How do viruses mutate? Can humans eliminate them? | Virus Super Topic

After reading today's article, you will understand the following questions:

1. How do viruses mutate?

2. How much does a virus have to change to be considered a new strain?

3. The Delta strain is more contagious, so why is its virulence not reduced?

4. Can humans eliminate the new coronavirus?

But before that, we need to talk about what "species" is.

Written by Li Qingchao (Shandong Normal University)

The new coronavirus has been mutating. The epidemic has been recurring, and everyone is worried. We hope that special medicines can defeat it, physical isolation can stop it, and vaccines can eliminate it, but it comes again, in a different guise. This time, the aggressive Delta strain appeared in India in October last year. How did it come about? How was it identified? It is so powerful, will there be a more powerful next generation? Its infectiousness has increased, will it evolve into a new virus? ...

Before answering these questions, we need to talk about the issue of "species".

Which came first, the chicken or the egg?

Which came first, the chicken or the egg? Aristotle could not give an answer, but biologists can give a definite answer.

Because when faced with this question, the concepts of "chicken" and "egg" in their minds are different. Aristotle was thinking about "chickens lay eggs, eggs lay chickens", and this infinite sequence of mutual cause and effect has no real origin [1]. Biologists will first ask what kind of eggs are "eggs" here, what is the definition of "eggs", and then they can give a more reasonable explanation. If "eggs" refer to bird eggs such as chickens and duck eggs, or even turtle eggs, dinosaur eggs and reptile eggs, these amniotic eggs appeared about 312 million years ago [2]. Chickens (Gallus gallus domesticus) are domesticated from red junglefowl (Gallus gallus), and may have appeared at most 8,000 years ago [3]. In this way, eggs appeared much earlier than chickens.

Let's be clear, what if "egg" refers to "chicken eggs"? It is generally believed that chicken eggs are "eggs laid by chickens", even if the egg can roll on the ground and a Nezha jumps out when it is split, it doesn't matter. In comparison, "being able to hatch a chicken" is not a necessary condition for becoming an egg. In this case, the egg must have an animal called a chicken to lay it, so logically speaking, the chicken obviously came first.

So where did this chicken come from? It was hatched from an egg, and this egg was laid by an animal that was very similar to a chicken, but not yet a chicken. Because in the concept of a chicken, although "hatching from an egg" is a fact, if it can be hatched from another egg, it does not prevent it from being a chicken.

What if we emphasize that this egg is an egg that "can hatch a chicken"? Then the answer is that the egg came first. Because under this understanding, the entire life process of the chicken is essentially extended to the fertilized egg stage. People know very little about the process of hybridization and domestication of various wild jungle poultry to produce chickens, so it is impossible to know for sure whether there is a clear transition point between the non-chicken ancestors of chickens and chickens. If an animal that is almost the same as a modern chicken (i.e., a primitive chicken) lays a fertilized egg with the same DNA as a modern chicken (because the mother's egg, the father's sperm, or the fertilized fertilized egg mutated), then this egg is already an egg (that can hatch a chicken). So from this perspective, the egg came first. It's just that this egg may have been laid by an "animal that is not a chicken."

Ok, what if this egg is a "chicken egg" and "can hatch a chicken"? Well, in this case, this question really returns to its original meaning: circular reasoning, without beginning or end.

The concept of species

From the above discussion, we can see that clarifying concepts and reaching consensus are prerequisites for effective discussions.

Concepts are sometimes vague. The vagueness of concepts is not because we have not read enough, but because concepts themselves are man-made objects, while the facts they describe are much more colorful. To put it in a way that "goes against the teachings of our ancestors": concepts are used by people to describe reality, but reality is not responsible for "growing" on concepts. Especially in life sciences, the concepts left by the "ancestors" are often broken through and expanded.

For example, the concept of “species” is extremely complex (when you see the Chinese character “种”, a series of ideas will come to your mind). The word “species” alone is enough to cause a lot of confusion (reproductive isolation? If it’s just that, then the pattern is small). John Wilkins, a philosopher of science, counted 26 concepts of “species” and further divided the concept of species into seven basic concepts [4]:

(1) Biospecies of sexual organisms based on reproductive isolation

(2) Agamospecies based on asexual reproduction (clonal populations)

(3) Ecological species based on ecological niche

(4) Evolutionary species based on evolutionary lineages

(5) Genetic species based on genetic isolation

(6) Morphological species based on phenotypic differences

(7) Taxonomic species, i.e. species identified by taxonomists.

