RT-qPCR is indeed the common detection method right now. RT (reverse transcriptase) converts RNA->DNA, PCR (polymerase chain reaction) doubles DNA by replicating it over and over in heat cool cycles. To a first approximation, you get 2^n copies of the RNA (it was converted to DNA) where n is the number of heat cool cycles. By adding a fluorescent tracer, you get the q (Quantitative), so you can see how much DNA exists at each cycle. You can then fit a curve and see how much RNA (via its DNA complement) existed in the original sample. It's not actually that slow, you can do this in a couple hours if you have the right setup. The bottleneck is you do need time for the heating and cooling cycles. You also need to extract RNA from the sample first, which could be another bottleneck. I'm not totally clear on the relative cost, a good ELISA would eventually be cheaper, but qPCR itself isn't very expensive. The benefit is that qPCR is extremely sensitive, you WILL see if there is virus in the bloodstream. You can even use swabs and avoid blood altogether. Also, the minute you have a viral genome, you can make a qPCR test, you just need the sequence. That said, if you cleared the infection you will be negative under RT-qPCR.
An ELISA works differently. In this case you would present a part of the viral protein, the patient's antibodies will bind to it, and you then use another antibody (this one is conjugated to some sort of readout method, fluorescent or biochemical) which binds to generic human antibody. Now you have a stack: viral protein <> patient antibody <> readout antibody. You read out the signal provided by your readout, usually some sort of colorimetric thing (see home pregnancy tests, also an ELISA, slightly different configuration though). This works fast, can be manufactured in bulk, BUT requires do you have a protein(s) (in this case the viral protein) that is/are universally recognized by patient antibodies. It's a little trickier to develop. You also need to produce that protein at scale which can take a little time as well. Major benefit: with a good ELISA you WILL see not only whether someone IS infected but whether someone WAS infected for some period after illness regardless of symptoms. This is essentially the only way you'll get a really good number for baseline infection rate. That said, you likely actually need a blood draw.
In short, we need both, we probably could do a lot better than we are doing with qPCR in testing volumes and we could also really use an ELISA.
Source: PhD biochemist, have personally run these assays in various forms.
Maybe one should note, that there are two possible Elisa based strategies. Yes, You can present some viral protein to detect antibodies produced by the body after serum conversion, as you said. This serum conversion takes at least a week to happen and you need a blood sample. On the other hand you can also immobilize antibodies specific to the viral proteins and directly detect the virus. This is possible immediately after infection and fluids like sputum or saliva can be used. Both strategies are under development for quick tests right now.
This is all true, but detecting the viral proteins directly with reasonable sensitivity and specificity is much more difficult. The reason is that there is just a lot less of it to detect. After seroconversion, the amount of antibody against the virus can be very high and relatively easy to check.
+1 the major advantage of RT-qPCR is it's a massively amplified test. Tiny amounts of virus can be detected. When you're detecting a patient's antibodies to the virus, the patient is producing massive amounts of it. That said, after clearing the infection that production will decline, but still should be detectable at least for a while.
Direct detection of viral particles is substantially harder because for N viral particles you basically get O(N) signal (to put it in CS terms). There are some caveats, your readout antibody can generate an exponential signal for example.
You still need to be presenting the right part of the capsid and have the right material. In the direct ELISA scenario, you need 2 antibodies. One to bind the capsid to your surface, the other to bind it again and either have a readout attached directly or be bound by yet another antibody with the readout (likely the latter). Fortunately, viral capsids are repetitive so you might be able to use the same antibody for both. You ALSO need those antibodies to have low cross-reactivity with sputum or whatever other rough sample you have. When you are looking for a patient's antibodies, the patient's immune system has already taken care of that for you. This is all tricky, obviously it's not THAT hard, but it's not trivial.
