Thread by @tomopencell

Sharing a 🧵 about our latest publication👇

https://twitter.com/medrxivpreprint/status/1497496008091213828

Our labs are in shipping containers at the airport on the Isle of Jersey and we have screened more than 500,000 passengers and residents. You can read more about how it works in our previous paper: biorxiv.org/content/10.110…

In our latest paper we show that by integrating a mobile PCR lab with DNA sequencing tech from @nanopore we can deliver a swab-to-sequence result in **under 30 hours**
This compares with weeks currently available by shipping samples to centralised labs.

The workflow (a in the figure) shows that by post RNA extraction we have actually gotten 1/3 of the way to doing a sequencing run! So integrating RT-qPCR with sequencing saves this step.

The issue is that direct sequencing of RNA is HARD. Check out @NetworkArtic for why.

Instead what we do is a reverse transcriptase step followed by an amplification. Then we "barcode" each sequence so that we can "pool" them later to be able to do 48 sequences at the same time!

Check out @Scalene (Quick et al. 2017) nature.com/articles/nprot…

This "pooling" is a super effective technique since it also brings down the cost per run to **sub £20** meaning it is economic when you include shipping costs etc.

Shout out to the supplementary section! medrxiv.org/content/10.110…

We use cycle threshold (Ct) as a proxy for viral load in this paper and essentially the higher the Ct the lower the viral load. Lower concentrations of RNA make it difficult to get a decent "read" and "coverage" of the genome reduces as the Ct pushes past ~25. This is unfortunate

We provide an in depth analysis of the dynamics of the outbreak across multiple waves and the public health interventions implemented to help mitigate.

Ultimately we show that the dominate variant during the third outbreak period was Delta. This corresponds with the intensity of the global outbreak at this period.

There is a LOT more to do here. Some areas for further work is optimising the base calling process by using "#guppy" on a optimised machine. The The MK1C @nanopore is the first portable instrument to integrate the @nvidia jetson developer chipset but sacrifices some performance.

We are HIRING by the way! If this thread excited you please get in touch. If you love software, hardware and biology then @OpenCellLondon is the place to be: opencell.bio/jobs