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Consensus sequences

All consensus sequences will be deposited on GISAID and on NCBI under BioProject ID PRJNA612578. metadata.csv contains collection dates, location, originating labs and sequencing metrics: coverage and average depth.

Location Number of Sequences
Alabama/Madison 1
Arizona/Maricopa 3
Arizona/Yuma 1
California/Alameda 8
California/Contra Costa 3
California/El Dorado 1
California/Fresno 1
California/Kern 1
California/Merced 1
California/Nevada 2
California/Placer 1
California/Sacramento 1
California/San Francisco 3
California/San Mateo 1
California/Santa Barbara 3
California/Santa Clara 10
California/Stanislaus 1
California/Ventura 1
Florida/Orange 2
Florida/Volusia 1
Illinois/Champaign 1
Iraq/Kurdistan/Duhok 535
Jordan/Amman 483
Jordan/Aqaba 41
Jordan/Irbid 58
Jordan/Mafraq 2
Jordan/Zarqa 5
Maryland/Montgomery 1
Mexico/Baja California 26
Mexico/Baja California Sur/Los Cabos 1
Mexico/Baja California/ 1
Mexico/Baja California/Ensenada 58
Mexico/Baja California/Mexicali 426
Mexico/Baja California/Reforma 1
Mexico/Baja California/Rosarito 12
Mexico/Baja California/San Quintin 1
Mexico/Baja California/Tecate 9
Mexico/Baja California/Tijuana 1449
Mexico/Chiapas/Baja California 1
Mexico/Chihuahua 9
Mexico/Chihuahua/Chihuahua 40
Mexico/Chihuahua/Ciudad Juarez 61
Mexico/Coahuila/Saltillo 135
Mexico/Coahuila/Torreon 170
Mexico/Durango/Durango 4
Mexico/Jalisco/Guadalajara 93
Mexico/Jalisco/Guadalajara Tetlan 1
Mexico/Jalisco/Puerto Vallarta 53
Mexico/Jalisco/Vallarta 14
Mexico/Jalisco/Zapopan 4
Mexico/Nuevo Leon/Guadalupe 75
Mexico/Nuevo Leon/Monterrey 195
Mexico/Nuevo Leon/San Nicolas De Los Garza 116
Mexico/Nuevo Leon/San Nicolas de los Garza 65
Mexico/Nuevo Leon/Santa Catarina 45
Mexico/Sinaloa/Culiacan 453
Mexico/Sinaloa/Los Mochis 123
Mexico/Sinaloa/Mazatlan 107
Mexico/Sonora 32
Mexico/Sonora/Hermosillo 62
Mexico/Sonora/Obregon 66
Mexico/Sonora/San Luis Rio Colorado 35
Mexico/Sonora/San Luis R������o Colorado 2
Mexico/Tamaulipas/Reynosa 1
Mexico/Tijuana 1
Mexico/Tlaxcala/Chiautempan 1
Michigan/Genesee 1
Minnesota/Dakota 1
Nebraska/Sarpy 2
Nevada/Clark 4
New Jersey/Union 1
New York/Bronx 1
New York/Kings 1
New York/New York 1
New York/Rensselaer 1
Oregon/Benton 1
Pakistan/Islamabad Capital Territory/Islamabad 51
Pakistan/Punjab/Lahore 7
Pennsylvania/Philadelphia 1
Texas/Collin 1
Texas/Fort Bend 1
USA/Alaska/Anchorage Municipality 1
USA/Arizona/Maricopa 2
USA/Arizona/Pima 3
USA/Arizona/Yuma 1
USA/California/ 2
USA/California/Alameda 13
USA/California/Bellflower 1
USA/California/City and County of San Francisco 1
USA/California/Contra Costa 6
USA/California/Cruise_Ship_1 8
USA/California/Cruise_Ship_2 32
USA/California/Davis 1
USA/California/Downey 1
USA/California/El Dorado 5
USA/California/Fresno 2
USA/California/Glenn 1
USA/California/Humboldt 1
USA/California/Imperial 280
USA/California/Inglewood 1
USA/California/Kern 5
USA/California/Long Beach 1
USA/California/Los Angeles 496
USA/California/Los Angeles 1
USA/California/Los Angeles County 72
USA/California/Madera 1
USA/California/Marin 2
USA/California/Mariposa 1
USA/California/Modesto 1
USA/California/Monterey 2
USA/California/Murrieta 2
USA/California/Napa 1
USA/California/Orange 280
USA/California/Orange County 9
USA/California/Placer 11
USA/California/RIverside 1
USA/California/Riverside 640
USA/California/Sacramento 6
USA/California/San Bernardino 84
USA/California/San Diego 96387
USA/California/San Francisco 20
USA/California/San Mateo 59
USA/California/Santa Barbara 5
USA/California/Santa Clara 9
USA/California/Santa Cruz 1
USA/California/Solano 3
USA/California/Sonoma 1
USA/California/Stanislaus 1
USA/California/Sutter 1
USA/California/Temecula 1
USA/California/Tulare 1
USA/California/Ventura 5
USA/Colorado/Boulder 1
USA/Florida/Saint Johns 1
USA/Hawaii/Honolulu 1
USA/Idaho/Ada 1
USA/Illinois/Cook 2
USA/Illinois/DuPage 2
USA/Illinois/Rock Island 1
USA/Indiana/Johnson 1
USA/Kentucky/Jefferson 1
USA/Louisiana/New Orleans 143
USA/Maryland/Anne Arundel 1
USA/Maryland/Montgomery 1
USA/Massachusetts/Middlesex 1
USA/Michigan/Wayne 1
USA/Minnesota/Anoka 1
USA/Minnesota/Ramsey 1
USA/Missouri/St. Louis 1
USA/Nevada/Clark 1
USA/Nevada/Douglas 1
USA/New Jersey/Monmouth 1
USA/New York/Dutchess 1
USA/New York/Orange 1
USA/New York/Warren 1
USA/New York/Westchester 1
USA/North Carolina/Durham 1
USA/Ohio/Clark 1
USA/Ohio/Hamilton 1
USA/Oklahoma/Tulsa 1
USA/Oregon/Klamath 1
USA/Pennsylvania/Allegheny 1
USA/Pennsylvania/Erie 1
USA/Pennsylvania/Montgomery 1
USA/South Carolina/Spartanburg 1
USA/Tennessee/Grainger 1
USA/Tennessee/Sumner 1
USA/Texas/Bell 1
USA/Texas/Montgomery 2
USA/Utah/Salt Lake 1
USA/Virginia/Fairfax 1
USA/Washington/King 3
USA/Washington/Kitsap 1
USA/West Virginia/Kanawha 1
USA/Wisconsin/Bayfield 1
USA/Wisconsin/Dane 1
USA/Wyoming/Albany 1
Utah/Utah 1
Virginia/Arlington 2
Virginia/Northumberland 1