Let's go back to the question of whether the chicken lays the egg. The chicken species evolved from the red junglefowl. The red junglefowl constantly mutated during the reproduction process and was selected, eventually forming the chicken we know today. But from which "generation" of the red junglefowl, or from which egg did the real chicken hatch? This answer is difficult to verify, and perhaps impossible to answer. The artificially defined, virtual longitude and latitude lines are precisely fixed, but the natural, real coastline is difficult to measure its true length. The concept is beautiful, but when you really use one concept after another to examine a real process of continuous change, it will feel very strenuous. Because the evolution of species is gradual and continuous, mutations need to change step by step.

The “change” of “species”: mutation and variant

When naming the new coronavirus, the main consideration is the evolutionary relationship between viruses.

On February 11, 2020, the International Committee on Taxonomy of Viruses (ICTV) announced that the new coronavirus would be officially named "severe acute respiratory syndrome coronavirus 2" (SARS-CoV-2) [5]. This indicates that the new coronavirus is a close relative of the SARS coronavirus (SARS-CoV) from a taxonomic perspective.

ICTV emphasized that the SARS in the name of the new coronavirus (SARS-CoV-2) is to highlight their evolutionary relationship with the original virus, rather than their relationship at the clinical disease level. This name is given by taxonomists, but it contains rich information such as phenotype (can cause pneumonia), morphology and taxonomic status (coronavirus family with crown-shaped virus particles) and close relationship (close to SARS virus). This name clearly defines the virus species that caused this epidemic.

mutation

Without mutations, there would be no colorful life, let alone humans. This "error" in the replication of genetic material that is latent in every cell proliferation, individual reproduction, and virus replication process creates differentiated "players" for natural selection and is the raw material for evolution.

Genetic information is stored in the primary structure of nucleic acids, just like this article, which is also composed of characters, except that the "characters" of nucleic acids are bases. The transmission of genetic material is the replication of base sequences. This process is completed by replicase.

Tips: Polymerase Vs Replicase

The transmission of genetic information in life requires the synthesis of new daughter nucleic acids (products) from nucleotides (substrates) according to the parent sequence (template) in the form of complementary base pairing. This reaction is catalyzed by polymerase.

Different polymerases can transfer genetic information to new genomes to perform the replication function, which is called replicase; or transfer genetic information to non-genomic functional RNA molecules (mRNA, etc.) to perform the transcription function.

Depending on the types of templates and progeny nucleic acids, polymerases can be divided into DNA polymerases (using DNA as a template to synthesize DNA), RNA polymerases (using DNA as a template to synthesize RNA), RNA replicases (using RNA as a template to synthesize RNA), reverse transcriptases (using RNA as a template to synthesize DNA), etc.

Mutation in a broad sense refers to the change of genetic information (nucleic acid sequence). Viruses are obligate intracellular parasitic microorganisms without cell structures, and their core components are genomic nucleic acids. The viral genome is likened to a book, and the replicase responsible for genome amplification is equivalent to a copyist. From the perspective of the entire viral genome, the types of viral mutations are:

1. Point mutation refers to a single base change, or the insertion or deletion of a small fragment. Point mutation is similar to the copyist being distracted and copying the wrong characters during the copying process. It is caused by the incorrect replication of the viral genome replicase and is a form of variation that may occur in all viral genome replications (all viruses have a genome replication process in their life cycle, and their replicases are prone to errors to varying degrees). Its frequency of occurrence mainly depends on the fidelity of the "copyist" viral genome replicase. For RNA viruses, their RNA replicase does not have proofreading activity - that is, it cannot proofread whether the replication is correct and correct it in time - so the mutation rate of RNA viruses is the highest. In contrast, the replicase of DNA viruses (such as smallpox) has proofreading activity, so the mutation rate is lower.

