Brilliant talk by Phill James @Grounded_circus on #SARSCoV2 genome sequencing using @nanopore sequencing. Giving humanity hope in these dark times. Here I will share some information from the talk. Thread.👇 
Why #Nanopore for Sars-Cov2 genome sequencing? @nanopore sequencing allows us to do real-time sequencing cost-effectively and with low instrument cost. In the #COVID19 context, it can help us monitor the #coronavirus spread and vaccine efficacy.
.@nanopore was used before for monitoring other viral outbreaks, such as #Ebola: nature.com/articles/natur… and #Zika: genomemedicine.biomedcentral.com/articles/10.11…
Here is the workflow overview for #SARSCoV2 genome sequencing, starting with RNA extraction, reverse transcription, PCR, barcode ligation, adapter ligation, and sequencing. Overall time, incl. sequencing: ~12 hours? @Grounded_circus
Primers come from @NetworkArtic. @nanopore suggest sequencing 400 bp amplicons that span the viral genome, because based on preliminary results, with higher amplicon size qPCR efficiency drops. #COVID19
As for barcode ligation, based on their protocol 95% of the amplicons will have both ends ligated (Great news! One problem I likely faced with my non-viral samples, lack of efficiency here).
As for when loading the library onto flow cell, 15-20 ng seems to be optimal. Another good news here: 100k reads give us good info on the viral genome! This is great.
Active research alert 1: Rapid barcoding approach currently not recommended, as it somehow fragments the library further. I can't wait to see optimized protocols on this.
Thank you @Grounded_circus and @nanopore for this amazing talk. Also, a shout out to open-source @nextstrain for the great scale of data on #nCoV genomes and rapid phylogeny analysis.
