At the end of 2019, a hitherto unknown virus, the so-called SARS-CoV-2, began to spread in our species at a dizzying pace . Simultaneously with the spread of the virus, fears also grew that it could mutate into a more contagious or deadly form. The successive appearance of new variants, more transmissible or partially resistant to the action of antibodies, shows us how natural selection exerts its action in real time. Today, the conclusion is that to end this pandemic we need to understand how the virus evolves and, in a certain way, anticipate it.
Continuing in the health field, another current problem is the rapid expansion of bacteria resistant to antibiotics , those molecules capable of inhibiting bacterial growth and that have been crucial in combating infectious diseases. Once again we are facing an example of how, in the presence of antibiotics, natural selection favors bacteria that have managed to acquire some resistance mechanism against them. According to recent estimates, approximately 700,000 people die each year from infections with this type of bacteria, a clear indication of the severity of the problem.
It has been more than a century and a half since Charles Darwin published his book The Origin of Species in which he established that evolution is a slow process, which occurs thanks to the accumulation of small changes that occur by chance and on which selection acts. natural, favoring individuals with the most advantageous modifications. How do we reconcile this slow and gradual evolution with the rapid changes that occur in viruses and bacteria?
The important microorganisms
Darwin focused his attention on comparing the physical characteristics of organisms observable with the naked eye. Although microorganisms were already known in his time, the difficulties in observing them made it difficult to identify differences between them, so that their enormous diversity and their importance in the global biosphere remained hidden for several decades.
In Darwin’s time, the mechanisms that allowed generating variability in living beings were not known either. The discovery in the first half of the 20th century that DNA was the hereditary material made it possible to link changes in the characteristics of organisms (the so-called phenotype) to changes or mutations that occurred in the DNA (the genome or genotype). This opened the door to the study of evolution through the comparison of the genomes of the different forms in which life manifests itself.
In the world of microorganisms —which includes viruses, bacteria, and archaea— comparative genomics has been a real revolution, since it has made it possible to verify that the mechanisms that generate variability can go far beyond the small changes I was talking about. Darwin. In addition to the mutations that occur in the DNA, as a consequence of the errors that occur during its copying or the damage caused by various agents, in the world of microorganisms there is great genetic promiscuity, which is manifested in the exchange of genetic material between members of the same or different species. In this way , evolutionary innovations are quickly transmitted and the species concept may even cease to make sense.
Another relevant fact is that, in general, the replication of the genomes of microorganisms takes place with higher error rates than those of multicellular organisms. This circumstance, together with their rapid reproduction and the high number of individuals that usually make up their populations, means that the repertoire of mutants on which natural selection can act is much broader than in other systems. The consequence is that evolution accelerates enormously, being able to be observed in real time.
Observing evolution live with RNA viruses
In the viral world there is something unique and that is that, in some cases, genetic information can be stored in RNA. This molecule is formed by the union of simpler units called nucleotides (which can be of four types: A, U, C and G), to form a chain that can contain thousands of them. The order in which the nucleotides are arranged is what determines the information, in the same way that the order in which the syllables and words follow each other in a text is what gives it meaning. DNA is a similar molecule but formed by the union of two chains in which the U is replaced by a T.
The peculiarity of RNA viruses is that the copying of their genome, something that happens whenever any virus multiplies, takes place with much higher error rates than those of DNA viruses. This is partly because the activities needed to copy RNA lack error-correcting ability (something that those that copy DNA do), meaning that for every 10,000 nucleotides copied, which is the typical length of an RNA genome, approximately one error occurs.
Other important mechanisms for the generation of variability in viruses are recombination and the rearrangement of genomic segments . Recombination occurs when genomic fragments from different viruses come together in the same genome. It is a very frequent mechanism in retroviruses and coronaviruses and can produce much more drastic changes than the specific errors that we have mentioned before. Finally, the reorganization of genomic segments takes place in viruses such as influenza, in which the genetic material is segmented. When the same cell is infected by two different viruses, the progeny viruses may contain a mixture of genomic segments from the two parental viruses. These new viruses can totally or partially escape recognition by the immune system , being capable of triggering pandemics.
