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https://80000hours.org/podcast/episodes/cassidy-nelson-12-wa...

"At the moment, the most common types of testing are PCR testing, which is polymerase chain reaction, and it allows you to detect a pathogen that has a certain section of its genetic code match this test that’s very limited in terms of anything new that comes out. You always have to know about the pathogen beforehand, have to have designed and validated a test against that.

In the last few years though, some new technologies that have come out that are based on metagenomic techniques, which are pathogen agnostic diagnostics. So you don’t need to know anything about the pathogen beforehand. You can put a clinical sample on and it will tell you all of the DNA that is in that sample. And so you’d be able to do things like bioinformatics testing on this and be able to actually work out, “Oh, it matches against my RSV or CMV or other known viruses, or this is completely new and it doesn’t match anything in my bioinformatics data set…

It sequences everything. So you’d imagine like 98% of it is just human DNA, but bioinformatically you just push that out and you usually don’t care about the human DNA, and then everything that’s left over you’re able to analyze…

This would mean that not only would you be able to have a reliable diagnostic from the get-go before an outbreak begins and then for those first few cases, you might actually be able to instead… on average globally, we have about a 20 day lag in between first outbreak cases and detection of an outbreak for new emerging diseases. That’s way too long. If you could detect those first handful of cases of a new disease, you’re much, much more likely to be able to contain it...

Robert Wiblin: Is this affordable?

Cassidy Nelson: So this has started being used in places like in 2014 in West Africa when there was some diagnostic conundrums going on in the Ebola epidemic going on there. Metagenomic sequencing, especially based on nanopore technology, which is a fascinating way to do this is quite expensive in terms of the reagents that are being used, but the costs of that are coming down and the accuracy of it is going up. I personally think though that these platform agnostic ways of looking at pathogens is really the only way forward if to be on top of diagnostics. There’s really always going to be a one step behind type picture if we have to wait to characterize a new pathogen and then design a new test for it based on PCR type methods today.

Robert Wiblin: So the idea is we would just make this the normal way of diagnosing people with contagious diseases. So people come into hospital, they’ve got symptoms and you’d do the sample and you try to sequence everything. You see all the viruses that are going through there. And then you can see whether any of them are weird and whether there’s a pattern of some new disease showing up, hopefully really quickly.

Cassidy Nelson: Yeah, and there’s been great studies that have come out looking at like fever in return travelers, for example: 60% of them never get a diagnosis, but there’s something causing their fever. People have gone on using metagenomic techniques and have gone, “What is the pathogen here? What do we actually have”, as well as other diagnostic conundrums. So people have been starting to do this. It hasn’t been adopted on a wide scale yet, but I’d love to see this adopted and you’d be able to have this in all healthcare settings. So you could have this in your emergency department. You may first limit it to just severe cases. So if you have a severe case of pneumonia or another disease, you don’t have any etiology that you’ve been able to find, you’re able to do these types of tests.

Cassidy Nelson: This would mean that not only would you be able to have a reliable diagnostic from the get-go before an outbreak begins and then for those first few cases, you might actually be able to instead… on average globally, we have about a 20 day lag in between first outbreak cases and detection of an outbreak for new emerging diseases. That’s way too long. If you could detect those first handful of cases of a new disease, you’re much, much more likely to be able to contain it."