2. Recombination, that is, the exchange of large fragments of genomic molecules between different strains of the same virus. Recombination is equivalent to a copyist changing a book halfway through copying, with the upper half of the new book being "Journey to the West" and the lower half being "A Dream of Red Mansions". When the same cell is infected with two (or more) closely related viruses, recombination exchange or transfer of genomic replication templates may occur between genomic molecules, leading to recombination mutations.

3. Reassortment, which is the reassembly of the genome molecules of segmented genome viruses. Reassortment is similar to packing Harry Potter books 1 to 4 together with The Chronicles of Narnia books 5 to 7. Reassortment is a special form of recombination that exists in segmented genome viruses such as influenza viruses. When two (or more) closely related viruses are infected in the same cell, the segmented genomes are redistributed during the virus packaging process to produce new viral offspring.

Figure 1. RNA, DNA structure and their base types. Under normal circumstances, the bases in nucleic acids are paired according to A=T, C≡G. In RNA, U is A=U and C≡G. The dotted lines in the figure represent hydrogen bonds. Source | wikipedia

In fact, using the metaphor of "copyist" to describe replicase is not accurate enough. It is more like a small hand arranging building blocks. According to the base arrangement sequence of the template chain (or parent chain), it selects appropriate bases based on the principle of base complementary pairing to arrange the new chain (daughter chain). Template chain 1 and new chain 2 are in a complementary pairing relationship. When the new chain 3 produces its own daughter chain 3 according to this process, the sequence of 3 is exactly the same as the original template chain 1. ؏؏ᖗ乛◡乛ᖘ؏؏Perfection.

No!

Whether it is DNA replicase or RNA replicase, the nucleotides incorporated during the replication process are not always accurate. In other words, the little hands on the row of building blocks always put some wrong building blocks on it... If these wrong bases are incorporated and left in the new chain, it is a base mutation.

Too many mutations will make the genome information unstable and affect the function of the genome. Therefore, DNA polymerases often have proofreading activity, which is a 3' to 5' exonuclease activity that can cut off the wrong base and then continue to connect the correct base. The fidelity of DNA polymerase can reach an error only once for every 107 to 109 bases copied, which is equivalent to copying a 1 million-word novel 100 times before an error occurs (Dream of Red Mansions is about 790,000 words).

In contrast, RNA polymerase has no proofreading activity, and an error may occur once every thousand to one hundred thousand bases in replication. This error-proneness is a characteristic of RNA virus replicase (God intended it). In addition, the RNA virus genome content in the patient's body is very large, and the RNA virus replication cycle is short and the replication level is high, and a large number of RNA virus genomes containing different mutations are produced every day. All of this creates the extremely high genetic diversity and variability of RNA viruses. Not to mention environmental mutagenic factors (radiation, chemicals that can modify bases, special bases or base analogs, etc.), host RNA editing enzymes (adenosine deaminase, etc.) and other factors will further increase the mutation rate of RNA viruses.

Figure 2. DNA polymerase catalyzes the extension of a new DNA chain and has proofreading activity. [6]

Figure 3. The replicase of the new coronavirus. Adapted from illustration by Cognition Studio, Inc. [7]

It should be pointed out that for point mutations, since they are caused by erroneous replication of the viral genome replicase, this error occurs randomly, so the virus mutation can occur at any site.

So, when we detect the virus sequence, can we see mutations randomly distributed throughout the genome? It depends on where the mutation is located and what consequences it causes.

Generally, the non-coding sequence region of the virus (where proteins are not expressed) will have many important sequence-based elements, while the coding sequence region mainly plays a role in protein function after encoding proteins (three nucleotide codons in a specific order determine one amino acid). Based on the effect of the mutation on the coding sequence, point mutations can be divided into frameshift mutations and substitution mutations.

In a frameshift mutation, the reading frame shifts after the coding sequence is inserted or deleted (not in multiples of three), the original protein coding sequence is destroyed, and the protein cannot be expressed normally. This situation is similar to a five-character quatrain ancient poem. After inserting or deleting a few words, you will not understand what it means if you read it according to the five-character sentence.

Substitution mutations are point mutations that do not affect the reading frame, and the consequences of the mutation depend on what changes occur in the codons.

Synonymous mutation: Some amino acids have multiple codons, and the changes between the codons encoding the same amino acid do not affect the type of amino acid.

Missense mutation: A change in a codon results in a change in the type of amino acid it encodes.

