Zika virus Genomics

Summary

Zika virus sequence data from the 2015-2018 epidemic in the Americas.

Data

Sequences | Alignments | Trees | BAMs

Samples

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.
  • HKY_Γ 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 Repo

Florida NCBI BioProject

Cuba NCBI BioProject

NextStrain – Zika virus

WHO – Zika Virus

PAHO – Zika Virus Infection

PAHO – Regional Zika Epidemiological Updates

PAHO – Zika Cumulative Cases

CDC – Zika Virus

CDC – Areas with Risk of Zika

Genomic Epidemiology Reveals Multiple Introductions Of Zika Virus Into The United States
Nature 546(7658):401-405 (2017)

Establishment And Cryptic Transmission Of Zika Virus In Brazil And The Americas
Nature 546(7658):406-410 (2017)

Zika Virus Evolution And Spread In The Americas
Nature 546(7658):411-415 (2017)

Multiplex PCR Method For MinION And Illumina Sequencing Of Zika And Other Virus Genomes Directly From Clinical Samples
Nature Protocols 12(6):1261-1276 (2017)

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