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
Jordan/Amman 483
Jordan/Aqaba 41
Jordan/Irbid 58
Jordan/Mafraq 2
Jordan/Zarqa 5
MEX/Baja California/Ensenada 16
MEX/Baja California/Mexicali 254
MEX/Baja California/Rosarito 1
MEX/Baja California/Tecate 7
MEX/Baja California/Tijuana 857
MEX/Sonora/San Luis Río Colorado 35
USA/Alaska/Anchorage 1
USA/Arizona/Yuma 1
USA/California/Contra Costa 3
USA/California/Cruise_Ship_1 8
USA/California/Cruise_Ship_2 32
USA/California/Davis 1
USA/California/El Dorado 2
USA/California/Fresno 1
USA/California/Imperial 151
USA/California/Kern 2
USA/California/Los Angeles 109
USA/California/Modesto 1
USA/California/Orange 19
USA/California/Riverside 91
USA/California/Sacramento 1
USA/California/San Bernadino 6
USA/California/San Diego 13615
USA/California/San Mateo 1
USA/California/Santa Barbara 4
USA/California/Santa Clara 1
USA/California/Sonoma 1
USA/California/Sutter 1
USA/California/Ventura 3
USA/California/DuPage 1
USA/California/Rock Island 1
USA/Louisiana/New Orleans 143
USA/Minnesota/Ramsey 1
USA/Ohio/Hamilton 1
USA/Oklahoma/Tulsa 1
USA/Pennsylvania/Allegheny 1
USA/Tennessee/Grainger 1
USA/Texas/Montgomery 1
USA/Utah/Salt Lake 1
USA/Washington/King 3
USA/Washington/Kitsap 1
USA/West Virginia/Kanawha 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]


NextStrain builds we maintain to display our data in context of other publicly available data:

San DiegoCalifornia, Mexico, Mexico-California border region, New Orleans/Louisiana, New Mexico, Jordan.

Nextstrain Narratives


Age distribution of COVID-19 cases in San Diego County

| Data, Narrative | No Comments
To understand the spread of COVID-19 in San Diego, we looked at the age distribution of COVID-19 over time (Figure 1). Data for this analysis was provided by the Epidemiology and Immunization Services Branch of the County of San Diego Health and Human Services agency through the San Diego Open GIS Data Portal. The visualization was inspired by Gytis Dudas's…

Narrative 2 | Cross-border virus transmission

| Data, Narrative | No Comments
English: To gain insights into the the emergence, spread, and transmission of COVID-19 in our community, we are working with a large number of partners to sequence SARS-CoV-2 samples from patients in San Diego and across the border in Tijuana. In this preliminary analysis we look at the how the outbreaks are connected between California, USA and Baja California, (more…)



San Diego Partners
SEARCH Alliance, San Diego

San Diego County Health and Human Services Agency
Tracy Basler, Jovan Shephard, Raymond Chinn, Nikos Gurfield, Brett Austin, Eric McDonald

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

California Department of Public Health
Debra Wadford, 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

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

Sharp Healthcare, 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

Jeremy Kamil, Vaughn Cooper

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

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

GitHub Commits






scripps research