My poem is an adaption of the children’s classic “We’re going on a bear hunt” by Michael Rosen. This is one of my daughter’s favorite books.
We’re going on a fossil hunt, We’re gonna catch a big one, What a beautiful genome, We’re not scared. Oh, no! An ancient herpes virus. We can’t ignore it, We are all infected by it, We’ll have to investigate it. Computer beeping, computer whirring.
If you have read any of this blog, you know that I’m fascinated by all sorts of strange fossils. I have done my share of novice fossil hunting, but I don’t get many opportunities to find really unique fossils.
Well, there’s a very recent form of fossil hunting that I have gotten to partake in to some small extent, and I can do it while sitting in front of a computer screen! With some computer skills and some knowledge of animal genomes it isn’t difficult to join this hunt for fossils inside the genome of living organisms.
Just like hunting for fossils in rocks though, most genomic fossils really aren’t that unusual. However, a recently discovered fossil caught my attention. Scientists have dug-up the ancient remains of a herpes simplex virus in the genome of a small primate. While not found in the human genome, our genomes do contain huge numbers of similar fossils which have been uncovered and investigated. Lets spend a moment exploring these molecular fossils and this herpes fossil in particular.
What are molecular fossils and what can we learn from them?
These huntable fossils are called molecular fossils. Molecular fossils are portion of a genome that are remains of dead genes or genetic elements inserted into a genome from a foreign source. They have been passed on, from parent to offspring, to the present day. Over time, these pieces of the genome accumulate errors through mutation, making them harder and harder to recognize. They are like traditional fossils in that they can start out as very clear impressions of something, but over time they can be compressed, eroded, or chemically altered—which makes them more difficult to identify.
Molecular fossils are little time capsules inside the genomes of all organisms. They tell us something about their past.
Recently, molecular fossil hunting has become more popular and successful with the advent of massive genome sequencing. Think of it as a large road cut through a mountain ridge, which makes the layers of rock that used to be covered by a forest accessible to geological investigation. Most of the genome of an organism is not coding (gene) sequence. Rather, these “other” sequences are hundreds of thousands of pieces of duplicated non-functional genes, viruses and other mobile genetic elements (MBEs). Our genomes consist of 2% code that actually makes the basic products that make us up and 98% other stuff much of which is fossil genetic material.
These fossils tell a story of an organism’s past, just like a fossil in a rock can tell us a story. Because of astounding technological advances in sequencing DNA it is possible to analyze the entire genome of hundreds of organisms. As a result, we can search though the hundreds of billions of pieces of the genome to find pieces of DNA sequence that represent remnants of coding sequence that we think an organism might have used in the past but no longer needs. We can even look for evidence of past interactions with viruses that might have left something behind in our genome.
Molecular fossils are found in all genomes
Genomes of all organisms contain pieces of old discarded genes and remains of viral infections. For example, last year, I wrote about a molecular fossil found in vampire bats (They have the Gene but Blood is Not Sweet Nectar to Vampire Bats). Around the same time, my biology class took on a project to find what they predicted would be a molecular genetic fossil in whales: the umami taste gene. Marine mammals aren’t expected to need to taste their food if they are swallowing it whole, but if whales have ancestors that were once on land, they may still have the remains of genes that they once used while on land.
Those remains would be molecular fossils buried inside their genome.
My class was able to obtain sequences of DNA from two whales and show that the genes did exist in their genomes, but the sequences of those genes were so altered by mutation that they couldn’t possibly function as they should. Just as my students predicted, these whales were unlikely to be able to taste umami. Further work done in another lab has now confirmed that whales can’t taste sweet either.
These types of nonfunctional fossil genes, often referred to as pseudogenes, are extremely common. And so, in a way, they are a bit boring—like the abundant fossils shells you can find seemingly anywhere.
But there are other genetic fossil hunters we might call paleovirologists who search for more exotic molecular fossils. Yesterday, in the journal PLOSOne (ref 1), a molecular fossil of the herpes virus was found in the genome of several primates. This molecular fossil is notable because although the virus that causes herpes is very common in humans and primates, this virus is not known to integrate into our genome. Instead, it lives separately in our cells.
Fig. 1. The structure of a herpes simplex virus. Like almost all viruses it consists of a coat of proteins surrounding the genetic material. The DNA holds the instructions for how to make all the proteins and assembly them back into a new virus. But the virus can not make a copy of itself without entering into a host cell and getting it to read its DNA and carry out the instructions. All viruses can be thought of as parasites on living cells.
Finding a fossil herpes virus
Herpes simplex virus (HSV-1, Fig. 1) is a very common virus with an estimated 95% of the human population infected. You probably contracted the virus in the first few years of your life. If you have ever had a cold sore, mostly likely in the mouth area, then you are infected with the virus. And even if you haven’t had a cold sore breakout in a long time, it is almost certain that this virus still lies within you, hibernating like a bear inside a neural cell body near the location of your last outbreak.
Another kind of herpes virus, herpes simplex virus 2 (HSV-2), is associated with genital herpes, though outbreaks can occur on nearly any part of the body. This virus is not as common in the human population and the virus is most similar to Chimpanzee herpes virus (ChHV). It is thus thought to have crossed species, infecting humans sometime in the past.
Fig. 2. Simplified virus life-cycle showing a virus infecting and using a bacteria to make more viruses. The herpes simplex virus is similar. It uses the cell machinery like a parasite to make copies of its self.
While almost all of you reading this have the HSV-1 virus hiding in some cells of your body right now, the viral genome is not actually integrated into the genome of your cells. It remains separate from your cells DNA (Fig. 2). It causes a cold sore when that genome is activated and, as all viruses do, commands your cell to read its code and make more viruses. Because the virus is not part of our cells, we don’t inherit the virus directly from our parents, but rather obtain it from our environment which is quite easy to do since it is spread even more easily than a cold virus.
