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#TestingMethods2020

PopMax testing whole country. https://popmaxcovid.com/Testing-the-population-for-Covid-19.pdf

A: Not for current challenges

**We are non profit no affiliation no personal gain**.   Using end point pcr allows mass pcr in the millions per day easily. Proven at Kbioscience LGC every day for last 15 years. 1.5 million pcr tests per day every day.

We have 100% concordant data from Lighthouse rtPCR covid samples and reagents to prove this approach. 

Also on Antibody test we accept a smudge YES/NO answer but on RNA rtPCR test we are told we clinically need a curve telling us how much then throw data away to give the same YES/NO..

Now we can prove end point is 100% concordant with slow expensive rate limiting rtPCR.

Sampling the killer as we all know. Tubes have to go out and come back with zero packaging. Amazon etc already have bar code scanners but they got a day job.. Uber now going back to work..

So how ?  Well there are 750,000 nhs volunteers sitting at home doing nothing. I know I’m one of them. Volunteered to drive prescriptions to elderly etc. Then there are another level of NHS volunteers who are more medical competent who trained in defib etc who. Both these could be utilized to expedite getting samples to houses and back in whole population testing. It’s not beyond the wit of man/women to have the Driver and Medical volunteer to deliver and pick up tubes in a large sharpie type bio secure tube barrel. The house/family would drop it in. So not touched..

The app already runs the whole process of giving out tasks locations pick up directions instructions.. Just piggy back on the back of it.  See attached image its just my local tiny village.. huge UK coverage. 

Then dump contents of barrel in an auto step or bowl feeder to orientate, bar code read, decap and fill with media.. Industry solutions required not lab auto.. Not as expensive as single Tecan but huge throughput.  Using “UK volunteering service” not long term sustainable but would work to kill R number.. And test million per day save lives.

Saliva swab. Q tip. Mass Gamma irradiate Q tips place under tongue for 30 seconds then place in pool tube. Gama irradiation is done by the ton in food industry. Cheap and could process million Q tips per day. FDA approves Q-tip-like swabs to allow patient self-testing for COVID-19” FDA already tested.. Then drop into pooled tip tube which is automation friendly.

Q tips cotton so will not cross contaminate but can be mass gamma radiated to sterilise. Food industry solutions. !.

All to feed PopMax.

Just quoted large x 5 Hospital trusts for testing 3000 staff every three days for a month at £50k total. Or £2.50 per test NOW.

Wuhan now need to Mass test 11,000,000 people due to new outbreaks in ONE city.. We are not prepared for this.

 

Have you validated this method, if so, how and what were the results of the validation?

Yes when at the Lighthouse labs last week see slide deck. 

FDA approved Q tips.

GoodSAM app network in place.

How quickly could this be deployed and what are the dependencies?

Hugely deployable re-purpose existing  liquid handling uses same thermo reagents

GoodSAM app needs additional functionality.

Q tips available.

 

 

What is the likely production volume?​

800k per day with three systems all documented costed. All available now off the shelf

Q tips are available off the shelf

GoodSAM network app already working with 750,000 volunteers on it..

 

 

What are the risks and barriers to using this at scale?

ZERO risk but Wuhan now testing 11,000,000 in one city due to reoccurrence  

Proven over 15 years of 1.5 million pcr tests per day at KBioscience now LGC

 Proff of concept immediately available with existing pcr equipment.

Who are you already partnering with on this?

NHS trust x5 hospitals East Kent Hospital Trust

Cost £50k to test 3000 staff per three days for a whole month 25,000 tests.

At £2.5 per test !!  Not the NHS price of £54 ea

 

Tagged users
edited on May 13, 2020 by Jon Curtis
Jon Curtis

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acjwd3 5 months ago

I am not qualified to comment on the validity or appropriateness of this strategy, but I can confirm the concordance data presented from the MK labs appears to be a screenshot from one of our ABI7500s. (By the way, we're technically called a Lighthouse lab, not a 'Megalab', that's just a term that happened to be on one of our whiteboards the day ITV came round.)

