Covid-19. Stuff I have written
COVID-19
What a time.
Here just a reminder of the virus in question.
Quite pretty image. Spikes sticking out.
I have written much in various places. Here are most tomes .
´Vaccine stuff
A` vaccine is commonly used. There are at least four different ´platforms` and strategies for protection being developed. This will lead to confusion in the marketing and faith in the safety and efficacy of ´vaccines`.
Safety is really only measured when practicing vaccination (large scale studies at least), so the rush to get the vaccines out will not improve the chances of a safe product and mass vaccination will be a lottery of the feedback (if complications are allowed politically).
Vaccines work best (assuming they induce protection) only if a large percentage of the population is vaccinated in a short time period. This gives the term ´herd immunity` its true meaning as gleaned from the animal vaccination campaigns e.g. rinderpest, a disease that was eradicated by vaccination campaigns. The derived percentage of a herd (population) that needs to be immune, to best eliminate virus, is around 75-80%. Figures of 65% are too low. Even lower figures are very dangerous and would maintain the virus.
If the vaccination is more sporadic, pockets of immune people mingled with non-immune (non vaccinated) can be problematic in that mutation selection of viruses by the antibody pressure induced by vaccines may produce more virulent strains.
So, it is important to get the vaccination strategy right even with a potent vaccine and I can well see the mess we could be in with the various advocates involved in the politics of disease.
(I underline this last point since it may be the only one you can use due to the brevity of the article).
My quote then.
`A potent vaccine is only half the problem, the other half is how you use it`.
or
`A potent vaccine is only 10% the problem, the other 90% is how you use it`.
This factor is what I wrestled with for many years in dealing with protecting animals from virus disease and ends up being a political debate. God forbid that this spills over into COVID territory.
Maybe the human vaccinologists should consult more with animal virologists. I, of course, could wrote another 1000 words on why!
Down-play and play-up.
Viruses infect cells. The cells are factories of virus replication. Cells die and release virus to infect other cells. This imposes damage to the whole organism infected. The extent of damage depends on how much virus is produced in time and which organs are affected. The effects then vary from a runny nose to severe organ failure and death.
The virus has the full spectrum of human beings to play with, a massive, highly variable, genetic pool (ocean more like). The genetics and the consequential immunological variation in humans faced with virus attack, as well as the health issues already inherent in individuals, determine the relationship of virus to man.
A high contagion rate means that the virus has an easy time infecting a large number of people, an easy time spreading helped by the variation in people´s attention to preventative practices.
Underlying conditions (known and unknown) complicate the ´cause of death` and can be used to down-play or to emphasise the the COVID-19 damage being wrought. COVID associated deaths are a fact. The cause of death is really a lottery, dependent on the extent of damage associated with virus infection, the health ´faults` already inherent in the individual and the knock-on effects of the body defending itself. People rarely die of cancer (general term) but rather the effect of specific cancerous cells multiplying without check and affecting organs that fail. Liver failure cause of death vs cancer of liver causing liver failure, a recording issue.
Recording deaths ´due to` and trying to compartmentalise these is hardly that useful especially when trying to get people to stop the spread using simple methods. Is the purpose of reducing the extent of COVID-19 caused deaths to a fraction of the current observed death toll (COVID associated) an attempt to down-play the severity of this contagion? I suppose the unanswerable question is ´how many of the people who died, would not have died, had they not contracted (had a test to confirm) COVID-19`.
As a virologist, it is clear that the COVOID-19 has many tricks to evade host defences, as well as the ability to infect a wide range of cells in the human hence, many organs, that make it a super predator as distinct to the more ´normally identified ´ COVID cold viruses. The lasting complications of those recovered is testament to this and the death toll is not the only statistic that needs review.
Flu and cold
A term describing clinical signs of the results of being infected with an Influenza virus.
We also have general term a ´cold`.
A cold can be caused by one of many types of virus and can be included under flu of course according to clinical signs. All depends on the diagnostics used. So if a distinct virus is measured associated with clinical signs (symptoms) then we move into a different recording area.
Test for Influenza are honed since we have studied this beast for many years. It is a complicated virus and has the ability to recombine its major proteins H and N producing different strains e.g. H1 N1, H3 N5 etc. This means that populations can be exposed to changing cassettes of virus and consequently the virus can gain advantage over populations where there are antibodies produced against past strains that had specific H and N´s. This major change is termed antigenic shift. So seasonal flu thrives through the ability of the virus genetic material to change. It is even more complicated since major changes in H and N can also be associates with smaller antigenic changes in the specific H or N proteins. So an H an be an H1 and also a slightly changed H1. This is termed antigenic drift`.
So we have the possibility of a rapidly changing virus (major to minor changes) that evolves to be able to overcome a population that was exposed to a past virus. The overcoming is the an ability to by-pass any protective antibodies produced on the previous infection OR from a vaccine used with a specific antigenic (H and N) cocktail.
The major mechanism for virus change is, in fact, through the selection of mutations in infected individuals (or animals). I have talked about amounts of virus produced on infection as well as the mutation rates before in another thread, but basically many thousands of mutations are produced on virus infection due to the inherent rate of mutation of all things containing DNA or RNA (1 in 10,000 replicative events). So for every 10,000,000 viruses we have 1000 mutants. Most mutants are defective but some can have an advantage in overcoming a host´s immunity and may be selected to become the dominant infecting agent (hence a new strain emerges). This is one reason why we cannot eradicate flu and try and second guess the emerging strain to formulate more relevant vaccines. Here we can also look at strains of flu in animals that might emerge and take steps to have vaccines of the more appropriate H and N genetic make up. Again not fool proof and also affected by the unknown of the effect of any minor antigenic changes on the H and N (drift).
The situation for COVID-19 is different although, the same pressures on the virus-host are the same.
For a start, the virus is smaller and produces more virus particles on infection than with flu. So it has high replication value that affects the ability to spread (contagiousness). With this comes the time course for replication that is faster than flu. So the virus can progress through high production of virus particles at a quicker rate.
Antigenically the COVID-19 is totally different to ´flu`. The changes associated with the virus should be considered as antigenic drift (small changes on specific proteins). Some of the proteins are associated with cell attachment e.g. the spike protein and this is a marked candidate for attention since preventing cell attachment would prevent progression of disease. So the attention in vaccines and therapeutics has concentrated on this spike either by manufacturing the spike proteins in bulk as separate entities from virus to act as proteins inducing anti-spike antibodies, or using the nucleic acid that codes for the profiles in a vector or by raising humanised monoclonal antibodies against the spike protein and using these to inject into patients to act as neutralising antibodies against the virus.
