On Feb. 12, New York City Health Commissioner Thomas Frieden announced that a New York resident in his mid-forties, who had last tested HIV-negative in May 2003, had been diagnosed in December with advanced AIDS by clinicians at the Aaron Diamond AIDS Research Center.

The man is infected with an HIV strain that combines two features: strong virulence and multidrug resistance. Those are independent features of a given HIV strain, but that combination, while rare, is worrisome.

The strain appears to have caused a very rapid onset of AIDS. While full-blown AIDS usually occurs more than a decade after initial infection with HIV, the New York City Department of Health and Mental Hygiene estimated that in this case, onset appears to have occurred "within two to three months, and at most 20 months, after HIV infection."

The strain also is susceptible to drugs from only two of the four major classes of antiretroviral drugs. While multidrug resistance is a common consequence of HIV treatment, it is rare in newly diagnosed patients who have yet to be treated.

Act One: What Is Known

After initial tests suggested that the viral strain might be multidrug resistant, the isolate was sent to South San Francisco-based biotechnology company ViroLogic Inc. for more extensive investigation.

ViroLogic examined the virus with both genotypic and phenotypic assays. The Aaron Diamond Center already had done genotypic testing, and ViroLogic's genotypic testing was mainly confirmatory.

But ViroLogic also used a proprietary phenotypic assay, PhenoSense, to test for drug resistance. For phenotypic testing, the sequences encoding protease and reverse transcriptase are isolated from the patient sample and inserted into a resistance test vector, together with a reporter gene.

"It confers the properties of the patient's virus on the laboratory strain," Christos Petropoulos, vice president of research and development at ViroLogic, told BioWorld Today. "We then test the concentration of a drug it takes to inhibit the virus, and compare it to typical wild-type virus."

Based on the relative concentrations, a given drug can be classified as fully active or partially active, or the virus can have full resistance.

Overall, testing showed the virus to be highly resistant to nucleoside reverse transcriptase inhibitors and protease inhibitors. The picture was mixed for non-nucleoside reverse transcriptase inhibitors - the strain showed resistance to some members of the class, but was susceptible to Sustiva (efavirenz, Bristol Myers Squibb Co.). It was also susceptible to the entry inhibitor Fuzeon (enfuvirtide, Trimeris Inc. and F. Hoffmann-La Roche Ltd.), which is the only member of its class to date. (See BioWorld Today, March 17, 2003.)

Based on those findings, the patient is being treated with a combination of Sustiva and Fuzeon. It is too early to tell whether the regimen will be effective.

Additionally, ViroLogic tested the virus with its replication capacity assay, which determines a virus' ability to replicate, and HIV co-receptor tropism assay, which identifies the preferred cell receptors used for virus entry. Normally, when a viral strain becomes drug-resistant, it also becomes less able to replicate, Petropoulos explained.

"The enzyme has evolved to form a certain optimal structure," he said. "You get drug resistance from mutations that distort the normal shape, but in distorting the enzyme, you've also made it less able to perform its normal function." The end result is that replication is less efficient. That was not the case in the current isolate, which sports a replication capacity comparable to that of wild-type strains.

Finally, ViroLogic tested which co-receptor the virus attaches to. Normally, HIV enters the cell by attaching to a CD4 molecule and one of two chemokine co-receptors. The new strain can use both co-receptors; like multidrug resistance, that is not unique, but unusual in a virus from a newly diagnosed and as-yet untreated individual.

Act Two: What Is Not

What the tests cannot determine is why the disease is progressing so rapidly in that particular patient. Both the viral strain and the individual contribute to overall disease progression. So while perhaps the new strain is unusually virulent, the patient didn't help his own cause, having reported "multiple male sex partners and unprotected anal intercourse, often while using crystal methamphetamine," the health department said. Crystal meth is not exactly an immune system booster.

Individuals also vary in their genetic susceptibility to infections, and the N.Y. patient's immune system might simply be weak independent of his drug abuse.

Given that multidrug-resistant HIV strains are rare in newly infected patients, a possibility is that the man was infected by someone who already was on antiretroviral medication. One way to assess the strain's inherent virulence is by checking whether the progression to AIDS occurred as rapidly in the N.Y. patient as in other people who might be infected with the same strain. To answer that question, the health department is making efforts to identify and contact the infected man's sexual partners. A search of ViroLogic's archives also turned up a blood sample with a strain of HIV that is closely related to the N.Y. man's strain. California officials are looking for the patient the blood sample came from, to determine whether the disease progressed rapidly in him, as well.

What testing the sample cannot show is the public health risk posed by the viral strain. That is partly because a single case report does not give enough information on overall virulence, and partly because infectivity is yet another independent viral feature. Petropoulos said that little is known about the strain's infectivity to date, though what is known suggests it is probably within the normal range.

For the public's benefit, the health department is taking a better-safe-than-sorry approach. On Feb. 24, Commissioner Frieden said that "we are encouraging drug resistance testing for all persons newly infected with HIV," and said the public health community needed to improve its monitoring of HIV drug resistance. He also has said that "patients who are on treatment for HIV/AIDS and are doing well do not need susceptibility testing unless advised to by their physician."