The Lurker: How A Virus Hid In Our Genome For Six Million Years
In the mid-2000s, David Markovitz, a scientist at the University of Michigan, and his colleagues took a look at the blood of people infected with HIV. Human immunodeficiency viruses kill their hosts by exhausting the immune system, allowing all sorts of pathogens to sweep into their host’s body. So it wasn’t a huge surprise for Markovitz and his colleagues to find other viruses in the blood of the HIV patients. What was surprising was where those other viruses had come from: from within the patients’ own DNA.
HIV belongs to a class of viruses called retroviruses. They all share three genes in common. One, called gag, gives rise to the inner shell where the virus’s genes are stored. Another, called env, makes knobs on the outer surface of the virus, that allow it to latch onto cells and invade them. And a third, called pol, makes an enzyme that inserts the virus’s genes into its host cell’s DNA.
It turns out that the human genome contains segments of DNA that match pol, env, and gag. Lots of them. Scientists have identified 100,000 pieces of retrovirus DNA in our genes, making up eight percent of the human genome. That’s a huge portion of our DNA when you consider that protein coding genes make up just over one percent of the genome.
Scientists have studied these so-called endogenous retroviruses both in humans and in other species, and the evidence all points to the same scenario for how they genetically merged with us. Our ancestors were infected with retroviruses on a regular basis. On rare occasion, a virus infected a sperm or egg and managed to end up in an embryo. Every new cell in the embryo inherited the retrovirus DNA implanted in its genome. And then the embryo grew up into an adult, which then had offspring of its own, and passed the virus DNA on as well.
At first, the virus still retained some of its old powers. Its DNA could sometimes still give rise to new viruses. Mutations arose in the viral genes, and they might prevent it from making shells. Yet the dying virus could still make a new copy of its genes and insert them back into its host genome. That would explain why it’s possible to classify our many endogenous retroviruses into different families. The families are made up of new copies of an ancestral virus.
Eventually, however, the endogenous retroviruses got so hobbled by mutations that they became nothing more than baggage. (In some cases, we’ve domesticated their genes, co-opting them for our own functions, such as building a placenta.) Given that many matching endogenous retroviruses can be found in other primates, this process has been going on for millions of years–even tens of millions.
The world of our inner viruses is still a murky, mysterious one that scientists are still surveying. And Markovitz’s discovery enabled him to add considerably to our understanding of these shadowy creatures. He discovered new members of a particularly interesting class of endogenous retroviruses–ones that, even today, can still have life breathed into them.