Again mutation and selection takes place as a result of high replication during infections, the production of mutations and their ads vantage over exe listing populations of virus. This is the way viruses perpetuate. The problem with COVID-19 is that although many `stable`mutations have been recorded during the pandemic these are mainly based on nucleic acid and not antigenic comparisons. Only antigenic comparisons will give us a handle on the likely pathogenicity of strains and will help devise effective virus vaccines. Basically we need to type the COVOIDs and subtype them using antigenic comparisons.
In my time studying foot and mouth disease I identified that a single amino acid change in an antigenic site was enough to massively alter the major antigenic characteristics of a virus and hence its pathogenicity and ability to escape previous antibody pressure.
More Virology forthcoming.
Strangely enough we turn to animal virology (non human) to look at factors involving virus transmission. We have the dubious advantage in being able (rightly for wrongly) to experiment on animals in a way unacceptable on humans. So, we get better data and these can be extrapolated to the human condition and the relationship between viruses and man.
We can measure virus in and virus out in real time in the actual disease targeted animals. We can use different routes of infection e.g nasal or intravenous or a jab in skin.
We can monitor the effect of the virus on the animals by invasive methods and not only non-invasive methods (as in human case).
We can use different characterised strains of virus to infect animals and see what effects changes in the virus have on disease progression.
We can harvest virus from all organs of an animal and assess variation in viruses during an infection.
We can use vaccine formulations and test these with challenge of live virus by whatever route to test efficacy of the formulations.
We can make proximity experiments to measure aerosols and assess what conditions best encourage or discourage contagion.
We can therefore control many of the factors that cannot be controlled with a human disease.
Minimum infectious dose.
In the case of COVID-19, we cannot measure just how much virus is needed to set up an infection. This value is the minimum infectious dose (MID). This figure can be established in animals. The results can show a degree of variation depending on the virus studied, the route that virus is introduced and the innate variation in animals (as would be in humans too). Theoretically, a single virus could cause disease but often figures ranging around 100-1000 infection virus particles are needed to guarantee infection.
As the challenge from a virus in terms of the numbers of virus infectious particles in a challenge ´dose` increases, then statistically the greater the chance of infection. The MID is the minimum needed.
Disease progression is then on the cards. The route of infection is important here as well as the amount of virus challenging the victim. Basically there should be normal distribution of effect from mild to severe and this is not essentially related to the dose. So we can have a person infected with a low amount of virus having a rapid and more deadly disease, as well as person infected with a high amount showing a slow disease progression and possibly few clinical signs. The distribution between for the two scenarios is normal so statistically saying anything about the amount of virus needed to set up a more deadly infection is futile. We do not have figures anyway for the MID of COVID-19. Where am I going you ask?
Well, despite not knowing figures of MID for humans (to my knowledge), we do know that there is threshold value for infection based on animal models. So reducing virus challenge is essential in limiting the spread of virus through infecting people and the subsequent massive amplification of virus. Logical this, reduce the amount of virus and reduce the possibility for infection (with caviat as above).
Three dimensional considerations.
There are several ways that COVID-19 spreads.
- By aerosols, I include droplets here, as well as anything flying out of mouth (fomites is technical word). Animal models e.g. for foot and mouth disease, does show that droplet size is important in virus spread.
2. By contaminated surfaces directly where virus survives probably associated with contaminants such as food proteins and can enter body through minute skin scratches.
3. By touching contaminated surfaces and then touching mouth and nose introducing virus.
Route 2. has not been dealt with, to my knowledge, but introduces an interesting area where by the direct entry of virus into the blood, allows the virus almost immediate access to every organ that blood passes through! This might account for the different progression of disease see. Again there is evidence from animal disease to support this.
Note that 2. Also might figure with people who develop infections after 1 or 3 and then contaminate surfaces and reinfect themselves though the blood barrier. Double the challenge.
Social distancing.
We have to consider social distances and need to see a sneeze or cough as eliciting a ´cloud`of possible infectious virus more in 3 dimensional terms. If we take the source of virus as the mouth and define someone as pushing out say 1,000,000 virus particles in a 1 cc ´plume` of virus, we can see that as the this spreads from the mouth, the virus becomes less concentrated. Assuming just for now that a sphere of virus is put out, then the virus is ´diluted` in air by a cube root function of instance from the mouth. So at 1 meter from the infectious source the concentration of virus is massively ´diluted`.The 1.000,000 per 1 cm at ground zero is now spread to a sphere one metre in diameter so the concentration of virus is now subject to the volume in which is contained
i.e. At one metre the volume in which virus is ´contained ` is now 523,599 cc. On this basis we have a concentration of only around 2 viruses per cc.
At two metres, using the same ´logic, we have a volume 4,188,790 so diluting the virus to significantly less one virus particle per cc.
So distance matters even without knowing the MID.
Of course the perfect sphere is not totally applicable in that plumes are produced that are more directional. So a hemisphere is better considered and this halves the volumes given above for the two distances however, even limiting the volumes considerably dilutes the virus concentration. ( to 4 viruses at one metre and still less than one and two metre, respectively).
Masks.
I am not sure what Rein meant `Masks can stop a virus coming from me to the other person, which seems plausible. But not the other way around!
Back to MID and anything that can possibly reduce how much virus is pushed out or taken in. Masks, per se, are treated as a general theme, but intrinsically there are many versions of masks and ways of wearing them. If a large amount of virus is thrown at you then there is little protection from a mask, however sophisticated in design. However, although the pore size in all masks is much greater than a COVID-19 particle, virus tends to aggregate, increasing their ´profile so that theoretical considerations on size have to be dealt with. Most studies have used purified viruses where aggregation has not been considered. Nor is it easy to replicate ´live` virus transmission especially in humans!
Basics then would be proper social distancing, rigid 2 metre separation for a while. iris mis hardly ever maintained as man the social animal seeks personal cantacts.
Interesting to note that at say 40 cms apart and putting this into the equation for virus concentration, we have a figure for a hemisphere of of about 16,700 ccs, so the 1,000,000 virus particles are diluted to around 60 viruses per cc. Probaby enough to achieve the MID?
Of course if we increase the amount produced on a sneeze etc., to 10,000,000 then it is more critical to get that 2 metre distancing.