Nonsense mutation: An amino acid codon becomes a stop codon, which can lead to premature termination of protein synthesis.

Figure 4. Base pairing and point mutation

The consequences of the mutation may be reflected in the phenotype in the following ways.

Loss of function mutations, also called inactivating mutations, result in a gene product with less or no function (partial or complete inactivation).

Gain of function mutations, also known as activating mutations, change gene products, making them more potent (enhanced activation) or even acquiring abnormal functions. Experiments that increase the toxicity of pathogens or infect new hosts are generally not allowed. The probability of such mutations occurring in nature is extremely low, but the impact is the most far-reaching.

Dominant negative mutations produce a gene product that is antagonistic to the wild-type gene. These mutations usually result in an altered (usually inactive) molecule and are characterized by a dominant or semi-dominant phenotype.

A lethal mutation is a mutation that causes the death of the organism carrying the mutation.

Back mutations are point mutations that restore the original sequence and therefore the original phenotype.

Mutations in a virus may affect the coding of proteins and the sequence of RNA or DNA elements necessary for viral replication, so a large number of mutations are often harmful - harmful to the virus itself. These viruses containing harmful mutations cannot replicate themselves and are eliminated.

In addition to harmful mutations, a considerable number of mutations are "synonymous mutations", that is, they have no effect on the virus before and after the mutation. In the end, only a few mutations have a positive effect on the virus's adaptability and are enriched and fixed.

In short, the virus is constantly mutating randomly, but many mutations will cause the virus to "die faster" and only a small number of mutations will survive.

Since the viral genome is generally short and has low information redundancy, and is limited by the virus's own survival and replication needs, the host's innate immunity and adaptive immune pressure (adaptive) screening, most of the mutation sites in the viral genome are concentrated in certain areas of the viral genome - usually the antigenic determining regions of its structural proteins. Therefore, the distribution of viral mutations that we can detect on the genome is uneven. For example, a large number of mutations of the new coronavirus are concentrated in its spike membrane protein encoding gene.

Figure 5. Schematic diagram of the genetic mutation sites of the alpha strain of the new coronavirus. The mutations are marked at the bottom of the figure, mainly concentrated in the second half. Source | The New York Times

The highlight of virus mutation research is the change in the antigenicity of pathogenic viruses. There are two proprietary concepts of "virus antigenic variation", namely antigenic drift and antigenic shift. The former refers to relatively subtle changes, while the latter refers to huge changes in antigenicity. Of course, some mutations left over from positive selection also exist in non-coding regions or non-structural protein coding regions.

variant

The new coronavirus is still changing, and new variants have emerged. Variant viruses are viruses that carry genetic mutations. If there are enough mutations, the virus can be divided into different genotypes, subtypes, mutant strains, etc. based on sequence differences. The standard for division is the size of the sequence difference, and the classification standards for different viruses are different.

In fact, a virus infecting the same patient also undergoes various mutations during the process of continuous replication, so there are also differences in the sequences of different viral genome molecules in the body. In other words, different viral gene sequences will be detected in a patient (see "Where do the new coronavirus variants come from? Chronic infected people may be human incubators" for details).

The existence of this virus in a large number of variant groups is called a quasispecies. The above-mentioned classification of existing virus genotypes describes the genetic diversity of the virus; and the various variants that are being produced in the quasispecies describe the high variability of the virus. Genetic diversity is the result of viral evolution under the combined action of mutation and natural selection.

The new coronavirus variants we have discovered so far have not yet separated into "types", let alone new virus species. It's just that these mutants pose a greater threat to public health - they are more contagious, cause more severe symptoms, or are more resistant to vaccines - and they need to be taken seriously.

Among them, four known variants are of greatest concern and have been included in the WHO’s list of variants that require attention[8].

The Alpha variant (B.1.1.7), first discovered in Kent, England, has spread to more than 50 countries and regions and may still be mutating.

The Beta variant (B.1.351), first detected in South Africa, has spread to at least 20 other countries

The Gamma variant (P.1), first discovered in Brazil, has spread to more than 10 other countries/regions

The Delta variant (B.1.617.2), first discovered in India, has spread to 92 countries.

