Medical What makes the current coronavirus different from the others?

[jim mcnamara]

@mfb @jedishrfu

Re: vaccines
per https://nextstrain.org/ncov There are 880 reported genotypes (strains), this is a compendium of those genotypes.

As of
20-March-2020.

RNA viruses have high mutation rates.

This is the same reason why there are dozens of extant influenza genotypes, and we create trivalent (or quadrivalent) vaccines which work against a fraction of them. This is also the reason the flu shot in 2018 did not match very well and flu mortality was much higher. Mortality appears, based on current data, to be higher for Covid 19 than the last bad bout of flu in the US. So a vaccine miss puts us back behind the eight ball mortality-wise for either flu or nore so for Covid 19.

So what I am saying is the "vaccine" can be created and tested. But we are in a situation where a random happenstance we cannot control may and will render it less than perfect and and the "miss" will be far worse than most flu epidemics have ever been. Assuming the same clinical progression as we see now.

Or, how about:
The flu sucks and so does Covid 19. Neither is something we humans want in any, way, shape for form. Our vaccine approach needs to change. And simply saying 'a vaccine is coming' is not a true panacea.

 

[mfb]

If you check the virus in hundreds of people you can find hundreds of variants. Not surprising. Most mutations won't be relevant for a vaccine.
If you click on "clock" you can see that these strains differ by single mutations, or sometimes don't even differ at all but still count as separate strain.

 

[TeethWhitener]

I don't find the theory that the Covid 19 could have been an ongoing epidemic before 2019 until someone in China isolated this novel virus, too outlandish.

The low phylogenetic divergence makes it extremely unlikely that this virus has been circulating in humans for much longer than has already been observed.

 

[Ygggdrasil]

@mfb @jedishrfu

Re: vaccines
per https://nextstrain.org/ncov There are 880 reported genotypes (strains), this is a compendium of those genotypes.

As of
20-March-2020.

RNA viruses have high mutation rates.

This is the same reason why there are dozens of extant influenza genotypes, and we create trivalent (or quadrivalent) vaccines which work against a fraction of them. This is also the reason the flu shot in 2018 did not match very well and flu mortality was much higher. Mortality appears, based on current data, to be higher for Covid 19 than the last bad bout of flu in the US. So a vaccine miss puts us back behind the eight ball mortality-wise for either flu or nore so for Covid 19.

So what I am saying is the "vaccine" can be created and tested. But we are in a situation where a random happenstance we cannot control may and will render it less than perfect and and the "miss" will be far worse than most flu epidemics have ever been. Assuming the same clinical progression as we see now.

Or, how about:
The flu sucks and so does Covid 19. Neither is something we humans want in any, way, shape for form. Our vaccine approach needs to change. And simply saying 'a vaccine is coming' is not a true panacea.

I agree with @mfb here, the fact that we observe different genotypes have because the virus has accrued various mutations, does not mean that there are different strains of the virus. As an analogy, human individuals differ by ~20 million base pairs, but (as far as we know) all are equally susceptible to the Coronavirus (so to the virus, there is only one strain of human). Only very specific mutations could allow a human to be immune from the virus (e.g. in the case of HIV), and likewise, only very specific mutations in the SARS-CoV-2 virus would allow it to evade immunity in vaccinated individuals.

Thus, many mutations will not have any effect on the virus, and we would mainly care about mutations that affect the behavior of the virus. So far, we have not seem much meaningful change to the viral genome:

Since the start of the pandemic, the virus hasn’t changed in any obviously important ways. It’s mutating in the way that all viruses do. But of the 100-plus mutations that have been documented, none has risen to dominance, which suggests that none is especially important. “The virus has been remarkably stable given how much transmission we’ve seen,” says Lisa Gralinski of the University of North Carolina. “That makes sense, because there’s no evolutionary pressure on the virus to transmit better. It’s doing a great job of spreading around the world right now.”

There’s one possible exception. A few SARS-CoV-2 viruses that were isolated from Singaporean COVID-19 patients are missing a stretch of genes that also disappeared from SARS-classic during the late stages of its epidemic. This change was thought to make the original virus less virulent, but it’s far too early to know whether the same applies to the new one.

https://www.theatlantic.com/science/archive/2020/03/biography-new-coronavirus/608338/
(note: this article from the Atlantic is a great, popular press summary of what we know about how the virus differs from other coronaviruses, and how those differences may lead to its success in spreading across the globe).

