by Frank Ryan
Just as we saw with hummingbirds and flowers, viruses and humans are changing one another's evolution. This is the pattern one would expect in a symbiotic evolutionary situation.
It doesn't imply that the virus is not also evolving selfishly, any more than it implies the same for the human population. At one and the same time, natural selection is operating selfishly in virus and in human, but it has also begun to act at the level of the partnership. Virologists term this pattern of parasitic interaction a “co-evolution.” From a symbiological perspective, we are witnessing how symbioses often begin with parasitism, but the evolutionary situation can progress, in some cases, to one of mutualism.
The HIV-1 virus selectively hunts down an immune cell known as a CD+T helper lymphocyte. This cell has a key immunoglobulin type of chemical on its surface membrane, known as CD4, which allows the viral surface envelope to fuse with the cell membrane. The viral genome now enters the cell nucleus where the virus's own chemical enzyme, known as “reverse transcriptase,” copies the viral RNA genome to its DNA equivalent, and this, with the help of another viral enzyme known as “integrase,” integrates the viral genome into the cell's nuclear genome. This remarkable virus–host genomic fusion is an essential step before the virus can instruct the host genome to manufacture daughter viruses that will spread to other cells and repeat the process; meanwhile the virus spreads widely through the blood stream and tissues of the infected individual.
We note in passing the importance of the retroviral capsular envelope in evading the host immunity, then finding the target cell and fusing with the cell membrane to allow the virus to invade the host cell. As part of this process of spread, the virus will again make use of the envelope to evade the human immunity that is trying to fight it, at the same time infecting and killing more and more CD4 cells. As the disease progresses, the virus reaches the stage where billions of new viruses are created every day, meanwhile these daughter progeny are also mutating, through copying errors, at an extraordinary rate. It is this vast production and simultaneous mutational evolution of the virus within its infected host that makes it so difficult for the human immune system to defeat the virus without medical treatment. And during this proliferation phase, the virus will also preferentially find its way to the gonads—the ovaries and testicles—and it will find its way to the glands that make seminal fluid, vaginal secretions, and saliva to maximize its potential for spread to other hosts.
In the same way that a retrovirus is capable of inserting its genome into the CD4 cells, many retroviruses have the astonishing potential of inserting their genomes into the germ line of their infected hosts, the ovum and the sperm. We are observing this happening right now in a retroviral epidemic that first infected koalas in the eastern side of Australia roughly a century ago. We witness the terrifying effectiveness of sexual transmission of this so-called “emerging infection” first hand, with virologists confirming that all of the animals in the north are infected, and the wave of transmission is passing southward, where, other than isolated island populations, all of the koalas are likely to be infected with the virus in time. It is causing a horrific wave of mortality, from leukemia and lymphosarcoma. But though biologists were initially worried that the retroviral epidemic might cause the extinction of the Australian koala, it is now unlikely that this will happen. Already the retrovirus is inserting into the germ cells of the koala, so that living koalas have anything up to 40 or 50 viral loci in their chromosomes, which will now be passed down as part of the inheritance of future generations. Since this holobiontic genomic union is taking place within the nuclear genome, unlike that of the mitochondrial, the koala retrovirus inserts will be inherited in classical Mendelian manner.
To date, HIV-1 has not been seen to invade the human germ line. Some virologists had believed that this would prove impossible because HIV belongs to a subgroup of retroviruses, called lentiviruses, which were not known to “endogenize.” But recently, lentiviruses were found in the germ lines of European rabbits and Madagascar lemurs, the latter a primate. Whether HIV will eventually become part of us remains to be determined. A multitude of other retroviruses have entered the human and prehuman primate germ lines, to contribute to the evolution of the human genome in this way, so that roughly 9 percent of our human genome is now made up of retroviral DNA. Retroviruses that have invaded the genomes of their mammalian hosts are known as “endogenous retroviruses” or ERVs, as opposed to free-ranging infectious viruses, which are known as “exogenous” retroviruses. Our human endogenous retroviruses, or “HERVs,” comprise between 30 and 50 families, depending on definition, and these families are further subdivided into more than 200 distinct groups and subgroups. The most recent of these lineages to invade the prehuman genome, known as HERV-Ks, include ten subtypes that are exclusive to humans.