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Jon Curtis 5 months ago

Hi we were called in to improve the lighthouse process flow which is not the way we would have done it.. Im Jon curtis and retired have zero affiliations and do not gain in any way.. Yes we ran lighthouse samples and reagent on our water bath mass PCR system to end point and read on your machine. .. With 100% concordance. My co founder and I ran 1.5 million pcrs a day every day and the company still does.. We have been asked by Dr Moses East Kent to run 3000 staff every day for a month at £2.50 per test. NHS price £54. We are zero profit not even an organisation just trying to pass on free of charge improved methodology.. No strings attached..
My name is Jon curtis and happy to expand chat. Im on linkedin. joncurtis7@hotmail.com
https://www.linkedin.com/in/jon-curtis-9286b019/
07912 842821

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acjwd3 5 months ago

I'd be very surprised if you responded to all of these questions, but I've written out my thoughts and attached them.

This is to give you an idea of what someone like me might think on reading your current slide deck, and the sort of questions I'd try to understand to get a better insight into your proposal, based on the material currently presented.

I have a molecular biology background but not lots of instrumentation evaluation or PCR expertise, with a couple of years of low-level project management work.

If any of them strike you as helpful/worth clarifying I encourage you to incorporate answers into your slides. Good luck with your work!

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acjwd3 5 months ago

Yikes, that file came out a bit mangled once posted. I will copy-paste the text here.

Let’s assume I’m already persuaded that population testing is an essential good, and a
goal that we should definitely be pursuing.

Part 1: Method differences
My understanding so far of how this method achieves that goal: the headline difference in using this method is that you are using endpoint PCR, not RT-qPCR. So, trying to explain that to myself, you look at the level of detectable viral DNA at the end rather than looking at a curve of viral DNA amplification and the point in time at which the cycle threshold (number of rounds of amplification) at which the amount of viral DNA exceeds a pre-defined threshold. So you lose the ability to do quantification and melting-curve analysis with endpoint PCR. The argument made is that it's not necessarily limiting in SARS-CoV-2 detection, because the information you want is not relating to quantitative information like viral load but instead you want a binary yes (lots of virus detected at one time point) / no (no virus detected at one time point).

**So, the biggest assumption/assertion 1 is that an endpoint PCR assay is sufficient for diagnosis of SARS-CoV-2 vs. RT-qPCR.**

I am not really qualified to assess this difference and wouldn't quite know what questions to ask to establish this.

Part 2: Efficiency gains in processing
Then there come the detail on efficiency gains: you're suggesting switching from manual handling to a fully automated decapping process. Presumably you'd still need tubes debagged in a class II microbiology safety cabinet, and as tube sizes vary you'd have to triage them for the type required in the decapping automation [they come in a range of different sizes]. I'm interested that the automated transfers work with swab in tube as that would very much help. There's no information I can see in your documentation about the technical details of how this would work. I can confirm this stage would be great to speed up and would love to see how this could work. At this stage I also imagine would be a need to triage barcoding and have a separate process for correcting badly coded tubes as there's no way they'll be applied to the tubes consistently.

The second gain here is using 384 well plates rather than 96. This isn't specifically a limitation for RT-qPCR vs. endpoint PCR, but seems to be emerging from the availability of equipment for 384-wells for RT-qPCR process (e.g. Tecans, KingFishers, Tecans again, ABI7500s are all set up to work with 96-well plate formats). So the gain here would be that if you use a endpoint PCR process that you can provide sufficient volumes of equipment for that method that does handle 384+ samples per plate, and the consumables to match. But could there be 'halfway' improvement - e.g. if there was insistence on remaining with RT-qPCR, could the equipment be implemented for steps from decapping through to PCR reagent plating, then have it be loaded into real-time PCR equipment that can handle 384-well plates? Would that still provide at least some benefits? Or would there be losses - e.g. maximum volume limits - that would make this infeasible?

Your documentation also mentions a applying different RNA extraction method - more information on that would be welcome too (currently as you probably know it's using MagMax kits).

Then to the actual endpoint PCR: water-bath/thermocycler seems pretty straightforward, and I have no reason to assume this equipment wouldn't be capable of handling the temperature changes required. Presumably also the detection systems are well-established and validated technology.

Part 3: How do we know all this could work?
I guess I'd also be curious about how you'd plan to do the validation studies - presumably a scale-up from the existing sort of concordance data you have with many more sample plates? The current data is of course nice to see and I imagine quite difficult to obtain, but a 'next step' ask in terms of getting more concordance data would provide a clear direction for someone sufficiently well-resourced and motivated to evaluate your proposal further.