Now, that is not to say that the virus won't or cannot mutate to evade immunity. These types of mutations are certainly possible, and people are monitoring virus sequences to monitor for that possibility. Because the immune system recognizes the protein on the surface of the virus (the spike protein), it is very important to monitor changes to the spike protein as these types of mutations do carry the possibility of altering how our immune system recognizes the virus.

 

[jim mcnamara]

@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.

 

[Laroxe]

This reports on a study that seems to have galvanized the UK and US governments, not surprising really considering the picture it paints.
Currently the case figures are unreliable, the rate of testing is very different in different countries and this makes it impossible to get an accurate estimate of mortality. It seems as if stressing the risk to the elderly might have been a bit of a mistake, a significant number of younger people become seriously ill and the facilities needed to treat these people will likely be overwhelmed in most countries, this will impact on the mortality rate.
I don't thing that the way in which death is attributed to corvid19 is a major problem, the illness seems to run a fairly characteristic course, the pneumonia is usually as a result of the virus rather than a secondary bacterial infection and may be associated with a "cytokine storm" like that seen in SARS.
There have been some drugs that have shown promise but so far none can be recommended but trials are going on everywhere, Meplazumab is a monoclonal antibody and like all of the new biologics will be horribly expensive, its unlikely that it could be used outside of very specific situations in wealthy countries.
Even if infection only produces weak immunity there may be some hope in the new vaccine technology that instructs the bodies own tissues to produce the antigens, this would probably produce an extended exposure and a better immune response.
I suspect that the study reported may be biased towards a worst case situation, we still have very limited information really, but its easy to see why things are changing so quickly.
https://www.ft.com/content/16764a22...1W0zHgVCcFBjkCOa9VWzQ0WfWVFGDcvbKhjoZwRb8rxNo

 

[Ygggdrasil]

I don't find the theory it is plugging up the healthcare situation very convincing either, according to this paper, https://www.sciencedirect.com/science/article/pii/S1201971219303285, about 20,000 people die over there too because of the flu, you still take these patients to the hospitals, ICUs etcetera. They had ample time over there to develop a remarkable healthcare system to cope with all the flu patients. I mean the numbers alone are crazy.

Comparing annual deaths to influenza across the whole country versus the number of COVID-19 deaths over the course of a small amount of time at an early stage of the epidemic is misleading. Current figures from Italy show over 500 deaths per day, which is 10x higher than the estimated number of influenza deaths per day (~55 deaths per day based on 20,000 deaths per year). Furthermore, these deaths are concentrated in certain regions of the country, so the burden on hospitals in these regions is even 10x higher than the normal burden from influenza. Given that it takes about 2-3 weeks for an infection to lead to a death and the number of deaths per day keeps increasing, we are likely to see things get worse (>10x the burden on hospitals than influenza).

 

[Astronuc]

Most of the SARS-CoV-2 genome resembles bat coronaviruses, expect for one protein encoded by the viral genome, the spike protein (which is the element that helps the virus bind to the host cells). The spike protein more closely resembles the spike protein from coronaviruses found in pangolins. Therefore, from this data, scientists infer that the SARS-CoV-2 virus resulted from recombination between a bat Coronavirus and a pangolin coronavirus. When and where this recombination took place remain yet to be understood.

Here are some preliminary, non-peer reviewed pre-prints that present genetic analysis of various Coronavirus sequences making the case that SARS-CoV-2 likely resulted from recombination of bat and pangolin coronaviruses:
https://www.biorxiv.org/content/10.1101/2020.02.07.939207v1
https://www.biorxiv.org/content/10.1101/2020.02.17.951335v1
https://www.biorxiv.org/content/10.1101/2020.02.13.945485v1

https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30251-8/fulltext

Findings
The ten genome sequences of 2019-nCoV obtained from the nine patients were extremely similar, exhibiting more than 99·98% sequence identity. Notably, 2019-nCoV was closely related (with 88% identity) to two bat-derived severe acute respiratory syndrome (SARS)-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21, collected in 2018 in Zhoushan, eastern China, but were more distant from SARS-CoV (about 79%) and MERS-CoV (about 50%). Phylogenetic analysis revealed that 2019-nCoV fell within the subgenus Sarbecovirus of the genus Betacoronavirus, with a relatively long branch length to its closest relatives bat-SL-CoVZC45 and bat-SL-CoVZXC21, and was genetically distinct from SARS-CoV. Notably, homology modelling revealed that 2019-nCoV had a similar receptor-binding domain structure to that of SARS-CoV, despite amino acid variation at some key residues.

