@freed_nikki | 1,545 followers
If you are sequencing Omicron (B.1.1.529) COVID genomes with the “Midnight” panel (e.g. using @nanopore) it looks like there might be one region that is dropping out, based on the sequences submitted to GISAID (N=68). Potential quick fix 🧵 (work with @osilander)

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Es ist absolut faszinierend, der globalen wissenschaftlichen Gemeinschaft live dabei zuzusehen, wie ihre Mitglieder sich über Twitter mit Erkenntnissen versorgen, um Omikron besser zu verstehen.
 
🙏 @freed_nikki and @NetworkArtic for ongoing rapid response. Users can still detect omicron using the current @nanopore Midnight method, however we strive for full, *complete* genomes. We are preparing to supply materials to cover the region, and we value user feedback. 1/2
 
In reply to @freed_nikki
We see genomes with NNNs in region 28, suggesting a dropout. This seems to be caused by a mismatch in the 3’ end of the Midnight Left_28 primer. pic.twitter.com/V0Xf28onf4
 
Thanks for this! Worth noting that none of Omicron's defining mutations occur in this region, meaning Midnight protocols are not less powered to detect it.
 
Some problems in the sequence...
 
In reply to @vinodscaria
Sequencing coverage issues with #Omicron on Midnight assay on @nanopore and how to work around twitter.com/freed_nikki/st…
 
El bitxo continua posant les coses més difícils, també a nivell de genòmica.
 
 
Info for those using the Freed/Midnight primers for SARS-CoV-2 sequencing
 
 
 
 
 
 
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