At 10,000,000 per sneeze 1 metre gives around 40 viruses per cc.
At 10,000,000 per sneeze 2 metres gives 2´3 viruses per cc.
We do not know how much virus is produced in a good sneeze, that would be handy.
I have a PhD. in virology and worked as a researcher in UK at Pirbright for 20 years on animal virus diseases and also those affecting man (zoonoses). I was a UN scientist in Vienna working for FAO and the IAEA helping development and setting up of serological and molecular diagnostic tests in member states around the world to aid disease control. Credentials then to set the scene
A few thoughts/ questions.
1. The ´test(s)?` People keep saying ´the test`. What are the exact details of the test?
2. Are all countries using the same test(s)?
3. Are the people doing the sampling using fully protected covering.
4. How are people trained to perform sampling?
5. What do we know about antibody produced after infection with the corona virus?
6. What are the opinions on use of highly successful anti viral nasal sprays used against ´common cold`viruses.
1. Details of test.
I assume this is what is called a real time PCR (RT PCR). Stands for REAL TIME POLYMERASE CHAIN REACTION. Here minute amounts of virus, in this case Corona, are amplified so that the large product can be more easily identified. The test relies on an initial ´primer` that is taken from the virus or a related strain and which can identify a complementary region in a test sample. The primer then determines the specificity of the test, identifying only (in this case the active disease agent Coronavirus). In the current situation am I to assume that a definitive primers elucidated from the particular Coronavirus that is causing the outbreaks? If not, which primer is being used?
2. Relevant to point 1. Are all countries using the same primers? In fact are all countries using the RT PCR?
3. The RT PCR has the advantage that it can amplify a single copy of the target millions of times resulting in a large product. This exquisite sensitivity means that contamination of the sample even by a tiny amount results in a problem. Let us say the sampler is infected then it is highly likely that his or her samples are contaminated if there is no precautionary measures i.e. full protective gear to stop any contamination from the tester as well as to avoid contamination from the sample. An infected sampler can result in false positives.
4. This links to point 3. Without training this could be a disaster. The sample itself is a problem. Blood, saliva, tracheal swabs. all problematic due to cross contamination of sampler and samples. If samples are taken from people in close proximity then it is easy to cross contaminate samples from an infected person to samples that are from non infected.. The high sensitivity of the RT PCR does the rest. Result is false positives.
So the whole sampling regime has to be checked. The handling of the samples once deposited is also highly problematic and they must be kept well separated and sorted under conditions where there can be no cross contamination, this also included handing of samples i.e. handing them on mass. A whole laboratory can be contaminated from a single, poorly handled positive sample and this is a disaster. I have direct evidence for this from my time as an active UN scientist dealing with PCR.
5. Antibodies. I am trying to find out when and what antibodies against the Coronavirus are produced. Not much in the news about this. When do they first appear (days after infection)? What type of antibody is produced e.g is there an early IgM say after 4-5 days followed by increasing levels of IgG.
I say this because it gives the chance of developing a rapid antibody test for confirming Corona infection e.g. ELISA. (I have a written text books on ELISA-if interested see by Googling name J. R. Crowther and ELISA). I also would like some discussion about what the general antibody levels are in humans and animals against other Coronaviruses. Relevant maybe as a factor in protection of some and also the carrier state where people show no clinical signs of diseases but ar infectious.
6. The nasal spray I am thinking of was developed by a friend´s company and is now on sale in Europe but not in USA. It uses a concoction based on simple sugars. There is good likelihood that the mechanisms for protection proven against other ´cold`viruses will work against Coronavirses. Enough said, but it does protect against many of the cold viruses (Corona being just one of the hundreds of viruses that have been implicated in cold clinical signs), I have no commercial interests at all but the product can be tested fairly quickly tissue culture conditions and might be effective in protecting people.
Viruses mutate.
Viruses are subject to mutation as does anything with DNA or RNA (as with Coronavirus RNA). The mutation rate is about 1 in 10,000 replicative events.
So a virus yielding say 10 to the power 6 (1000,000) viruses in a replicative cycle in a cell will have 100 mutations. The greater the number of cells infected the higher the number of mutations. If 1000,000 cells are infected they would yield 1000,000,000,000 viruses so 100,000,000 (1 in 10,000 of the total yield) mutants would be possible. Viruses ´thrive` due to their capacity to produce vast numbers of copies.
Reducing the numbers to say 1000 viruses per cell and infecting 1000,000 cells still means 100,000,000 viruses and 10,000 possible mutants!
Mutations are then are subject to selection pressures of the host. This can be through humoral antibody or cellular factors and sometimes there is a great advantage to the virus mutant over the ´dominant `population` affected by the pressures.
So this ´new`virus could outstrip that original population. The result is that in next cycles the mutant dominates, being able to overcome the selection pressures. We then see a change in the virus ´strain`and possible properties. This has already been noted for the Coronavirus and the new version seems less virulent than the original.
This was predictable and is somewhat linked to the virus survival ´strategy`in that killing hosts is not good for the virus evolution and less death means more virus hosts. It could also mean that the virulence for humans is ´blunted`. However, mutations can work in the opposite direction and strains more pathogenic can arise!
From Health 24.com
On Thursday Health Minister Zweli Mkhize announced that the first South African had tested positive for the new coronavirus.
A 38-year-old man had tested positive a few days after returning from a trip to Italy.
The minister stressed, however, that despite this first confirmed positive case, there was no need to panic.
With that in mind, researchers in China have found that there are two different types of the new coronavirus (designated as L and S type) that are causing infections worldwide.
The preliminary study was published on Tuesday 3 March 2020 in the journal National Science Review and was conducted by scientists at Peking University’s School of Life Sciences and the Institute Pasteur of Shanghai.
The researchers found the L type virus was prevalent in the early stages of the outbreak, and was more aggressive. The frequency and virulence of the virus have since decreased since early January.
The S type, they said, was found to be the ancestral strain – evolutionarily older and less aggressive.
The researchers stated that new variations of the coronavirus causing Covid-19 could be caused by “mutations and natural selection besides recombination”.
“These findings strongly support an urgent need for further immediate, comprehensive studies that combine genomic data, epidemiological data, and chart records of the clinical symptoms of patients with coronavirus disease 2019 (Covid-19),” they said.
Morbility and mortality.