 

[Laroxe]

Flu really doesn't seem to be a good model for understanding possible vaccines for covid19. The influenza viruses have made something of a fetish of changing their surface antigens and this can involve several different processes. The viruses can change due to antigenic drift, antigenic shift and the change driven by the selective pressures of the new host. Antigenic drift reflects changes that can occur due to random mutations that occur during replication, while these are common, particularly in RNA viruses the specific mutations needed to effect the surface antigens are not. This means that influenza type B and C and now apparently covid19 tend not to undergo major changes, so far Covid 19 seems to be remarkably stable.

The same can not be said of influenza type A which appears rather less choosy about its hosts, a virus can jump from one species to another and does so fairly frequently. There are a number of variables that influence the likelihood of cross species transmission perhaps the most important being the degree of exposure of a weakened host. It is also possible for type A viruses from two different species to infect the same intermediate host and even the same cell, this can lead to anew subtype with a mix of surface antigens from both (or more) of the infecting viruses. This leads to a major reorganisation of the surface antigens and its this that causes the problems in developing effective vaccines. Viruses are then subject to the selective pressures of the host and the requirement to optimize the effects it has on the host to improve its own fitness.

We now have the technology to identify potential surface antigens from the genetic code and use a variety of methods to expose an individual to a number of these, the choice appears particularly important in Covid 19 as the effectiveness of the antibodies varies a great deal and some may facilitate an abnormal response the so called cytokine storm. However targeting several different surface antigens makes it difficult for the virus to adapt and avoid the effects. Interestingly its only now that these technologies are being used in flu vaccines and one is already undergoing trails that specifically targets the antigens shared by most strains. These appears to offer broad protection against flu, but the most recent technologies remain unproven.

When considering the effects on health resources covid19 is not offered as an alternative to flu, the flu is still circulating and continues to cause illness. Generally the serious illness caused by flu can be treated and the seriously ill that recover tend to use critical care facilities for shorter periods of time. Up to 20% of Covid 19 infections result in hospitalisation with around 6% requiring intensive care often over several weeks. I thought you might be interested in all of the treatments and vaccines being studied. Currently the most promising is the use of hyper-immune gamma globulin from the blood of people who have recovered, this will become more available as the pandemic develops but doesn't really represent a treatment for the majority. Sorry for rambling.

https://milkeninstitute.org/sites/default/files/2020-03/Covid19 Tracker 032020v3-posting.pdf

 

[Phil Core]

All kinds of interesting stuff here but does not directly address original questions

Upfront it must be acknowledged that the CoronVirus is a single strand RNA virus that reverse transcribes.

Have heard that an upper bound is 32,000 nucleotides.

1. " Ability to make new viruses - apparently 1000 times more prolific than flu." Where is this number of 1000 times coming from? Actually I think it is related to 3 - "If I remember this right, its "spike proteins" cling more strongly to the cell membrane." But how scientific is using 1000 times?

It was noted by Chinese researchers that the the CoronVirus is distinguishable from other very similar RNA viruses by nucleotide coding at the end of the RNA chain. Not sure if the coding is for a protein or ? My understanding was that whatever this appendage was it made it easier for the virus to penetrate cellular integrity. How convenient to have a protein that does this. Of interest is that this novelty appears at the end of the RNA chain. To me meaning newer.

2. "Unlike flu viruses, it does not appear to mutate because it has a "proofreading enzyme" that repairs mistakes in replication of its RNA. " Does anyone know with RNA how this might work? I always thought proofreading was a DNA to RNA function. I originally suspected that if it was an RNA virus it would be more amendable to mutation.

