HIV can develop resistance to gene-editing tool

Mutating HIV with the gene-editing platform CRISPR/Cas9 may inhibit viral replication, but it can also lead to the creation of viruses that are resistant to gene editing and more difficult to target, scientists say.
Researchers who used CRISPR/Cas9 to mutate HIV-1 within cellular DNA found that while single mutations can inhibit viral replication, some also led to unexpected resistance.
Researchers from McGill University, University of Montreal in Canada, Chinese Academy of Medical Sciences and Peking Union Medical College in China believe targeting multiple viral DNA regions may be necessary for the potential antiviral aspect of CRISPR/Cas9 to be effective.
Upon entry into a cell, HIV's RNA genome is converted into DNA and becomes entwined with the cellular DNA. From here, CRISPR/Cas9 can be programmed to target a DNA sequence and cleave viral DNA.

The problem is that HIV is notoriously good at surviving and thriving with new mutations, so while many viruses are killed by the targeted approach, those that escape the CRISPR/Cas9 treatment become more difficult to target.
"When we sequence the viral RNA of escaped HIV, the surprise is that the majority of the mutations that the virus has are nicely aligned at the site where Cas9 cleaves the DNA, which immediately indicates that these mutations, instead of resulting from the errors of viral reverse transcriptase, are rather introduced by the cellular non-homologous end joining machinery when repairing the broken DNA," said Chen Liang, senior investigator at the Jewish General Hospital.

"Some mutations are tiny - only a single nucleotide - but the mutation changes the sequence so Cas9 cannot recognise it anymore. Such mutations do no harm to the virus, so these resistant viruses can still replicate," said Liang, who is also the Associate Professor of Medicine at the McGill University AIDS Centre.

The study serves as a cautionary tale for those who hope to apply CRISPR/Cas9 as an antiviral.
Liang does not believe the effort is futile, however, as there are strategies that could overcome this limitation.
For example, targeting multiple sites with CRISPR/Cas9 or using other enzymes aside from Cas9.

Once a solution is identified, the next barrier will be identifying ways to deliver the treatment to patients.
The study was published in the journal Cell Reports.