Culminating a 10-year research effort, researchers track how fitness landscapes constantly shift in the ongoing struggle for survival — ScienceDaily

Scientists believe that if the original strain of SARS-CoV-2, the virus that causes COVID-19, had remained unchanged, the pandemic would have largely ended by now. Instead, the virus has mutated several times, leading to more contagious strains and ongoing waves of COVID infections.

Culminating 10 years of research, a study by University of California, San Diego scientists has revealed an intriguing new understanding of how viruses and the hosts they infect develop new innovations to outwit each other. Animesh Gupta, formerly at UC San Diego’s Department of Physics (now at Generate Biomedicines Inc.), School of Biological Sciences Associate Professor Justin Meyer, and their colleagues developed new technologies and conducted a series of experiments to detect the changes that viruses and hosts undergo in their constant competition for survival.

Researchers provide new evidence for the role this coevolution plays in driving new adaptations. As described in the journal eLife, the researchers found that coevolution drives changes in the overall fitness of the organism. Bacteria, for example, are known to evolve resistance to viral infections, which prompts viruses to adapt to work around the resistance, leading to new mutations that create a new entry.

“There is a back-and-forth dance of adaptation and resistance. First the virus changes and increases the pressure on the bacteria, then the bacteria respond by evolving resistance, and the virus innovates to overcome the resistance,” said Meyer, a researcher in the department. of Ecology, Behavior and Evolution. “Viruses being able to innovate in an evolutionary genetic sense is happening much more often and faster than we expected because of this ongoing evolutionary arms race.”

Since the days of Darwin, scientists have known that during the struggle for survival, species are known to develop new functions in order to adapt to new ecological challenges and opportunities. But many of these ideas were based on the evolution of a single, isolated organism. Much less is known about how the evolution of one species affects the evolution of another, since all organisms are constantly evolving. Theories had suggested that coevolution between species increases the prospects for new innovations by changing the organism’s “fitness landscape,” a broad measure of genetic fitness.

When Meyer and his colleagues first explored these concepts 10 years ago, the technologies did not exist to adequately measure the details of how such fitness landscapes might change in a Darwinian sense. As technologies developed, Meyer used the new technology of gene editing and high-throughput phenotyping, which enabled him and his colleagues to precisely measure the fitness landscapes of hundreds of viruses (bacterophages) and their coevolution with their hosts. them (bacteria Escherichia coli or E. coli).

The resulting new technology allowed scientists to track interactions mutation by mutation. The results provided new perspectives on changes in the contours of the bacteriophage virus fitness landscape.

“By connecting multiple technologies, including genome engineering with next-generation sequencing that allowed us to count the mutants, we could measure how they were competing against each other,” Meyer said. “We could see the changes during coevolution and witness what new mutations were allowing.”

The results revealed that the fitness of almost every viral genotype depended on the infected host, making the metaphor of a static “landscape” to describe the evolution of fitness. Instead, researchers began using the fitness term “seascape”—reflecting the constant waves of dynamic change—as a much more accurate descriptor.

“This study provides direct evidence for the role of coevolution in driving evolutionary innovations and provides a quantitative framework for predicting evolution in developing ecological communities,” the authors write in their study. “Our studies show that a parasite’s fitness depends on complex genetic interactions within its own genome and with the genomes of interacting hosts. These interdependencies result in highly random evolution…”

With their new technology and new knowledge in hand, Meyer and his colleagues will now focus on different types of fitness seascapes, their structures, and the types of evolutionary fitness that unfold.

With viruses such as SARS-CoV-2, new avenues of research are poised to help define the general principles of how such organisms evolve. This information could eventually help scientists make better predictions about the paths of viral evolution.

“We would like to know more about the mutations in the next round that allow the virus to escape future immunity,” Meyer said. “Can we understand not just one cycle, but several cycles into the future?”

Co-authors of the study include: Animesh Gupta, Luis Zaman, Hannah Strobel, Jenna Gallie, Alita Burmeister, Benjamin Kerr, Einat Tamar, Roy Kishony and Justin Meyer. Funding for the research was provided by the National Science Foundation (1934515), the James McDonnell Foundation, and the Max Planck Foundation.

Leave a Comment

Your email address will not be published.