 

[TeethWhitener]

Upfront it must be acknowledged that the CoronVirus is a single strand RNA virus that reverse transcribes.

Coronaviruses do not reverse transcribe.

 

[TeethWhitener]

Unlike flu viruses, it does not appear to mutate because it has a "proofreading enzyme" that repairs mistakes in replication of its RNA. " Does anyone know with RNA how this might work?

The error checking is provided by an exoribonuclease. Here’s one paper from a while back:
https://pubmed.ncbi.nlm.nih.gov/23966862/

 

[TeethWhitener]

Only tangentially related to the thread, but quite related to my last post:
https://pubmed.ncbi.nlm.nih.gov/29511076/
Apparently, as of a few years ago, remdesivir was being evaluated for its potency against SARS-CoV, as it interferes with the exoribonuclease and its proofreading activity. Furthermore, mutations in the exoribonuclease that confer resistance to remdesivir are also associated with loss of fitness in SARS-CoV.

 

[Phil Core]

My bad on the reverse transcription. That has to do with the way the virus is tested for. Still do not know why you need to reverse transcribe to detect the virus.

https://www.vox.com/2020/3/20/21188266/coronavirus-test-us-united-states

The most commonly used test is a nasopharyngeal swab, where a special Q-tip is put up your nose to take a sample. This swab is then sent out to a laboratory that can extract the virus’s RNA. The virus that causes Covid-19, SARS-CoV-2, is an RNA virus, which means it uses ribonucleic acid as its genetic material. It requires a process called reverse transcription, or RT, to transcribe its RNA into DNA.Because there’s not very much material in one sample, a polymerase chain reaction (PCR) is used to rapidly make billions of copies so it can be analyzed. The DNA is dyed a fluorescent color, which glows if SARS-CoV-2 is present. Most of the available Covid-19 tests use this process. The virus has about 32,000 nucleotides, so there’s a variety of tests, each looking for different parts of the virus’s genome, and they use different chemicals — there’s not one test every country is using.

 

[TeethWhitener]

Still do not know why you need to reverse transcribe to detect the virus.

Google RT-PCR. It’s the gold standard technique for COVID testing right now.

Edit: your post is strange. You ask and then answer your own question. Are you still not sure why PCR requires reverse transcription?

 

[Phil Core]

Most of what you are quoting is over my head.

But

1. I always thought the continuity of genetic information was a function of the double helix. Wrong in one, correct in the other.

I am a strong advocate of incremental analysis. So how does this correction function work? Having only 1 strain makes it hard for me to imagine. Is it the biochemistry that does not work or is there a master blueprint that must be adhered to?

2. As far as testing. Why can you not directly test for the RNA in a cell? The way I understand it you have to take the RNA - reverse transcribe - and then make millions, billions of copies. Seems very inefficient.

 

[TeethWhitener]

1. I always thought the continuity of genetic information was a function of the double helix. Wrong in one, correct in the other.

I am a strong advocate of incremental analysis. So how does this correction function work? Having only 1 strain makes it hard for me to imagine. Is it the biochemistry that does not work or is there a master blueprint that must be adhered to?

I’m not sure what any of this means.

Why can you not directly test for the RNA in a cell? The way I understand it you have to take the RNA - reverse transcribe - and then make millions, billions of copies. Seems very inefficient.

It’s a lot easier to detect billions of something than one of something.

 

[BillTre]

PCR, the basic technique involved here, only works on DNA, not RNA.
You have to turn the RNA sequence into DNA sequence in order to PCR it.
Being able to do PCR opens a lot of doors for you analytically, that could not be done with RNA.

If you are unsatisfied with that, you might want to develop a RNA based PCR-like method yourself.

 

[Phil Core]

I’m not sure what any of this means.

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.

 

[Phil Core]

PCR, the basic technique involved here, only works on DNA, not RNA.
You have to turn the RNA sequence into DNA sequence in order to PCR it.
Being able to do PCR opens a lot of doors for you analytically, that could not be done with RNA.

If you are unsatisfied with that, you might want to develop a RNA based PCR-like method yourself.

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.

 

[Ygggdrasil]

Is there something that makes the CoronVirus unique? Yes. Apparently it is the ending sequence. Search for that.

