Below information is from Katherine Melville, Oxford Nanopore Technologies.
Hi All- This is Katherine Melville from ONT. I am sorry we missed the call
earlier- I had an overlap but would like to join future meetings-- and am happy
to address any questions that come up. Thank you Anoja for inviting us to the
channel. I did want to follow up with some information and links for you all.
ONT have been working to support our public health customers in sequencing the
virus. Our customers have generated some protocols that we can share with you
for sequencing SARS-CoV-2 to help you get started. As you may know, ARTIC have
released a protocol that uses tiled amplicon enrichment against SARS-CoV-2.
Their protocol can be found here: https://artic.network/ncov-2019
We have posted a derivative of their protocol into our Community page, which
can be viewed here:
https://community.nanoporetech.com/protocols/pcr-tiling-ncov/v/PTC_9096_v109_revB_06Feb2020
Please do also note that improvements to this protocol are likely to be made as
time progresses. There are several labs globally that are working on iterating
this protocol as of now, and new primers have already been released to address
an observed primer dimer issue in one of the pairs. The ARTIC group also built
a workflow featuring reference guided assembly and variant call approach that
is available as a Docker container through the above links.
Outside of the targeted approach that we recommend, there are also metagenomic
approaches that have been released by our customers which enable detection of
potential co-infections. These include both SISPA from PHE
(https://www.medrxiv.org/content/10.1101/2020.03.05.20032011v1) and Dr. Charles
Chiu's MSSPE enrichment protocol
(https://www.nature.com/articles/s41564-019-0637-9.pdf?draft=collection). Dr.
Chiu has released primers specifically for SARS_CoV-2 as part of his MSSPE
enrichment protocol (https://twitter.com/cychiu98/status/1221341348218822657).
All updates on progress of using ONT for COVID-19 will be released here, so I
do recommend tracking this page:
https://nanoporetech.com/about-us/news/novel-coronavirus-covid-19-information-and-updates
I would stress that labs are applying our R9.41 flow cells, LSK-109 kit, and if
they wish to multiplex, they use our native barcoding kits (EXP-NBD104 and
EXP-NBD114) for their sequencing. People have used our new R10.3 flow cells,
but these are beta flow cells and therefore we cannot reliably supply them.
There are also some sites that have used Flongles, but I would recommend that
you use R9.4.1 as this is our most stable flow cell with reliable shipment. To
render the experiment cost-efficient, you can use the native barcoding kits
above (up to 24 samples, https://store.nanoporetech.com/sample-prep.html/).
Please let me know if you have any questions! If anyone is considering using
ONT, please feel free to contact us through this page:
https://nanoporetech.com/about-us/news/novel-coronavirus-covid-19-information-and-updates
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