Zika virus genomic data

Summary: Zika virus sequence data from the 2015-2017 epidemic in the Americas. Data here.

Data

Sequences | Alignments | Trees | BAMs

Samples

Scripps IDDateSample typeQuality score% CoverageLocation of infection
FL001Sa2016.03.22Saliva***99.71Martinique
FL008U2016.06.21Urine***90.07Puerto Rico
FL010U2016.06.22Urine****97.69USA: Florida
FL016U2016.07.03Urine***99.88Puerto Rico
FL021U2016.07.19Urine***97.45USA: Florida
FL022U2016.07.16Urine***97.77USA: Florida
FL030U2016.08.02Urine***99.75USA: Florida
FL032U2016.08.05Urine***99.75USA: Florida
FL036Se2016.08.04Serum***99.73USA: Florida
FL038U2016.08.04Urine***99.76USA: Florida
FL039U2016.08.17Urine****99.75USA: Florida
Hu0015Sa2016.08.24Saliva***99.75USA: Florida
FL01M2016.08.22Mosquito****99.75USA: Florida
FL02M2016.08.23Mosquito****99.74USA: Florida
FL03M2016.08.23Mosquito****99.83USA: Florida
FL04M2016.09.04Mosquito****99.72USA: Florida
FL05M2016.09.09Mosquito****99.74USA: Florida
FL06M2016.09.20Mosquito****99.71USA: Florida
FL08M2016.10.05Mosquito****97.70USA: Florida
ZC188Se2016.01.16Serum****98.26Colombia
ZC192Se2016.01.07Serum****98.36Colombia
ZC204Se2016.01.06Serum****99.74Colombia
ZC207Se2016.01.09Serum****96.68Colombia
ZC199Se2016.01.10Serum***97.44Colombia
Hu0046Sa2017.04.18Saliva****98.20Cuba
FL046Se2017.07.26Serum**82.50Cuba
FL047U2017.08.08Urine**80.40Cuba
FL049U2017.09.24Urine****96.00Cuba
FL051Se2017.07.17Serum****98.40Cuba
FL052U2017.08.05Urine**86.50Cuba
FL055Se2017.08.13Serum****96.80Cuba
FL057U2017.07.17Urine**93.80Cuba

Quality

**** Complete coding sequence, no apparent contamination in aligned bam file
*** Complete coding sequence, some contamination in aligned bam file (confident in consensus)
**  Partial coding sequence, no apparent contamination in aligned bam file
*   Partial coding sequence, some contamination in aligned bam file

Sequencing

  • Library construction was performed using an amplicon-based approach amplicon-based approach.
  • Sequencing was performed on the MiSeq.

Coding-complete genomes

  • Downloaded from NCBI, ViPR, and NextStrain. Only new genomes are added to later folders.
  • Consensus sequences sequenced in our lab are added to the root of the 'consensus_sequences' folder.

Alignments

  • Created using MAFFT.
  • Trimmed to just contain the ORFs.

Maximum likelihood trees

  • Created using the fast algorithm in RAxML using 200 bootstraps.
  • Orange = travel-associated cases; Red = local transmissions.
  • We root trees on KX447517 from French Polynesia.

Time-scaled trees

  • Made with BEAST using the following parameters:
    • Uncorrelated relaxed clock with lognormal distribution, CTMC rate prior.
    • HKYΓ substitution model with codon partitioning.
    • SkyGrid, 50 parameters, time at last point = 4.
    • 30,000,000 states.

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]

GitHub Commits

Resources

Publications

Links

USAMRIID Zika virus sequences on GitHub
By: Jason Ladner, Mike Wiley, Gus Palacios

NextStrain
By: Richard Neher, Trevor Bedford

Virological.org
By: Andrew Rambaut

ZiBRA Project
By: Nick Loman and crew

ZEST – Zika Real-Time Experiments
By: Dave O’Connor

Funding

NIH_CTSA
PEW

Main Collaborators

Florida Gulf Coast / Tulane
Lauren Paul
Amanda Tan
Scott Michael
Sharon Isern
Robert Garry
Florida Department of Health
Leah Gillis
Stephen White
Marshall Cone
Edgar Kopp
Kelly Hogan
Andrew Cannons
Mario Porcelli
Chalmers Vasquez
University of Miami
Diogo Magnani
David Watkins
Paola Lichtenberger
Mike Ricciardi
Varian Bailey
USAMRIID
Jason Ladner
Mike Wiley
Gus Palacios
Broad Institute
Sabeti Lab
University of Birmingham
Josh Quick
Nick Loman
Oxford University
Julien Theze
Moritz Kraemer
Nuno Faria
Oliver Pybus
The Hutch / Edinburgh
Gytis Dudas
Trevor Bedford
Andrew Rambaut