Can coronavirus RNA fit our genes?

Sars-CoV-2 in our genes? This is a frightening prospect by a US MIT study published on May 6, 2021 in the journal PNAS by researcher Rudolf Janisch, a highly respected specialist in genetics and epigenetics in his field. This research has revealed genetic abnormalities during virus sequencing in infected people: hybrids where the RNA of the virus is mixed with human genetic material, which scientists call “chimerus”. Jainisch’s team therefore comes to the conclusion that the RNA fragments of the virus may insert themselves into the genomes of these people (forming the said chimers), which may be at the core of the long forms of Kovid-19.

But barely a week after its publication, another study by the American Institute of Health (NIH) in collaboration with Purdue University and the University of Michigan (United States) came to counter these results. These 3 teams claim that these chimeras are only artifacts – in other words, accidental and insignificant results of sequencing – due to sequencing techniques and that there is little chance that RNA from coronaviruses can integrate into our genome. .

To better understand this mess, Science and future Questioned the researchers who led these four studies: Rudolf Janisch of MIT, who therefore believes in the integration of coronavirus RNA into human DNA, and researchers opposed the hypothesis: Ben Afzali (expert in immunoregulation at NIH), Cristian Vobus (virologist specializing in interactions between Sars-CoV-2 and humans at the University of Michigan) and Majid Kazemian (specialist in high-level sequencing at Purdue University). Even though they still differ on this potential genetic integration, they all agree on another question of great importance: it is highly unlikely that the same could happen with the RNA of vaccines from Pfizer and Modern. Here are the reactions of scientists, who reacted independently of each other Science and future.

“Integration of genetic information from viruses into the human genome has already taken place in development, although this is rare”

Science and the future: Do we know of other viruses that can fit into the human genome?

Christian Vobus: Viruses such as DNA viruses and retroviruses (like HIV) can integrate into the genome, but have never been seen with other coronaviruses or other RNA viruses such as SARS-COV-2, whose replication cycle occurs in the cytoplasm. In other words, far away from the DNA that is in the nucleus. So it’s much less likely that a polymerase (Protein that assembles nucleic acids to form RNA strands, editor’s note) Can initiate its action in the cytoplasm and then go into the nucleus and continue there. This makes the Chimerus hypothesis very unimaginable. Even RNA viruses that replicate in the nucleus, such as influenza viruses, which have been known for more than a century, are not integrated into the genome when it is much more likely than coronovirus Will be. .

Rudolf Janisch: Integration of genetic information from viruses into the human genome is something that has occurred earlier in development, although this is rare. It is entirely possible that a cytoplasmic virus, such as Sars-CoV-2, is converted into DNA and may enter the genome.

Majid Kazemian : In the long run of development, i.e. millions of years, it is possible that anything and everything can be integrated into the genome. Therefore, we can see the integration of these coronaviruses in absolute terms. But these are extremely rare events; They cannot explain the abundance of chimers that one has the impression of finding in sequencing (since they are found in almost all the samples studied).

“Such experience must be verified by other means”

Science et Avenir: What could be the mechanism for this possible integration of coronaviruses?

Rudolf Janisch: Our genome contains transposable elements. These are pieces of DNA Those who can go there: They break away from one place and establish themselves elsewhere. Speaking, These “transposons” produce RNA and retrotranscriptase, ie. Enzymes that convert this RNA into DNA and Allow it to be reintegrated elsewhere in the genome. For example, LINE1 transposon (For long-connected atomic elements, editor’s note) Represent 17% of our genome; They are capable of such a mechanism. And not only can they reconnect, but they can also integrate other RNAs, such as Sars-CoV-2. We recognize these integrations by signatures of LINE1: a repetition of ten to twenty base pairs and a recognition sequence by an endonuclease, which cuts DNA and initiates integration. These two signatures are present in most integrations that we see in our genome. It is a major mechanism for integrating viral RNA. And we see these signatures with Sars-CoV-2 in the sequences of these chimers, indicating that it is in fact an integration mediated by these transposons.

I am Afjali: The idea that a transposon in the nucleus can take RNA from the cytoplasm and convert it into DNA and then return it to the nucleus and integrate it into the genome is very unlikely. Dr. Jainish has shown this possibility by overexpressing LINE1s, but when we overexpress them in this way it is bound to create things we don’t really see. Because these additional transposons will integrate all RNAs that have been added to the culture, not just Sars-CoV-2. Such experience must be verified by other means, they do not prove much in themselves.