Advantageous conditions
Given the speed with which viruses multiply and the large size of their populations, which can be made up of more than 10-12 individuals, it is easy to intuit the large number of mutants (also called variants) that are accessible at any time. natural selection. Most of these mutants will be similar to the original virus or may even be worse. But with such high numbers, it is inevitable that from time to time an advantageous one will emerge that will quickly be favored by natural selection. And what can be advantageous for a virus? The most obvious responses include expanding its host range , enhancing its transmission in the population, evading the immune response, or resisting antiviral treatments , but there are many other characteristics that a virus can improve in order to remain stable in a population.
The speed of viral evolution has meant that, throughout history, events have occurred that might seem impossible, such as waterfowl, chimpanzee or bat viruses that have managed to transform into typically human viruses that cause diseases such as influenza, AIDS, COVID -19 or common colds.
A hallmark of evolution at error rates as high as those possessed by RNA viruses is that the best-fitting genome never completely dominates the population . There will always be a more or less broad spectrum of mutants surrounding that most optimal genome. Despite this great diversity, it is easy to obtain a consensus sequence, corresponding to the most represented nucleotide in each genomic position in the set of viruses that make up the population. The same consensus sequence can be obtained for different virus populations, which shows its limited value. It can be very useful to determine which mutations are becoming the majority, but it does not show us many of the changes that occur in the spectrum of mutants, which is where the true evolutionary potential of the population lies.
In most cases we do not know how many viral particles are needed to cause an infection. When this number is very low, the genetic diversity of the population is greatly reduced, although the replication of the virus in the new infected organism can regenerate it again. Viral evolution during an epidemic process involves the alternation of millions and millions of population bottlenecks —as many as new infections— followed by the subsequent exponential amplification of the virus. It is difficult to integrate all this at the population level, so it can be difficult to predict the direction an epidemic will take. Sometimes mutations that do not provide any advantage will also be fixed, simply reflecting the success as a propagator of the person who was infected with a particular variant.
Bacteria and their conquest of almost all ecological niches
Like viruses, bacteria also mutate faster than the cells of multicellular organisms, giving rise to very diverse populations in which there may be variants that facilitate their adaptation to new environments. In this way, bacteria have managed to conquer practically all possible ecological niches and explore a wide variety of metabolisms. There are bacteria capable of living at more than 100 ºC , in the deep sea or in extremely dry conditions. There are also bacteria that feed on the remains of living beings, that carry out photosynthesis or that obtain their energy by oxidizing inorganic compounds. The human being is very proud of his intelligence and ability to modify the environment making it more favorable for his survival. Bacteria play with different weapons, but it cannot be said that they are less successful.
In the bacterial world, evolution has a very powerful ally: mechanisms for exchanging genetic material, something that allows evolutionary innovations to be quickly shared by the entire community. The process is called horizontal gene transfer , as opposed to vertical gene transfer, which occurs from parent to offspring. The most common horizontal transfer mechanisms in bacteria are conjugation, transformation, and transduction. Conjugation requires contact between two bacteria and is carried out using a special structure, through which genetic material is transferred. Transformation consists of the uptake of exogenous DNA, which is in the environment and normally comes from dead cells. Finally, the transduction is carried out by certain viruses that infect bacteria, the so-called bacteriophages , which have the ability to include part of the genetic material of the bacteria they infect within their capsid. This material may be transferred to another bacterium and, by various mechanisms, end up forming part of its genome.
An important consequence of lateral gene transfer is the existence of important variations in the gene content of individuals of the same species. The process could have been fundamental in the very origin of life, if we consider that our last universal ancestor could have consisted of a consortium of primitive cells that exchanged genes in a very promiscuous way, so that they could all take advantage of the innovations that were emerging in each one of them.