Morbidity is an indicator how infectious a virus is as a index of the number of targets exposed that become infected. Mortality is an index of how many infected targets die. Relevant because deaths always and rightfully grab the headlines. but these factors almost impossible to estimate accurately in this outbreak. Basically the potential to infect the planet population is stated and so the current assessed death rate of 3 to 6% is all we have. Result is a horror story here by possible death of 3-6% in billions and that is the panic button we have pressed.
Developing vaccines and protective strategies.
See thus article to see the wide array of approaches being made.
https://www.clinicaltrialsarena.com/analysis/coronavirus-mers-cov-drugs/
The development of concoctions to prevent or treat Coronavirus infection is either by vaccination inducing protective responses (e..g. antibodies) blocking the virus from infecting the host (hence prevention) or by treating the host with chemicals (antiviral drugs) that specifically target the virus and reduce and /or eliminate it from the host (reduction of the virus load to reduce risk of severe disease).
Molecular biological methods offer rapid and detailed examination of viruses and also potentially many vectors that can be used to deliver viral molecular species. It is highly likely that a product(s) will be available to combat this specific Coronavirus The main problem for rapid development is with the clinical trials necessary to establish their safety and efficacy. There is a danger that the human panic and economical consequences of the current pandemic drives development into short cutting the established rules governing the process of validation.
Anectode
There is always a danger for both man and animals concerning virus infections. When the first cases of a pig disease happened in Italy, infected material was sent to my laboratory for identification. It was not foot and mouth disease. Material was injected into British pigs and they were susceptible and soon showed clinical signs of disease. The infected pig handlers and a laboratory staff member who examined the infected tissues then suffered severe disease and almost died. The virus was Swine Vesicular Disease (SVD) and continued to cause problems spreading all over Europe . The initial virus was related to Coxsackie viruses in man, common enough and most do not cause a major problem. Turns out that the virus went from man to pig, then mutated to a form that was far more infectious to man than the virus that first infected pigs! The virus kept mutating and through process of selection pressures drifted more and more from the Coxsackie lineage. The relatively high antibody levels of humans against Coxsackie virus probably played a role in limiting the infections of humans (coupled to virus mutating even more and away from pathogenic threat to humans).
There could be further complications with this Coronavirus if other animals contract the disease. New cycles of infection and mutation could pose a threat to humans as well as animals infected.
Coronaviruses infect many animals including pigs, domestic and wild birds, bats, rodents, dogs & cats, and cattle. These viruses are divided into three groups and have been known for more than 50 years to cause various diseases in animals depending on the group and strain of the virus. They cause acute and chronic diseases in animals such as respiratory and gastro-enteric diseases; neurologic diseases; and liver disease. Lord help us if pets get infected!!
The wheel turns.
ARS-CoV that affected humans in 2003 world-wide and the Middle East respiratory syndrome coronavirus currently affecting people in the Middle East and Europe are said to have an animal origin. Although the exact animal vectors are not known, recent discovery suggests that bats could be the natural reservoir for that group of virus (SARS-CoV). Many of these animal origin coronaviruses can infect humans and cause mild to severe disease including death.
China
https://www.newsweek.com/what-started-coronavirus-outbreak-c ... ts-1483627
The virus was first reported among people who worked at a seafood market in the Hubei Province city, where live animals were sold. As information about the nature of the virus emerged, experts updated their view that it could only spread from animals to humans, to state it could spread from person to person.
Paul Hunter, a professor in medicine at the U.K.'s Norwich School of Medicine, University of East Anglia, told Newsweek that it is still not clear what the source of the virus was, and "it may never be definitively proved."
He said: "The virus has already been detected in both bats and snakes prior to this outbreak and the strains in both bats and snakes are similar to each other and the strains from human cases. Human cases are more like the strains in snakes so that is the more likely."
To understand the source of a virus, Hunter explained, experts compared the gene sequence of the new virus with those that already exist.
"This is probably as good evidence as we will get," he said. "Ideally we would like to isolate the virus from food animals in the market, but it is likely that the infected batch of animals are long gone.
Round and round.
Let me begin again with the reason for new strains arising from infections.
As I indicated earlier, the mutations possible are due to an error rate in the process of copying nucleic acids (DNA and RNA). This error rate is approximately 1 in 10,000.
So for every 10,000 copies of the nucleic acid there is one error statistically.This is true of almost everything living as well as for viruses who rely on the living cells to propagate.
The error rate is due to a complex of conditions and can be considerably altered where mutagens (inducers of mutation events) are present. In animals, including humans, there are mechanisms for repairing abnormal replication events. As we get older or are affected by mutagenic substances these repair mechanisms can be outstripped and hence errors left unrepaired. It may be that the errors give rise to something that is detrimental to the host, hence cancers and the ageing processes are complications.
The error rate then for viruses is 1 in 10,000.
Now we have to contend with the massive numbers involved when viruses infect cells and the statistics of error rates.
Back to the example of a virus producing 1,000,000 new viruses in a cell.
Back to the error rate of 1 in 10,000 so there is a potential to have 1000,000 divided by the 1/10,000 errors i.e. 100.
This is a single cell.
So we now infect 1000,000 cells and they produce the 1,000,000 viruses each we have 1,000,000,000,000 viruses.
The potential now for errors is that number divided by 10,000 i.e. 100,000,000 errors.
Now most of the errors are redundant in terms of producing viable viruses. Viruses unable to infect or process events after infection.
Most will be useless viruses.
But some could have altered the nucleic acid to code for some factor giving an added advantage over the main genome of the original viruses. The advantage could be factors such as a faster infectivity cycle; a change to be able to use a new receptor in host cells; a change to alter which cells can be affected (a changed so called tropism).
The alteration of host range is included in this hence the transmission of the ´new`Coronavirus in the first place from the animal market to humans. What was once say, a bat virus, mutates and can then infect man. It must be remembered that a the number of cells infected are far more than the million I simply used in the above example therefore, far more errors are possible.
Any ´mutant` is an error modified virus and if armed with any advantage can compete and outstrip the original virus population to become the dominant virus. It is that which can be observed in tests comparing the old strain nucleic acid structure to the new ´strain`nucleic acid structure. This, as said in my first description, has been demonstrated already, a new strain having been identified.
I think that the comment made as you reported for Raina MacIntyre needs clarification.
I see this as being able to map the structure of the RNA and show changes. The more changes noted as compared to the original structure, the more the virus has evolved through the error and mutation process.
