RT-LAMP is the right way to scale diagnostic testing for the coronavirus

post by Kevin · 2020-08-04T10:05:29.718Z · score: 38 (16 votes) · LW · GW · 6 comments

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  RT-LAMP is the right way to scale diagnostic testing for the coronavirus
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6 comments

RT-LAMP is the right way to scale diagnostic testing for the coronavirus

by Kevin Fischer

kfischer $& gmail *( com

RT-LAMP compared to RT-PCR is a less versatile and more recently invented laboratory technique. LAMP is more suited to actual diagnostic testing at scale than PCR but never became industry standard despite its demonstrated superiority. Labcorp/Quest/One Medical use PCR for their coronavirus diagnostic tests and they currently have delays as long as two weeks for issuing results which is totally unacceptable for fighting this pandemic. Color in San Francisco has one of few widely available RT-LAMP tests for the coronavirus and they generally give results back in one to two business days and are not bottlenecked by laboratory procedure.

An open access RT-LAMP coronavirus diagnostic toolkit was published at the end of July and I believe presents a solution to scaling diagnostic testing to where it needs to be. A rapid, highly sensitive and open-access SARS-CoV-2 detection assay for laboratory and home testing

What steps can we take to help national testing capacity switch to RT-LAMP instead of RT-PCR? There are parallel approaches here -- bottom up development suggests distributed citizen science RT-LAMP labs to fill in gaps in testing capacity, top down distribution suggests convincing the major industry players to devote resources to switching to RT-LAMP over RT-PCR. I'm going to take the bottom up approach; can anyone else figure out how to help Quest and Labcorp switch over to the superior testing method?

Does anyone else want to set up their own RT-LAMP operation? I'm going to give it a try and will write a guide on what to buy once we're operational. One of my business partners was an innovator in LAMP primer design over ten years ago and we still own the lab equipment needed for the simple procedure. Presumably as non FDA approved citizen science it will have to be "for research only" and not for diagnostic testing purposes but it's possible the FDA is being cooperative and that actual FDA licenses could be issued on a timeframe that is reasonable.

6 comments

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comment by Kevin · 2020-08-04T19:58:21.560Z · score: 4 (2 votes) · LW(p) · GW(p)

Does this not get front paged because of coronavirus saturation?

comment by Raemon · 2020-08-08T20:05:56.181Z · score: 3 (2 votes) · LW(p) · GW(p)

It's actually a somewhat different thing where, normally frontpage is supposed to be stuff that's more timeless, that people might presumably still care about in 5 years. Part of the whole point is to avoid LessWrong being news-driven.

Early in the pandemic, the mods decided that coronavirus was important enough to frontpage lots of stuff about it, and it did take over the site for awhile. Later, it happened that a) people were talking about it less, and b) it felt like we'd 80/20d the covid discussion and it was no longer urgent enough to break our frontpage guidelines for.

(Note that personal blogposts still get a fair bit of visibility, the point is mostly to avoid having it be the first thing people associate with LessWrong when they first show up. Frontpage posts tend to get 2-3x the traffic, mostly from newbies and people not logged in. Zvi's weekly covid posts get a fair number of comments.)

I do think this topic seems quite important if true (haven't evaluated it myself yet), and am glad you posted it here.

comment by zby · 2020-08-08T19:47:55.370Z · score: 1 (1 votes) · LW(p) · GW(p)

OK, but do you have a more through comparison between PCR and RT-LAMP or is it just based on your intuitions?

And there are even more methods: https://www.cebm.net/wp-content/uploads/2020/04/CurrentCOVIDTests_descriptions-FINAL.pdf

comment by AndHisHorse · 2020-08-05T01:56:01.124Z · score: 1 (1 votes) · LW(p) · GW(p)

Why _haven't_ they already switched? Presumably, these companies are full of people with some vague incentives that point at maximizing efficacy, but they're leaving a "clearly superior" product on the table. It may be that the answer is that this is some sort of systemic, widespread failure of decision-making, or a decision-making success under different criteria (lower tolerance for the risk of change, perhaps, than these same systems have now) rather than a reflection of some inadequacy of RT-LAMP, but "the folks with the expertise and incentive to get it right are all getting it wrong and leaving money on the table" sounds like a more complex explanation than "there are shortcomings to RT-LAMP that I haven't considered", and I'd like to see some further evidence in favor of it.

comment by Kevin · 2020-08-05T07:47:28.174Z · score: 5 (3 votes) · LW(p) · GW(p)

I think until recently throughput issues PCR was basically good enough and some scientists were attached to their hard learned PCR skills, LAMP was new and scary and unfamiliar enough that lots of scientists just didn’t know it was easier and better. Primer design was a serious obstacle in the early days of LAMP but is easy with modern computer primer design tools.

LAMP is also only better than PCR for the things that it is better at. PCR has general applications to biological science and LAMP is only good for an important subset of possible PCR diagnostic tests. I think mainstream scientists lack the understanding of what LAMP can and can’t do and for something as sensitive as HIV testing I can understand that people don’t want to rock the boat and switch to LAMP from PCR.

It’s also relevant that LAMP is only recently leaving patent protection. I’m not sure what the licensing cost structure used to be but now there are no patent license fees pushing through adoption is simpler:

I am going to try and scale towards selling RT-LAMP kits to US states in very high unit amounts; I’m feeling optimistic.

comment by bgold · 2020-08-04T21:27:14.828Z · score: 1 (1 votes) · LW(p) · GW(p)

I'd be quite interested in reading that guide!