Viruses from a test tube
Is it possible to make a biological weapon out of a virus and why clone SARS-CoV-2
Killer viruses actively developed in secret laboratories are a constant topic of speculation among supporters of conspiracy theories. In fact, viruses have been studied in laboratories for a very long time, and there is no mystery about it. Post-science asked virologist Sergey Alkhovsky to tell about whether it is possible to clone a virus or create it from scratch, what technologies are available for this, as well as about the threats that viruses promise to humanity.
Biological weapons or a ridiculous accident?
In 2015 , scientists from The University of North Carolina and the Wuhan Institute of Virology reported that they artificially created a hybrid version of the coronavirus, codenamed SHC014-MA15. Studies have shown that it is able to infect the epithelium of the human respiratory tract, as well as cause pneumonia in mice. Some scientists criticized the experiment, because the experiments carried out gave very little to understand viruses, but at the same time created a potential threat to humanity in the event of a leak from the laboratory. Other researchers, on the contrary, pointed out that such experiments are carried out constantly, and apocalyptic scenarios, which often excite the public, have never been implemented.
Most likely, this story would have been forgotten quite quickly, if not for a fatal accident. At the end of 2019, an outbreak of a new type of coronavirus SARS-CoV-2 unexpectedly occurred in Wuhan, China, and a few months later it turned into a pandemic. Events developed very rapidly and, against the background of a lack of information about the virus, they became overgrown with conspiracy theories. Many of their supporters assumed that such a rapidly spreading threat simply could not have arisen naturally, which means that the virus is an artificial development directly related to SHC014-MA15.
In fact, SARS-CoV-2 is not some unique phenomenon in nature. This is one of the many coronaviruses that have been circulating in the human population for a long time. For the first time, one of them, HCoV-B814, was detected back in 1965, and since then it has been established that up to 15-20% of all colds are caused by coronaviruses. In addition, coronaviruses have already demonstrated that they are not limited to the common cold. SARS-CoV, known as SARS, caused local epidemics in the countries of the Far East: the total number of infected by the end of July 2003 reached 8096 people, 774 of them died. If this virus has not infected people in its natural habitat since then, then the Middle East respiratory syndrome, known as MERS and also caused by coronavirus, is still diagnosed in up to a dozen cases per year.
Another pillar of conspiracy theories about viruses is the belief in the incredible power of modern science, capable of unlimited manipulation of the genetic code. The truth, however, is that with the current level of knowledge, virology has more questions than answers.
What exactly do scientists know about viruses?
Viruses were discovered quite late, and bacteria were considered the only possible causative agent of diseases for a long time. Only in the 90s of the XIX century, scientists Dmitry Ivanovsky and Martin Beyerink independently showed that the extract of a diseased plant retains infecting properties, even if all bacteria are removed from it. This directly indicated the presence of some tiny infectious agent that had not been detected before. Beyerink called them viruses. Finally, it turned out to confirm their existence in 1939, together with the first photo of the virus, which was taken using an electron microscope.
Today we know for sure that in its simplest form, a virus is a specially formed nucleic acid, in the form of RNA or DNA, and located in a capsid – a protein shell. The virus cannot definitely be called alive, because it is able to function only when it is in another organism. When the virus enters the cell, it infects it, unpacks and begins its vital activity. In the cell, its RNA or DNA is recognized by cellular ribosomes, and with their help, the synthesis of viral proteins is started. As soon as a sufficient number of proteins have been synthesized, the viral RNA polymerase (responsible for copying the genome, that is, the structure of RNA) begins to produce many copies of the viral genetic material. A copy of the RNA is packed into a capsid, leaves the cell and is sent to another – and the process repeats from the beginning.
The structures of viruses are very different. Coronaviruses, for example, have one of the "longest" RNAs, their genome consists of 28 thousand nucleotides. Most viruses "fit" into 5-10 thousand. The sequence of nucleotides of each individual sample of a virus of a particular species is formed into a specific genotype, which directly determines its biological properties, that is, the phenotype, for example, the ability to infect not only bats, but also humans.