It might be easier to understand the workflow if there was a detailed case study showing how it was already applied successfully to a diagnostic process (from the information in the deck it seems this is already being done at scale with some customers).

Part 4: What limitations aren’t considered here?
Of course, there's another limit on population sampling at the scale suggested here that is outside your control: sample collection in terms of swab administration and logistics. Presumably this procedure still uses nasopharyngeal swabs taken as the source material? We already have a lot of challenges surrounding taking these swabs from c.100,000 people, let alone 16 million pooled samples. Would be good to see this clearly spelled out in the slides and some consideration given to this challenge (even if just to point out that it will exist as a significant limitation that needs to be overcome with a lot of supply chain / logistics support).

I imagine another limitation might be reagent availability - sure, it would be great to get the increased throughput with 384 wells and faster times from sample to result, but does the endpoint PCR method make the available reagents go further vs. the current RT-qPCR system and allow for scale-up even with that limitation?

Part 5: Money
On cost savings: the headline saving of £2.50 vs. £55 is obviously a big improvement. I know little about how the costing of this sort of thing works, but where is that saving coming from? (e.g. is it from less staff, cheaper reagents, cheaper equipment, reduced consumable bills, all of the above?) It might be easier to think about that reduction if it's mapped back to the concrete 'visualisable' places where the money is being saved.

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Jon Curtis 5 months ago

See *******answer******* below.

Part 1: Method differences
My understanding so far of how this method achieves that goal: the headline difference in using this method is that you are using endpoint PCR, not RT-qPCR. So, trying to explain that to myself, you look at the level of detectable viral DNA at the end rather than looking at a curve of viral DNA amplification and the point in time at which the cycle threshold (number of rounds of amplification) at which the amount of viral DNA exceeds a pre-defined threshold. So you lose the ability to do quantification and melting-curve analysis with endpoint PCR. The argument made is that it's not necessarily limiting in SARS-CoV-2 detection, because the information you want is not relating to quantitative information like viral load but instead you want a binary yes (lots of virus detected at one time point) / no (no virus detected at one time point).

**So, the biggest assumption/assertion 1 is that an endpoint PCR assay is sufficient for diagnosis of SARS-CoV-2 vs. RT-qPCR.*

******YES.. Talking and working in rtPCR for years and end point yes yes yes.. Can cycle to 50 cycles we have band width.. Most labs ignore over ct 35 anyway******

I am not really qualified to assess this difference and wouldn't quite know what questions to ask to establish this.

Part 2: Efficiency gains in processing
Then there come the detail on efficiency gains: you're suggesting switching from manual handling to a fully automated decapping process. Presumably you'd still need tubes debagged in a class II microbiology safety cabinet, and as tube sizes vary you'd have to triage them for the type required in the decapping automation [they come in a range of different sizes]. I'm interested that the automated transfers work with swab in tube as that would very much help. There's no information I can see in your documentation about the technical details of how this would work. I can confirm this stage would be great to speed up and would love to see how this could work. At this stage I also imagine would be a need to triage barcoding and have a separate process for correcting badly coded tubes as there's no way they'll be applied to the tubes consistently.

*****Im the engineer of our old company who specialised in Genomics genetic mass PCR etc so de-caping is easy throw into bowl feeder which orientates and presents to a bar code reader de capper then dispenser. .. https://alphamation.co.uk/vibratory-bowl-feeders/ sort of thing all basic factory stuff.
We have our own pooling tube design which is automation friendly as well*********

The second gain here is using 384 well plates rather than 96. This isn't specifically a limitation for RT-qPCR vs. endpoint PCR, but seems to be emerging from the availability of equipment for 384-wells for RT-qPCR process (e.g. Tecans, KingFishers, Tecans again, ABI7500s are all set up to work with 96-well plate formats). So the gain here would be that if you use an endpoint PCR process that you can provide sufficient volumes of equipment for that method that does handle 384+ samples per plate, and the consumables to match. But could there be 'halfway' improvement - e.g. if there was insistence on remaining with RT-qPCR, could the equipment be implemented for steps from decapping through to PCR reagent plating, then have it be loaded into real-time PCR equipment that can handle 384-well plates? Would that still provide at least some benefits? Or would there be losses - e.g. maximum volume limits - that would make this infeasible?