If you want to read about what scientists know about what makes the current Coronavirus unique, here's a good article that summarizes some of the current research: https://www.theatlantic.com/science/archive/2020/03/biography-new-coronavirus/608338/

A good exerpt:

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.

 

[Ygggdrasil]

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.

The process of replicating the coronavirus' genetic information is a multi-step process. As you stated, the virus's genetic information is stored as a single-stranded RNA molecule and, after the virus enters cells in our bodies, that RNA gets read by the machinery in the body to produce viral proteins. Some of these proteins can assemble to begin the process of copying the single-stranded RNA. This process starts by converting the viral RNA into a double-stranded RNA. (A bit of notation, we refer to the original viral RNA molecule as the positive (+) strand because it is capable of being read by the ribosome to make protein. The strand that gets synthesized opposite the (+)-strand is called the negative (-) strand).

During this copying process, a certain viral enzymes can check for replication errors in the way that you suggest; the enzyme can detect places in the double helix where bases are mismatched, cut out the mismatched nucleotide, and let replication continue. After synthesis of the (-)-strand RNA, the viral enzymes can separate the two strands of RNA, then take the (-)-strand and begin copying that to produce new (+)-strand RNA. Again, during this process, the enzyme is converting single-stranded RNA to double-stranded RNA, so the same proof-reading enzyme can detect mismatches in the double helix and cut out mismatched bases. These new (+)-stranded RNAs can either be read by ribosomes in the cell to make more viral proteins or be packaged into new viruses and will serve as the genetic material for the new viral particles that are exported from the cell.

One additional note about the mutation rate of coronaviruses. I recently read a paper that states the following:

although 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.

https://marlin-prod.literatumonline.com/pb-assets/journals/research/cell/Online Now PDfs/CELL11322_S5.pdf

So, even though coronaviruses seem to show lower mutation rates than other RNA viruses (like influenza), they seem to evolve at similar rates.

 

[Phil Core]

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

 

[Ygggdrasil]

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

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.

 

[lavinia]

@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.

So because the virus is more contagious than flu it has the chance to mutate more and this makes a vaccine less effective. So are we at risk of a new Covid pandemic every year?

 

[jim mcnamara]

No. It just means that, unless we are able develop universal vaccines, the antigens present more of a moving target. When you have a higher mutation rate. Kind of like what we saw in 2018 flu - not a perfect match. It is still a win, just not a slam dunk. I am now seeing reports showing less mutation rate for the Covid-19 pathogen than reported earlier. We need to see.

Ewald's book discusses some of this, mostly using HIV for examples:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5587421/
Paul Ewald, 'Evolution of virulence and emerging diseases' 1998
This is a pdf link, I am not sure about copyright concerns.

In fact we are at a small risk for this kind of pandemic every year. If governments learn from this current pandemic, then we should be able to contain new outbreaks before they become a global problem. Earlier, I posted a link to Larry Brilliant's TED talk about how we stopped smallpox. The ring concept to stop the spread of new pathogens -- is discussed there as well.

 

[Phil Core]

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.

This is what I was thinking of. Works directly on the RNA.

Abbott Labs Unveils COVID-19 "Gamechanger": Portable Test Can Detect Virus In Under 5 Minuteshttps://www.zerohedge.com/geopoliti...the+survival+rate+for+everyone+drops+to+zero)

 

[TeethWhitener]

This is what I was thinking of. Works directly on the RNA.

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]

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.

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.

In the article quoted, there is some amplification involved but it seems to be far less than previous tests. I am sure not having to reverse transcribe helps.

From the article in case you did not read the whole thing.

"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. "

Would appreciate your opinion on how the detection time was reduced from days to mins.

Abbott Labs Unveils COVID-19 "Gamechanger": Portable Test Can Detect Virus In Under 5 Minuteshttps://www.zerohedge.com/geopolitical/abbott-labs-unveils-portable-test-can-detect-covid-19-under-5-minutes?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed:+zerohedge/feed+(zero+hedge+-+on+a+long+enough+timeline,+the+survival+rate+for+everyone+drops+to+zero)

 

[TeethWhitener]

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.

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.

Would appreciate your opinion on how the detection time was reduced from days to mins.

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.