One easier way to understand selection pressure on virus is the development of antibodies. If these can neutralise virus then, by definition, they act to eliminate the virus. However, an error derived ´mutant` could have properties that resist the antibodies produced and be left to infect cells and produce high numbers of viruses and hence notable infection. This is also a complication with vaccines that depend on producing neutralising antibodies where the selection pressure can induce selection of mutations that are a disease threat.
At last your question.
From what you said, does that mean it takes 10,000 generations of the virus for each mutation? Which would mean 10,000 "DNA errors" to cause the mutation?
By generation I am meaning the production of virus. A single cycle of infection is one generation and enough to produce the high numbers quoted above.
10,000 generations (my meaning the production of 10,000 viruses and not 10,000 separate cycles of infection) would statistically result in the production of a single error at the rate of 1 in 10,000.
The 10,000 DNA (RNA virus note) errors point made would require that 10,000 (I error) x 10,000 viruses are produced (as in above argument). So we need 100,000,000 (a hundred million) viruses produced to get to the possibility of 10,000 errors mixed in with the virus population. This number is feasible even in one cycle of infection. Such rather astronomical figures are well within the scope of most viruses. I
The mutant would be one (or more) of these errors with a significant advantage over the non error replicated viruses and hence might produce a new strain when amplified into being the major population.
Viruses are complex inert chemical entities that only replicate in living cells. The main strategy for most is to produce high quantities and then rely on mutation and selection to further their ´existence`. This gives rise to genetic evolution and the production of strains, types, subtypes as catalogued by man and determined through molecular and serological studies.
With all this hijacking of cells and replication they damage cells and can cause a disease. The exact nature of the disease depends on very simply on how many cells and in which organs are infected during the viraemia and how the body reacts to the threat through defence mechanisms.
Viruses are, in the main, statistical pathogens interweaving in the biochemistry of living beings.
Ramble over.
Let us go back in time.
Not so long ago too, when sophisticated molecular based tests were not available.Where viruses were not easily differentiated in minute detail.
Tracing an epidemic then was usually through case studies of clinical signs helped mainly through some serological testing. Virus infections could probably be assigned only to a particular type, a gross overview of what viruses might be causing extra problems.
The relationship between possible epidemics and death was then more difficult to assess.
Information was not well correlated.
The clinical signs of a ´cold`are too generalised to get people excited and linking deaths to a specific pathogen was not easy. This lack of awareness even of a pandemic is not surprising given the tests available. Generally it was a serological retrospective approach (more below on this) that led to an understanding of what HAD happened and not WAS happening.
So the panic was caused by deaths in the horrendous flu epidemics often quoted and the disease agent was not monitored on a day to day basis (as is now with insertion of panic buttons every day). Not so much of the ´beware its coming`.
Now we have the sophisicated molecular based tests and can dissect a virus genome too allow direct comparisons. This tells us of differences in RNA in the case of Coronavirus but does not tell us if the significance of the differences (changes).
What do I mean?
Well seeing differences in a linear stretch of viral genome RNA cannot be translated into knowing what the differences mean in terms of serological reponses to a virus nor the infectivity profile nor the virulence. These are factors wrapped up in the three dimensional folding of proteins that the RNA codes for.
Relevance?
The epidemiological significance then comes in following an outbreak, a new strain is identified and the monitor of the effect of this strain on say the human population is to follow the severity of infections, as we do now. Then we are up and running evolving data that modify our idea as to the morbidity (how many people infected) and mortality (how many infected die). The figures change as we add new data.
The accuracy of the data is hard to assess. Why?
1. Well first we have to be sure that an ill person has the specific Coronavirus in question. We need tests that are accurate (only pick the Coronavirus in question). There are some who question earlier tests as being accurate. What is known about the cross reactivity of the test with other Coronaviruses (test specificity in question. Could lead to over diagnosis.
2. I hinted at test sensitivity and the problems associated with using RT PCR (cross contamination of samplers and those sampled, as well as contaminating samples on sampling site as well as in laboratories. This leads to mis- diagnosis.
3. People showing no clinical signs may carry the ´new`virus due to previous infections with related Coronavirus (possibly locked on through antibody pressure) . Without testing almost everyone (an impossibility) we do not have figures on this. Could be an underlying threat.
4. Some serological test are needed to assess patients as to the development of antibodies against the new strain. What is timeline for production of the species of antibodies produced?
This would also allow rapid testing of individuals in say a dip stick assay (like a pregnancy test). This at least would confirm that people had developed a symptom associated with the new Coronavirus.
I read that we already have humanised monoclonal antibodies that react only (specifically) with the new Coronavirus and these could be used in a very sample test to confirm or otherwise a patients infecting agent. Retrospective test in that we are confirming disease agent though post infect analysis , but it would be a great epidemiological tool for monitoring the increased spread or contraction of cases.
This might considerably help the self-isolation equation too. Cold symptoms usually occur sometime after infection by whatever agent. If the serological test was made say 3 to 5 days after noticing the cold when antibodies should apparent then a simple test (a 30 minutes top test) would either confirm the Coronavirus or rule it out, allowing the self isolation to be lifted. Would be nice to have an off the shelf self testing kit.
The cold.
The ´common`cold is named aptly as about 100 virus have been associated with its clinical signs (symptoms in layman speak).
In the UK There was a Common Cold Research Unit at Porton Down, a recognition of the importance of the ´syndrome`cold. A recognition also as to the underlying importance of the wide ranging economic and social effects of the ´cold´on society. Unfortunately there were normal breakthoughs in research.
The Common Cold Unit (CCU) or Common Cold Research Unit (CCRU) was a unit of the British Medical Research Council which undertook laboratory and epidemiological research on the common cold between 1946 and 1989. It was set up on the site of the Harvard Hospital, a former military hospital at Harnham Down near Salisbury in Wiltshire. Common colds account for a third of all acute respiratory infections[where?][when?] and the economic costs are substantial in terms of sick leave.
Thirty volunteers were required every fortnight during trial periods. The unit advertised in newspapers and magazines for volunteers, who were paid a small amount. A stay at the unit was presented in these advertisements as an unusual holiday opportunity. The volunteers were infected with preparations of cold viruses and typically stayed for ten days. They were housed in small groups of two or three, with each group strictly isolated from the others during the course of the stay. Volunteers were allowed to go out for walks in the countryside south of Salisbury, but residential areas were out of bounds.