******got to think about man power to run 200+ rt machines vs 5 end point and a stacker.. twister plate stacker ************

Your documentation also mentions a applying different RNA extraction method - more information on that would be welcome too (currently as you probably know it's using MagMax kits).

*******we sold our company to LGC who are world class in rna extraction purified and crude.. we ideally want crude**********

Then to the actual endpoint PCR: water-bath/thermocycler seems pretty straightforward, and I have no reason to assume this equipment wouldn't be capable of handling the temperature changes required. Presumably also the detection systems are well-established and validated technology.

Three water baths and robot arm https://www.youtube.com/watch?v=FXv_WOjEKJE
This is Carly she joined us at 14 for weekend work with her mum. Now 30 and married !…. Using mass PCR hydrocycler.

Part 3: How do we know all this could work?
I guess I'd also be curious about how you'd plan to do the validation studies - presumably a scale-up from the existing sort of concordance data you have with many more sample plates? The current data is of course nice to see and I imagine quite difficult to obtain, but a 'next step' ask in terms of getting more concordance data would provide a clear direction for someone sufficiently well-resourced and motivated to evaluate your proposal further.

*************carrying out pilot which is a lot more than pilot in East Kent Dr Samuel Mosses.. 3000 staff every there days for a month at £2.5 per test including extraction..***************

It might be easier to understand the workflow if there was a detailed case study showing how it was already applied successfully to a diagnostic process (from the information in the deck it seems this is already being done at scale with some customers).

**********forget diagnostic clinical we are telling people to go home, not clinical. All our work is higher than clinical workflow as its a million data points a day and cant ever make mistake ever. Lots of work practises are above clinical. Lighthouse is way below any clinical accreditation HAND pipetting into tubes WOW ************

Part 4: What limitations aren’t considered here?
Of course, there's another limit on population sampling at the scale suggested here that is outside your control: sample collection in terms of swab administration and logistics. Presumably this procedure still uses nasopharyngeal swabs taken as the source material? We already have a lot of challenges surrounding taking these swabs from c.100,000 people, let alone 16 million pooled samples. Would be good to see this clearly spelled out in the slides and some consideration given to this challenge (even if just to point out that it will exist as a significant limitation that needs to be overcome with a lot of supply chain / logistics support).

********** Yes massive problem BUT AMAZON etc have bar code scanners and got to get rid off all packaging at pick up by AMAZON.. A van with one way containers so nothing gets out etc.. Like a big CAT 3 sharpie bin..**************


I imagine another limitation might be reagent availability - sure, it would be great to get the increased throughput with 384 wells and faster times from sample to result, but does the endpoint PCR method make the available reagents go further vs. the current RT-qPCR system and allow for scale-up even with that limitation?

***********There are other reagents plus would be in 5ul NOT 25ul. Its being tested at 1ul. Though we start at conservative volume************..


Part 5: Moneyknow little about how the costing of this sort of thing works, but where is that saving coming from? (e.g. is it from less staff, cheaper reagents, cheaper equipment, reduced consumable bills, all of the above?) It might be easier to think about that reduc
On cost savings: the headline saving of £2.50 vs. £55 is obviously a big improvement. Ition if it's mapped back to the concrete 'visualisable' places where the money is being saved.

********clinical world rips you off for everything. Staggering for no more quality then commercial testing. Half our £50k project is clinical swabs ***********************


You have got to think this is not science any more with virologists etc its industrial engineering like backed a bean factory

Happy to chat as easier I'm Jon curtis
joncurtis7@hotmail.com
07912 842821

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Jon Curtis 5 months ago

Also I volunteered to be one of the 750,000 nhs volunteers and guess what Sod all happened.. Im bloody sure they would love to help with getting tests to and from houses. Etc..There are two levels one being like me a driver then more semi qualified in defibrillators etc. These could be trained in taking swabs to houses.. And retrieving them.. yep that works..

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Bev Matthews 4 months ago

Hello Jon, Thank you for sharing this solutions with us, we're already pursuing these options but appreciate your time to ensure that the assessors are aware. please do keep an eye out for our future challenges. Thank you. Bev

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Bev Matthews 4 months ago

Status label added: A: Not for current challenges

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Jon Curtis 4 months ago

Mass testing data handling 10,000,000 ++ per day

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