BOO!

Why aren't scientists banned from creating new contagious viruses?

Polina Loseva, N+1

Recently, scientists from Boston University showed the results of their experiment — a hybrid coronavirus (article by Chen et al. The role of spike in the pathogenic and antigenic behavior of SARS-CoV-2 BA.1 Omicron is published on the bioRxiv website). "Skeleton" is from the Wuhan variant, "spike" is from omicron. Chimera BOO (as it was dubbed on Twitter by the name of the university) turned out to be fatal for 80 percent of infected mice. Now virologists are discussing whether it can really be dangerous for humans. Social media users are worried, and the US National Institutes of Health are outraged that they found out about the experiment after the fact — although scientists had to bring the protocol of experiments for approval in advance. There have been a lot of such scandals over the past ten years: now with the flu, then with one coronavirus, then with another. And although everyone says that it threatens new strains and new epidemics, no one has banned these studies so far.

In about half of their work, genetic engineers add some new property to the body (and in the other half, on the contrary, they select it). Experiments of this type are called "gain of function" (abbreviated as GOF), endowing with a function. Sometimes this allows you to "improve" the object of research. For example, more recently, scientists have made dogs glow to track how the genetic editing system works in them. And other scientists have added a fragment of rabbit DNA to the genome of the plant — to teach the plant to break down volatile carcinogens.

As long as it concerned bacteria and laboratory animals (and did not concern organisms that can be eaten), these works did not cause anyone any big questions. But in 2012, the scientific community wondered whether it was worth banning the endowment of some objects with new functions — after it was tried on viruses dangerous to humans.

Disgrace in ferrets 

In 2011, Dutch virologists conceived an experiment with the avian influenza virus, H5N1. They decided to find out what prevents him from having an epidemic among mammals — for example, ferrets (and there it's not far from humans) — and how many genetic changes separate him from this.

A ferret can pick up the usual H5N1 virus from a bird — through its saliva or excrement. But in order to infect the next ferret, the virus needs to start being transmitted by airborne droplets, which it cannot do by itself. To help the flu acquire this skill, the researchers made three substitutions to its genome: two to the hemagglutinin gene (so that the virus better adheres to the receptor on ferret cells) and one more to the polymerase gene (so that it works better at low temperatures; ferret lungs are eight degrees colder than birds). This mutant virus multiplied well in the respiratory tract of infected ferrets, but still was not transmitted to the neighbors in the cage.

Then scientists gave him the opportunity to evolve himself inside ferrets and accumulate the mutations that he needed. They helped only technically — they transferred the virus from one animal to another. And after the tenth transfer, they arranged a test drive, planting a healthy ferret to an infected ferret. It turned out that the influenza virus, which initially carried only three point replacements, acquired two more mutations in hemagglutinin over ten generations — and thus learned to be transmitted by airborne droplets.

The scheme of the experiment with generations of ferrets. The first six times the scientists transferred tissue homogenate: they euthanized the animal, cut out its nasal passages, crushed the tissue and isolated viral particles from there. The next five times they managed to flush from the nasal cavity. Herfst et al. / Science, 2012

The height of the barrier (more precisely, the length of the path from the bird to the ferret) was really determined by scientists in this way. It turned out that an outbreak of influenza among birds is separated from a possible pandemic among humans by only five amino acid substitutions. This is quite a bit: for example, ten times less than omicron acquired compared to the Wuhan coronavirus. And this estimate is probably overstated — in the same 2011, another American group conducted a similar experiment with the same flu and ferrets, and taught it to be transmitted through the air in just four substitutions. But it was not the height of this barrier that scared the American authorities and the scientific community — but the fact that virologists took the liberty to help the virus jump over it.

Some scientists worried that the results of such studies could not be published openly — God forbid someone decides to reproduce the experiment with malicious intent. But from this, the editors of Science and Nature, where the articles were published, immediately reinsured themselves — they hid technical details in the texts so that they did not look like instructions for use.

Others admitted that they don't really trust their colleagues - and the security measures they take. American and Dutch flu "trainers" worked in BSL-3 certified laboratories (this is the second class in terms of rigidity of restrictions), and no one doubted their honesty. But safety also depends on the extent to which local regulators issuing certificates monitor compliance with international standards. And other BSL-3 laboratories — and there are hundreds, if not thousands of them in the world — may not be so well protected. And leaks have already happened: smallpox, coronaviruses, and possibly even viral encephalitis have escaped from scientists in different years.