Each of these HERV families and subfamilies appears to represent an independent genomic colonization event—and therefore a genomic invasion during a historic retroviral plague that infected our ancestors. Given what we have seen of AIDS and the koala retrovirus epidemic, it suggests a grim story of ancestral survival through epidemic after epidemic. When two different sets of scientists recreated the likely original genome of our most recent human retrovirus invader, the human endogenous retrovirus HERV-K, they discovered a highly infectious exogenous retrovirus with pathogenic potential in tissue cultures. It's salutary to reflect that we are the descendants of the survivors. But now we need to consider the consequences of retroviruses entering the evolving human genome.
When a retrovirus invades a germ line cell it does so as a selfishly driven parasite. The host genome will fight back against the alien invader. This battle will continue, even if the defensive weaponry must change, when the viral genome has colonized the germ line to create “viral loci” scattered throughout the chromosomes. Antibodies are no longer effective here within the genome, but other measures, aimed at shutting down the viral loci, will come into play. One such measure is “epigenetic silencing” (I shall explain more about this in a subsequent chapter). But such epigenetic measures as “methylation” of the viral locus are not a permanent solution to suppressing an infectious pathogenic virus. Permanent silencing will require mutations, whether through damage to the viral genes and regulatory regions, or through the insertion of an unwanted genetic sequence into the viral genome. Meanwhile, the continuing presence of viral genome within the host germ line, often in many copies distributed throughout the chromosomes, introduces a new possibility for symbiotic genetic interaction between the two very different genomes. Over the fullness of evolutionary time, many such opportunities will arise.
We should recall that while virus and host are separate evolutionary entities, with very different evolutionary pathways, they are not unknown to one another. In fact, they share an intensely interactive parasitic history. During this history, the virus has evolved many different strategies for manipulating host immunity and cellular physiology, strategies in which the viral envelope, coded by the viral env gene, has played an important role. Meanwhile the human genome—and in particular its protective immune systems, some innate and some highly changeable and adaptive—has also evolved many strategies for hunting down and disabling the virus, its alien proteins, and its alien genes.
Within the HERV loci—which comprise whole viral genomes embedded in the human chromosome—many viral genes have been silenced over millions of years by mutations. This led an earlier generation of geneticists to dismiss all viral components as “junk DNA,” but now we know that many viral loci have remained “active,” in a number of different ways. Retroviruses have their own regulatory sequences, known as “long terminal repeats,” or “LTRs.” In the viral loci embedded in the chromosomes, these are bordering stretches of DNA enclosing the viral genes. Retroviral LTRs are regulatory dynamos capable of taking over the bureaucratic control of nearby human genes. They are also capable of interacting with other genetic sequences, including epigenetic and regulatory sequence
s. We also know that the huge chunks of the genome known as LINEs and SINEs are structurally related to HERVs, and, as shown by Professor Villarreal, they appear to work in a complex coordination with the HERV component. Between them, the HERVs, LINEs, and SINEs account for some 45 percent of our human DNA. This raises some important questions. What role has this vast retroviral legacy played in the holobiontic evolution of the human genome? What role is it playing in our human embryology, our day-to-day physiology, including our susceptibility to diseases?
