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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Double, double toil and trouble: a tale of two infections

Wordle of text from Ben-Ami et al 2011

What are the evolutionary consequences of parasite superinfection (i.e. simultaneous infection by multiple parasites)? When parasites are genetically distinct, coexistence within a host generates conflict because of limited resources. How this conflict is resolved is the source of evolutionary research on the evolution of parasite life history traits such as virulence, the negative effects on the host caused by infection, and transmission mode, how parasites infect a new host. The transmission mode of a parasite is often characterized as occurring in one of two different modes: vertical or horizontal. With vertical transmission, an offspring obtains its parasites directly from its parents. In contrast, with horizontal transmission, infections occur either directly from the environment or contagiously by infection from other individuals.

My interest in the evolution of transmission mode in parasites and symbionts led me to a recent paper (Ben-Ami et al. 2011), which addresses the consequences of superinfection by two different parasites with different transmission modes of the waterflea, Daphnia magna, on virulence and parasite fecundity. Pasteuria ramosa is a castrating, horizontally transmitted, blood-infecting bacterium where spores are produced from the cadaver of the host Daphnia. Octosporea bayeri, a microsporidium, utilizes both vertical transmission to eggs and horizontal transmission via waterborne spores.

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