You can think of viruses as nature’s shapeshifters. To adapt to environmental pressures and more effectively infect their hosts, viruses gradually accumulate beneficial mutations—a phenomenon we are currently seeing with the rise of Delta and other SARS-CoV-2 variants.
The human immunodeficiency virus (HIV), however, takes shapeshifting to the extreme, rapidly accruing seemingly random mutations due to an error-prone enzyme involved in replication called reverse transcriptase. Some of these mutations allow the virus to become resistant to anti-HIV drugs, rendering them ineffective. Consequently, developing treatments that lower transmission risk or suppress viral levels throughout a patient’s lifetime remains a challenge.
Given the complexity of HIV drug resistance, the relationship between viral genetics and both when and where mutations occur had long eluded scientists. Historically, studies on the occurrence of mutations in HIV relied on reporter genes: segments of foreign DNA sequences that, when expressed by the virus, produce easily measurable signals that allow scientists to predict HIV’s mutational dynamics.
But according to experts, this experimental strategy does not always paint a clear picture of when, where and how mutations that cause HIV drug resistance arises. “Studying native genes is the only way to get this information,” explained Samuel Gan, Senior Principal Investigator at the Antibody and Product Development Lab of A*STAR’s Experimental Drug Development Centre (EDDC) & Bioinformatics Institute (BII).
To bridge the gap, the Gan lab studied a panel of HIV genes encoding the Gag and protease viral proteins. These components are crucial for assembling the virus once it begins to divide inside an infected host cell. They also examined mutations in the p66 sub-unit of HIV reverse transcriptase.
Fascinatingly, the scientists found that HIV mutations were not as random and unrestrained as previously thought. Far from being random, they instead observed that certain genes naturally accumulated mutations at particular hotspots. The mutations generally did not occur in gene regions with a significant impact on function, such as the active site of the HIV protease—a critical molecular pocket within the enzyme responsible for viral maturation.
Notably, Gan’s team observed that these mutations occurred even without selection pressures, like the presence of the immune system or antiviral drugs. These findings suggest that even early in infection, HIV may already be laying down the genetic groundwork for drug resistance. Indeed, native codon usage by the virus appears to control the emergence of such mutations and where they occur.
When it comes to dealing with highly adaptable, rapidly mutating viruses such as HIV, it seems that prevention remains better than a cure. “Fortunately, most viruses are less adaptive,” reassured Gan, “The next key step would be to study why some HIV proteins can tolerate specific mutations and not others.”