“I don’t see the need”: Severinov biologist about mass testing for coronavirus and prognosis of the spread of the disease

- Konstantin, let's talk about testing with you. What is the problem of testing for coronavirus in general?

- Yes, there is no particular problem. There is a problem in general testing. That is, you want to determine a very small amount of some foreign agent, for example, by ribonucleic acid or by proteins, in the case of a virus, against the background of a very large number of molecules that are in biological fluid.

- That is just rubbish.

- Garbage, yes. And you want to do it for sure. You may have a false positive reaction, you say that there is a pathogen, but it really is not. And there is another mistake - the reaction is false negative: you say that there is no pathogen, but it is. The price of the issue, especially in the current situation, is high. Therefore, you want to make the test reliable. In addition, it must be certified, it must show a certain accuracy, it must be fast, cheap, it must work like a clock, which is very important. To be made not once on the knee, but mass produced. Wherever possible, appropriate equipment should be supplied, people should be trained. All this means that there must be a system.

- Now in Russia testing for coronavirus is carried out by one single method - polymerase chain reaction.

- With reverse transcription, yes.

- Why?

- I do not know why. In fact, there are two ways. A virus - it has a genome - a nucleic acid, RNA or DNA, and it is packed in a protein coat. And there are two ways to test for the presence of the virus. You can determine the presence of a nucleic acid, this is the first option. And this is done with the help of such a polymerase chain reaction, a very elegant procedure, which, if there is information about the DNA or RNA sequence of an infectious agent, amplify, multiply specific sequences corresponding to this agent, and then simply detect the presence of such an amplified multiplied sequence.

So that’s what it is. That's all very fond of genomes. The genome is a text. We have four letters of the nucleic acid - AGCT. You can read and put in the database. Specifically, in the case of coronavirus, in my opinion, about 900 genomes were already received yesterday. That is, samples from sick people were isolated, and a sequence of 30 thousand letters was determined, this is the coronavirus genome. These isolated coronaviruses, or rather, certain genomes, are slightly different in different people, because the virus tends to change. But, comparing these sequences that are received, you highlight certain blocks that do not change, they are almost always the same. Scientists call them conservative. And this, in a sense, piece of biological text - it is such a marker for the presence of the virus. Because we don’t have such nucleic acid sequences in our DNA. Accordingly, you can come up with a procedure that will specifically recognize just such nucleic acid sequences. And if there are such sequences, you will have some system that will say: yes, it is there. Since we are still talking about very small quantities, it is useful to multiply the signal. You know how these amplifiers used to be, when you listen to music and stuff, you amplify, multiply. So, this polymerase chain reaction is just a certain biochemical procedure that allows you to exponentially accumulate, increase the amount of the original nucleic acid, provided that it corresponds to the sequence that interests you.

- They started testing by PCR - correct me if I am mistaken - which is usually used to, for example, determine the viral load. In order to determine how much virus ...

- It is not quantitative. Mostly quality. There are variants of the polymerase chain reaction, which is quantitative.

- And there is another principle - this is the principle of antibody. That is an enzyme-linked immunosorbent assay. That is why an immuno-enzyme analysis is not being done on coronavirus in Russia now? This is the main test in the world.

- Yes and no. In both China and other countries, tests based on the polymerase chain reaction are more widespread because they are very cheap. They are easy to make, they are easy to implement.

- PCR is cheaper than ELISA?

- For the polymerase chain reaction of the test, you do not need to know anything except to have the virus genome sequence on your computer, and then you do some actions that allow you to develop this system. And there is an appropriate base, there are powerful laboratories throughout the country, including ours, which can put this on stream. We have clinics like InVitro that test people for various diseases using this test. Your whole procedure remains exactly the same. The only thing that changes is the reagent, which is necessary to determine this particular nucleic acid. Look, this is all built on the beautiful principle of complementarity. You know: here is the DNA, the double helix. One chain corresponds to another. And, if you know the sequence of nucleic DNA or RNA in one strand, you can develop another strand that will fit it. And all you need to detect coronavirus is to find the area that will be suitable.

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- That is, there the price is exclusively in this reagent, which is designed for any specific nucleotides?