In 2000, a year before the draft human genome was released, Dr. John M. McCoy and his colleagues in the United States and Dr. François Mallet and his colleagues in France discovered that a human protein they called “syncytin” is coded by the envelope gene of a retrovirus locus, called ERVWE1, which is embedded in human chromosome 7. We might recall that this gene codes for the envelope protein that not only coats the virus with a kind of protective membrane but also plays a key role in the ability of the virus to find and penetrate the host target cell membrane, meanwhile evading and outwitting the complex wiles of the human cellular barriers and our white cell and antibody immune defenses. Not only is syncytin coded by the viral envelope gene, or env, its expression is controlled by the virus's own promoter within the viral regulatory LTR. In other words, the viral locus is functioning as a viral genomic unit within the overall human genome. The viral protein, syncytin, does not code for an enzyme or structural protein, as many of our human proteins function. Syncytin changes the fate of the cells in the placental interface between the maternal and fetal circulations so that a cell called a “trophoblast” is turned into a “syncytiotrophoblast.” This enables the human placenta to create a fused multi-cellular membrane, called a “syncytium,” that acts as an extremely fine filter between the maternal and fetal circulation so that nutrients from mother to fetus and waste products from fetus to mother are obliged to pass through cellular cytoplasm. This helps to create the most deeply invading of all known mammalian placentas as well as what is the finest barrier—microscopically thin, as only a single cell layer can be.
Further research confirmed that the original retrovirus, which endogenized into our genome as the locus ERVWE1, invaded the primate cell line roughly 30 million years ago. Since it arrived before the divergence of the evolutionary lines of the great apes from a common primate ancestor, we humans share the ERVWE1 locus, and its placental function, with chimpanzees, gorillas, and orangutans. This is why there is no “H” for “human” in the locus name. Were it exclusive to humans, we would add the H, so the viral name would then read HERV-WE1. And that tells us that the virus is a member of the HERV-W group. Today we also know that the virus inserted itself some 650 or so times into the genome. But the remaining 649 viral loci, spread over many different chromosomes, have all had their envelope genes switched off through mutations under the influence of natural selection. This is not merely necessary as a precaution against unwanted invasive viral emergence, it is also vitally important to avoid a conflict of envelope gene expression in such a pivotal role as reproduction. I would go further to insist that it must be this way because the ERVWE1 locus, and its expressed syncytin gene, must be recognized as “self” by our human immunity throughout our lifetime.
Within a few years of the discovery of syncytin, two more viral loci were identified as contributing their expressed proteins to placental structure and function. The virus HERV-FRD was found to code for a protein designated “syncytin-2,” which appears to help protect the fetus from maternal immune attack through the placental barrier. ERV3 was found to complement the cell fusion role of syncytin, now redesignated “syncytin-1.” In time, a fourth virus, a member of the human-associated HERV-Ks, was found to contribute to placental function. It seems likely that there is a protective overlap in function between the four retroviruses since a small number of the population have a mutation in the ERV3 env gene yet they appear to be protected from sterility by the overlapping cover of the other viral genes.
Today we can list at least twelve different viral loci that contribute in one way or another to human reproduction. We still don't know what some of these viruses do, but one of these expresses its gene if a mother has a Cesarean delivery, while another expresses its gene during a natural birth. Further research on the viruses HERV-FRD and ERV3 also confirms the same pattern of mutational suppression of all potentially rival loci of these viruses scattered throughout the human chromosomes. Only the selected loci can be regarded as self.
In May 2012, it was my pleasure to make a trip to the historic Uppsala University in Sweden, famous for its association with Carl Linnaeus, who devised the system of the classification of life still used by biologists. I came here at the invitation of my friend and colleague, Erik Larsson, professor of pathology at the University Hospital, who is an international expert on human endogenous retroviruses. I was already aware that Professor Larsson and his colleagues had conducted important pioneering research on the role of HERVs in human embryology and on their contribution to important aspects of normal physiology, particularly in relation to placentation and human reproduction. I wrote about this extensively in my book Virolution.
Professor Larsson's research pointed to a major role of HERVs in human evolution as well as in human diseases such as cancers and the autoimmune diseases. To get a better understanding of both these roles, we needed to know what viral genes might be contributing to normal human embryology and physiology. In particular, we needed better techniques of searching for viral gene expression in different human cells, tissues, and organs. Until recently, scientists had been limited to looking for the expression of viral genes as messenger RNA. This had given us important clues as to what was happening at tissue level, but we needed to develop accurate deep sequencing techniques that would allow us to show viral proteins at work in the human cells. This has been the focus of research in Uppsala for many years.
