designing PCR for COVID19
I read the False Negative of PCR test for COVID19 is high compare to expensive CT scans.
https://pubs.rsna.org/doi/10.1148/radiol.2020200642
I was curious if experts can comment on why and what makes it difficult to design more accurate PCR given the COVID genomes is out there.
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Hello Quak!
We believe that this post does not fit the main topic of this site.
Not a bioinformatics issue.
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.
Cheers!
IMHO it is an important topic. Any country has at least a few patients now. And very few articles discuss experimental procedures and provide some details. Where else is it possible to find some current scientific information, if not here?
Thank you!
You've not addressed the reason why the post was closed.
I believe there are already multiple posts related to designing qPCR primers here. The who idea of designing primer AFAIK is a bioinformatic tasks, there are multiple bioinformatic pipelines and method. Of course, I can rephrase the question, remove the COVID19 and make it less sensitive. I don't mind if you do so.
Viruses evolve VERY rapidly, so my concern with a single set of primers for it are that they'd quickly be wrong. Presumably one would have to design a LOT of them to add some robustness.
Thanks for your comment - I wish the question was not closed to discuss in a better formatted place. Here are a few questions, If 96% sequence similarity exist with other SARS-like coronavirus strains, does that mean, it is not possible to find a "universal" primers ? is there any computational way to assess the performance of https://www.biobasic.com/coronavirus-covid-19-primers primers for example ?
Please note that there is not (to my knowledge at least) anyone on this site with experience developing assays for virus monitoring, so any replies related to this are pure supposition.
This is a terminology debate - qPCR kits are assays and one can find tons of posts here about designing qPCR primers.
Please show us a few examples of posts that match the following criteria:
your 4 answers 1 - and you 2 sounds weird - I feel I am bullied, without any construction feedback on where to go and why this is not a bioinformatics question. Yes I am asking it elsewhere :). Thank you again for moderating here - I love this place no matter what.
I apologize for coming off too strong. As Devon said, there are not a lot of experts on PCR here, so you'll have better luck if you asked elsewhere. PCR primers are on the border of wet lab and computational biology, and we focus a lot more on the computational aspects of the field than the wet lab aspects. Closing your question was to help you as fast as we can, because we know this is not the right place for your question.
Thank you - I agree and understand.
CDC has primer probe sequences available here. CDC probably has access to more genomes than what is available in public databases so these should be authoritative.