Human coronaviruses, which are responsible for about 10% of common colds, were first isolated from volunteers at the unit in 1965. The CCU continually recruited volunteers for research into the common cold until its closure in 1989. The final director was David Tyrrell, whose autobiography describes his work at the CCU from 1957.
The CCU was sometimes confused with the Microbiological Research Establishment at nearby Porton Down, a military unit with which it occasionally collaborated but was not officially connected.
Worth looking at possibilities, the coronavirus certainly gets around!
Hopefully we shall not see similar diseases progressions in man, as some below.
This is a good reason to take this virus seriously, the mutation, selection and emergence of strains to alter their hosts as well as target organs and hence move from a cold to something far worse.
Diseases caused
Coronaviruses primarily infect the upper respiratory and gastrointestinal tract of mammals and birds.
They also cause a range of diseases in farm animals and domesticated pets, some of which can be serious and are a threat to the farming industry.
In chickens, the infectious bronchitis virus (IBV), a coronavirus, targets not only the respiratory tract but also the urogenital tract. The virus can spread to different organs throughout the chicken.
Economically significant coronaviruses of farm animals include porcine coronavirus (transmissible gastroenteritis coronavirus, TGE) and bovine coronavirus, which both result in diarrhea in young animals.
Feline coronavirus: two forms, feline enteric coronavirus is a pathogen of minor clinical significance, but spontaneous mutation of this virus can result in feline infectious peritonitis (FIP), a disease associated with high mortality.
Similarly, there are two types of coronavirus that infect ferrets: Ferret enteric coronavirus causes a gastrointestinal syndrome known as epizootic catarrhal enteritis (ECE), and a more lethal systemic version of the virus (like FIP in cats) known as ferret systemic coronavirus (FSC).[58]
There are two types of canine coronavirus (CCoV), one that causes mild gastrointestinal disease and one that has been found to cause respiratory disease.
Mouse hepatitis virus (MHV) is a coronavirus that causes an epidemic murine illness with high mortality, especially among colonies of laboratory mice.
Sialodacryoadenitis virus (SDAV) is highly infectious coronavirus of laboratory rats, which can be transmitted between individuals by direct contact and indirectly by aerosol. Acute infections have high morbidity and tropism for the salivary, lachrymal and harderian glands.
A HKU2-related bat coronavirus called swine acute diarrhea syndrome coronavirus (SADS-CoV) causes diarrhea in pigs.[61]
Prior to the discovery of SARS-CoV, MHV had been the best-studied coronavirus both in vivo and in vitro as well as at the molecular level. Some strains of MHV cause a progressive demyelinating encephalitis in mice which has been used as a murine model for multiple sclerosis.
Significant research efforts have been focused on elucidating the viral pathogenesis of these animal coronaviruses, especially by virologists interested in veterinary and zoonotic diseases.
LET US JUST SAY.
A devil´s advocate approach.
What we know and what we fear?
Fear of the unknown.
Fear of the known.
What is best for the world?
What is wrong with our collective disease preparedness?
Alternative scenarios. (Note, these are for discussion).
Let us just say that there was no identification of the Coronavirus strain now causing havoc.
What would have, or be, happening now?
Would there be an increased awareness that there there more colds?
This would depend on how colds were and are monitored.
We could look at past figures and examine them against current reports I doubt whether this would have yielded anything significant. Death rates could also be examined. Hospital receiving patients with acute respiratory signs might have been an alert as to spotting a circulating agent. but the figures might be buried in the other causes for such respiratory illnesses.
In other words the outbreak we are witnessing might not have been obvious.
It is the very fact that the agent was identified in detail that led to the panic factors now prevalent. Patients showing severe symptoms would still be treated (as in the olden days when the etiological agent was far less understood). In the case of virus diseases that have no cure, then it is in the hands of fate whether people survive or not. Nursing care and palliative medicines are the only option anyway.
It could be argued that the economic and social consequences of alerting the worlds population are proving far more damaging to that population than the disease itself. The knock on effect of the measures being taken probably far out way the damage that the virus might do (is doing) .
Financial ruin, attacks on ethnic groups and ´diseased`individuals, suicidal instincts awakened, dare I say looting possibilities, conspiracy theory derived hatred, severe depletion of cash floe to the individual, etc. All add to this soup of uncertainty. Disruption through fear. Social mayhem. It will get worse.
The situation has been handled badly politically.
Science should try and be 2 years ahead of possible pandemic causing agents. In most countries proposed prophylactic measures are ignored. In fact it is hard to get through to politicians that spending a large amount in case something bad happens is worthwhile and cost effective, since saving money in preparing for what might happen (hoping it never will) is an easy way out.
This includes the nature of the agent itself (e.g. the influenza variant that might appear) as well as a system for dealing with a massive outbreak situation. Generalised vaccine and anti viral drug development and research (downplayed in USA in recent years) should be increased taking note of possible sinks of infection that might lead to trouble e.g. by constant epidemiological screening of populations where the risk of transmission from animal to man and then man to man is deemed highest.
Stockpiles of protective gear should be made available, as for tests, hardware for sampling; consistent specialist training and selection of task forces, specialised hospital overflow units divorced from ´normal´hospitals to avoid contaminating other patients, (the novel drive through testing stations I noted today in Os). All needs planning before an outbreak. These outbreaks are a constant threat and there will be more.
Will we have learn our lessons? Never be short sighted and plan for the worst. Never down play the risk as a numbers game but give best case scenarios. Encouragement of best practice without hysteria.
Too late now in the current situation.
I am sure that several waves of disease agents not unlike the Coronavirius have been ignored by Governments in the past.
As I said initially, points made are thrown out (maybe) to incite discussion.
Thank you for reply highlighting the profiteering angle. As a scientist i am frustrated to say the least at the headless chicken approaches taken. Nothing is a surprise with this virus as compared to other viruses. Nothing. It is highly contagious and infecting the most awkward population to deal with man. This is why it is a problem. We should have a test by now that measures both the quantity (titre) of antibodies as well as their quality and also be able to relate serological results to neutralisation data to allow us to predict how long people with various titres can be expected to be protected.
So.
1. What antibodies are present on patients sera?
2. Whether these are specific antibodies to covid-19 or against another related pre-pandemic cold virus corona?
3. The quantity of antibody (titre) to allow a prediction of when antibodies disappear through natural decay rate.
4. The tire of antisera against the spike proteins as a measurement of neutralising activity
6. Virus neutralisation results on many patients sera to relate to serological tests.
All needed too in relation to vaccine development.