 

[Phil Core]

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.

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."

 

[TeethWhitener]

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).

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.

That’s not to say it isn’t useful. It certainly is. But unless Abbott can crank out thousands of these devices, the logistical bottlenecks regarding testing will still exist.

One other thing: reading Abbott’s own literature is enlightening. They claim positive results in as little as 5 minutes, and negative results in as little as 13 minutes. Those words are very important. I imagine the 5 minute case is for someone with an extremely high viral load, such that a detectable signal begins to show up after 5 minutes. Whether that signal can be considered confirmatory is a different question, but those types of issues don’t make for sexy headlines.

 

[Phil Core]

Truce.

You are right. They are leaving out some details.

I have been framing a body of thought about the virus. A beginning was how to speed up testing.

I enjoyed our back and forth. I learned a lot and perhaps you learned a little.

 

[Laroxe]

I wonder if we are missing an important point when we are discussing the changes in Covid 19. It is like most viruses, subject to genetic drift but this represents a bit of a mess really, it represents random changes in many parts of its genome. Most of these will disable the virus and of those that don't the possibility of causing changes in the surface proteins that act as antigens is low and multiple changes would be needed to effectively disable an antibody response.

This is simply not comparable with flu, which has a number of immunologically distinct species and has the capacity through immunological shift, when two different types of flu infect the same cell to totally rearrange their surface proteins. These cause of the so called pandemic flu outbreaks. This ability to rapidly change its antigen profile is not available to the Covid 19 virus.

There is also the fact that its establishment in humans exposes the virus to a whole new set of selective pressures to optimise its own survival, these will have a far greater impact at their population level than changes just talking about the mutations.

 

[Ygggdrasil]

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."

Isothermal RNA amplification methods, such as those used in the Abbott test, involve a reverse transcription step to convert the viral RNA into DNA. The main difference with RT-qPCR is in how the resulting cDNA molecule gets amplified. Here's a description of the RT-LAMP technique that the Abbott test is based on: https://en.m.wikipedia.org/wiki/Reverse_Transcription_Loop-mediated_Isothermal_Amplification

See Figure 1 from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4313160/ for more information on the Nicking Enzyme Amplification Reaction technique that the Abbott test is based on.

 

[TeethWhitener]

@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.

 

[Ygggdrasil]

@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.

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.

However, the main point of the previous post stands. The NEAR technique still involves reverse transcription of the RNA into DNA before it can be amplified.

 

[Phil Core]

I was very wrong and everyone has been right. However, no one, has reveled why the RNA must first be transcribed into DNA before a virus best can be tested for. Would appreciate some details.

Why must RNA be converted to DNA to test for virus?

As an aside. I was in a tangential kind of way correct in suggesting that a quicker test was the first key in addressing the virus.

No one mentioned antibode. Truth - Antibode tests are not that reliable to me.

The more we dwell on a topic the more that is revealed. Why this is true only ...

 

[TeethWhitener]

Why must RNA be converted to DNA to test for virus?

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.

 

[snorkack]

In the normal virus multiplication, RNA virus uses viral ferments to amplify directly from RNA to RNA, without reverse transcription, correct? The only indispensable intermediate is the negative sense chain, but I think the negative sense chain is RNA, not DNA?
So why does PCR testing need to reverse transcribe RNA into DNA rather than directly breed the RNA?

 

[TeethWhitener]

What is a viral ferment?

At any rate, PCR uses a special DNA polymerase that is thermally cyclable in the amplification step. As the name suggests, DNA polymerase amplifies DNA, not RNA.

 

[atyy]

Also, in general RNA is fragile, while DNA can contain equivalent information but is chemically more stable.

Question: would RNA survive the heating step in PCR? When RNA has to be preserved it is common to keep samples cold, which is why I think many versions of the COVID-19 swab test require samples to be refrigerated, eg. https://stanfordhealthcare.org/heal...covid-19-test/covid-19-molecular-testing.html "Specimen must be kept at 2-8°C (refrigerated/cool) or frozen"

There seems to be an all RNA-version of PCR https://www.pnas.org/content/113/35/9786 (not sure how practical this is).

 

[Phil Core]

Stability and ability to sustain more heat make sense. Thanks