Such differences in properties are the result of constant mutations. RNA and DNA of viruses, as well as nucleic acids of living organisms, can be copied with errors. This directly affects the properties of the virus and makes it more or less adapted to the environment. At the same time, it is advantageous for the virus to infect a certain type of living beings quickly and stably, without causing fatal harm to their health. The rapid death of an animal or plant means that the virus will have fewer opportunities to be transmitted further, which means that the risk of its extinction will be higher.
And yet, SARS-CoV-2 is the result of an interspecific mutation that turned out to be extremely successful (for the virus). Therefore, today scientists do not take their eyes off viruses and are constantly looking for which one of them can provoke the beginning of a new pandemic.
Where to look for viruses?
Human activity is one of the key factors that influences the mutation of viruses. All human viruses are former animal viruses that mutated at some point and acquired the ability to infect people. HIV, hepatitis viruses, influenza viruses are former zoonoses. These transitions occur due to the incessant and unavoidable contact between humans, wildlife and viruses inhabiting it, since such interaction creates evolutionary incentives for viruses to infect people.
In some areas of activity, people are particularly at risk of catching the infection from animals. In agriculture, we constantly have to deal with rodents – a stable source of hantavirus, which excites hemorrhagic fever with renal syndrome (HFRS). In Russia, 10-12 thousand cases of this severe infection are detected annually. But, in addition to this hantavirus and many others, a dozen more types of viruses live in the natural reservoir of rodents. There is absolutely no guarantee that one day an option capable of infecting people will not appear from this variety. Exactly the same situation happened with SARS-CoV-2. Horseshoe bats are carriers of a large number of coronaviruses that are completely safe for humans. However, in the process of constant evolution, an option may always unexpectedly arise that will acquire the ability to infect a person. And having infected one person, the virus will inevitably spill out into the human population.
Progress does not always somehow allow us to resist this process. On the contrary, it often only contributes to the emergence of new viral diseases. People are increasingly intruding into those natural areas where they did not exist before. An example is tick–borne encephalitis. Until the 20s of the XIX century, such a disease was not heard of at all. The problems began with the development of the Far East and Siberia: as soon as people started coming there, the first epidemic outbreaks appeared. Today we have to get vaccinated against encephalitis every time we go camping.
Another similar example is the Ebola virus, first discovered in the 70s of the XX century. It is carried by flying foxes, winged foxes, which have been the only natural reservoir for it for 10-20 thousand years. As people developed territories near the habitat of the bats, they cleared the jungle and created plantations with fruit trees in their place. Fruit-eating bats flocked there for food, and because of the unnatural abundance of food for them, their populations grew to huge flocks. All this greatly increased the likelihood of human contact with the products of the vital activity of the bats (saliva, blood, feces), and therefore with the virus.
The ecology of viruses deals with the study and tracking of such threats. This is an attempt to understand what we are living with, what we are in contact with, and to find out what viruses we can detect in natural reservoirs, or more precisely, to understand the patterns of virus spread depending on the natural and climatic conditions of the area and the interactions of representatives of its flora and fauna. The ultimate practical goal is to learn how to control the spread of viruses.
One of the main tasks of modern virus ecology is to determine the total number of viruses that can leave the current distribution area and move into the human population. According to preliminary estimates, there may be up to 400 thousand such viruses.
Today, however, people are quite far from achieving this goal. We do not know the full diversity of viruses and do not understand how the mechanisms of their mutations are arranged, because of which variants of viruses with altered properties constantly appear.
Viruses under the microscope
The ecology of viruses is largely a "field" discipline related to the study of the properties of a particular environment. The direct study of the structure of viruses is engaged in another key section of virology – the molecular biology of viruses. Molecular biology itself studies a much broader set of objects and problems, but the study of viruses plays a special role in it. Viruses are a very convenient model on which it is easy to conduct research. In the 1960s and 1970s, it was bacteriophages, bacterial viruses, that made it possible to discover the principles by which replication (copying) takes place DNA in the cell.
The study of differences between variants of the same virus, the mechanisms of virus penetration into the cell, the development of the immune response – all these are topical topics for the molecular biology of viruses. This field is inextricably linked with medical virology – the direct study of cases of infection with viruses, the development of infection, and its treatment.
In fact, the genome of viruses is of most interest to scientists: it determines their properties, and with them the principles of influence on living organisms. It is possible to determine the function of each section of the RNA or DNA of the virus by comparing the original sample of the virus with its modified version. To do this, a molecular clone is created – a copy of the virus, which is modified and then compared with the original.
