig, and Lisa A. Waddell. Eastern Equine Encephalitis Virus: A Scoping Review of the Global Evidence. Vector-Borne and Zoonotic Diseases.May 2021.305-320.http://doi.org/10.1089/vbz.2020.2671 but with some supplementation from references detailed in the CSV. Used to generate Skygrid covariate starting values for before 2003.
Shapefiles for maps were obtained from gadm.org
Post-2003 case data has also been removed as it was obtained from ArboNET - available on request from https://wwwn.cdc.gov/arbonet/maps/ADB_Diseases_Map/index.html
Figure one: A) Arbonet data B) [state]_melanura_ir.csv C) Arbonet data D) Arbonet data
Figure two: A) study_dataset.csv B) study_dataset.csv C) study_dataset.csv D) combined_DTA_all_states.mcc E) DTA_all_states.jumps.csv
Figure three: A) new_introductions.tree B) introduction_times.csv C) location_outbreaks.csv
Figure four: introduction_times.csv new_introductions.trees location_outbreaks.csv subtree_[XX].csv
Figure five: A) Arbonet data and [state]_mosquito.csv B) combined_data.csv C) D)
Figure S1: tempest_export.tsv
Figure S2: A and B) Arbonet data and [state]_melanura_ir.csv C) mosquito_abundance_by_week_CT_all_mosq.csv D) combined_data.csv
Figure S3: All of the skygrid log_files
Figure S4: Celis-Murillo, A., Malorodova, M., and Nakash, E., 2022, North American Bird Banding Program Dataset 1960-2022 retrieved 2022-07-14: U.S. Geological Survey data release, https://doi.org/10.5066/P9BSM38F.
Figure S5: Arbonet data
Figure S6: Model output data