Majority of HIV Proviruses are Defective: They Will Not Reactivate the Virus

A new study conducted by researchers at John Hopkins Medicine has found that most of the proviruses in the latent HIV reservoir are defective but the current methods used to measure size of reservoirs, PCR and QVOA, are not precise in their measurements in that their results often count proviruses with and without defects.

A new study conducted by researchers at John Hopkins Medicine has found that even if patients diagnosed with HIV receive antiretroviral therapies (ART) early on, they will still have a reservoir of rapidly accumulating proviruses; however, these proviruses are found to be mostly defective. In addition, the methods that are currently widely used to determine the size of the reservoir of dormant HIV in patients are not precise in their estimations, according to a press release.

The study showed that even in the earlier stages of the disease, more than 90% of the latent proviruses were so mutated that they were no longer able to function. These findings implicate the need for the development of new ways to count just the proviruses that are not defective, the ones that can reactivate infection.

Study author Robert Siliciano, MD, PhD, infectious disease physician and molecular biologist at the Johns Hopkins University School of Medicine said, “To cure HIV, you want to get rid of the proviruses without defects. But our work shows that the standard assays used to do that are measuring forms of the virus that are not really relevant to these cure strategies.”

ART is currently used to treat patients with HIV, a virus that attacks the body’s immune system, destroying cells that help the body fight off infections and other diseases. According to the press release, over 36 million people are HIV-positive worldwide and 17 million people are currently being treated with ART. ART works to reduce the amount of HIV in the body by preventing the virus from infecting new CD4 cells and simultaneously works to increase CD4 cell count in the body, thus strengthening the immune system, according to the CDC. Even though it prevents the virus from producing more viruses, latent forms of the virus remain hidden inside certain cells in the immune system where they do not replicate or produce chemical signals that ART would notice and target.

Some proviruses in the latent virus reservoirs have the potential to become active after patients have finished ART, making the effort to effectively remove these reservoirs a priority among virologists. New experimental drug strategies are currently being developed to eliminate these proviruses as a way to cure HIV. Siliciano adds that the best way to test the effectiveness of these new strategies is to take what he calls “snapshots” of the latent virus reservoirs before and after treatment is administered by using a technique called polymerase chain reaction (PCR). PCR measures the presence of obvious HIV genes, however, proviruses that are defective are also counted if they contain those specific genes.

Previously, scientists have made breakthroughs in targeting dormant or latent HIV cells through the use of a sugar-binding protein and ImmTavs protein in order to prevent reactivation of the cells. However, now researchers feel that many of the proviruses being detected were likely to be defective. A quantitative viral outgrowth assay (QVOA) is a more arduous method that can be used to measure the amount of proviruses that are not defective as well as the size of the latent HIV reservoir.

Siciliano and his team took a closer look at 19 men and women between the ages of 20 and 76 years of varied race who had been on ART for at least 8 months and who had started the therapy either more than 180 days after infection or less than 100 days after acquiring the infection. By sequencing the genomes of a number of proviruses in these individuals, they aimed to determine how effective the 2 techniques, PCR and QVOA, were at counting the proviruses that had the potential to reactivate.

The researchers found that despite when the patient had started ART, within weeks or years of becoming infected by the virus, 90 to 98% of the proviruses from any patient were defective, and thus, were incapable of reactivating the virus.

Upon comparing the data of the proviruses in the patients conducted with both techniques, the researchers found that “…PCR overestimates the true size of the latent reservoir by a median of 188-fold in patients who began treatment more than six months after their infection with HIV, and 13-fold in patients who began treatment earlier, while QVOA underestimates the reservoir by a median of 27-fold in patients who began treatment late and 25-fold in those who began treatment early,” according to the press release.

Due to the high cost of the effective sequencing method that Siciliano and his team used to yield these results, it makes using the method on a broader clinical scale impractical, which means that the two current methods, PCR and QVOA, methods that are not as precise in their results, are all that researchers have to rely on when it comes to measuring the reservoir of latent proviruses.

On speaking of the how their results can be used to better understand the results yielded by PCR and QVOA methods, Siciliano said, “With current counting methods, it looks like you can bracket the true size range. But we’d like to figure out better ways to do the measurements.”