The Virus Hunter of a bygone Era

Clarence James Peters (knowns as CJ (great name if you ask me)) was a virus hunter. Back in his time, that mean spending time in the field, in remote parts of South America. Virus hunting today has changed. There is still adventure to be had, but there are more rules, and they are enforced more strictly.

Want to hear CJ Peters story, and worry about viruses in the world around us?

Read about it here!



Mystery Parrot Disease Virus Identified

A disease that has terrified parrot breeders for the last few decades has been identified as a virus that is new to science. This discovery will allow scientists to find the source of this virus, to control its spread, develop a vaccine and to find a cure.

Want to know more? Read about it here!


Another Bacteria that Causes Lyme Disease

Sure, finding new and interesting species and describing them is exciting.

But finding new bacteria that cause a well understood disease? Equally if not more exciting (my little parasitic loving heart is all aflutter!).

While it has long been thought that lyme disease is caused by one bacterium (Borrelia burgdorferi), researchers at Mayo Clinic found something floating around in blood samples of people suspected of having Lyme disease that is totally different.

It has been named Borrelia mayoniiand it is remarkably similar to it’s lyme disease causing brethren. But it also has some important differences.

Read all about it over at NPR


Life, um, finds a way—except when it doesn’t

This week the LA Review of Books has my review of Unnatural Selection, a nifty new book in which ecological toxicologist Emily Monosson describes how living things evolve their way around the things we humans do to try and contain them.

… the introduction of the insecticide DDT rapidly led to the evolution of resistant mosquitoes, houseflies, and, yes, bedbugs. Decades of farming with the herbicide glyphosate, better known under the brand name Roundup, have led to the evolution of resistance in dozens of weed species. One after another, Monosson ticks off cases, dividing them into chapters corresponding roughly to biological classification. She goes beyond these headline examples to describe lesser-known triumphs of “resistance evolution,” such as viruses evading human immune responses and inadequate vaccination, cancer cells overcoming chemotherapy, and fish that survive water polluted by biochemical toxins.

This hits some of the same themes as that recent review about using evolutionary biology to solve major problems in the coming century, though I might have liked it if Unnatural Selection spent a bit more time discussing the cases when life doesn’t find a way—the myriad reasons we’re in the middle of the sixth mass extinction in the history of the planet. But I highly recommend the book for the folks in your life who may not realize how personal evolutionary biology can be.

Random Natural History: Ebola

through a glass, darkly

Currently there is a catastrophic outbreak of Ebola happening in West Africa. Over 1700 infections have been recorded with nearly 1000 deaths, making it the deadliest outbreak of ebola known. Infection results in a hemorrhagic fever, which starts out a bit like the influenza, but can result in bleeding from mucous membranes, organ failure, and ultimately death. But what is Ebola?

Ebola is a Filovirus. Filoviruses are a small group of viruses only known to infect mammals. They are so named because of their filamentous shape. They have tiny genomes, only ~19,000 base pairs in length, containing only seven protein coding genes and two regulatory regions. By contrast, the human genome is over 3 billion base pairs, contains around twenty thousand genes and has innumerable (by which I mean as yet unnumbered regulatory regions). Because of ebola’s simplicity, (as with all viruses), it cannot reproduce without commandeering the cellular machinery of its hosts. In the words of Cormac McCarthy, These anonymous creatures… may seem little or nothing in the world. Yet the smallest crumb can devour us.

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Estimating dates using HIV evolution patterns

In this post we see how we can track mutation rates to estimate when people were infected with HIV and even when the virus first crossed over into humans.

HIV is an evolution machine

Its polymerase enzyme is pretty sloppy and has an error rate of about 1 mistake for every 10 thousand nucleotide bases copied.

For a virus with a genome about 10 thousand bases in length, that means that basically every time HIV replicates itself, it makes a mistake.

Sometimes these errors result in a defective virus, but sometimes they give the virus some new property its predecessor didn’t have, such as resistance to an antiretroviral agent (the drugs we use to treat HIV). The high mutation rate of HIV has also led to extensive worldwide diversity in the epidemic, leading to groupings of related viruses called clades that are named with the letters A through K, and sometimes with two letters where it looks like two clades have recombined into a spliced version of HIV. The different clades are shown in this phylogenetic tree. Also shown are how they relate to other immunodeficiency viruses that infect other primates, as well as how HIV (more precisely, HIV-1) is related to a distinct virus that also infects humans and causes AIDS, called HIV-2, which is mostly confined to west Africa.

This extensive diversity also makes it very difficult to develop an HIV vaccine.

Although the high mutation rate makes things difficult for scientific and medical advances in HIV, it does allow us to see evolution in action, and can lead to some pretty interesting discoveries.

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