Thanks; that is a good question. In our laboratory, we have a ratio of 10:1 for PCR to qPCR instruments. In the new laboratory that we are constructing, the ratio is 50:1. It was similar at Stanford academic laboratories during my PhD. Standard PCR instruments are inexpensive and very common. qPCR instruments are definitely not as common, as they are very specialized instruments for a few use-cases.
Most clinical laboratories would have 10 to 50 PCR instruments that they can use to run the initial amplification reaction in parallel before Sanger sequencing. Also, Sanger sequencing uses a plate feeder, so you can add new plates on top as the second round of PCR reactions finish.
But, more importantly, the qSanger can by-pass RNA extraction, which seems to be an important bottleneck in the RT-qPCR workflow.
$15 is half the price of even the bare minimum qPCR kits (e.g., TaqPath). We need to buy the reagents from NEB, IDT, and others and work with a contract manufacturer to mix it into a reaction. Reagent, manufacturing, quality control, and fulfillment cost already add up to ~$11/reaction. That does not take into account any costs associated with developing the assay, supporting the assay, getting it through EUA, customer service, bioinformatics help. And we have to pre-pay for all of the reagent costs in the anticipation of the volume. I anticipate that we will likely end up net negative with this work, and even if it ends up being slightly net positive, it will not impact our valuation in a positive way.
The current equipment owners are already the clinical laboratories. It is unused capacity for them. Other owners are sequencing service providers. The full cost of running an end-to-end Sanger reaction as a provided service is $2-$6, so at the $50 reimbursement price, the laboratories will still be incentivized.
Thanks for the question. Last week, I sent half-a-page of instructions in a hastily written e-mail to a scientist working for the Switzerland government response team, and they told me that it worked beautifully in their first try this week.
With the details described in the manuscript, the onboarding can be only a few days (or even self-onboarding based on instructions). The only part that is somewhat tricky is the bioinformatics algorithm for positive vs. negative calls, which we can supply.
I think we can scale it to significantly more than 1M a day, but it would require the relaxation of certain regulations that currently prevent collaboration between clinical laboratories and other institutions that have Sanger instruments. FDA and CMS require that clinical laboratories process the sample end-to-end, so it prevents a distributed model of initial processing in the clinical laboratory followed up with send-out for Sanger sequencing.
California CLIA and FDA regulations for COVID-19 testing have been relaxed significantly over the last few weeks, so the above is perhaps not impossible.
Roche 6600/8800 instruments are state-of-the-art automated RT-qPCR machines. We need them as well as other COVID-19 testing instruments.
That said, it is easier to ship the test kits than scale the instrumentation. Both Roche and Abbott still need to build hundreds of their instruments before the kits that they are shipping out this week can be used on the daily rate that they are trying to get to. I am not sure with Roche, but Abbott estimates the end of June to have enough machines shipped to achieve 50K per day capacity on their instruments.
Another potential problem with new instrumentation is that reimbursement for COVID-19 tests is very low ($30-$50), so it becomes financially difficult for hospitals and laboratories to buy very expensive instruments and also pay for test kits that cost $30-$50 per test, on par with reimbursement.
We try to avoid both issues by utilizing a currently unused Sanger install base and low-cost reagents.
We have the data both with extraction and without and show that it does not make a difference with qSanger. In Figure 4, we add VTM directly to PCR reactions. Seracare VTM samples has SARS-CoV-2 viral RNA in a different capsid to prevent infections in a research setting, but otherwise it reflects real-world VTM samples (and much more realistic than even what EUA requires).
By the way, this robustness is completely expected, as any impurities in VTM would impact spike-in and endogenous viral amplification equally for end-point PCR (so their ratio stays the. same). This is not necessarily true for qPCR where an impurity (caused by lack of RNA extraction) can potentially cause a positive sample look like a negative when the viral RNA does not RT-PCR.
Both the methods and David's twitter clearly describe the linear regression as the method and how it works with spike-in. In practice, it is a lot more complicated, as the signal-to-noise ratio can interfere with the regression and primer N-1 synthesis errors need to be accounted for. That is why we are willing to help other laboratories with our bioinformatics pipeline.
If it is specific to COVID-19 testing, we will not seek anything, as long as the end-user is not financially benefiting from it or importantly, selling qSanger kits.
If they need our bioinformatics automation & help with set-up, we would license the method for COVID-19 testing for $3-$5/sample as part of each sample that is being put through our pipeline.
If they ask for 96-well plates with all reagents that are ready to use (so that they just need to add VTM), we would work with manufacturers to produce the reactions and plates, and the price of kit (~$15 per test) would include limited license to use our automated bioinformatics calling pipeline.
I don't think we are in any way undervaluing the serological tests. A great serological test would be very useful. However, because of the indirect measurement, they tend not to be very sensitive or specific, so it is fair to say that they become more important not at the peak of the pandemic but at the post-pandemic period.
By the way, as a company, we really don't have much to gain from this test. If it does not get adopted, we'll go back to building our core business which has been growing 100% quarter over quarter. We have poured resources into the current development, because it is the right thing to do. No investor in our Series B round will take into account any non-recurring sell-almost-at-cost revenues that we get from a once-in-a-century pandemic.
We have already generated and put into our scientific manuscript the data that FDA requires for EUA. As a high-complexity CLIA-licensed clinical laboratory, we don't see significant risk in getting the authorization in 2 weeks. However, we need to start working with clinical laboratories across the country today if this is going to scale to hundreds of thousands of tests as soon as we get the EUA. Also, international laboratories don't need EUA and can start using the test immediately. We did not think it would be responsible to hold off on making the technology public when every day is so critical in our response to the current pandemic.
Most clinical laboratories would have 10 to 50 PCR instruments that they can use to run the initial amplification reaction in parallel before Sanger sequencing. Also, Sanger sequencing uses a plate feeder, so you can add new plates on top as the second round of PCR reactions finish.
But, more importantly, the qSanger can by-pass RNA extraction, which seems to be an important bottleneck in the RT-qPCR workflow.