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
Jordan/Amman 223
Jordan/Irbid 6
Jordan/Mafraq 2
MEX/Baja California/Mexicali 1
MEX/Baja California/Tijuana 152
MEX/Sonora/San Luis Río Colorado 2
USA/Arizona/Yuma 1
USA/California/Cruise_Ship_1 8
USA/California/Cruise_Ship_2 32
USA/California/Imperial 125
USA/California/Los Angeles 2
USA/California/Riverside 2
USA/California/San Diego 1962
USA/California/Santa Barbara 1
USA/California/San Bernadino 1
USA/Louisiana/New Orleans 123

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 data@andersen-lab.com

Phylogeny

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.

Nextstrain Narratives

narrative

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…)
narrative

Narrative 1 | Genomic Epi in San Diego

| Data, Narrative | No Comments
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 infected patients in San Diego. This is our first preliminary analysis. (more…)

People

Collaborators

San Diego Partners
SEARCH Alliance, San Diego

San Diego County Public Health Laboratory
Tracy Basler, Jovan Shephard, Brett Austin, Raymond Chinn, Nikos Gurfield, 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 Rees-Stealy, San Diego
Aaron Harding, Jacquelyn Berumen, Cathy Woerle, Liam McGinnis, Art Mendoza, Omid Bakhtar

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

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

Data

Protocols

Funding

NIAID

ctsa

scripps research