Zika virus genomic data

Summary: Zika virus sequence data from the 2015-2018 epidemic in the Americas. Data here.

Data

Sequences | Alignments | Trees | BAMs

Samples

Scripps ID Date Sample type Quality score % Coverage Location of infection
FL001Sa 2016.03.22 Saliva *** 99.71 Martinique
FL008U 2016.06.21 Urine *** 90.07 Puerto Rico
FL010U 2016.06.22 Urine **** 97.69 USA: Florida
FL016U 2016.07.03 Urine *** 99.88 Puerto Rico
FL021U 2016.07.19 Urine *** 97.45 USA: Florida
FL022U 2016.07.16 Urine *** 97.77 USA: Florida
FL030U 2016.08.02 Urine *** 99.75 USA: Florida
FL032U 2016.08.05 Urine *** 99.75 USA: Florida
FL036Se 2016.08.04 Serum *** 99.73 USA: Florida
FL038U 2016.08.04 Urine *** 99.76 USA: Florida
FL039U 2016.08.17 Urine **** 99.75 USA: Florida
Hu0015Sa 2016.08.24 Saliva *** 99.75 USA: Florida
FL01M 2016.08.22 Mosquito **** 99.75 USA: Florida
FL02M 2016.08.23 Mosquito **** 99.74 USA: Florida
FL03M 2016.08.23 Mosquito **** 99.83 USA: Florida
FL04M 2016.09.04 Mosquito **** 99.72 USA: Florida
FL05M 2016.09.09 Mosquito **** 99.74 USA: Florida
FL06M 2016.09.20 Mosquito **** 99.71 USA: Florida
FL08M 2016.10.05 Mosquito **** 97.70 USA: Florida
ZC188Se 2016.01.16 Serum **** 98.26 Colombia
ZC192Se 2016.01.07 Serum **** 98.36 Colombia
ZC204Se 2016.01.06 Serum **** 99.74 Colombia
ZC207Se 2016.01.09 Serum **** 96.68 Colombia
ZC199Se 2016.01.10 Serum *** 97.44 Colombia
Hu0046Sa 2017.04.18 Saliva **** 98.20 Cuba
FL046Se 2017.07.26 Serum ** 82.50 Cuba
FL047U 2017.08.08 Urine ** 80.40 Cuba
FL049U 2017.09.24 Urine **** 96.00 Cuba
FL051Se 2017.07.17 Serum **** 98.40 Cuba
FL052U 2017.08.05 Urine ** 86.50 Cuba
FL055Se 2017.08.13 Serum **** 96.80 Cuba
FL057U 2017.07.17 Urine ** 93.80 Cuba
FL082 2017-10-09 Urine ** 98.20 Cuba
FL257 2018-01-18 Urine ** 98.30 Cuba

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]

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