The idea that an improved flu could also leak out of the laboratory looked frightening. Especially considering that the previous flu, swine flu, swept the world quite recently, in 2009. Some virologists suggested locking up such experiments in the most secure laboratories, BSL-4 — where they usually work, for example, with ebolaviruses. But there are only a dozen such laboratories in the world, all flu researchers will not fit there. It was clear that there would be no quick agreement, so the authors of the sensational articles called on their colleagues to suspend work with well-transmitted flu strains. At least for two months.

It didn't work out in two months — we had to revise safety standards for another year and weigh the pros and cons of GOF experiments. The American Biosafety Advisory Council gave the green light only in early 2013, and the research continued - but not for long.

Confusion in terms 

In 2014, the US government announced the following moratorium. The reason for it was given by several American laboratories at once, which did not show themselves from the best side. Employees of one forgot smallpox vessels in the pantry, scientists from the other did not kill anthrax, in the third a sample of a "weak" strain of influenza was contaminated with a "strong" H5N1. And although these incidents did not lead to casualties, and the pathogens were the most common, not "improved", flu researchers got it again, and also those who worked with the SARS and MERS coronaviruses (the outbreak of which was just on the rise at that time). The authorities were afraid that the offspring of GOF experiments would also run away somewhere, and suspended funding for their projects - which in American science actually means a ban on work.

However, by this point it was no longer entirely clear what kind of experiments were meant. Having moved from biologists to regulators, the term "gain of function" has lost its original meaning. It has ceased to mean work with glowing dogs and useful plants — only research with potentially dangerous pathogens. In addition, in the process of moving, the values of both gain and function blurred. For example, if after manipulation, the virus became better transmitted through the air, but at the same time it is worse to kill its victims, then it is unclear whether this can still be called gain. And if the initially contagious virus simply increased its contagiousness, then you can argue about whether it is worth seeing a new function in this.

The 2014 moratorium stopped studies "that confer such properties <...> that the virus will have increased pathogenicity for mammals or be better transmitted by respiratory means." But it was not very clear what exactly "gain of function" means in the name of the moratorium order itself: intention or result? Virologists who taught the flu to be transmitted between ferrets obviously expected to change its properties from the very beginning. But what about those who planned to just take a closer look at the properties of the virus and accidentally raised a monster?

Studded hybrid 

In 2016, the government's Biosafety committee revised its definition to avoid terminology confusion. In the new version, instead of the usual GOF, the abbreviation GOFROC (gain of function research of concern; however, it did not particularly catch on) was introduced — that is, a study that causes concern. Concerns were caused by the work, as a result of which there were:

• infectious pathogens that can spread widely and uncontrollably among people,
• pathogens that cause high morbidity or mortality.

This definition seemed to remove most of the questions. It only deals with really dangerous strains and studies that are relevant to humans. After it was adopted, in 2017 the government lifted the moratorium. Now, in order to get money for research, everyone who planned work that fit the definition of a GOF experiment had to approve their protocol in advance at the Institutes of Health. But it quickly became clear that this procedure does not work either.

The scheme was broken by a study of the same 2017. Virologists have studied how natural bat coronaviruses are potentially dangerous to humans (which now, of course, sounds ironic). Since "wild" coronaviruses do not always grow well on laboratory cultures, scientists have proposed to grow a chimera. As a skeleton, virologists took the already well-known coronavirus WIV1, which binds to the ACE2 receptor and multiplies well in human cells. Then, the virus' own spike proteins were replaced with spike proteins of various newly discovered "wild" coronaviruses and checked whether they help it to penetrate cells. And we found out: some really help. Spike proteins of two previously unknown bat coronaviruses turned out to be sticky for human cells — which means, theoretically, these viruses are able to jump to a person from a bat.