For more specific variant characteristics, please review "The Delta variant of the new coronavirus fights back strongly, and epidemic prevention needs to draw on real-world data of vaccines丨117 Three People".

The most aggressive Delta strain was first discovered in India in October 2020. This new variant carries E484Q and L452R mutations, which may lead to immune escape and increased infectivity. The World Health Organization named it B.1.617, and on May 31, 2021, it was named with the Greek letter δ (Delta). In fact, B.1.617 contains a total of 15 mutations, 6 of which occur on the spike protein, and 3 of them are more critical: L452R and E484Q mutations occur in the region where the spike protein binds to the angiotensin-converting enzyme 2 (ACE2) receptor of human cells. L452R increases the virus's ability to invade cells, and E484Q helps enhance the virus's immune escape; the third mutation, P681R, also enables the virus to enter cells more effectively. The combined effect of these mutations allows the virus to partially avoid some neutralizing antibodies and increase its infectivity several times [9].

The vaccines currently available are still effective, at least they can prevent severe illness and reduce deaths.

Now we know that when developing drugs or vaccines for the new coronavirus, virus mutation is an issue that must be considered, because virus mutation can cause changes in its drug sensitivity and antigenicity, thereby affecting the therapeutic effects of drugs and the protective effects of vaccines.

Some people ask, isn't it true that the more contagious a virus is, the less virulent it is? Why is Delta as easily spread as chickenpox, but its virulence remains the same? (For details, see "The Delta strain that hit Nanjing is as easily spread as chickenpox, and one person can infect eight or nine people")

The direction of viral survival evolution should be to "pursue" higher adaptability by "optimizing" virulence, that is, maximizing the virus transmission coefficient R0, and the so-called "optimization" of virulence may be enhanced virulence or weakened virulence. For a certain virus, whether natural selection increases or decreases the virulence of the pathogen depends on the specific combination of the host, virus and environment. Therefore, the evolution of the virus does not necessarily lead to an increase in the virulence of the virus; the increased infectivity of the new coronavirus variant does not necessarily lead to an increase or decrease in virulence.

Can the virus be eradicated by “destroying” the species?

Infectious diseases are caused by pathogens, so they can be eradicated by eradicating pathogens. In fact, humans have successfully eradicated a terrible infectious disease: smallpox. On May 8, 1980, the 33rd World Health Assembly officially announced: "The people of the world have won the victory and eradicated smallpox." The human feat of eradicating smallpox was not achieved by chance. Its realization was the result of a series of factors:

1. The pathogen only infects humans, with no other hosts or virus reservoirs. This means that only humans need to be managed, not wild animals that are difficult to control.

2. The incubation period after infection is short, the disease develops quickly, and the symptoms are obvious. This means that it is very easy to make differential diagnosis when monitoring the source of infection, and there will be no asymptomatic infected people who are difficult to prevent and "silently spread the virus".

3. After self-healing from infection or vaccination, strong and lasting immune protection can be obtained, which means that the disease can be effectively prevented and controlled through vaccines.

4. The pathogen has poor variability. This means that the pathogen "smallpox virus" will not quickly develop mutations such as antigenicity and drug resistance, which would cause problems for the prevention and control effects of existing vaccines or drugs.

5. Education, social psychology, government decision-making, international cooperation, and other political, economic, and social conditions. The public understands, society attaches importance to, the decision-making is correct, and the world acts in unison.

In summary, smallpox is a well-known, ferocious virus that has only one killer weapon and does not change. In this case, it is feasible to eliminate the virus.

In fact, in the fight against other infectious diseases, mankind has also achieved great victories, but for some reasons, the goal of eliminating these diseases has not been achieved as planned. For example, polio is still endemic in Afghanistan, Pakistan and Nigeria. The World Health Organization believes that as long as there is a child infected with the polio virus, children in all countries are still at risk of contracting the disease.

The reason why the polio virus has not been eliminated is that it does not meet the second and fourth items mentioned above - polio virus infection may only cause mild diarrhea and be ignored; the attenuated live vaccine itself has the ability to mutate and become stronger.

Humanity has also achieved significant victories in the prevention and control of measles. Based on the characteristics of the measles virus, it is also a virus that is expected to be eliminated by humans. However, it does not meet Article 5: people do not take measles very seriously. After all, in most cases, measles does not cause serious symptoms.