After looking at two very similar viruses, one of which can infect a certain type of cell, and the other cannot, how do you understand which elements in the structure of surface proteins are responsible for this? It is necessary to compare their genomes and look for differences in them. If it turns out to detect a difference in the structures of DNA or RNA that encode 2 or 3 amino acids, then we can say for sure that it is this feature that sets the properties of one virus that are absent from the other. For example, SARS-CoV-2 has mutations that are responsible for the ability of the surface S-protein ("crown spike") to bind to the cell receptor. This allowed him to infect people.
Until the 2000s, research was severely limited by technical capabilities. It was necessary to carry out very extensive field and laboratory work to detect the causative agent of any infection. It was necessary to go on an expedition, collect materials – for example, to get a fragment of human tissue, presumably killed by the virus. Then add it to the artificially created cells, and then isolate a pure culture of the virus, free of foreign elements in the sample. It was not always possible to do this quickly, because the cells might not be infected – it took more time to understand the conditions in which infection occurs.
Because of this, by 2000, only 1500-2000 viruses had been studied well enough. Now the situation has changed dramatically. Technologies of genome-wide sequencing (Next-Generation Sequence) appeared, which made it possible to "read" several sections of the genome at once using a specially prepared device (sequencer), which means to obtain information about all genomes in the studied sample with viruses. Thanks to this technology, it is possible to omit the stage of isolation of a pure virus culture and directly proceed to the analysis of its genome. Now scientists are sequencing, for example, sewage or ocean waters and can find several thousand new viruses only in one study – and there are hundreds and thousands of such studies.
Is it possible to create a new virus in the laboratory?
The study and work with virus genomes has reached a new level today, and this in many ways fuels the public's fear of laboratory research. However, the level of development of modern science sets clearly defined boundaries of the possible and the impossible.
Absolutely all serious virologists have a negative attitude to the hypothesis of the artificial origin of the SARS-CoV-2 virus. Even during the SARS-1 epidemic in 2002, it was found that this virus came to the human population from bats. In the caves of Yunnan, where dozens of coronaviruses were found, their variants were also found, in which certain positions in the genome structure coincided with SARS-1 and SARS-2. So there is no fiction in the fact that one day the puzzle was formed and these viruses splashed out into the human population.
Unfortunately or fortunately, this does not mean that it is impossible to create a dangerous virus in the laboratory. In 2012, a high–profile study "Transmission of influenza A/H5N1 virus by air between ferrets" was published, related to studies of the avian influenza virus - H5N1. Some of its varieties are very pathogenic, and their mortality is about 60-70%. People are saved from this threat by the fact that H5N1 can be infected only through close contact with a very high infectious dose of the virus, which is why factory workers are infected with avian flu in the vast majority of cases, for example, when cutting sick poultry. Such dangerous forms of influenza, as a rule, are able to infect a person only through the lower respiratory tract. However, only a few relatively small mutations can make a difference.
Ron Fouchier, a scientist from Erasmus University in the Netherlands, has been researching the transmission of the H5N1 virus from animal to animal for a long time. He infected one ferret with the avian flu virus, took a swab from him and infected the next ferret with this swab. Each time the virus slightly mutated: its properties changed during transmission from one animal to another. After the tenth transmission of the virus through a smear, Fouchier noticed that those ferrets that were sitting in neighboring cells with already sick, without the participation of a scientist, also began to become infected. In an article written in 2011, Fouchier concluded that only five mutations can give the H5N1 avian influenza virus the properties of a serious airborne pandemic virus.
This article was sent to Science and Nature, reputable scientific journals. A large-scale scandal broke out. On the one hand, many accused Fouchier that his experiments were conducted in insufficiently safe conditions, where a leak could potentially occur. On the other hand, many perceived the article proposed for publication as instructions for creating a killer virus, which they are going to place in the public domain. After pressure from the scientific community, it was decided that such articles should be published only with partial concealment of information, so that no one could repeat the results of the study with malicious intent.
The following picture is emerging: creating a new virus from scratch at the current level of technology development is impossible – it simply will not be possible to invent and arrange 28 thousand nucleotides in the right order to obtain SARS-CoV-2 artificially. However, it is quite possible to make minor modifications to the genome of well-studied viruses.
