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The middle of a viral pandemic is one time when evolutionary theory seems unusually salient. Mostly we think of evolution as happening over unimaginable stretches of deep time, but not so for viruses. The reason that new flu vaccines are offered to the vulnerable every year is that the various populations of these viruses evolve in subtle ways over weeks and months in ways that enable them to elude our immune systems. Although it still seems that Sars-2-CoV does not evolve as rapidly as many viruses, including flu, recent mutations have made it clear that it is highly likely that it will eventually evolve strains increasingly resistant to first generation vaccines and the immune responses of early victims.  

 The evolution just mentioned is classically gradualist, in the manner beloved of the mid-twentieth century biologists who constructed the classic theory of evolution, the Modern Synthesis. A mutated nucleotide here and another there, and a subtle change in protein structure leaves a molecule unrecognised by our immune systems. But Covid-19 is famous for the opposite: the saltatory (Latin: salto, saltare, to jump or leap) evolution generally rejected by the Modern Synthesis. The virus, on current theory, quite literally jumped from a bat to some other animal (possibly a pangolin or a palm civet) to a human. The virus that jumped from the bat was perhaps the purest case of what Richard Goldschmidt, the great defender of saltatory evolution, called a hopeful monster. Equipped with an otherwise useless change to its RNA (the genetic material used by this class of viruses) it landed on the hapless pangolin and found, to its amazement, that its chance mutation or mutations had left it perfectly equipped to slide inside the unfamiliar cell. And another such hopeful monster, at some later time, jumped from pangolin to human. (Or so it was speculated.)

 The story just told features an individual, the monstrous virus, and its lucky leap.  But almost as in quantum mechanics, one can think of viruses either as a stream of individuals, or as the flow of a process. And in this case the latter, I suggest, is more fundamental. The flow of a virus lineage through the bottleneck from one species to the next requires an individual, the lucky virus particle that landed on the unfortunate pangolin. But one cannot think of the flow of viruses as merely the flow of particles. [1]

 The viral particle, the virion, is a single-stranded RNA genome (some viruses have double-stranded or DNA genomes), surrounded by a protein casing. In the case of Covid-19, this coat includes the spikes that we have all seen in representations of the virus.  The virion is largely inert. It can survive in this state for days or weeks, doing nothing. But for the active phase of the viral flow, the particle, the virion, ceases to exist. Having penetrated the cell, the virion dissolves into the cell and its RNA genome begins to hijack the molecular activity of the cell for its own reproduction. At the end of a complex chain of chemical interactions, the cell starts to make new virions, and eventually the cell is destroyed, releasing the virions into the host environment.

 The viral flow, then, consists of both chemical activity in host cells and the movement of virions from cell to cell and from host to host. A unique event such as the transfer of a suitably equipped virion from pangolin to human can open up a whole new environment that the process can begin to invade.

 Within this flow, of course, evolution happens. Because of the vast number of reproductive events and the short time frame within which they happen, this can happen very rapidly. Although the Dawkinsian picture of evolution as a battle among selfish bits of nucleic acid has been largely rejected, [2] it is substantially appropriate in application to viruses. This is simply because they are little more than sequences of DNA or RNA, attached to a few of the proteins for which the nucleic acids code.

 Happily, however, selfish does not necessarily mean nasty. Covid-19, having just entered this vast empty space of human life, is evolving mainly to spread effectively. Since Covid-19 spreads by coughing virions at passing hosts, the last thing it needs to do to this end is kill its host: dead hosts do not cough. On the other hand, it has only a limited time before the immune system of its current host is geared up to eliminate it from the body. If the time it takes to kill the host is similar to this time, from the virus’s point of view there is no great harm done.

 If it can spread itself, which means roughly that R0 (R-naught), the average number of new hosts infected by every infected host, is > 1, a major selective pressure will be towards increasing R0, and spreading faster. This will, for example, select strongly against variants that kill the host too quickly.

 But a virus successful at spreading soon enough runs into another problem. As it runs through a population it will leave a higher and higher proportion of the population with immune systems trained to recognise and destroy it. The more of these there are, the lower R0 becomes, until it falls below 1, and the virus begins to decline. At this point various strategies become possible.

