In this project we aim to understand evolution and spread of Powassan virus by sequencing viruses isolated from ticks in the Northeastern United States.
Ticks were collected at different locations by colleagues at the Connecticut Agricultural Experiment Station, Colorado State University, Cornell, Maine Medical Center Research Institute, New York State Department of Health, Tufts, and Upstate Medical University.
- Library construction was performed using an amplicon-based sequencing approach.
- The Powassan LII primer scheme can be found in the primer_schemes folder
- Sequencing was performed on the NovaSeq, paired-end 150.
- iVar was used to generate consensus genomes.
- Created using a 75% treshold and at least 10X coverage.
- Uploaded in folder consensus_sequences.
Some of our analyses were performed using the nextstrain (augur) pipeline. These results can be visualized using auspice, accessing the links below:
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!
Grubaugh Lab | Yale School of Public Health (YSPH) | https://grubaughlab.com/