- Yes. Another question for this to work well is all sorts of subtleties. There is a problem with antibody tests. What is the meaning of the antibody test: in people who have a disease, pathogens appear in the bloodstream, our immune system responds to this disease by producing antibodies. Antibodies are special proteins that interact with a foreign agent and help us inactivate it. Such a very specific antibody recognizes only the antigen to which it corresponds. In our case, it will be a coronavirus. Accordingly, if someone had a coronavirus infection, there will be antibodies specific to this virus in the bloodstream.

- We need a lot of biological material ...

“And we need to detect these antibodies.” We must be able to find them. Because this way you can detect those people who, for example, have already been cured, but they had an infection. They might not know that they are sick, but they formed antibodies that resolved this virus. Detecting such people is much more useful in terms of epidemiology and the development of control methods. They no longer have DNA or RNA virus. There are antibodies left. This is what provides our immunity. The memories of the body and some way to fight the infection if it suddenly arises.

- In general, an amazing, of course, story that the basis of this test is memories.

- Yes. But in order to be able to do such a test, you need to collect blood from people, and detect the presence of an antibody specific for the virus in this blood. So, you must have some kind of substrate on which you lay the surface proteins of the virus. You need such a protein, this S7, to be produced by genetic modification, isolate it in large quantities and start to be applied to some pieces of paper so that you can then drip blood samples from various people on these samples and test. In any case, this is much more complicated - you just need to produce a large amount of viral antigen, know what it is in order to detect antibodies.

- How far do these tests differ around the world? Is our analysis being done in Russia the same as the analysis being done in Italy?

- There is some published information. For example, the CDC, the American Center for Disease Control, they simply suggested, they made some standard of their test. Obviously, all the other people who are developing these tests use this information to make their own clones, but perhaps they are improving this business. Regarding our tests ... In fact, no one has done benchmarking like this.

- How much do you need to test everyone? The Spaniards took and tested all.

- I absolutely do not understand why this was necessary if people have no symptoms.

The fact that I was healthy yesterday does not mean that I did not get sick today. Field testing, besides the fact that there will be a huge load on the healthcare system, is unlikely to give anything.

- How ready is Russia for large-scale testing?

- In my experience, at least in Moscow, a network of commercial clinics has been developed, there is the Institute of Epidemiology, in which such analyzes are put on stream - not in connection with coronavirus, but they can be easily reassigned. Another question - if you test everyone, then this opportunity will be satiated very soon. And there will be problems.

- What do you think, how many tests will be done?

- There is no problem translating this into tens of thousands; I see no problems at the country level. I do not see the need to do this. The test is needed to confirm the diagnosis, and not just in order to gain some peace of mind and then go to work and then break all possible rules.

- A man lies in Kommunarka. All the assumptions that he might have a coronavirus. Indeed, the first test shows coronavirus. Why would he do three more tests? Or, for example, the first test does not show coronavirus. Why do two more tests?

- If you look at the genome of the virus, there are quite a lot of genes, it is still a very large virus, it is one of the largest RNA genomes. And you look at the presence of a positive response in several parts of the viral genome. Because if you look at only one section, you may be mistaken. And the standard system - you look at two places, if both negative - everything is fine, if both positive - everything is bad, if positive - negative, you want an independent laboratory to verify this, repeat it again, etc.

- How will the situation with the epidemic in Russia develop?

- Obviously, there will be a very large increase in the coming weeks, and maybe even months. In New York, now more than 10 thousand. We are just like New York. Why should it be any different? The question is about ordinal growth. If not sick, then people with a positive diagnosis.

We, of course, are a country protected by God, but why should we have 500, and in other places tens of thousands?

In fact, here such an interesting scientific part begins. The fact is that if serological testing were widely organized, you could estimate how many people have already gone through this. And it is precisely on this layer that it will be possible to predict when it will begin to bend - when new cases appear with less frequency, because the virus simply has nowhere else to live.

“You say if we had serological testing.” Why don't we have this?

- Because, unlike the test with a chain polymerase reaction, which allows you to simply make such a plug-in - you took a different nucleotide sequence and use it in standard kits for the detection of coronavirus, - serological tests, ELISA, immunological tests require much more preliminary work on receiving antigen.

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“But they are all over the world.” There are Korean tests ...

