Phil Core said:Is there something that makes the CoronVirus unique? Yes. Apparently it is the ending sequence. Search for that.
The structure of the virus provides some clues about its success. In shape, it’s essentially a spiky ball. Those spikes recognize and stick to a protein called ACE2, which is found on the surface of our cells: This is the first step to an infection. The exact contours of SARS-CoV-2’s spikes allow it to stick far more strongly to ACE2 than SARS-classic did, and “it’s likely that this is really crucial for person-to-person transmission,” says Angela Rasmussen of Columbia University. In general terms, the tighter the bond, the less virus required to start an infection.
There’s another important feature. Coronavirus spikes consist of two connected halves, and the spike activates when those halves are separated; only then can the virus enter a host cell. In SARS-classic, this separation happens with some difficulty. But in SARS-CoV-2, the bridge that connects the two halves can be easily cut by an enzyme called furin, which is made by human cells and—crucially—is found across many tissues. “This is probably important for some of the really unusual things we see in this virus,” says Kristian Andersen of Scripps Research Translational Institute.
For example, most respiratory viruses tend to infect either the upper or lower airways. In general, an upper-respiratory infection spreads more easily, but tends to be milder, while a lower-respiratory infection is harder to transmit, but is more severe. SARS-CoV-2 seems to infect both upper and lower airways, perhaps because it can exploit the ubiquitous furin. This double whammy could also conceivably explain why the virus can spread between people before symptoms show up—a trait that has made it so difficult to control. Perhaps it transmits while still confined to the upper airways, before making its way deeper and causing severe symptoms. All of this is plausible but totally hypothetical; the virus was only discovered in January, and most of its biology is still a mystery.
Phil Core said:Others are saying that this virus is not a good candidate for mutation. Somehow it self corrects. How is this done?
Although I never fully appreciated it, I imagined that with a double helix, if there was a problem with one strand in some way it might check the other to see if there was a more efficient method available.
How is a single strain RNA being self corrected? Has to be a lot of something in the chain to do that.
https://marlin-prod.literatumonline.com/pb-assets/journals/research/cell/Online Now PDfs/CELL11322_S5.pdfalthough coronaviruses likely have lower mutation rates than other RNA viruses because of an inherent capacity for some proofreading activity due to a 3’-to-5’ exoribonuclease (Minskaia et al., 2006), their long-term rates of nucleotide substitution (i.e. of molecular evolution) fall within the distribution of those seen in other RNA viruses (Holmes et al., 2016). This suggests that lower mutation rates are to some extent compensated by high rates of virus replication within hosts. Although there is no evidence that this capacity to mutate (common to RNA viruses) will result in any radical changes in phenotype - such as in transmissibility and virulence - as these only rarely change at the scale of individual disease outbreaks (Grubaugh et al., 2020), it is obviously important to monitor any changes in phenotype as the virus spreads.
You're welcome. As someone who is publicly funded to do biomedical research, I think it's important to try to better explain science to the public, especially at times like these. Plus, I'm currently locked out of lab, so I have plenty of time and energy to devote to other things at the moment.Phil Core said:Yggdrasil - You are the best. You have devoted a lot of your time and energy to helping others. I found the articles you referenced to be excellent.
Thanks Big Time
jim mcnamara said:@Ygggdrasil Yes But.
You are correct that it does not mandate genetic change that impacts the clinical aspects of vaccination. It just starets off with a big disadvantage.
This is a nice textbook example of R selection - with genetic drift and mutation at work in populations with little selection pressure. A sort of free-range virus sortie.
There are four main branches on the phylogenetic tree per GISAID data sets as of right now. (link below) Instead of wild ducks like influenza has, this virus has 7+ billion humans to facilitate genetic drift and mutation.
See R & K Selection for a definition: https://en.wikipedia.org/wiki/R/K_selection_theory
A virus with 'a whole new world' to itself, is a model of R selected activity for what we are seeing. This virus population is going to rapidly diverge genetically. Based on the GISSAID data. As you know RNA viruses mutate rapidly. There exist four primary branches now.
