For a month now, samples delivered to the Disinfectology Research Institute of Rospotrebnadzor from all regions of Russia have been showing the same ratio of Delta and Omicron strains. This was told in an interview by the chief researcher of the Research Institute of Disinfectology of Rospotrebnadzor, Corresponding Member of the Russian Academy of Sciences Elena Ilyina. She explained why oxygen therapy contributes to the development of nosocomial pneumonia, and assessed the effectiveness of drugs for COVID-19. — Elena Nikolaevna, you work at the Research Institute of Disinfectology of Rospotrebnadzor and are engaged in reading the genomes of coronaviruses that are currently circulating. How many virus samples are sequenced per week, per month?

— We have reached the capacity of 2,000 genomes per week. And there are a lot of such organizations that are actively sequencing. Therefore, now in the Russian database there are already about 14 thousand omicron genomes, and the total number of coronavirus samples is about 90 thousand. We see both “omicrons” of the BA.1 line and a small amount of BA.2. Samples come from all regions.

Therefore, it cannot be said that "a wave is coming" across Russia. It is rather a general flash, approximately the same from all sides. I expected to see some difference between Moscow and remote regions, but it turned out that there was none.

- How does the ratio of the number of samples with "omicron" and "delta" change, if we take the past month and a half?

- When we went on New Year's holidays, we had a ubiquitous "delta". When we returned from the New Year holidays, we saw the widespread dominance of the "omicron". But the "delta" has not gone away completely, it has remained. And the ratio between "delta" and "omicron" is approximately the same in all regions for a whole month after the New Year holidays.

- It turns out that "omicron" does not displace the "delta"?

“He didn’t push her out until the very end. We see about 70% -80% "omicron" and about 20% "delta". For a month now, the ratio of "omicron" and "delta" in the population has remained the same. It cannot be said that the "delta" is leaving.

- How many "omicrons" sequenced by you belong to the BA.1 line?

- Approximately 95%. And 5% is the second line. We did not find the third one.

- And the number of "microns" of the second line also remains the same? Can't we conclude that BA.2-"omicron" is more contagious?

- Not yet. We see genetic differences, but the presence of BA.2 does not increase. And in the clinic, the second line is not particularly different.

- Some time ago there was a publication by Cypriot scientists who discovered the recombinant "deltacron". Have you seen such mutants?

- Indeed, there was such a publication, but soon after its release, comments appeared that it could be contamination (contamination). Since we are seeing the simultaneous circulation of the "omicron" and the "delta", I think that the scientists may indeed have mistaken the mixed population for the recombinant.

Omicron and Delta are quite far apart. By their origin, these are parallel lines.

Given the fact that there was only one scientific publication and the question of the existence of the "deltacron" was not raised, this is most likely a mistake.

— Do you obtain viruses for sequencing from swabs?

- Yes, exclusively nasopharyngeal swabs. They are collected in different regions of Russia from patients. Then they are tested on the spot, answering the question: do these swabs really contain the target virus - in this case, coronavirus? Then the samples are delivered to us by special transport companies for in-depth testing.

- How many samples fit into the sequencer, if we mean one batch? How long does sequencing take?

— As a rule, we load about 400-600 samples every day. Since we have a rather powerful PromethION Oxford Nanopore sequencer, we work on the third generation, it reads these 600 samples for 8–9 hours. At night he reads, in the morning we shoot, and the next download. It has 24 cells, each holds 96 samples.

- You sequence them, and then what?

— Then we put all genomic sequences into the Russian database VGARus. It has been operating in Rospotrebnadzor since June 2021. This database is constantly being filled, its data can be analyzed, to look at some patterns in the variability of the virus. This is where patient data comes in.

- You have studied microbiomes, so I especially want to ask you about pneumonia, which often follows infection with SARS-CoV-2. Some doctors say that with COVID-19, bacterial pneumonia often joins the viral one. Other doctors, on the contrary, believe that attachment of this kind occurs infrequently and therefore do not prescribe antibiotics. What are you observing?

- It is worth distinguishing between viral pneumonitis (or alveolitis) and pneumonia itself - inflammation caused by a bacterial infection. In severe cases, a bacterial infection joins this very pneumonitis or alveolitis. That is, the pneumonia that is a complication of the coronavirus infection is no longer viral pneumonia. It is always bacterial.

- And what bacteria usually join?“The same bacteria that traditionally cause hospital-acquired pneumonia. This list is the same all over the world. These are, as a rule, Acinetobacter - different, mainly Acinetobacter baumannii, Pseudomonas aeruginosa, Klebsiella pneumoniae, staphylococci. Most of these pathogens originated from soil bacteria, from which they have retained the ability to survive in common areas, on toilets, on sinks, and on other surfaces. Oxygen therapy often contributes to the addition of a bacterial nosocomial infection.

- Why is this happening?

- As soon as you turn on any mandatory ventilation of the lungs, and the oxygen supply is mandatory ventilation, you promote the exchange of bacterial flora between the upper and lower respiratory tract.

There are always a lot of bacteria in the human mouth and nose. But the mucosa performs a barrier function, it absorbs microorganisms in a normal state. When using oxygen therapy, you willy-nilly carry bacteria from the nose and mouth into the trachea and lungs with the airflow.

— How quickly do coronaviruses develop resistance to drugs based on monoclonal antibodies?

“These are targeted drugs. This is their plus and minus. Monoclonal antibodies are matched to a specific type of virus. And therefore, it is not at all a fact that monoclonal antibodies that work great, for example, against the Delta strain, will work against the Omicron. The problem with monoclonal antibodies is precisely this - they are very specific.

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