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May 16 2013

The viruses hidden in our DNA

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 paceā€¦ 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.

5 comments

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  1. 1
    Reginald Selkirk

    Another example of a retrovirus: the chicken pox virus. Or, as it’s also known: the shingles virus. The virus responsible for chicken pox, Herpes zoster, can hide away in the DNA of nerve ganglia cells. If the virus breaks out later in life, it is known as shingles.
    .
    Another biological thing that will blow your mind: transposons.

  2. 2
    J. Quinton

    The pattern of endogenous retroviruses is actually one of my favorite evidences for evolution. We share the most ERVs with chimps, less with primates, lesser still with mammals, etc. fitting the pattern of nested hierarchies.

  3. 3
    Kevin

    @1: That’s pretty much a different subject entirely.

    What he’s talking about are ancient retroviruses that have become part of the DNA of humans that is transmitted via germ cells (egg and sperm). They have become part of what is accepted as human DNA. In some cases, as noted above, the genetic material is being used to do some kind of work.

    They’re really not “viruses” anymore. They’re genetic sequences in our human DNA that once were viruses. In other words, they don’t ever “wake up” and start making copies of the virus that they descended from. The sequences have been integrated into human DNA forever and ever, not as virus-making sequences.

    Herpes is a DNA virus that is, as you say, a forever part of you. But only in certain “somatic” cells (in other words, a cell that isn’t a sperm or an egg). Therefore, it’s not integrated into human DNA as human DNA. And can’t be passed on from parent to child (at least, not during the act of procreation – kids can get infected with herpes during childbirth; it’s sometimes fatal).

    Fundamentally, it’s difference between germ cells and somatic cells.

    The point is, one of the many, many, many creationist canards is “no new information” in DNA. They don’t see how “mutations” in DNA can give rise to new function. Well … this is one way. A rich source of new sequences that can adapt to do some work in the body…or to just propagate to the next generation forever.

    Duplication, translocation, transposition, and deletion are other sources of new information for DNA sequences, FWIW. Retroviruses aren’t the only source of new/additional genetic material. Just an interesting one.

  4. 4
    Reginald Selkirk

    Dear Kevin: don’t try to lecture me on biology.

  5. 5
    thebookofdave

    Dear Reginald: others also read the bottom half of the internet. Try to get over yourself.

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