During my visit, it was also my pleasure to meet Professor Larsson's colleagues, the molecular biologists Professor Fredrik Pontén and Dr. Per-Henrik Edqvist of the Rudbeck Laboratory. One of the great mysteries of human embryological development is how, from the original pluripotent cells of the fertilized ovum, all the different cells that make up the various tissues and organs arise. For many years, Pontén and Edqvist have been working with other Swedish molecular biologists in exploring this mystery. In particular, they have screened the cells of different human tissues and organs to see how the expression of proteins might differ between, say, a nerve cell and a blood cell, or a cell from the liver or kidney. This enormous undertaking, which is a natural follow-up to the Human Genome Project, is known as the “Human Proteome Project.” At the time of my visit, it was nearing completion, and it had provided fascinating insights into how the day-to-day machinery of the different tissues and organs work. In essence, they arrived at two related conclusions: each specific tissue cell had a small number of proteins that were exclusive to the cell type, on average perhaps six or seven, but the major difference between the cells of the various tissues and organs was in the variations of the overall expression profile of a very wide range of proteins that were common to most.
Pontén and Edqvist also cooperated with Professor Larsson and his Department of Pathology, in looking for the expression of HERV-derived proteins. To do so, they devised a new system involving extensive tissue screening with a pair of antibodies raised against protein sequences derived from two different sections of HERV envelope gene. The Uppsala-based scientists now extrapolated this system to study three retroviral loci in the human genome, ERVWE1, ERV3 and HERV-FRD, looking for significant expression of their envelope genes in a wide range of human cells, tissues, and organs. What they discovered was original and astonishing. These virus-derived envelope proteins, pre-evolved to interact at a deep level with our human physiology, were being expressed at a significant level—one that suggested physiological function—in many different human cells, tissues, and organs other than the placenta, inclu
ding the brain, the liver, the bowel, skeletal muscle, the heart, the skin, the adrenal glands, the salivary glands, the insulin-secreting islets of Langerhans in the pancreas, and the testis, as well as in multinucleated inflammatory cells found in the blood as part of the reaction to foreign invaders, such as bacteria and infectious viruses.
This was powerful supportive evidence for virus–human symbiosis at genomic level. In each case, the viral envelope gene was under the control of the viral promoter sequences, which were conserved by natural selection within the virus's own regulatory LTRs. It seems likely that these pioneering Swedish colleagues and others will extend this type of study to other viral loci within the human genome. We still have a great deal to learn about what such viral proteins might be doing in these many different tissues and organs, both in terms of normal physiological function and in terms of disease.
So-called because it shows up as a starry shape within the substance of the brain, the astrocyte is a support cell involved in local immune responses within the brain and central nervous system. The Swedish scientists confirmed that syncytin-1, the envelope protein of ERVWE1, is normally expressed in modest amounts in these cells. Other scientists in France, Italy, Germany, and America have discovered that the same viral protein appears to be over expressed in the local astrocytes within the disease-affected parts of the brain and central nervous system in patients with multiple sclerosis. Italian scientists have also shown that during the first acute attack of MS, a virus closely resembling ERVWE1 appears in high levels of intensity in the blood. In other laboratory tests, it has been shown that the affected astrocytes secrete a chemical that is lethal to a type of brain cell called the oligodendrocyte, which manufactures myelin, the substance that coats nerve cells like the insulation on an electrical cable. Damage to myelin is the central pathology of MS. This same virus falls to unmeasurable levels in patients who respond well to beta-interferon therapy. Could it be that a defective regulatory control of the ERVWE1 viral envelope gene expression in the astrocytes is playing some role in the pathology of MS?