This is a wonderful resource using GISAID data sets, please play around with it.
https://nextstrain.org/ncov
This is a discussion of genetic drift and mutation in R & K selected populations of Eukaryotes (birds)
https://royalsocietypublishing.org/doi/full/10.1098/rspb.2015.2411
As of this writing there are 946 genome samples in the chart. I am not claiming anything "wierder" than what we see in influenza genomes over the course of a year, just that the magnitude of rate of change not like flu. Humans are the "wild duck populations like the flu has" in this model. We speed up the change by losing the intermediate steps that flu has to go through.
Such that vaccine expectations are misplaced, IMO. For a vaccine to be effective in 6 months when trials begin, and will continue later to work in the wild on virus populations that have changed. A lot. This will result in misses like we have had in the past two years with flu vaccines. A vaccine miss here is and order of magnitude worse than for the flu given the current virulence and infection transmission data.
It is not that we cannot make vaccines it is how well they work over time.
Plus, SARS patients apparently lose immunity after 1+ years. Assuming that same limited immunity obtains here: This translates to a somewhat limited duration herd immunity.
FWIW I really object to the concept 'but it is like the flu'. This denigrates a horrible disease (flu) which we should have been able to get a handle on by now. We have simply slowed it down. Example: 2018 was a bad flu year in part, due to a vaccine/antigen mismatch.
This in turn speaks negatively to getting a vaccine handle on a more transmissable and virulent disease via vaccines. Antivirals may really be a better choice.
This link shows that we can isolate very early new flu outbreaks with TamiFlu rings. And we do not do it proactively and widely. At least there are no reports other than this one on H1N1 in Singapore 2009.
https://www.nejm.org/doi/full/10.1056/NEJMoa0908482
It has been successfully used in nursing homes:
https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1532-5415.2002.50153.x
For Covid 19 -- Even if we come come up with an anti-viral that works as well as TamiFlu, we will then need to proactively contain it with rings. Or give out billions of pills every year. Or as an alternative, try to keep a series of vaccines current for all forms. And re-vaccinate as needed. We can do it. Somewhat. But the way it was referenced in the posts that triggered this discussion was not correct, IMO. It is not like the flu.
This is what I was thinking of. Works directly on the RNA.Phil Core said:I guess I could develop my own test but I would not want to deprive someone else of the adventure.
I am unfamiliar with PCR. However, RNA DNA both composed of nucleotides.
Is there something that makes the CoronVirus unique? Yes. Apparently it is the ending sequence. Search for that.
I think you have a fundamental misunderstanding of these technologies. All of the technologies (PCR, this isothermal method, etc) require amplification of the nucleic acid to have any hope of detection at all. Saying “works directly on RNA” is meaningless, because all of the methods are literally looking for a few molecules of RNA in a huge quantity of interfering media (including the RNA already present in the media). To be able to detect anything at all requires increasing that number of RNA molecules from a few to several billion.Phil Core said:This is what I was thinking of. Works directly on the RNA.
Using the word "meaningless" is very close minded. True I do not have an extensive scientific background but I believe I made a contribution by suggesting that the RNA be analyzed directly.TeethWhitener said:I think you have a fundamental misunderstanding of these technologies. All of the technologies (PCR, this isothermal method, etc) require amplification of the nucleic acid to have any hope of detection at all. Saying “works directly on RNA” is meaningless, because all of the methods are literally looking for a few molecules of RNA in a huge quantity of interfering media (including the RNA already present in the media). To be able to detect anything at all requires increasing that number of RNA molecules from a few to several billion.
My point is that the fundamental method is the same as PCR. "RNA be analyzed directly" is vague at best, meaningless at worst. Do you mean analyze RNA directly extracted from the patient? I've already described how that's impossible. Several times. Do you mean amplify the RNA extracted from the patient in order to detect it? Then that's what both methods (PCR and Abbott's method) already do. This is why I think you're fundamentally misunderstanding the techniques. You're suggesting things that are either 1) already being done, or 2) impossible in practice.Phil Core said:Using the word "meaningless" is very close minded. True I do not have an extensive scientific background but I believe I made a contribution by suggesting that the RNA be analyzed directly.
