Yep, ok .. I agree that the SARS-CoV-2 virus is too big for RT-PCR to decode the entire genome ( .. my bad).
I was incorrectly recalling
this study about how they used an RT-PCR System to generate genome
sequences, (not the entire genome directly .. as I recollected), of the Foot and Mouth Virus (which is only about 8.3kb in length):
Right, which is why I started that sentence with "diagnostic RT-PCR". There's all sorts of shotgun or tiling approaches to full length sequencing, but they are too expensive, time consuming, non-scalable and, well, pointless, from a diagnostic perspective.
The metagenomics thing is a bit of an esoteric red herring for this conversation. It basically means sequencing all of the organisms in a biosample, then using bioinformatics to tease out what organisms were present.
Yes .. and thus such 'false positives', (as far as the infection potential is concerned), still remains as a viable explanation for 'positive' (PCR-RT) results for recovering patients(?) - Ie: partial protein sequences, once amplified, might provide partial match-ups with SARS-CoV-2 sequences, and thus register as 'positives'
Firstly, this is all R/DNA. We aren't amplifying, measuring or doing anything at all with proteins (antibody tests aside). Secondly, (I don't know the full details of the tests but) we are not doing any matching of the product, we are just asking "is there a product". Which is to say measuring the presence of DNA after the RT-PCR..or indeed during the PCR reaction via something like UV light absorbance at 260-280nm, or more likely the dequenching of fluorophores.
TaqMan - Wikipedia
.. but I'm not sure how this could happen where the immune system initiated the apoptosis process .. its hard to find what happens to virion molecules after they've gone through this process - are they recognisable afterwards?
Virions are particles, not molecules. Cov2 looks like a spikey soccer ball dipped in lard. And getting out of an apoptopic cell is probably a bit like flying an x-wing out of an exploding death star.
Anyway, once they're out they don't fly wings and fly away, they just, like, hang around. Given for this disease they tend to form at the bottom of the lung but the test collects material from the nose, one might argue there's a delay between virion formation and expulsion...at least in the absence of coughing.
Uh .. ok .. my understanding is that the E gene produces the E protein in the envelope, which was thought to be be 'an essential' for the CoV virus to gain access to the inside of a host cell(?) This study shows that's not necessarily the case and so, a partially functional virus, with a gene artificially deleted, can still cause infection and penetrate the cell membrane (by other means).
Well...it's obviously not essential in this case. Previous studies have shown that it is essential for some coronaviruses and not for others. But regardless this has absolutely nothing to do with the topic of false positives, or positives after recovery, or any of the other stuff we were discussing.
I was thinking of a particularly infectious part (functionally) of the envelope .. not the entire envelope - (my mistake).
E gene is an ion channel that allows ions (usually K+ or Na+) to enter the virion to trigger conformational change as a part of the viral uncoating during the virus life cycle (at a guess, I haven't looked that up). Don't read too much into the fact it's call the "envelope protein".
What I mentioned above .. ie: 'a partially functional virus, with a gene artificially deleted, can still cause infection and penetrate the cell membrane (by other means)'.
I'm not aware of the mutant virus using "other means". Given it replicates at 100 to 1000 lower levels than the wild type, it's more likely it uses exactly the same means, just no where near as well. If it is, as I refuse to check, an ion channel driving conformation change, that would fit the evidence.
The infection rate, with that gene deleted, also looks to be slower and more targetted at specific cells too (ie: less infectious?). I'm wondering if this may be a partial explanation for why some people seem to have more 'severe infection' than others(?) (Apart from different levels of viral loads different people may encounter when becoming infected?)
It isn't. The mutant is 100 to 1000 times less effective. It would be like sending the New York Yankees (the wild type virus) out to bat against the Springfields Under 5 B team. Any virus that badly adapted relative to wildtype will be out competed and gone, unless there was a selective pressure that made the mutant survive better, which is why anyone that actually wants to understand evolution should read about the development of DDT resistance in fruit files. What we are seeing with COVID19 is entirely a wild type virus versus varying immune systems and comorbidities, not pockets of oddly deleted virus.
Also, we are doing a heck of a lot of full genome sequencing. If there was a deletion mutant out there, we'd have found it.