Rudolf Janisch: It should be remembered that although LINE1 is normally very poorly expressed, it may be more active under stress, such as cancer or infection. We have already seen this in patients, including those with Kovid-19. This hyperactivity may facilitate integration, as may be the excess of LINE1 in our experiments. Furthermore, we also confirmed these results from cells that did not overexpress LINE1.

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I am Afjali: But the best evidence is the patients, and no evidence to that effect has been found among them.

“This was verified by mixing RNA from flies with human RNA”

Vigyan et Avenir: However, we can clearly see these chimers in sequences made with patient samples…

Majid Kazemian : We also saw these chimers for some time. We have already thought that it is probably artifacts where virus RNA combines with human RNA into the tube where we are preparing the sequencing, but we wanted to be sure. This hypothesis was verified by mixing RNA from flies with human RNA in test tubes. That is, in situations where integration into the genome is impossible because there is no human DNA, only RNA. And yet, we find the same percentage of these chimers as seen in Kovid’s sequences. Quite simply because these techniques are very sensitive and able to detect very small by-products such as these chimeras. Furthermore, we looked in libraries of sequences for other viruses and we see similar rates of these chimers, which never exceeded background noise levels. This confirms that they are artifacts.

Christian Vobus: Polymerase used to amplify nucleic acids during these sequencing can make mistakes. From time to time, they can release their matrix and cling to other molecules nearby, forming these RNA hybrids. This is the basis of recombination in viruses. But this is possible only with molecules that are nearby, not between the nucleus and cytoplasm. On the other hand, when we burst cells and mix everything in a tube to be sequenced, RNA molecules of different origin (virus and human) are found nearby and can therefore form these hybrids.

“What we’ve seen with cells in culture makes us very confident”

I am Afjali: We confirmed this hypothesis by increasing the amplification of viral RNA. Imagine looking for a very special needle in a bundle of straw where there are other common needles, and this gold needle represents 1% of the total needles. If we use a very powerful magnet, we should be able to take out these needles and if we increase the capacity of this magnet then we should see their volume increase. However, the amount of normal needles increases, but not the gold needles, indicating that they are most likely artifacts.

Rudolf Janisch: The newspaper pressured us to publish the preprint in December, where we were talking only about patient scenes. This is something that I regret, yet there was no direct evidence of genomic integration in the preprint. Chimeric tapes were found in many patients’ sequencing, but it was very likely that this was due to artifacts caused by polymerase errors during sequencing. So this argument of chimers found in these sequences does not stand on its own, we have to be honest to that. But we have since found other arguments. For example, we have demonstrated these chimeras in cultured cells infected with coronaviruses, using three different sequencing techniques. Including nanopore techniques that do not require PCR and therefore will not accidentally create these chimeras. So even if we do not have direct evidence of this integration in patients (which can be very difficult to find) what we have seen with cells in culture is very reassuring to us.

Majid Kazemian : Almost all high-throughput sequencing technologies available produce some background noise, artifacts that make us see ghosts … including nanopore technology. In addition, this technique has been used only with cells overexpressing LINE1 and so have problems associated with this overexpression.

“Dr. Jainish is a highly respected member of the National Academy of Sciences”

Science et Avenir: So, does coronavirus RNA integrate into our genome or not?

I am Afjali: We do not think there is a possibility. But this is only a scientific and intellectual discussion of the nature of interactions between cells and viruses. It is important to understand that even if this happened and fragments of Sars-CoV-2 fit into the genome, they would be so small that they could not regenerate proteins that could reconstitute the virus or have any effect on human health There can be consequences.

Rudolf Janisch: I think our results are reassuring. What the other paper shows is that sequence libraries may have chimera artefacts found in them, meaning they only refute our pre-printing arguments. And on that, I agree. But his article does not refute the arguments made later. So they cannot deny integration, it makes no sense.

Majid Kazemian : Dr. Jainisch is a highly respected member of the National Academy of Sciences and takes what we say very seriously, even if we do not agree on it. Furthermore, I believe the criticisms he received after pre-printing and publication are exaggerated.

Sciences et Avenir: What about RNA vaccines like Pfizer and Modern? Is it possible that this RNA fits into our genome?

Rudolf Janisch: This is much less likely to happen to vaccines, as these vaccines do not represent stresses such as infection, so there will be no activation of LINE1 and very unlikely integration without it.

I am Afjali: For vaccines, it is clear that there is no possibility that the RNA present in them may integrate into the human genome.

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