The same is true for herpes viruses that infect other primate species. All great apes and many other primates studied are susceptible to getting herpes viruses, but each species is only infected by a particular “species” of herpes virus. In other words, there is a chimpanzee version of herpes, but it only can infect chimpanzees. And there is a separate macaque virus for each macaque species. Humans are unusual in that there are two different “species” of herpes virus that can infect us. The figure below shows the genetic relationships of some herpes simplex viruses and their hosts.
Fig. 3. Wertheim et al. 2014, figure 1, comparing HSV phylogeny (ie. relationship tree) to primate phylogeny. Original caption: “General pattern of co-divergence for primate herpes simplex viruses and their Simiiforme hosts. Underlined viral taxa indicate phylogenetic incongruence, implying cross-species transmission events. Dashed lines connect virus to host species.” The human and chimpanzee sequences are on top.
The authors of the paper published in PLOSOne reasoned that, although the herpes virus doesn’t normally attack and insert itself into our genomes, unlike a virus like HIV which causes AIDS (Fig 4), there should be accidental integrations of the viral genome into the host organism genome once in a while given that there have been hundreds of trillions of herpes infections in history. On that rare occasion that the viral genome might be accidentally incorporated into the DNA genome of the sex cells that are passed from one generation to the next, then the viral genome could be passed down from your distant ancestors all the way to you today.
This HIV virus which causes AIDS in humans integrates its genome directly into the host cells genome. There it can stay dormant for days, months or years before activating and making new viruses. When the later occurs the symptoms of AIDS appear. It is these viruses that integrate their genomes into their hosts genomes that are more likely to become molecular fossils.
In effect, the viral genome can become part of a populations or species DNA from that time that it integrates with the cells. But there is a catch. The viral DNA inserted into an animal genome would almost certainly be non-functional, and so it would be more susceptible to mutation degradation over time. As a result, the more generations that the viral DNA is passed along, the more different that virus sequence should become relative to active “living” viruses.
The right side of this figure shows an example of what to expect when a virus integrates itself into the genome. Once integrated the viral DNA is a part of a host genome and so is passed down from parent to offspring. It may become common in a species and if the species splits into two then both species will have the ancient viral DNA contained in their DNA. I this case it will be obvious that the two rabbit species had a common ancestor more recently than with the third species of rabbit since the third didn’t share an ancestor with the viral integration. EVE is an acronym for Endogenous Viral Elements. Figure from Ref 2.
So scientists have set off on a hunt to see if they could find evidence of past herpes virus genome integrations into the genome of a primate. And there’s no need to go to some far off place for this fossil hunt. Looking for viral genomes only requires that you get comfortable in front of a computer. What do you have to do? Using freely available databases, you search through hundreds of billions of base pairs of genome sequence of many primate genomes.
This is very similar to a paleontological expedition in search of dinosaur bones, where you look for a certain type of rock to find the types of fossils you want to find—but, of course, there’s no guarantee that they’ll be there.
In the case of the hunt for viral genomes, searching finally paid off through the examination of the genome of a certain wide-eyed tiny primate: the tarsier.
It turns out that the viral DNA in the tarsier’s genome was like a fossil jawbone sticking out of the face of a cliff. Once scientists identified a small piece of the viral genome in the tarsier’s genome, they started to dig around more carefully. Eventually, they were able to retrieve remains of nearly the entire genome of a herpes virus! To double-check their results they tested it by getting a second tarsier individual and finding the same virus in its genome in the same location. Clearly the two had inherited this viral DNA in their genomes from their common ancestor however many generations in the past that may have been.
Like most of the bones of a dinosaur fossil, most of the genes of this viral genome were broken into sizable pieces—in the case of DNA, there were many individual mutations. Or the genes were completely shattered, which means that they were missing entire portions of the gene.
The remains of the virus, just like a few hundred bones from a T. Rex, were enough to make it obvious that, at one time, there must have been a complete herpes simplex genome present in the tarsier’s ancestor. But today, all that remains are non-functional genetic pieces of the virus that have been passed down from one generation to the next. Passed down and down and down, for a very long time with each passing resulting in small changes to the original DNA sequences.
Scientists also compared sequences from the genes of this “fossil” virus to modern viruses. They found the fragments of viral DNA within the tarsier’s genome where more similar to today’s herpes viruses in primates than any other known virus. Nonetheless, the sequences were far different that any living virus yet identified.
So far, even though nearly all humans are living with the herpes virus in some of their cells, no herpes simplex viral genome has been found to have been integrated into our own genome. However, each of us does carry with us hundreds of thousands of pieces of other viral genomes, which exist as fossilized viral relics of past infections. At one time, our ancestors were once infected, and the viral genomes have been passed down to all of us today. Each time we pass these viruses to our children, though, we are apt to make mistakes in the copying process, causing it to be more and more difficult to recognize these molecular fossils over time. Today, about 8% of each of our genomes has been identified as pieces of ancient viral infections. With a genome of about 3 billion nucleotides (ATCGs) this means that all of us are carrying around at least 240 million nucleotides in our genome that are not really “human.” It sounds a bit scary but don’t freak out, 99.9% of this DNA is non-functional and isn’t likely to have any effect on us.
Unlike the children’s book that ends with the line “We are never going on a bear hunt again,” I am most definitely interested in going on a molecular fossil hunt no matter where it might lead. These fossils present us with difficult but detectable mysteries, and each one of them contains a fascinating story.
Naturalis Historia 