Hybrid viruses (second and fourth row) reproduce in cells as well as the original WIV1 (first row). Cells are colored blue, viral proteins are colored red. Hu et al. / PLOS Pathogens, 2017

Formally, there was nothing special about this job. The WIV1 virus has not acquired any new functions: before hybridization, it did an excellent job of penetrating human cells itself. There was no reason to think that in the hybrid version it is much more dangerous than before the manipulation. But scientists and officials again did not agree on whether it was worth starting such experiments at all. It turned out that the definition of 2016 did not solve the problem. Some officials give out grants for those studies that seem safe to them. And others still see them as a threat and continue to be outraged.

A new reason to clarify the definitions was the covid pandemic, after which there was talk about the laboratory origin of SARS-CoV-2 (we talked about them in the text "You yourself are artificial"). Moreover, the leak of the coronavirus was blamed on the very laboratory that had been engaged in transplanting thorns to the WIV1 virus a few years earlier. The debate about the origin of covid continues even now, and the work of scientists from Boston University with a hybrid coronavirus has added fuel to this fire.

BOO! 

Boston virologists took an omicron spike and transplanted it onto the skeleton of the very first, Wuhan coronavirus. Thus, they tried to understand why omicron is so good at avoiding antibodies, but causes such low mortality.

It turned out that it was the thorn — but only partly. The Wuhan virus with omicron spike protein did not really react to antibodies isolated from the blood of vaccinated people. At the same time, it turned out that the omicron spike does not make the virus less deadly. Usually mice do not die from omicron, but 80 percent of animals died from chimera BU.

Perhaps the Boston scientists in vain focused on the mortality of mice in the abstract of their article. If they had described their results mildly, they could have done without noise. At least because this is not the first study of this kind (in the article Liu et al. Spike protein-independent attenuation of SARS-CoV-2 Omicron variant in laboratory mice the crossing of omicron with the Wuhan ancestor is also described). And also because it is again unclear whether it can be considered a GOF.

Firstly, there is no question of any new properties — this is still the same coronavirus, just another kind of it. There have already been a lot of such hybrids, they appear in the population by themselves and do not always cause new outbreaks. The same deltacron is a chimera from a much more dangerous delta than the Wuhan variant, and a much more contagious omicron. A lot was written about it in the spring of 2022, but it could not withstand competition with other varieties of omicron and disappeared without a trace.

Secondly, it is not very clear whether it is possible to talk about strengthening properties. If measured by the Wuhan standard, the chimera BU is most likely more contagious. At the same time, it is clearly less pathogenic, since one hundred percent of mice died from the Wuhan variant itself. That is, the omicron spike reduced it — by as much as 20 percent. On the other hand, if we take omicron as a reference point (from which there is only a thorn in this chimera), then the mortality rate has grown, and from this the authors concluded that pathogenicity is determined by the skeleton rather than the thorn.

Finally, all this work has been done on mice — and special mice that are literally stuffed with human ACE2 receptors. That is why they die in such numbers from the coronavirus, which for people was not so deadly even at the beginning of the pandemic, when it was unclear how to treat it. This means that one can hardly expect the same pathogenicity of the chimera BU in humans, even if it escapes from its BSL-3 laboratory.

However, now scientists doubt that this work made sense at all. The fact that mutations in the omicron spike allow the virus to hide from antibodies has been known for a long time, we have not learned anything new here. And the second conclusion — about how the thorn affects pathogenicity — could be valuable, but it is unclear how legitimate it is to project mouse results on humans here.

There is a communicative failure: if the authors had not focused on high mortality, they would have heard neither criticism from colleagues nor reproaches from the public. There would be no problems with the National Institutes of Health — which can now leave these scientists without funding.

*** 

There will be new inspections, new moratoriums, new formulations — and new scandals. Bans and committees will not prevent virologists from figuring out where new abilities come from viruses. At least because some scientists believe that new pandemics need to be prepared in advance. Predict strains, test medications, and adapt vaccines. To do this, you need to run a little ahead and get new viruses before they occur in nature.

Therefore, the work on "gain of function", no matter who defines it, will not go anywhere. We will discuss again and again whether our misfortunes are caused by the leakage of some of these experiments. However, over the past hundred years, scientists have never proved that at least some kind of epidemic was caused by a laboratory pathogen. And even if virologists in a particular America agree with their officials, submit reports on time and carefully monitor safety procedures, there is always a chance that something will go wrong with other researchers - who do not inform the National Institutes of Health about their plans.

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