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There are some which again and again talks the benefits of getting herd immunity against Covid-19. It is often postulated as the situation when about 60% of the population has been infected (and survived) and thereby have gained an immunity against Covid-19.
There is just one problem with this idea: it probably won’t work.
The issue is that the mutation rate of Covid-19 appears to be too high to make this ideology work in practice. All known sequence analyses of the coronavirus 2 can be found at https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/. And it is fairly simple to make a sequence analyses of the different samples. In principle then you don’t need to know anything about genes to do this sort of analyses. Because several samples contain a description of the complete gene sequence. And by comparing the different gene sequences, you will get a quite clear impression of how equal the sequences actually are.
If you do so, and for instance choose to look at the first 100 complete sequences in the gene bank, you will find that 25% of the samples appear to a duplicate of at least one of the other. Far the most of the first 100 samples (exactly 95%) are so much alike that the only different between them appear to be single letters in the gene sequence which are exchanged. And then there are 5% of them which appear to have actual alterations in the gene sequence, such as addition or subtraction of genes or other alterations in the gene sequence beyond a simple exchange.
An immunity will require that your body is able to recognize the gene sequence as something dangerous. But will you be able to do that, if the part of the gene sequence is significantly altered, which appear to be the case in 5% of the cases? That would be itself require a more detailed analysis, which would involve some knowledge of the genes.
But even if we neglect the 5% alterations, then there is still the question of the consequence of all the small changes. It may not sound as much if you just exchange a few letters in the gene sequence, but the case is that the genome of the virus is quite small. The total sequence length is of about 30.000 letters, so changing a few letters is actually a noticeable change in the sequence for as such. So if we compare the 100 first samples in the gene bank, and we ignore all differences in the first and the last part of the gene sequence (it contains only noise anyway), then we will notice that there is an average difference between the 95% of the gene samples which only contain no or small changes, is about 0.027%. It may not sound as much, but this difference has to be associated with the mutation rate of the virus. So, if the mutation represents the average mutation over 1 cycle, then simple math will tell you that over 1000 cycles, then the virus would have mutated into something which is about 76% different from what it looks like now. A difference which clearly indicate that it might be quite difficult for your body to recognize the virus again.
By this we have not said anything about how long 1 cycle is. To get a better impression of the length of 1 cycle, then we could take a closer look at the samples which are totally alike. And it appears as if almost all the samples which are alike could be related to the same source. This could therefore indicate that it is quite likely that the virus would mutate for each time it spread to another person. A conservative estimate would therefore be that in average 1 letter is exchanged when the virus spread from one person to another. That would be equivallent to a change of 0.0035%. The earliere average of 0.027% would then represent the change in a chain of 8 persons (8 letters).
We don’t know exactly how much it will take before a virus cannot be recognized. But we do know that SARS from 2002 and Covid-19 is about 70% equal, and they are characterized as two different virus. So even less most likely will do it, then we will reach the 70% after about 9000 letters has been exhcanged, which we assume will be achieved in a chain of a similar length. If one person in average infect 2.5 persons, then a chain of 9000 persons is reached when the total of the world population has been infected once. However, if we keep distance and we are careful, so each of us will only infect 1 other person, then it may take longer time before we all will get infected, but the mutation rate pr. million infected people will increase accordingly. Because if we only infect 1 other person, a chain of 9000 will therefore only involve 9000 people. More than one chain may though exist at the same time, which implies that several different branches of the virus may achieve the 70% benchmark independently of each other.
The thought that we will be able to achieve a herd immunity is therefore challenged, partly by the 5% of the samples which appear to have more significant changes than just an exchange of a single letter, and partly by the sum of small changes which appear to happen quite often.
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Categories: Reflection
Tags: corona, corona-19, coronavirus, covid, covid-19, covidupdate, herd immunity
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Northern Dragon 
Interesting. And frightening, since that presents a real problem for vaccines.
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This text is specially focused on the idea of herd immunity.
In case of vaccines, then yes, mutations do definitly also constitute a significant problem. However, there may be ways to come around this sort of problems for a vaccine.
The journal Nature has brought a very intersting article about how to make a universal flu vaccine (see: https://www.nature.com/articles/d41586-019-02751-w). The idea is that not all part of the genome of the virus is equally likely to change. At least for the flu, it may thus be possible to target some of those more stable areas and thereby create a universal flu vaccine (still on its way, but results looks promising).
So something similar could possibly also be the case for the Corona virus. But since it is very obvious that the virus do mutate, we have to take account for it and not just take it for granted that we will become immune just because we have got the virus once.
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