Forum:COVID19 testing - can we/should we use NGS?
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4.3 years ago
liorglic ★ 1.4k

Hello all,

So I had this thought and would like to hear other people's opinion.

I am usually working on plant genomics, so I know very little about virology or diagnostics. Also I'm not deeply familiar with the molecular aspect of lab work.

So, as far as I understand, one of the main efforts in current COVID19 outbreak is to do massive testing to detect cases. The main method used right now is (again AFAIK) RT-PCR, and health authorities have been making huge efforts to perform as many tests as possible. The method is fairly simple and quick, but the throughput isn't great - basically you have to test samples one by one (although I did hear suggestions that pooling could work).

What if we apply NGS for testing multiple samples at once? We could use some multiplexing method (e.g. as offered by iGenomX - can multiplex up to 960 samples) for pooling many samples together. The procedure could be something like:

  1. Collect samples
  2. Library prep - including creating cDNA, multiplexing and optionally PCR using some virus-specific primers
  3. Sequencing using short reads
  4. Demultiplexing
  5. Alignment of reads to the virus reference genome to determine if it's present, per sample

Of course this would take much longer than RT-PCR, but I'm wandering if the higher throughput could be worth it. Additionally this method has the bonus that while we do testing we can also collect sequence information that can tell us about virus evolution and strain divergence.

I tried googling for such ideas, but only found this commercial option. Maybe it wasn't done yet because there are difficulties that I didn't think of...

What do you think? Can it work?

Thanks!

NGS covid19 diagnostics • 1.1k views
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Hello liorglic!

We believe that this post does not fit the main topic of this site.

This is wetlab / clinical diagnostics, not bioinformatics.

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!

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Hello. I'm glad to see you are making efforts to keep this great forum relevant. However, I believe this topic should stay open.
Although this is not a pure bioinformatics question, I think wet lab and bioinformatics are in many cases inseparable. If you read my post carefully, you can see that bioinformatics are indeed involved (e.g. demultiplexing and short reads alignment). Moreover, due to the urgency and importance of the topic, I think some flexibility is in order. Please let the community decide - if this topic is of no interest to the forum members it'll probably not get answers/attention.

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Fair enough, even though I do not agree that some bioinformatics buzzwords make thread bioinformatics-on-topic. Please remember (all those who are going to comment/answer with or without expert knowledge on clinical settings) that clinical testing requires certification of a method with extensive validation of the protocols and of the potential edge cases plus proper positive and negative controls. Also, when you comment I encourage to provide references over anecdotal evidence, just my two cents.

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4.3 years ago
Joe 21k

We can, and are using NGS.

However, its not cheap or fast enough to be a routine test at this point.

Additionally, the big problem with the qPCR tests, are that the patient requires quite a high viral titre for the assay to work. NGS needs quite a lot of input material still, so this would likely be prohibitive. The best point-of-care diagnostics tend to be serological assays.

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Apparently I'm not the only one who had this idea: https://docs.google.com/document/d/1kP2w_uTMSep2UxTCOnUhh1TMCjWvHEY0sUUpkJHPYV4/edit?usp=drivesdk

Still unclear if it's a good one though...

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The obvious limiting step in that looks to me to be having enough reliable barcodes, but I can't say ive paid much attention.

There's a long road to proving it's clinically valid however....

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