 Some viruses respond by mutating fast enough repeatedly to surprise the immune system. Hence the colds and flus that recur seasonally in subtly ever-changing variants. Another way to go is to become so contagious as to reliably hunt down all new hosts as they join the host population, as with the pathogens for measles, mumps or chicken pox. Unfortunately for them, specialising in contagiousness rather than mutability has left them susceptible to mass vaccination programmes, and only the gullibility of the human population and the venality of those who make their livings by perpetuating invented harms has saved the measles virus, in particular, from extinction. A final strategy, followed by retroviruses such as the various herpes viruses and HIV, is to hide in the host genome, attempting bursts of reproductive activity when circumstances seem propitious.

 This last strategy points to one final but very important fact about viruses. Contrary to their uniformly bad press, most of them are harmless and many may even be beneficial. Contrary to the still common picture of nature red in tooth and claw, a great deal of the biological world is cooperative. As is equally little understood by right wing politicians, generally the best way to survive and even thrive is to cooperate, and this is true even for viruses.

 Most biological systems appear to contain about ten times as many viral particles as cells, which implies that a typical human body contains about 400 trillion virions. If these were all out to get us we would be in serious trouble. In fact, the large majority of these viruses are phages, viruses for which the hosts are bacteria. The populations of phages are likely to be essential in stabilising the bacterial populations that are increasingly recognised to be an essential part of the human system. Phages are also found to be highly concentrated on mucous membranes, where they are presumably beneficial in attacking potentially pathogenic bacteria invading the body. And various other health benefits have been attributed to human viral populations. [3]

 The phenomenon of phages in human bodies points to an important fact about biological pathogens and mutualists (beneficial symbionts): these designations are relative to a particular scale. To a gut bacterium a phage is a pathogen; to the human system as a whole it is a mutualist. To those who believe in Gaia, as an actively self-maintaining biological system, the disturbing thought suggest itself that what seems to us humans a dangerous pathogen, such as Covid-19, might to Gaia be a mutualist, trying to control an out of control and dangerous population.

 The longer-term fate of Covid-19 remains to be seen. There have been suggestions that it is likely to join the ranks of seasonal respiratory infections; if so, one hopes at least that it will gradually evolve in the direction of lower virulence. But there are also reports that Covid-19 is rather stable, in which case it may, like measles or smallpox, be successfully defeated by a global vaccination programme.  At present the first scenario seems more likely.

 Since this was written as part of a collection of reflections on evidence, I should end with some thoughts on why the reader should believe anything I have just written. Of course, I’m sure that not everything I have said is true, but I’m strongly convinced that a good deal of it is. The reason, I suggest, is what I shall call consilience.

 By consilience I do not mean, as the word has often been used, that we are heading towards one, unified science. Quite the contrary. What I mean is that a story such as that I have just sketched is able to draw on a remarkable diversity of models, techniques and findings, and where these intersect they speak, by and large, with one voice.  I have appealed to evolutionary theory, epidemiology, molecular biology, pharmacology, and so on. The sequencing of viral genomes and the relation of these sequences to protein structures that may themselves be analysed with a wide variety of techniques, are practices that have been applied on organisms from jellyfish to elephants and from bacteria to sequoias. Biology speaks with a huge variety of voices, but in the end those that do not fit into a bigger developing picture will be kicked out of the choir. Whether I have correctly heard what the choir is singing is no doubt open to debate. But it is worth a careful listen.

John Dupré 

[1] John Dupré and Stephan Guttinger (2016). “Viruses as Living Processes”. Studies in History and Philosophy of Biological and Biomedical Sciences, 59: 109-116.

[2] See, e.g., Special issue of Interface Focus, on New Trends in Evolutionary Biology: biological, philosophical and social science perspectives. Edited by Denis Noble, Patrick Bateson, Nancy Cartwright, John Dupré and Kevin Laland. August, 2017.

[3] https://theconversation.com/viruses-arent-all-nasty-some-can-actually-protect-our-health-117678