Abbott's technology is proprietary, so most of the details are trade secrets. However, isothermal nucleic acid amplification is well-known (a simple google search will likely tell you more than Tyler Durden and Zero Hedge will). It's an umbrella term encompassing a number of different techniques, but in general, it involves using a specific set of enzymes for nucleic acid amplification at a single temperature as opposed to the thermal cycling generally required by PCR.Phil Core said:Would appreciate your opinion on how the detection time was reduced from days to mins.
TeethWhitener said:My point is that the fundamental method is the same as PCR. "RNA be analyzed directly" is vague at best, meaningless at worst. Do you mean analyze RNA directly extracted from the patient? I've already described how that's impossible. Several times. Do you mean amplify the RNA extracted from the patient in order to detect it? Then that's what both methods (PCR and Abbott's method) already do. This is why I think you're fundamentally misunderstanding the techniques. You're suggesting things that are either 1) already being done, or 2) impossible in practice.
Abbott's technology is proprietary, so most of the details are trade secrets. However, isothermal nucleic acid amplification is well-known (a simple google search will likely tell you more than Tyler Durden and Zero Hedge will). It's an umbrella term encompassing a number of different techniques, but in general, it involves using a specific set of enzymes for nucleic acid amplification at a single temperature as opposed to the thermal cycling generally required by PCR.
Edit: it's also important to point out that normal PCR only takes about 45 min-1 hour to run. The "days" for testing is due more to the logistics of getting the samples to a well-equipped enough lab that actually has the tests to run, not the time for the tests themselves. These logistical problems will still exist, regardless of the method used for testing.
Unless you have a real citation for this, you don’t know whether it’s true. Even the article you linked to says nothing about whether the RNA is amplified directly (very doubtful). It merely says that the device tests for a particular RNA sequence. Which is exactly what PCR does. My guess is that the amplification step is almost certainly DNA amplification. Also, based on what’s written in the article, I bet they use the exact same primers and probes that PCR methods do. In fact, reading it more closely, I’m prepared to wager a guess that the only feature that differentiates Abbott’s technology from any of the other nucleic acid tests is the isothermal nature of the amplification scheme.Phil Core said:True, methods mentioned are the same because they all test for the virus. However, the Abbot method uses the RNA directly while the prior method you were mentioning took the RNA and reversed transcribed it into DNA and them analyzed the DNA(amplified in a different way).
Phil Core said:1. I certainly never intended to imply I invented a new method. I was just offering a direct RNA vs an indirect reverse transcription for thought. I had not read the quoted article at the time.
2. True, methods mentioned are the same because they all test for the virus. However, the Abbot method uses the RNA directly while the prior method you were mentioning took the RNA and reversed transcribed it into DNA and them analyzed the DNA(amplified in a different way).
3. For the less imaginative the article I referenced actual has a picture of the testing device. I am sure it could be used in the field.
"The test starts with taking a swab from the nose or the back of the throat, then mixing it with a chemical solution that breaks open the virus and releases its RNA. The mixture is inserted into an ID Now system, a small box weighing just under 7 pounds that has the technology to identify and amplify select sequences of the Coronavirus genome and ignore contamination from other viruses."
Actually, it is not based on RT-LAMP. My previous reply was based on a Tweet suggesting that the test was RT-LAMP, but reading a little deeper into the literature, the test is actually based on the nicking enzyme amplification reaction (NEAR) technology. See https://www.alere.com/en/home/support/product-demos/alere-i.html and Figure 1 from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313160/ for more information on the technique.TeethWhitener said:@Ygggdrasil where did you find that the Abbott test was RT-LAMP? I couldn’t find any info on the exact nature of the test.
PCR amplifies DNA, not RNA. Therefore, to be able to amplify the virus’s genetic information, the viral RNA must be reverse transcribed to DNA.Phil Core said:Why must RNA be converted to DNA to test for virus?