First - why is this important for diagnostics?
First First though... what do I mean by diagnostics?
Diagnostics are what doctors use to know why someone is sick. They are a specific kind of test. Vs. a surveillance or public health test that indicates something.
2/
First First though... what do I mean by diagnostics?
Diagnostics are what doctors use to know why someone is sick. They are a specific kind of test. Vs. a surveillance or public health test that indicates something.
2/
A diagnostic that a doctor orders must be very good to do what it is meant to do - determine if someone is sick for a specific reason. So it needs to be high sensitivity and high specificity, there's little wiggle room. This is different than a public health indicator test.
3/
3/
OK, I won't harp further on diagnostics. Why is the SalivaDirect a good step forward for DIAGNOSTICS?
Two main barriers have gotten in the way of diagnostics in this pandemic: Swabs/tubes/media for sample and importantly, RNA extraction kits that prepare the RNA for PCR test
4/
Two main barriers have gotten in the way of diagnostics in this pandemic: Swabs/tubes/media for sample and importantly, RNA extraction kits that prepare the RNA for PCR test
4/
The SalivaDirect uses saliva - abrogating need for a swab/tube/media. Simply spit in a plastic tube without any other buffer or diluent needed. Simple as that - but then it MUST GO TO A LAB (more later)
5/
5/
So removal of the need for a swab and transport media removes a crucial step that has plagued numerous testing efforts. While swabs haven't really been too limiting lately, the choice between a deep nasopharyngeal swab and a more convenient front of nose swab is a tradeoff.
6/
6/
the deep nasopharyngeal swabs are difficult to perform - require a healthcare provider to do it, and are uncomfortable. The anterior nare (front nose) swabs are easier to self-perform, don't hurt, but don't catch as much virus as the deep nasopharyngeal swabs.
7/
7/
Use of saliva is a nice intermediate. It seems to catch potentially more virus than a self-collected anterior nasal swab but it's up for debate still how well it does against a nasopharyngeal swab. Either way, it doesn't require a swab/media, can be self collected, and works.
8/
8/
So to sum up point 1, SalivaDirect is an improvement by removing the need for a swab/tube and removed need for a healthcare worker performed nasophayrngeal swab - although self-collected frontal nose swabs have also already been approved.
Now on to why it is good for the lab
9/
Now on to why it is good for the lab
9/
A major hurdle in lab diagnostics for COVID19 has been a step in the qPCR process called RNA extraction. The RNA extraction kits were one of the first lab items in March to become limiting. Never did the world expect the number of RNA extraction kits that would be needed...
10/
10/
The RNA extraction process not only has proven to be a bottleneck in terms of supplies, but also adds an extra step in the laboratory that is almost as, or more burdensome as the qPCR test itself... so removal of it would be welcomed...
11/
11/
What is RNA extraction?? It is a preparatory step before qPCR that gets the specimen ready for the qPCR test itself. Essentially, the RNA is inside the virus and inside the cells that are in the swab. For the qPCR test to work, it must have access to the RNA...
12/
12/
The RNA extraction step essentially strips away the cellular structures and virus proteins etc and leaves just the naked RNA - which can then be added to the qPCR test for optimal detection....
13
13
The SalivaDirect assay includes a straightforward and welcomed step around the formal RNA extraction step. Instead of using true RNA extraction kits/materials, it simply adds a very common chemical (Proteinase K) and some heat to liberate the RNA much quicker and easier.
14/
14/
While this method has been used for a long time in PCR, SalivaDirect is the first EUA approved qPCR lab based assay for COVID19 to remove the formal RNA extraction for a simpler solution. This frees up reliance on limiting reagents and simplifies the protocol...
15/
15/
All great improvements! But it is important to note that despite use of saliva and simplifying the RNA extraction - SalivaDirect remains a laboratory based test that must be performed in highly specialized high-complexity CLIA clinical laboratories. It is not a rapid test.
16/
16/
I've found there is much confusion between the terms used for #COVID19 tests.
For example, use of saliva does not equate to a rapid test. i.e. SalivaDirect is not a rapid test, it is a high-complexity CLIA laboratory based test.
Even within rapid tests there are branches
17/
For example, use of saliva does not equate to a rapid test. i.e. SalivaDirect is not a rapid test, it is a high-complexity CLIA laboratory based test.
Even within rapid tests there are branches
17/
If a test needs a lab, it will necessarily not be rapid and will hit limits in volume. Only a certain number of tests fit through a doorway each day and onto a robot. With the right technology, like @Ginkgo is thinking about, a lab based test can get to very high numbers...
18/
18/
But it will necessarily not return a result in minutes (must travel to the lab) and the lab will hit its limits in terms of volume.
So rapid tests are a whole different idea. It is distributed testing - with results back in minutes, on the spot. There are different kinds.
19/
So rapid tests are a whole different idea. It is distributed testing - with results back in minutes, on the spot. There are different kinds.
19/
Some rapid tests are true diagnostics - they need some healthcare involvement, including doctors prescription of some sort, and are going to hit high levels of sensitivity because they are for medical diagnostics. @BDandCo Veritor, @AbbottNews IDNow are two
20/
20/
The tests with diagnostic labels will usually be more $$ too because they can be reimbursed by insurance (at least in US).
There is another kind of rapid test, which we have been calling for. These are first and foremost for public health - and can be done at home...
21/
There is another kind of rapid test, which we have been calling for. These are first and foremost for public health - and can be done at home...
21/
Non diagnostic rapid tests might use saliva or will use frontal nose swabs. They will hopefully not have a full diagnostic claim because they will serve to indicate if someone may be transmitting virus, but will not be used by a doctor to diagnose. These are different.
22/
22/
For more info on those kinds of rapidtests, you can check out rapidtests.org (linked below) or read this wonderful piece that covers all of this by @alexismadrigal in the Atlantic
theatlantic.com/health/archive…
To sum up...
23/
theatlantic.com/health/archive…
To sum up...
23/
SalivaDirect is a wonderful and hugely needed addition to the arsenal of laboratory based diagnostics. It will improve capacity to test in other CLIA labs too!
It is however not a rapid test that's going to be done at home with an answer in minutes. These are different.
24/24
It is however not a rapid test that's going to be done at home with an answer in minutes. These are different.
24/24
Last point, thanks @SaadOmer3 for reminding. By removing RNA extraction, SalivaDirect test can be made considerably cheaper than most lab based qPCR tests today. Likely <$5 vs $15-$50 in materials, making qPCR more accessible in low and middle income countries.