The genome of a virus is a sequence of nucleotides. If this sequence is known, then it can be synthesized chemically. Therefore, if it was possible to create a molecular clone of a virus, it means that there is already a template that can be easily modified for relatively little money for such a task - only about 100 thousand dollars.
And yet there is no preliminary recipe by which the virus can be modified. Fouchier did not calculate the necessary components to change H5N1, he obtained them empirically. That is why serious modifications of the virus are impossible without a preliminary experiment.
There is also a difference in the degree of knowledge of various viruses. On the one hand, there is a huge layer of work with different subtypes of the influenza virus, on the other hand, much less similar data has been collected regarding coronaviruses. It has not yet been possible to obtain a molecular clone for SARS-CoV-2. Therefore, it is simply impossible to imagine a way to seriously modify it in any way. News that scientists from Sienas have improved the coronavirus so that it has become immune to standard antibodies – a very big exaggeration. The study was carried out with the help of virus-like particles into which certain proteins were embedded. This is valuable work, but you should not draw wrong conclusions from it.
The theory about the artificial creation of SARS-CoV-2 does not stand up to criticism. However, the pandemic unfolding on the planet may still have a laboratory origin. The possibility of a banal leak can never be ruled out.
Can the virus "escape" from the lab?
Modern requirements for the security of working with viruses are very strict. In the 1960s and 1970s, there were indeed cases of laboratory infection, for example, infection through ventilation. Today, technology allows you to keep the virus in the laboratory, even if a leak does happen.
The laboratory that works with pathogenic microorganisms does this in accordance with very strict standards. Inside there must be "clean" zones for employees and "contagious" zones where all work on viruses is carried out. The laboratory itself is located either in a separate building or in a separate building altogether, depending on the danger of viruses stored in it. Doors and windows are sealed, and ventilation systems are equipped with special filters made of thin, concertina-folded fiberglass fibers, where, in case of leakage, particles that need to be retained settle. All manipulations with viruses are carried out in special laminar fume hoods with illuminators, ultraviolet lamps and a sterile air supply system, as well as in biological safety boxes. Boxes protect employees from infection, and laminar cabinets primarily create sterile conditions for the viruses themselves.
All viruses, depending on the danger to humans, are divided into four groups. The fourth (in the WHO classification – the first; in Russia, the reverse order of deduction is adopted) – the safest, it includes strains of microorganisms that are not capable of infecting humans, or causing mild diseases: ectromelia virus, enteroviruses types 68-71, cowpox virus and others. The third category includes viruses that cause diseases of moderate severity: herpes simplex of the first and second types, Epstein–Barr virus. The second group includes dangerous viruses that can cause diseases with a risk of death: tick-borne encephalitis, HIV, yellow fever, hepatitis C and others.
Finally, the first group of viruses are hemorrhagic fevers, smallpox, Ebola and Marburg viruses. This is the most dangerous category. There are only two centers in Russia that have the right to work with these viruses: the Vector Center in Novosibirsk and the military Institute in Sergiev Posad. Here, the staff changes clothes before entering the laboratory, and then necessarily takes a shower, clothes are completely disinfected. The production equipment in the laboratories is isolated from other premises, there are additional ventilation and waste disposal systems.
Some viruses are treated in different conditions depending on the type of research. SARS-CoV-2 is assigned to Group II. But when it comes to experiments not related to the accumulation of the virus (reproduction in cells), SARS-CoV-2, like other such viruses, is considered as a category III virus. However, all security procedures are maintained in this case.
Interestingly, the laboratories still store stocks of viruses that humanity has long coped with, such as the smallpox virus. On the one hand, they haven't had smallpox since 1979. Is it worth keeping its samples, because, despite all security measures, it is impossible to exclude the factor of banal human error?
On the other hand, there is no guarantee that one day smallpox will not return to a person for purely natural reasons. Smallpox affects sheep, goats and those closest to us evolutionarily, that is, monkeys. Therefore, even now there is a need to keep old stocks just in case: suddenly we need to urgently create a vaccine?
About the author: Sergey Alkhovsky – Doctor of Biological Sciences, Head of the Biotechnology Laboratory of the Institute of Virology named after D. I. Ivanovsky National Research Center of Epidemiology and Microbiology.
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