A great collaboration on direct RNA sequencing of SARS-CoV-2 transcripts using nanopore sequencing from Camilla Ugolini (Italian Institute of Technology) and colleagues, lead by Tomasso Leonardi (IIT) and Dave Matthews (Bristol) - I am a co-author. biorxiv.org/content/10.110…
(note; I and some other authors, eg, @AkesonUCSC have conflict of interests to declare as I am long standing consultant to Oxford Nanopore and shareholder).
Camilla looked at SARS-CoV-2 transcripts using a neat new protocol that both captures capped (full length) RNAs and can sequence through them, NRCseq, developed by @ettwiller (also a co-author). This means Camilla can distinguish full length from degraded transcripts.
The SARS-CoV-2 genome has a fiendishly clever "jumping" behaviour on the production of RNAs for its proteins (the outcome is a bit like splicing, but done via the polymerase). The capped sequences (but not "normal" direct RNA sequence) showed equal 5' to 3' RNA levels 
Armed with these complete RNA sequences, Camilla and colleagues could map out more of the potential ORFs, confirming the disputed ORF10 and having a subtype of ORF9 (ORF9d).
Perhaps unsurprisingly there are capped transcripts that don't start where expected - although rare these might be involved in regulation of the virus during its lifecycle.
The expression levels of the transcripts was consistent with northern blots (less common than one might think) and shows an inverse relationship between length and expression, suggesting there is a simple 'jump' probability between discontinuous sections.
As well as this exploration of SARS-CoV-2 biology, this technique shows great promise in helping to isolate capped RNAs from other RNA species in cells.
Great paper by Camilla, and also just shows the complexity of the SARS-CoV-2 (and Cornavirus in general) lifecycle.
• • •
Missing some Tweet in this thread? You can try to
force a refresh
