Virusphere. Frank Ryan

up in a protein’. While the hubris contains a grain of truth, there is rather more to viruses than being merely a source of mischief. So let us delve a little deeper! Do viruses rely on genes, and genomes, like all of the more familiar forms of life, from whales to humans and buttercups to the so-called ‘humble’ bacterium? The answer to that question is, ‘Yes!’ Viruses do indeed have genomes, which contain protein-coding genes. We shall discover more about those viral genomes in subsequent chapters when we shall also observe some important differences between the genomes of viruses and all other organisms.

      Do viruses follow the same patterns of evolution as, say, plants and animals? The answer again is, ‘Yes!’ But the patterns of evolution – the specific mechanisms involved – are heavily influenced by a facet of their organismal existence that is confined to viruses. Viruses can only replicate by making use of the host cell’s genetic apparatus, and because of this, viruses were formerly defined as ‘obligate genetic parasites’. But with our increasing understanding of viruses, and of their complex roles in relation to the evolution of their hosts, this definition is no longer sufficient to characterise them. A more adequate definition must take on board the fact that viruses are symbionts. Indeed, we now know that viruses are the ultimate symbionts, exhibiting many examples of all three patterns of symbiotic behaviour, namely parasitism, commensalism and mutualism. Moreover, since viruses will sometimes employ aggression as an evolutionary pattern of behaviour in relation to their hosts, they are also potentially ‘aggressive symbionts’.

      The more we examine viruses, in their evolutionary trajectories and in the influence of that trajectory on the evolution of their hosts, the stranger and more fascinating their story becomes. Is it reasonable to propose that viruses were born at the stage of chemical self-replicators before the actual advent of cellular life on Earth? If so, how then, from those primal beginnings, did viruses evolve, to interact with, and thus contribute to, the evolution of all of life on this planet?

      The aim of this book will be to enlighten readers through a step-wise progression, starting with a familiar territory: we shall confront the wide range of illnesses that are caused by viruses. For example, we shall examine what is really going on in the common cold, the childhood illnesses such as measles, chickenpox, herpes and mumps, rubella, as well as less familiar examples such as rabies, ‘breakbone fever’, haemorrhagic fevers such as Ebola, and virus-induced cancers such as Burkitt’s lymphoma. In such an examination we shall discover what makes viruses tick, exploring what’s actually going on inside us when we encounter the virus, how this gives rise to the symptoms we get from the infection, and, key to deeper understanding, probing what the virus itself gets from the ‘interaction’ with its human host. We shall employ the same virus-orientated perspective to explore important epidemic forms such as influenza, smallpox, AIDS and polio, which will illustrate how viral infections have impacted on human social history, from the wall paintings of the Ancient Egyptians to the colonisations of the Americas, Australasia and Africa. We shall also take a close look at vaccines as a measure to prevent epidemic infections, from the first introduction of vaccination against smallpox centuries ago to the recent controversy concerning the triple vaccine and the papilloma virus vaccine.

      The science of virology grew out of the study of viruses in the causation of disease. Through understanding the viruses already familiar to us, we shall widen our enlightenment by examining the role of viruses in the evolution of life, and in particular we shall explore the role of viruses in our human evolutionary history. We shall see how, throughout our prior evolution, we have shared our existence with these powerful invisible entities, and how they really have changed us at the most intimate level, to help make us human.

      I hope that, like me, you will come to appreciate the enormous importance of viruses to life, in its origins and complexity, while also marvelling at the existential nature of what is one of the great wonders of life on our beautiful blue-oceanic planet. Viruses, by and large, have had a bad press. This is understandable, given the experiences of earlier generations of virologists, whose only contact with viruses was in dealing with the infections caused by them. But today a major wind of change is blowing through the world of virology – so much so that recently a distinguished evolutionary virologist declared that we were witnessing what he called ‘The Great Virus Comeback’. What does he mean by this? Why have some of the modern pioneers of virology introduced the term ‘virosphere’ as the key to a new exploration of the importance of viruses to the entire biosphere? Could it be true that, as some would have us believe, viruses should now be seen as the ‘Fourth Domain of Life’?

       2

       Coughs and Sneezes Spread Diseases

      Historically, viruses were included with the so-called ‘microbes’ – tiny organisms that were originally discovered as the cause of infectious diseases in humans, animals and plants. Interestingly, there is a part of us that has long been intimately acquainted with microbes in general, and with viruses in particular. This is our inbuilt system of defences against infection: what doctors refer to as our immune system. It is perhaps as well that we possess this inbuilt immunological protection, because we inhabit a world that teems with microbes.

      A veritable zoo of such microbes covers our skin and other surface membranes. Biologists call this the ‘human microbiome’. Although it might cause some of us to squirm a little just to acknowledge its existence, this secret world is no real threat to us. It is an intrinsic part of our being, comprising a variety of bacteria, as well as other microbial forms, that inhabit our surface skin, mouth and throat, nostrils and nasal cavities, and in the case of women, the genital passages. Our bodies are said to contain roughly 30 to 40 trillion cells – if you are mathematically inclined, this is 3 to 4 times 10¹³ – which comprises the sum total of living cells that make up our living tissues and organs. Meanwhile our ‘microbiome’, which amounts to all of the microbes that inhabit our skin, gut, oral and nasal passages and throat, and genital tract in women, accounts for some ten times as many microbial cells, comprising such organisms as bacteria, Archaea and protists. It is natural enough, given our awareness of past epidemics and day-to-day troublesome infections, to assume that such microbes are invariably harmful; but these microbes that make up our personal microbiomes are not hostile. Some simply live off us in commensal fashion without causing us any harm; while many others help to maintain our normal health. For example, the zoo of microbes that inhabit our large bowels, or colons, play an important beneficial role in our human nutrition – such as in helping us to absorb vitamin B12 – as well as helping to protect us from invasion of our digestive tract by pathological visitors. The bodies of this ‘colonic flora’ account for no less than 30 per cent of the bulk of our faecal waste.

      There is also growing evidence that we benefit in a number of other ways from this microbial flora of our skin, and other abdominal cavities. This holistic realisation begs a relevant question: could viruses be a part of this human biome, capable of contributing to our human health? For any group of microbes to contribute to the nutrition or general well-being of a host, this would imply a lengthy period of symbiotic evolution with the same host. Immediately we even come to consider such a curious virus–host interaction, we are obliged to consider something profoundly different about viruses when compared to cellular symbionts, such as the bacterial flora of the human intestine or skin. Viruses inhabit the landscape of the host genome.

      This means that viruses are certainly not going to contribute, for example, to human vitamin digestion. What it really implies is that, if viruses are to contribute in some way to host health – or indeed host evolution – that contribution is likely to be much more subtle, involving, perhaps in the human host, an interaction with our immunological defences, or more profoundly still, an interaction with our human genetic machinery – or most profound of all, changing our very human genome, the repository of our human heredity, buried deep in the nucleus of every human cell. If this were to happen, viruses would have contributed to what makes us human.

      These are weighty questions. Perhaps many of my readers might be inclined to make the point that, so far as they are aware, only the less helpful kinds of viruses appear to have come their way.

      In