Overview

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
Iraq/Kurdistan/Duhok 535
Jordan/Amman 483
Jordan/Aqaba 41
Jordan/Irbid 58
Jordan/Mafraq 2
Jordan/Zarqa 5
Mexico/Baja California 26
Mexico/Baja California Sur/Los Cabos 1
Mexico/Baja California/ 1
Mexico/Baja California/Ensenada 53
Mexico/Baja California/Mexicali 420
Mexico/Baja California/Reforma 1
Mexico/Baja California/Rosarito 11
Mexico/Baja California/San Quintin 1
Mexico/Baja California/Tecate 9
Mexico/Baja California/Tijuana 1400
Mexico/Chiapas/Baja California 1
Mexico/Chihuahua 9
Mexico/Chihuahua/Chihuahua 39
Mexico/Chihuahua/Ciudad Juarez 54
Mexico/Coahuila/Saltillo 109
Mexico/Coahuila/Torreon 115
Mexico/Durango/Durango 3
Mexico/Jalisco/Guadalajara Tetlan 1
Mexico/Jalisco/Puerto Vallarta 51
Mexico/Jalisco/Vallarta 14
Mexico/Nuevo Leon/Guadalupe 62
Mexico/Nuevo Leon/Monterrey 97
Mexico/Nuevo Leon/San Nicolas De Los Garza 66
Mexico/Nuevo Leon/Santa Catarina 32
Mexico/Sinaloa/Culiacan 347
Mexico/Sinaloa/Los Mochis 119
Mexico/Sinaloa/Mazatlan 103
Mexico/Sonora 32
Mexico/Sonora/Hermosillo 61
Mexico/Sonora/Obregon 66
Mexico/Sonora/San Luis Rio Colorado 35
Mexico/Sonora/San Luis Río Colorado 2
Mexico/Tamaulipas/Reynosa 1
Mexico/Tijuana 1
Mexico/Tlaxcala/Chiautempan 1
Pakistan/Islamabad Capital Territory/Islamabad 51
Pakistan/Punjab/Lahore 7
USA/Alaska/Anchorage Municipality 1
USA/Arizona/Maricopa 2
USA/Arizona/Pima 2
USA/Arizona/Yuma 1
USA/California/Alameda 4
USA/California/City and County of San Francisco 1
USA/California/Contra Costa 5
USA/California/Cruise_Ship_1 8
USA/California/Cruise_Ship_2 32
USA/California/Davis 1
USA/California/El Dorado 5
USA/California/Fresno 2
USA/California/Glenn 1
USA/California/Imperial 198
USA/California/Kern 3
USA/California/Los Angeles 274
USA/California/Los Angeles County 72
USA/California/Marin 2
USA/California/Modesto 1
USA/California/Monterey 1
USA/California/Orange 152
USA/California/Orange County 9
USA/California/Placer 1
USA/California/Riverside 406
USA/California/Sacramento 2
USA/California/San Bernardino 43
USA/California/San Diego 66525
USA/California/San Francisco 18
USA/California/San Mateo 53
USA/California/Santa Barbara 3
USA/California/Santa Barbara 1
USA/California/Santa Clara 4
USA/California/Sonoma 1
USA/California/Sutter 1
USA/California/Tulare 1
USA/California/Ventura 4
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/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/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/Pennsylvania/Allegheny 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

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]

Data

Protocols

Collaborators

San Diego Partners
SEARCH Alliance, San Diego

San Diego County Health and Human Services Agency
Sarah Stous, Ashleigh Murphy, Raymond Chinn, Temet McMichael, Nikos Gurfield, JD Malone, Brett Austin, Eric McDonald, Seema Shah

San Diego Zoo
Patricia Gaffney, Laura Keener, Lauren Howard, Jennifer Burchell, Nadine Lamberski

Imperial County Public Health Department
Holly Maag, Stephen Munday, Paula Kriner

Los Angeles County Department of Public Health
Peera Hemarajata, Taylor Burleson, Sophia Serrano, Nichole Green

California Department of Public Health
Debra Wadford, Nikki Baumrind, Phacharee Arunleung, Kathleen Jacobson, Cindy Wong, Dominick Morales, John Bell, Sharon Messenger, Alice Chen

UCSD – Center for Advanced Laboratory Medicine
Jenny Shin, David Pride

UCSD – Division of Infectious Diseases and Global Public Health
Sara Browne

Rady Children Hospital, San Diego
Christina Clarke, Michelle Vanderpool, Teresa Mueller, Denise Malicki, David Dimmock, Charlotte Hobbs, Stephen Kingsmore

Scripps Health, San Diego
Ellen Stefanski, Ian Mchardy, Michael Quigley

Sharp Health, San Diego
Aaron Harding, Jacquelyn Berumen, Cathy Woerle, Art Mendoza, Omid Bakhtar

Helix, San Diego
Nicole Washington, Simon White, Geraint Levan, Kelly Schiabor Barrett, Elizabeth Cirulli, Alexandre Bolze, Charlotte Rivera-Garcia, Ryan Cho, Jason Nguyen, Sherry Wang, Jimmy Ramirez, Tyler Cassens, Efren Sandoval, Magnus Isaksson, William Lee, David Becker, Marc Laurent, James Lu

New Orleans
Allison Smither, Gilberto Sabino-Santos, Patricia Snarski, Lilia Melnik, Antoinette Bell, Kaylynn Genemaras, Arnaud Drouin, Dahlene Fusco, Robert Garry

Louisiana
Jeremy Kamil, Vaughn Cooper

Salud Digna, A.C., México
Abraham Campos Romero, Miguel A. Fernandez Rojas, Marco Antonio Luna Ruiz-Esparza, Jose Luis Moreno Camacho, Abraham Garcia Gil

Centro de Diagnóstico COVID-19, Tijuana, México
Idanya Rubí Serafín Higuera, Manuel Sanchez Alavez

Genomica Lab Molecular, México
Jonathan Gonzalez Garcia, Jose Roman Chavez Mendez, Jose Horacio Reyna Verdugo, Martin Gonzalez Ibarra, Luis Alberto Rangel Gonzalez

Infectolab, México
Samuel Navarro Alvarez, Carlos A. Cota Haros, Octavio Renteria Pacheco

Biolab, Jordan
Issa Abu-Dayyeh, Ahmad Tibi, Lama Hussein, Lina Mohammad, Zein Naber, Amid Abdelnour

Shifa Tameer-e-Millat University/Islamabad Diagnostics, Pakistan
Fouzia Sadiq, Muhammad Aslam, Rizwan Uppal, Umar Saeed

Analysis Partners
Marc Suchard, UCLA
Lauren Gardner, Johns Hopkins
Philippe Lemey, KU Leuven
Alexander Watts & Kamran Khan, BlueDot
Emma Hodcroft, Nextstrain

Funding

CDC