Wuhan coronavirus genome now on Genbank

[Reginald Smith]

Not sure if anyone here has experience with viral genome phylogenetics, phylodynamics etc. I am more knowledgeable about bacteria but for anyone's interest, the Wuhan coronavirus making the news now has full genomes in GenBank. It is small like most viruses (29 kbp). Several isolates seem available:

Wuhan seafood market pneumonia virus isolate Wuhan-Hu-1, complete genome

[Thomas Meany]

Thanks for pointing this out. We are hosting a Biohackathon at OpenCell London on this on Sunday: 

BioHackHereNOW - Wuhan 🧬 Virus 🦠

 

Short Notice *Biohackathon* Sunday 26th

 

The Wuhan virus genome has just appeared on Genbank. We would like to improve our understanding and contribute to the publics understanding.

 

This outbreak, occurring in one of the most populous and economically significant countries in the world, is serious. A case has also now been reported in the US. This is a short notice hack and would therefore require significant participation.

 

This isn't a "turn up and see what happens" event. Get in touch with us if you have an idea, an interest in the area or ideally a hack idea to bring to the table. As usual we can only take 10 people (slightly + for this one). If you want to join please *mail > he...@opencell.bio WITH subjectline [Biohackathon] * Give a short overview of your background, skills and interest and why you would like to take part.

 

Learn more about BiohackHereNow

[Reginald Smith]

Sounds cool, let us know how it turns out. Again, I do more with bacteria and claim no expertise, but housekeeping genes like polymerases seem to be pretty standard for phylogeny of viruses as well. Wuhan CoV isn't annotated well yet but doing some Blasts on other coronaviruses it seems the sequence below is part of the RNA polymerase and could be used for phylogeny etc. It looks most related to bat coronaviruses followed more distantly by SARS

      1 atgaggatca agatgcactt ttcgcatata caaaacgtaa tgtcatccct actataactc
       61 aaatgaatct taagtatgcc attagtgcaa agaatagagc tcgcaccgta gctggtgtct
      121 ctatctgtag tactatgacc aatagacagt ttcatcaaaa attattgaaa tcaatagccg
      181 ccactagagg agctactgta gtaattggaa caagcaaatt ctatggtggt tggcacaaca
      241 tgttaaaaac tgtttatagt gatgt
//

Reggie

[Reginald Smith]

On Twitter (via Dr. Rambaut below) I found out GISAID is where are the individual patient isolates of the Wuhan coronavirus sequences are going. That may give you all some more meat for a Hackathon. I assume you can just register an account.

Andrew Rambaut on Twitter (https://twitter.com/arambaut) is actually doing a lot of real time tweeting on phylogeny analysis and evolution.

Reggie

On Wednesday, January 22, 2020 at 4:24:04 AM UTC-5, Thomas Meany wrote: