Collaboration is a vital aspect of modern science. Trading ideas can lead to large breakthroughs in a project that would not be possible for a scientist working alone. As it turns out, this type of teamwork is common not only among researchers but among the viruses they study. Co-infection—when multiple viral particles enter and replicate within one cell—allows genome co-mingling and sometimes even cooperation between different viral strains to gain a fitness advantage that a single virus in isolation lacks.
Herpesviruses are large, double-stranded DNA viruses that use co-infection to increase their genetic diversity. They use homologous recombination, a process of exchanging DNA fragments with high sequence similarity between two genomes within one cell—even going so far as to sometimes recombine genomes between different herpesvirus species. This genome mingling contributes to the success of herpesviruses, which have co-evolved with humans for millions of years and continue to cause persistent infection in billions of people.
But what if there was a way to turn this viral advantage into a detriment? That’s the question that Dr. Marius Walter, a staff scientist in the lab of Dr. Keith Jerome in the Vaccine and Infectious Disease Division, is working to answer. In a study recently published in Nature Communications, Walter investigated where Herpes Simplex 1 (HSV-1) recombines in the body and engineered a way to propagate genetic changes during active and latent infections in mice.
The principle behind this study is gene drive, a technique that allows genetic editing on a population level. Gene drive was based on observations of how selfish genetic elements hijack inheritance patterns during reproduction to spread rapidly in a population, often to the detriment of their host species. Scientists have proposed using gene drive to propagate deleterious mutations that will eliminate invasive species or organisms that carry disease, and advances in genetic editing techniques like CRISPR-Cas technology have made these applications a possibility in the near future.
Gene drive was originally thought to be possible only in sexually reproducing organisms, but Walter was skeptical of this claim. He reasoned that all gene drive needs is two genomes that can homologously recombine in the same nucleus and a cassette that contains a gene editing enzyme. With their high levels of co-infection and recombination, herpesviruses are a perfect candidate for this technology.
During his postdoc at the Buck Institute for Research on Aging in San Francisco, Walter demonstrated that gene drive can work to hinder a related herpesvirus called human cytomegalovirus in cell culture models. He came to Fred Hutch to join the Jerome lab, which is a pioneer in using gene therapy to cure HSV infection in mouse models. Walter and his colleagues wanted proof-of-principle that gene drive could work in HSV and would translate from a dish to a mouse.
They started by building colorfully tagged viruses. The gene drive HSV contains a guide RNA and Cas9 to initiate recombination along with both red and blue fluorescent proteins. To control for natural genome mixing during infection, the wild-type virus expresses yellow fluorescent protein in a recombination-prone locus. The colors of virus after infection show how well the gene drive is functioning: if the proportion of red or orange (red+yellow) viruses increases over time, gene drive is occurring.
After successfully troubleshooting gene drive in cell culture, the authors moved into mouse models. During active infection, they found evidence of gene drive all over the brain, although the proportion of multicolor viruses depends on the location of replication. Walter points out that levels of co-infection predict whether gene drive will be efficient: in the retina, low co-infection tracks with low gene drive, but the high co-infection allows high gene drive in the brainstem and the ganglia. “The limiting step is coinfection, not recombination,” Walter emphasizes.
They next looked at gene drive during HSV reactivation from latency. To set up latent infection, mice were given yellow, wild-type HSV and then red and blue gene drive HSV a few weeks later. Excitingly, they found recombined viruses made up to half of all reactivation events. This raises the potential that co-infection can occur during latent infection and an incoming gene-drive containing virus could recombine with the genome of the latent reservoir.
In future work, the lab will attempt to make gene drive viruses that decrease HSV infectivity and reactivation—metaphorically, using fire to fight fire. Walter, however, is equally excited about what gene drive can reveal about the biology of herpesviruses. “The field had generally assumed that, just like some scientists, viruses were introverts that only occasionally mingled, but here we showed that they are in fact very extroverted and that co-infection and recombination are occurring at high frequency, both during acute and latent infection,” he says. “We’re looking to understand whether this high level of co-infection plays a role for viral fitness, and whether we can use it for therapeutic applications.”
The spotlighted research was funded by the National Institutes of Health and institutional support from the Fred Hutch Cancer Center and the Buck Institute for Research on Aging.
Walter, M., Haick, A. K., Riley, R., Massa, P. A., Strongin, D. E., Klouser, L. M., Loprieno, M. A., Stensland, L., Santo, T. K., Roychoudhury, P., Aubert, M., Taylor, M. P., Jerome, K. R., & Verdin, E. (2024). Viral gene drive spread during herpes simplex virus 1 infection in mice. Nat Commun, 15(1), 8161.
Hannah Lewis is a postdoctoral research fellow with Jim Boonyaratanakornkit’s group in the Vaccine and Infectious Disease Division (VIDD). She is developing screens to find rare B cells that produce protective antibodies against human herpesviruses. She obtained her PhD in molecular and cellular biology from the University of Washington.
For the Media