Zika virus in Florida

Data

Sequences | Alignments | Trees | BAMs

Samples

Scripps ID Patient ID Sample type Quality score % Coverage Location of infection
FL001Sa 001 Saliva *** 99.71 Martinique
FL008U 008 Urine *** 90.07 Puerto Rico
FL010U 010 Urine **** 97.69 USA: Florida
FL016U 016 Urine *** 99.88 Puerto Rico
FL021U 021 Urine *** 97.45 USA: Florida
FL022U 022 Urine *** 97.77 USA: Florida
FL030U 030 Urine *** 99.75 USA: Florida
FL032U 032 Urine *** 99.75 USA: Florida
FL036Se 036 Serum *** 99.73 USA: Florida
FL038U 038 Urine *** 99.76 USA: Florida
FL039U 039 Urine **** 99.75 USA: Florida
Hu0015Sa Hu0015 Saliva *** 99.75 USA: Florida
FL01M 7501 Mosquito **** 99.75 USA: Florida
FL02M 7719 Mosquito **** 99.74 USA: Florida
FL03M 7727 Mosquito **** 99.83 USA: Florida
FL04M 16-10416 Mosquito **** 99.72 USA: Florida
FL05M 16-3125 Mosquito **** 99.74 USA: Florida
FL06M Mosquito **** 99.71 USA: Florida
FL08M pool#8 Mosquito **** 97.70 USA: Florida
ZC188Se 423568715 Serum **** 98.26 Columbia
ZC192Se 423401315 Serum **** 98.36 Columbia
ZC204Se 424439915 Serum **** 99.74 Columbia
ZC207Se 423217515 Serum **** 96.68 Columbia
ZC199Se 4238001315 Serum *** 97.44 Columbia

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!

GitHub Commits

Protocols

MiSeq protocol for Zika virus sequencing
By: Josh Quick, Nick Loman, Nathan Grubaugh

MinION protocol for Zika virus sequencing
By: Josh Quick, Nick Loman, Team ZiBRA

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

Zika: Mapping The Emerging Evidence
By: WHO

Recent Data-related Blog Posts

Zika sequences from Miami mosquitoes

| Data, News | No Comments

Data here. Protocol here. Three pools of Aedes aegypti mosquitoes collected in Miami Beach on August 22nd and 23rd, 2016, were found to be infected with Zika virus. Through our collaborators, Scott Michael and Sharon Isern from Florida Gulf Coast University, we recently received samples of these mosquitoes for sequencing using our amplicon-based protocol for MiSeq.

Zika sequence from local Florida transmission

| Data, News | No Comments

Data here. Protocol here. In collaboration with Dr. Diogo Magnani in the Watkins Laboratory in the Dept. of Pathology at the University of Miami’s Miller School of Medicine, we recently received plasma and saliva from two people with Zika virus infections living in the Miami area. Using our amplicon-based approach previously used to sequence Zika virus from travel-related Zika virus cases in…

Travel-related Zika cases in Florida

| Data, Protocols | No Comments

Data here. Protocol here. In a collaboration with Scott Michael and Sharon Isern from Florida Gulf Coast University and Florida Department of Health, we have recently received several travel-related cases detected across Florida. We have now managed to sequence Zika virus genomes from three of these case and the data and analyses can be accessed here.

Collaborators

Florida Gulf Coast / Tulane
Lauren Paul
Amanda Tan
Scott Michael
Sharon Isern
Robert Garry
Florida Department of Health
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
Gytis Dudas
Trevor Bedford