Raw read files

Raw read files for both Illumina and Oxford Nanopore data are available on,

The sequencing is being performed using an amplicon-based sequencing scheme using PrimalSeq with artic nCoV-2019 scheme.

Nanopore data was processed using the artic-nCoV019 pipeline with minimap2 and medaka. Illumina data was processed using iVar (Grubaguh et al. Genome Biology 2019) with bwa.

Disclaimer. Please note that this data is still based on work in progress and should be considered preliminary. If you intend to include any of these data in publications, please let us know – otherwise please feel free to download and use without restrictions. We have shared this data with the hope that people will download and use it, as well as scrutinize it so we can improve our methods and analyses. Please contact us if you have any questions or comments – we’ll buy beers for #ResearchParasites that spot flaws and faults in the data and come up with improvements!

Andersen Lab The Scripps Research Institute La Jolla, CA, USA [email protected]

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During the winter of 2020-2021, a new genotype of highly-pathogenic (HP) H5N1 avian influenza A virus emerged in Europe, comprising a reassortant between the epizootic HP clade H5N8 and local low pathogenicity wildfowl strains. This new genotype caused record levels of infections in farmed poultry throughout Europe and quickly traveled, via waterfowl flyways, into North America, Africa and East…

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San Diego County Health and Human Services Agency
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San Diego Zoo
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Centro de Diagnóstico COVID-19, Tijuana, México
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Genomica Lab Molecular, México
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Lauren Gardner, Johns Hopkins
Philippe Lemey, KU Leuven
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