RT-qPCR is directly a O(2^N) signal. It's extremely sensitive, requires very little assay development, can be made very specific, can work with little sample prep, so it's a much better front-line, first-to-go test than direct ELISA. Still, we'd all love an ELISA, particularly to patient antibodies.
I definitely agree about the superiority of RT-PCR and the drawbacks of direct detection. Nevertheless, seroconversion can take between 5-12 days from symptom onset [1]. Therefore it's important to outline the different ELISA strategies (Thank you for doing so!), when discussing diagnostic tests.
The signal is actually more like N*2^C where C is the number of cycles (usually around 30). So a huge amplification, but still linear in the starting amount, i.e. O(N). That's actually more useful, generally, since ratios of amplified material stay approximately constant during amplification.
Yes, there are of course drawbacks. But the direct detection is applicable at the same stage of infection as a rt-pcr and therefore usefull for immediate disease diagnosis. Indirect tests after seroconversion are the easier alternative, and will probably be used extensively in the aftermath, to get solid epidemiological numbers.
One disadvantage to RT-qPCR I forgot to highlight, and an advantage to direct detection ELISAs (and ELISAs in general) is that ELISAs are relatively robust when fully developed. RT-qPCR requires a lot more gear. See pregnancy tests. Sits on a shelf for ages, all you need to do is pee on it, works reliably, needs no extra equipment.
Are the tests used in [1] (real-time RT-PCR) the same?
The false negative reported several times from the same patient is interesting, but may be more due to testing source (upper respiratory fluid vs. sputum or lower respiratory sources or blood).
Yes, the "q" is often used instead of "real-time" to avoid confusion with RT, which can also be "reverse transcriptase". RT in these cases is the enzyme that converts RNA to DNA.
I used to set up and run a large plate of qPCR (we didn't use the RT step in our particular use case) in an hour or so. Mind you this was for something like 200 samples. It took 2-3h to run the actual machine. If I was setting up such an assay, I'd order a bunch of different primers (you need DNA to make DNA) and run a bunch of plates with as many samples as I could to see what primers worked best. You'd include a bunch of negative controls, ideally some controls from patients/cultures infected with similar but not identical virus (for example a different coronavirus). To develop an RT-qPCR assay would take a week or two (rough guess), I think it took about a week to develop the WHO assay.
From what I can tell (mostly anecdotal and other data from friends I trust) the CDC assay used bad primers, they were noisy, showing a bunch of false positives. They also used a potentially dodgy fluorescence readout. I used to use the same readout, but our scenario was full of internal controls and the input sample was far more consistent. For human sample data a different fluorescent method that is more reliable should have been used.
Important ways this can be screwed up: it's helpful to use the same machine, the same protocol every time. This is because qPCR is an exponential assay, which means small errors can have big repercussions.
TLDR: Scale of fuckup here is massive. This really isn't that hard, and we could just have used what the WHO/others were using. I have no idea why they decided to go their own way.
An ELISA works differently. In this case you would present a part of the viral protein, the patient's antibodies will bind to it, and you then use another antibody (this one is conjugated to some sort of readout method, fluorescent or biochemical) which binds to generic human antibody. Now you have a stack: viral protein <> patient antibody <> readout antibody. You read out the signal provided by your readout, usually some sort of colorimetric thing (see home pregnancy tests, also an ELISA, slightly different configuration though). This works fast, can be manufactured in bulk, BUT requires do you have a protein(s) (in this case the viral protein) that is/are universally recognized by patient antibodies. It's a little trickier to develop. You also need to produce that protein at scale which can take a little time as well. Major benefit: with a good ELISA you WILL see not only whether someone IS infected but whether someone WAS infected for some period after illness regardless of symptoms. This is essentially the only way you'll get a really good number for baseline infection rate. That said, you likely actually need a blood draw.
In short, we need both, we probably could do a lot better than we are doing with qPCR in testing volumes and we could also really use an ELISA.
Source: PhD biochemist, have personally run these assays in various forms.
EDIT: Acronym expansion, source