“Yes, but they still need to be produced.” By the way, I don’t know how widely this is done. They appeared at the end of February, as I understand it, the first. It was still a significant delay.

- They say that now at every gas station in Germany you can take yourself to test.

- I do not know. We cannot go there now to say whether it is so or not. If this were so, they would definitely be told about it.

“Do we really live in a situation where no one understands anything?”

- Yes, I think so. And from all sides there is a variety of information. In the final analysis, everything will still become relatively clear, but in hindsight. We can hardly predict anything.

- But nevertheless, you look at what is happening around the world, you see some specific model that is developing. It develops there, in Italy, in this way. And in China, the epidemic is over. Why is it over?

- The common assertion is that strict quarantine measures were applied that helped at least stop the outbreak. This does not mean that it cannot begin again.

“Do you believe that?”

- The quarantine should work, it's true. It shows any mathematical model.

- Could a virus be made in a laboratory?

- No. In the laboratory, this is so difficult to do. Everyone uses this example that a mosaic virus was made when the receptor was changed, and it was shown that epithelial cells could become infected in the laboratory.

- There was a publication where it was said that an attempt was really made in the laboratory to reproduce ... What was done?

- Even earlier, in 2002, there was an outbreak of a similar virus, it was called SARS ... It also has a genome and more. A virus that was not previously practiced in humans, but now for some reason has acquired such an ability. Although it is known that such viruses live on these unfortunate mice. And the one who lives on mice, usually does not live on a person. And you, comparing the sequences of the genes of these two viruses and realizing in general that the ability to infect a cell is associated with the presence of receptors for the virus on the cell ... The virus has some spines, they interact with the cell, after such an interaction the viral genetic material gets inside the cell.

- The virus should recognize this cell?

“Yes, he must recognize her.” And you don’t need to be a scientist, any housewife will tell you what happens if I take a piece of the mouse virus that lives on a bat, which seems to be responsible for interacting with a person in the SARS virus, and change it. This will allow you to prove that indeed changes in the surface protein of the virus are all that is necessary and sufficient to change the circle of hosts. But you need to understand that you take a fairly large piece of genetic material and transfer it from one virus to another to its appropriate place. Well changed. You have a chimera. It means that most of this virus has one origin, but here is some other piece. And you really showed that under such conditions, the chimeric virus you received in nature that did not exist before acquired the ability to interact with human cells in culture.

- And they can then once - and fly?

- No. The fact is that if we take the current virus, the number of genomes of which is now going wild, we can compare the sequence of the genome of this virus with naturally occurring isolates. They are not identical, but close, and we can show that along the entire length of the genome of the virus some changes are relatively quietly accumulating relative to natural variants. But this was not an insert of some alien material - right in the middle.

- That is, you can always see the insert?

- Oh sure. Because the insert has a different sequence.

- So, now there is not a single artificial virus?

- There are a huge number of artificial viruses that scientists regularly receive in laboratories. But these viruses, they are also called recombinant viruses, simply contain pieces ... There is such a molecular biological concept as a “vector” - it is a carrier of genetic information. And you put in some kind of alien piece. Here are at least a dime a dozen. But this is done for highly specialized purposes. First, detecting this kind of manipulation is very easy. And secondly, it is impossible to make a targeted agent in such a way that would effectively spread over the population of people and infect them. Because we do not know what is needed for this. It is one thing when using a similar procedure - inserting a vector, a piece of foreign DNA - you can, for example, make a producer of insulin, or interferon, or something else. You created a new genetic construct, which, when introduced into a bacterial cell, will make it produce insulin and with the help of which we can then be treated. It can be done. Because we just added the insulin gene to some existing genetic system and made this gene work where it did not exist before.

And here you do not even know what you need to do. We cannot explain why this virus is like that. Looking at the mouse virus, or the camel virus, this MERS, or this one specifically, we cannot explain what happened.We do not understand why this virus suddenly - and spread to the human population. They are all kindred. Imagine that a certain long text, which ... if you start comparing them with respect to each other, then within 80%, maybe even 90% of the letters they will coincide. But there are many letters that differ. As a result, you’ll have 30 thousand differences on the genome, I don’t know, hundreds. Why and which of these differences is responsible for the new property, we do not know.