HIV and malaria are extremely difficult to eliminate because of the difficulty in developing vaccines and the variability of the pathogens that leads to drug resistance during treatment. As for avian influenza, it is extremely difficult to eliminate it because of its presence in wild animals.

SARS seems to have disappeared. This makes people wonder whether the new coronavirus can be eliminated. Let's take a look at the five conditions mentioned above:

1. Does the pathogen only infect humans?

It seems not. The new coronavirus can infect many animals besides humans, but fortunately, domesticated animals that have close contact with humans will not cause serious infection.

2. The incubation period after infection is short, the onset is rapid, and the symptoms are obvious?

Not really - after being infected with the new coronavirus, people may be asymptomatic or have mild symptoms. This group of people is difficult to detect and manage, making disease prevention and control difficult.

3. Can strong and lasting immune protection be obtained by self-recovery after infection or by vaccination?

At present, the effectiveness of the vaccine (mainly the protection rate against severe illness or death) has been tested and recognized, but the efficiency of protection (against reinfection) after new coronavirus infection or vaccination and the duration of sustained protection remain to be tested.

4. The pathogen has poor variability?

Obviously, the novel coronavirus is highly variable. It keeps changing and it is hard to guard against.

5. Can education, social psychology, government decision-making, international cooperation, and other political, economic, and social conditions work together?

This point shows a very sharp contrast in the fight against the epidemic in different countries. Everyone has been paying attention to it for a long time and should have a deep understanding of it.

The new coronavirus is not a rude and stupid person, but a cunning and fickle person. So should we "eliminate" it or "coexist" with it? This depends on whether we want to do it subjectively and whether we can do it objectively.

Subjectively, it should be "eradicated". If there is such a shiny slogan: "Viruses are also life and have the right to survive", this disease is probably incurable. Is it possible objectively? For this virus, there is no precedent and it is difficult, but it is not hopeless. And the more people believe in this "hope", the greater the hope (eliminating any disease requires global cooperation).

Since there is hope, should we do it? This depends on the trade-off. For example, in lottery, there is a probability of winning, and the cost does not seem to be high. After weighing the pros and cons, some people buy it, and some do not. This is normal. But if you win the lottery, whether you buy it or not, you will envy it. Except for China, a considerable number of people in the world have been forced to "coexist with the virus".

What can we do? In the short term, we do not seek to eliminate the new coronavirus from the entire human race, but at least one province or even a country can achieve "zero" within a considerable period of time. Even if the route of eliminating the virus is unsuccessful and eventually develops into "de facto coexistence" (vaccines or drugs are available, the spread of the virus and the mortality rate have decreased, but it has not disappeared), it is not too late to adjust the strategy.

Although "I" am a human being, humans do not have to be "I". Humans can coexist with viruses, and are coexisting with many viruses, but I do not want to be a human being tested by the new coronavirus. I should wear a mask, get vaccinated, and cooperate with epidemic prevention work. After all, with the attitude of "eliminating the virus", I have saved my life, and only then can we talk about coexistence or not.

References

[1] Sorensen, Roy (2003). A Brief History of the Paradox: Philosophy and the Labyrinths of the Mind. Oxford: Oxford University Press. pp. 4–11.

[2] Benton, Michael J.; Donoghue, Philip CJ (2007-01-01). "Paleontological Evidence to Date the Tree of Life". Molecular Biology and Evolution. 24 (1): 26–53.

[3] Benton, Michael J.; Donoghue, Philip CJ (2007-01-01). "Paleontological Evidence to Date the Tree of Life". Molecular Biology and Evolution. 24 (1): 26–53. doi:10.1093/molbev/msl150. ISSN 0737-4038. PMID 17047029.

[4] wikiwand.com/en/Species

[5] https://talk.ictvonline.org

[6] https://www.virology.ws/2009/05/10/the-error-prone-ways-of-rna-synthesis/

[7] https://meetings.ami.org/2020/project/sars-cov-2-rna-dependent-rna-polymerase-rdrp-and-remdesivir-mechanism-of-action/

[8] https://www.bbc.com/zhongwen/simp/science-57529842

[9] http://www.xinhuanet.com/2021-06/22/c_1127588313.htm