A couple of months ago I tweeted that we had our first Bedford lab wet lab (full disclosure: it’s a bench, but start small right?). Well I’m excited to say that we have just released our first bit of Bedford lab-generated sequence data and pushed results to Nextstrain Zika!
These data are 5 (draft) Zika genomes from clinical samples collected in the U.S. Virgin Islands. After getting some experience sequencing on the MinION down in Brazil, I spent the first two weeks of December getting amplicons and sequencing on island in St. Croix. The Caribbean in December, it’s rough, I know. This work is in collaboration with the VI Department of Health, who have generously given me access to their samples and let me take over their lab when I've been down. As a doctoral student in epidemiology, it’s an incredible opportunity to run a study from start to finish, not to mention investigate an outbreak in close to real-time. I’m really excited about it.
Importantly this has been a group effort. The fact that we have this data is a huge testament to the benefits of open science. I’m not a wet-lab scientist by training, and Zika is not the easiest virus to sequence. This project could have been really painful, and the fact that it hasn’t been owes a lot to the openness of other groups to share their knowledge, experience, and protocols. I’m so thankful to Josh Quick and Nate Grubaugh who were incredibly responsive when I had questions or needed help with the protocol, and Nick Loman for freely sharing his entire bioinformatic pipeline. Additionally my lab has been amazing both as a sounding board for ideas and for helping with the data processing and analysis. To have so many people come together to help a project succeed is wonderful, especially so when you’re a student trying to figure things out for the first time. Keep an eye out for more data coming out soon! We'll keep the zika-seq project updated with new sequences as we generate them.