Needs a keen research lab that can handle infectious corona viruses in tissue culture and expertise in ELISA. Three weeks to develop all??
Spread sheet
I suppose the politicians have to look at all angles.
So we have risk factors.
What % population will get sick?
How will sickness safest jobs?
What´ % of the sick will die?
What demographic for the dead?
How much can hospitals take?
as against
How catastrophic is shut down of whole economy?
As an animal virologist we have the dubious advantage of being able to control diseases by culling infected beings as well as cull those beings in contact. e.g. foot and mouth disease. Also we do develop vaccines that help…
WE are voting for a human cull though lifting contact restrictions. A complicated cull at that, but an admission that people will die in larger numbers due to allowing mingling.
Government has to respond to the true needs of their people and not to the will of blind freedom seekers and economic disaster mongers. What is best for us?
Maybe we could stand back on the economics as this is a worldwide problem where the base line is the same, stagnant economies altogether, therefore no differential advantages? maybe the rush to get back to work is the panic caused by seeing other countries getting their economies revved up?
Testing for antibodies against COVID-19
When a virus infects, the body has a number of responses to do with the host (human) immune system and the interactions are highly complex. One response is the production of antibodies mainly against the protein parts of the virus.
Virus are relatively simple in having a protein shell surrounding the genetic part that is DNA or RNA
The interaction between certain proteins on the surface of the virus and target host cells is key as to whether the virus infects cells.
Many different antibodies are produced against the virus in different quantities and time lines, so we should understand that the design of tests affects just which antibodies are measured and their relevance to the progression or otherwise of the infecting agent.
It is vital that we research what antibodies are produced and when, in individuals with varied clinical signs to help design test kits. This has been exemplified by the OIE, the World Organisation for Animal Health as 'Fit for purpose' that a kit has to be validated to show that the results can be interpreted to have a defined meaning in terms of diagnosis or another biological property examined.
Unfortunately due to the hurried panic in the pandemic and I suspect some commercial considerations, we are witnessing a large scale influx of `antibody tests` that have NOT fulfilled good practice criteria and are not sufficiently validated. Without the recognition of the need to pinpoint antibody populations, the tests are next to useless. Already there is bad press for many early test attempts.
There are three main needs for antibody tests.
1. Whether we have had this particular coronavirus infection. Note that there are other coronaviruses that cause common cold symptoms and people with such infections complicate the picture.
The test can be laboratory based whereby a blood sample is taken for testing.
Also a useful rapid point of care or home use test in the form of a single sample (pricked finger test). There are several developed either using a machine to read results or along the lines of a pregnancy test where one looks for a combination of lines appearing (or not) to determine positivity or negative results. Without laboratory based research to understand the quantity and type of antibodies produced in individuals with various clinical conditions, the rapid tests cannot be improved and already we have reports of such tests being unsuitable giving false results.
The ideal is a test(s) for estimating just how many people have had the virus and that can be used to examine those without clinical signs thus showing us a better picture of how many asymptomatic people had the disease. In scientific terms we can see what is the disease prevalence.
2. How much antibody has been produced against the coronavirus (the strength of the response or titre of antibodies in the serum). Also to measure which types of antibodies are produced and when they develop after infection and how long they last. This test would be laboratory based.
3. Whether there are virus neutralising (VN) antibodies in the serum and their strength (titre) as a guide to immunity and as in 2. above, how such neutralising antibodies develop over time and how long they last after infection. These antibodies are critical in preventing disease in the first place as well as ´attacking` (neutralising) the virus when it is produced from infected cells thus reducing the virus load and hence the impact of the virus infection (slowing progress, eliminating viruses). Establishing whether VN antibodies are present is essential as well as paving the way to understanding the mechanism of how they neutralise COVID-19.
Most viruses induce VN antibodies and understanding how these affect the various disease progressions in people is key to understanding immunity.
My moan.
Specific and sensitive tests can be devised for all three needs and devised quickly.
These should be with us already through their development in specialised research laboratories with the ability to handle live COVID-19 and perform tissue culture virus neutralisation testing, with serological techniques expertise and with access to many serum samples from various documented patients.
I am hoping that this is in hand but as a scientist and an outsider now like the general public, I am not impressed by the information forthcoming nor the scant descriptions of test reagents and test design approaches. The science is so far, at least that which leaks out, confused and based on too much guess work. Solid coordinated work is needed and definitely a referencing hand to oversee and make valid conclusions about the relationship of this virus to man.
I would love to delve deeply into the development of better serological techniques particularly the Enzyme Like Immunosorbent Assay (ELISA) that I have been involved since it was first developed for diagnosis. You will see this ELISA quoted more and more.
I would love to talk to the developmental scientists about methods using competition ELISAs to both measure antibodies of all kinds as well as determine the relative avidity (binding strength) of antibodies for various antigens of the COVID-19.
About measuring whether there are immune complexes in the blood and the complications of measuring both antibody and virus in such complexes that may explain why people show intermittent positive and negative results for virus.
About the difference in the clinical picture when the COVID-19 has direct entry into the blood through skin damage as agent the oral route.
About just now to relate quantitative serological results to protection and the duration of possible immunity.
Ah well. I am retired.
Use of Enzyme Linked Immunosorbent Assays (ELISA).
Measuring antibodies is an easy laboratory task.
Determining what amount of antibodies as well as the types of antibodies and their specific interaction possible using various systems of ELISA.
Mass testing is also possible due to the convenience of the ELISA plate systems.
Basics of ELISA
The ELISA key is the use of an enzyme attached to one of the components .
We have to define the antigen in any system as well as the antibodies being used and the target antibodies to be measured.
An antigen is anything that produce an antibody response in an animal.
Coronavirus then is the antigen or more correctly a whole package of different antigens.
The virus has proteins in an envelope surrounding the RNA genetic material inside.
When the virus infects it elicits a whole range of antibodies against these antigens. Such antibodies can then bind to the antigens and it is this that is harnessed in serological testing (including the ELISA).
The virus also infects and releases antigens that are disrupted and modified. Antibodies are also produced against these products.
Antibodies can be specific for a single strain and also, if the antigens on the coronavirus share properties with other strains, be cross reactive. So tests that measure specific antibodies to COVID-19 need to be measured against any ´background`of cross reactive antibodies.