The rapid evolution of microorganisms as selective pressure in the cellular world
What consequences does it have for the cellular world to have to deal with pathogens that change so quickly? For simplicity, we are going to detail what happens in the viral world below, although, with the necessary precisions, what has been described will also be valid for other rapidly evolving pathogens.
Bacteriophages constitute a very important selective pressure in bacterial populations, so that those that have some defense will quickly be favored. Among the most frequent defense mechanisms are the appearance of modified receptors, with which the virus cannot interact, or the appearance of systems that degrade the viral genetic material. In turn, the increase in the frequency of these resistant bacteria exerts a selective pressure on the population of bacteriophages, favoring those capable of eluding bacterial defense mechanisms. The repetition of this process over time supposes the appearance of concerted changes between the pathogen and its host, accelerating the evolution of both.
In the case of viruses that infect vertebrates, there is a similar scheme that has led, among other things, to the appearance of the adaptive immune system: the producer of antibodies . The mechanisms of variability of this system allow that, with a limited repertoire of genes, a very wide diversity of antibodies can be produced. It is not disproportionate to think that the adaptive immune system has arisen in response to the attack by agents as changeable as viruses. In turn, viruses can respond to this selective pressure by generating and selecting for escape mutants, which cannot be neutralized by antibodies.
Over time, a situation of peaceful coexistence between the virus and its host may occur, generating the so-called viral reservoirs , which are animal species that allow the multiplication of specific viruses without suffering symptoms of disease.
An important point is that, to complete their infectious cycle, viruses need to interact with a wide variety of cellular proteins. Any modification to these proteins that makes it difficult for the virus to use them may be an additional cellular defense mechanism. There are estimates that one-third of all adaptive mutations in humans have been selected for in response to viruses, making them a more important selective pressure than climate or diet.
Viruses, great creators of genes
High rates of genetic variation make viruses the best gene inventors in the entire biosphere. Viral genes can pass into the cellular world, thanks to the ability of some viruses to integrate their genetic material into the host genome, something that is very common in bacteria. When this happens, the viral genome duplicates at the same time as the cellular one, transmitting itself vertically from generation to generation. But the viral genome thus integrated does not behave as something static, but can affect bacterial gene expression through its regulatory elements. In this way, much more drastic evolutionary innovations can be produced than those that would be generated by the simple accumulation of mutations with a small effect.
When the integration of the viral genome occurs in the genome of the reproductive cells of vertebrates, the process is called viral endogenization and it is due to the fact that approximately 8% of the human genome is of viral origin, a greater part than that of DNA coding. Following integration, there is initially an amplification phase, which involves the generation of many copies of the viral genome and their distribution throughout the recipient genome. In the process, the copies undergo modifications that prevent new viruses from being expressed, but, as in bacteria, the presence of viral genetic material will also have consequences. For example, in our species, starch can begin to be digested in the mouth thanks to the fact that a regulatory element of an endogenous virus favors the expression of the amylase gene in the salivary glands.
A great evolutionary capacity
Some evolutionary leaps in the world of microorganisms have involved great transitions of complexity. The work of Lynn Margulis and other researchers has shown that the most complex cells, the so-called eukaryotes, arose as a result of endosymbiosis events between simpler organisms. Association with proteobacteria led to the appearance of mitochondria, while symbiosis with cyanobacteria led to the appearance of chloroplasts. The presence of mitochondria meant a considerable increase in the energy available for cellular functions, which could favor the great increase in complexity typical of the eukaryotic cell, thus opening the possibility of evolution towards multicellularity .
The conclusion is that a large part of the evolutionary innovations present in current life originated in microorganisms or arose as defense mechanisms against them, to the point of being able to affirm that the biosphere that currently exists is as it is thanks to the great capacity evolutionary of all those beings, invisible to our eyes, but that vastly surpass us in the ability to adapt to a changing world.
Esther Lázaro is a scientific researcher at the Center for Astrobiology (CSIC-INTA) and head of the “Studies of experimental evolution with viruses and microorganisms” group.
