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In the Real World

Research and Microorganisms: Viruses

The development of PCR techniques has considerably improved our ability to do virus research. One of the major advantages of new PCR techniques includes deep sequencing techniques, which allows scientists to identify DNA sequences from the oceans, or other remote locations. Because there is no need to culture cells or grow viruses, they can just simply randomly sample areas and just determine the sequences found in that area. So, if there are a lot of viruses, then you can identify virus sequences in that area.

Research identifying ocean viruses has led to some interesting gene discoveries. Viruses that have unique polymerase genes that are DNA-dependent DNA polymerases, similar to pox viruses, but belonging to their own group have been identified in the ocean. Viruses such as the mimivirus, a very large unique group of viruses found in the ocean are very large viruses. Mimiviruses infect ocean amoebas, and have diameters of approximately 400 nm in length (twice that of poxviruses), and has a 1 megabase long genome sequence.

Mimiviruses are larger than many very small bacterial genomes, and it is highly likely that through more deep sequencing we will also identify many viruses that are more like cellular life than the viruses we already know. This raises the question again on whether viruses are indeed living organisms, and perhaps we should revise the 3 domain architecture of life to create another level of organization to include viruses in the tree of life, to separate between ribosomal based life (cellular life), and non-ribosomal life (viruses).

While PCR techniques have dramatically improved our ability to detect virus sequences in the environment, this has also led to the detection of false positives. Many researchers have been looking for a virus origin of many chronic diseases that we don't understand, such as chronic fatigue syndrome. Recently, a group published a report saying that they identified a retrovirus called XMRV, which was found in the blood of patients with chronic fatigue syndrome, but not in normal healthy individuals.

While this provided a lot of hope for individuals diagnosed with this disease, it turned out that XMRV was not in fact found in the blood of these patients, and the XMRV sequences that they found were in fact contamination from mouse DNA. So, many people were taking antiretroviral drugs in the hope of treating their illness, only to discover that there was no viral origin for their disease. These types of mistakes have become more prevalent with the ease of PCR techniques to identify viral sequences. Misguided research on identifying virus causes for tumors has led to what many skeptics calling ironically "rumor" virology*, a pun on tumor virology, implying that much of this research is wrong.

*Unfortunately, we at Shmoop cannot fire the writer who came up with "rumor" virology. But boy would we like to.

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