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A New Strain of HIV?How many kinds are out there?

By Daniel Engber
Posted Tuesday, Feb. 15, 2005, at 11:05 AM ET

A new and perhaps aggressive strain of HIV was discovered last week in New York City. In the infected patients, the virus progressed with unusual speed and displayed the hallmarks of resistance to three of the four major classes of HIV drugs. Just how many strains of the virus are out there?

So many that scientists don't even count them all. The virus changes at a very rapid rate, in part because it mutates quickly, and in part because it reproduces so often. In an infected patient, billions of virus particles are produced every day, and the genetic makeup of the virus changes by about 1 percent every year. The point at which scientists decide to call a particular variant a new "strain" is not well-defined.

Researchers do classify strains of HIV more broadly. There is HIV-1, which is responsible for the global epidemic, and HIV-2, a milder form specific to West Africa. HIV-1 is very similar to a virus found in chimpanzees, and HIV-2 appears to have jumped to humans from the sooty mangabey.

Among the viruses that are classified as HIV-1, there are three different "groups": M (major), N (new), and O (outlier). Each group has just 40 percent or 50 percent of its genetic material in common with the other two. Group M is by far the most prevalent, while N and O are restricted to parts of Central Africa. Nine lettered subtypes of group M exist in various locations; these subtypes have about three-quarters of their genomes in common with one another. The drug-resistant strain identified in New York comes from Group M and Subtype B, which predominates in North America and Europe.

So, what do these distinctions actually tell us about the disease? Very little, at the moment. Many studies have tried to determine if one subtype is more easily transmitted or more deadly than another, but to no avail. Also, because most HIV research takes place in America and Europe, most drugs have been tested only on Subtype B; luckily, more recent efforts to use these drugs on other subtypes have so far proved successful.

Any subtype can develop resistance to a drug following exposure to it, and any longtime patient might develop drug resistance over the course of treatment. Scientists can test a particular strain for drug resistance in two ways. They can check its genome for specific mutations that would protect it from a given class of drugs, or they can test the drugs directly on an isolated sample.

Next question?

Explainer thanks Dr. Jay Dobkin of the Columbia University Medical Center and Dr. Feng Gao of Duke University.

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Daniel Engber is an associate editor at Slate. He can be reached at .
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Remarks from the Fray:

…Viruses like HIV mutate so fast that nobody who is infected really has one single "strain" in him like you might have a bacterial strain in a wound. Instead, we speak of a "quasi-species" or a diffuse cloud of geno- (and pheno-) types in a single patient. These related forms can cross breed, mutate and keep doing so. Attempting some subtle form of treatment doesn't work because it can only knock out part of the cloud, and some harsh treatment ends up 'pushing it around' for the most part, over the course of a many year infection. Inherently, many members of the cloud are dysfunctional. However, there can be several relatively successful, pretty different subtypes in any cloud. At the same time, you are unlikely to see the full suite of changes needed to move between, say, major serotypes or the big types (M,N,O) without a 'simultaneous infection.'

This is part, though, of why something like a careless HIV+ man having unprotected sex with other HIV+ men is so awful and insidious. He risks relatively little, in his mind, particularly if his virus is already drug resistant. However, this gives the HIV time to have a conference, trade tricks, and take their newfound knowledge to other patients. Suddenly, they can be drug resistant, or any other feature that we don't like in a virus.

--BenK

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