I have heard about retroviruses and that HIV belonged to that family but not being a biologist knew nothing more about what a retrovirus was and how it differed from any other virus. This article by Carl Zimmer explains what they are and in addition says that new research about them has revealed that we all have a lot of retroviruses that invaded our DNA a long time ago and that over time have mutated to become either inactive or dormant.
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.
But not all these endogenous viruses are mere baggage that we carry around. A few have the potential to become active and this is what the researchers found. By comparing the human genome with that of chimpanzees and Neaderthals, they were able were able to identify and locate the presence of one particular class of such endogenous retroviruses that they named K111. The human genome has about 100 copies of K111.
This finding suggests that between 6 million and 800,000 years ago, K111 was duplicated a few times at a fairly slow pace… It was only later, in the past 800,000 years, that K111 started proliferating at a faster pace.”
So why did we not know about the presence of these retroviruses in our DNA? It turns out that we have mapped just 95% of the human genome and many of these retroviruses lie in the yet unmapped parts called the centromere, which is the central region of the chromosomes, and which for various reasons is very difficult to study.