Neutralising antibodies are sought after since these probably offer protection in their ability to bind to virus and effectively stop it infecting cells before any infection (prevent disease) as well as mop up viruses once infections are underway.
Titration
The use of dilution ranges of serum in any test can determine the titire (strength) of antibodies.
So a test serum can be easily diluted e.f 1/10, 1/20, 1/40, 1/80 etc., or 1/10, 1/50, 1/250 etc.
In this way the activity of the serum in a serological assay can be measured and an end point determined where for example the last dilution showing a positive value is measured.
So a serum might be ascribed a value of 1/500 or 1/10,000 or 1/50,000.
Back to ELISA and here I am directing this with those who have expertise.
I wrote a brief effort showing all variations of ELISA, those interested can read this.
http://www-naweb.iaea.org/nafa/aph/public/ras-ai-elisai.pdf
I also published textbooks on ELISA
https://www.springer.com/gp/book/9781603272537
My main grouse at the moment is that although tests renewing developed there are no real details.
Here are some examples of what can be done with ELISA to test for and quantify antibodies. I hope experts can deal with them and indicate what is being produced.
1. Direct ELISA and competition.
I- = micro titre plate
Ag = antigenic mixture used.
Could be whole virus COVID-19 grown in tissue culture then inactivated.
Could be part of the COVID-19 capsid (envelope)
Could be polypeptide (s) from COVID-19
Ab or AB = antibodies
ENZ = enzyme linked to antibody
a. Set up direct ELISA
I-Ag + AB-ENZ——-colour (after adding a substrate that reacts wit ENZ to give a colour).
AB here is antibody to CORVID-19 taken form recovered patient and purified.
Or
I-Ag + AB-ENZ———colour
AB here is monoclonal antibody to CORVID-19 of defined specificity.
Easily titrated systems.
b. Competition with patient Antibodies.
The constant pre-titrated systems are challenged by addition of patients serum as a dilution range.
I-Ag +patients antibody and incubate.
Then
Add test system AB-ENZ
If there are specific antibodies in patients serum then these will bind to the Ag and prevent the test AB-ENZ from binding . Therefore no colour means competition and presence of Aantibodies.
The titre would be last dilution test serum that show inhibition of the colour reaction.
Use of a neutralisation site binding monoclonal antibody would be useful to assess patients sera and direct us more to seeing similar ned utilising antibodies in that serum.
Can be high volume test run on large scale in laboratories.
Gives a titre as a measure of amount of antibody produced.
Could be made specific for neutralising antibodies with use of specific monoiclojna antibodies.
Can be standardised easily with reference to Ag and AB used.
One excellent advantage is that the shapes (slopes) of the competition curves indicate differences in overall binding (avidity) for the polygonal systems,
Need a sample of serum!
2. Indirect ELISA.
Fairly typical response to developing antibody tests.
I am not recommending this.
Principle
1. Coat plates with defined amount of Antigen (see above for antigens)
I-Ag
2. Add patients serum as a dilution range and incubate then wash.
I-Ag + Ab.
If there is antibody then this will bind to the Ag.
I-Ag-Ab
3. Detect the Ab by adding anti human AB linked to any enzyme produced in another species (e.g. rabbits)
A colour means that antibodies were present in the sample and the titre is dilution at which there was no colour.
3. Capture Ag ELISA and competition.
Where there are difficulties in getting larger amounts of purified virus, then inactivated tissue culture fluids can be used.
I-Ab (anti COVID-19)
I-Ab -Ag (Covid-19 tissue culture)
I-Ab-Ag-AB-ENZ (added detecting system labelled with enzyme
Then competition as for 1.
4. Antibody Capture ELISA and then competition.
Antibodies from a patient can also be captured.
I-AB
I-AB-Ab
I-AB-Ab-Ag
I-AB-AB-Ag-AB-ENZ
I would add that immune complexes are a problem. Antibodies bind to virus and then these complexes aggregate. So we have both the virus and antibody as a target for serological tests (antibody detection) as well as antigen (coronavirus). While the virus is locked in through the binding of antibodies the complexes are subject to dis-association that might release the virus from the complex. The complexes are of course in the blood system and so infection after any virus release would be through contact with blood. The report of the positive and negative testing does not indicate what sample is tested and I assume that this is a swab but if blood is used then the immune complex problem arises.
The real time PCR is subject to many problems where there is a very large amount of virus in a sample as well as where there is very little.
Tests to determine immune complexes using ELISA can be assembled quickly and also tests to determine the species of specific antibodies evolved (IgA, IgM and IgG) in sera. Tests to determine specific neutralising antibodies can also be devised in a laboratory setting using current regents in association with parallel tissue culture virus neutralisation assays.
First the good news is that effective protection from infection is inferred that lasts 6 months. So immunity is highlighted and that is good news (although the study is hardly statistically viable). The duration of antibodies produced is directly linked to the amount of antibodies produced on infection (and also from a vaccine). The higher the titre the longer the antibodies stay in the blood stream. One can predict decay rates for antibodies from the maximum titre measured (that happens usually at round 21-28 days after initial infection). The question is what antibodies are being measured in any test as we need to know the neutralising titre since these antibodies are the ones that ´protect`in mopping up any virus that infects?) People will vary greatly in initial titres and therefore the duration angle is woolly at least. One thing not mentioned so far is the anamnestic response. Although antibodies might wane the body retains a memory of the virus and on attempted re-infection there is an almost immediate start to the antibody process so that large quantities of antibodies are produced in the first hours after infection rather than starting at 4-7 days on initial infection. This is important in assessing the protection of a population and typical of many virus vaccines. Nothing surprising her for virologists.
All viruses mutate at a similar rate (about 1 in 10,000 replication events). Viruses produce trillions of virus particles during infection. So as an example, a single cell might produce 100,000 virus particles and that means 10 mutations. If 1000,000 cells are infected then we have 10 x 1000,000 possible mutations i.e. 10,000,000 ! Most mutations go nowhere but some might be selected (through cell tropism and also antibody selection) with an advantage in infecting cells and become the dominant population, hence a new strain is observed. Whether the antibodies produced against the older, pre-mutant strain can still neutralise the new strain is the question that needs to be looked at. Already we have new stains noted with properties that differ significantly from the started virus. The key to success with viruses is mutation and selection to avoid host defence mechanisms. They change in antigenic properties to survive. The common cold spectrum of cold viruses illustrate this well.
