It has been a strange, exhausting year for many evolutionary virologists.
“Scientists are not used to having attention and are not used to being in the press and are not used to being attacked on Twitter,” Martha Nelson, PhD, a staff scientist who studies viral evolution at the National Institutes of Health, said in an interview.
Over the past year and a half, the theory of evolution has been thrust into the spotlight – more now than ever, perhaps, as the world is stalked by the Delta variant and fears arise of a mutation that’s even worse.
The origins of SARS-CoV-2 and the rise of the Delta variant have been debated, and vaccine efficacy and the possible need for booster shots have been speculated upon. In all these instances, consciously or not, there is engagement with the field of evolutionary virology.
It has been central to deepening the understanding of the ongoing pandemic, even as SARS-CoV-2 has exposed gaps in what we understand about how viruses behave and evolve.
Evolutionary virology experts believe that, after the pandemic, their expertise and tools could be applied to and integrated with clinical medicine to improve outcomes and understanding of disease.
“From our perspective, evolutionary biology has been a side dish and something that hasn’t been integrated into the core practice of medicine,” said Dr. Nelson. “I’m really curious to see how that changes over time.”
Pandemic evolution
Novel pathogens, antibiotic-resistant bacteria, and cancer cells are all products of ongoing evolution. “Just like cellular organisms, viruses have genomes, and all genomes evolve,” Eugene Koonin, PhD, evolutionary genomics group leader at the NIH, said in an interview.
Compared with cellular organisms, viruses evolve quite fast, he said.
A study published in the Proceedings of the National Academy of Sciences exemplifies evolutionary virology in action. In the study, Dr. Koonin and fellow researchers analyzed more than 300,000 genome sequences of SARS-CoV-2 variants that were publicly available as of January 2021 and mapped all the mutations in each sequence.
The researchers identified a small subset of mutations that arose independently more than once and that likely aided viral adaptation, said Nash Rochman, PhD, a research fellow at the NIH and coauthor of the PNAS study.
Many of these mutations were concentrated in two areas of the genome – the receptor binding domain of the spike protein, and a region of the nucleocapsid protein – and were often grouped together, possibly creating greater advantages for the virus than would have occurred individually, he said.
The researchers also found that, from the beginning of the pandemic, the SARS-CoV-2 genome has been evolving and diversifying in different regions around the world, allowing for the rise of new lineages and, possibly, even new species, Dr. Koonin said.
During the pandemic, researchers have used evolutionary virology tools to tackle many other questions. For example, Dr. Nelson tracked the spread of SARS-CoV-2 across Europe and North America. In a study that is currently undergoing peer review, the investigators found recently vaccinated individuals, who are only partially immune, are at the highest risk for incubating antibody-resistant variants.
C. Brandon Ogbunu, PhD, an evolutionary geneticist at Yale University, New Haven, Conn., whose work is focused on disease evolution, studied whether SARS-CoV-2 would evolve to become more transmissible, and if so, would it also become more or less virulent. His lab also investigated the transmission and spread of the virus.
“I think the last year, on one end, has been this opportunity to apply concepts and perspectives that we’ve been developing for the last several decades,” Dr. Ogbunu said in an interview. “At the same time, this pandemic has also been this wake-up call for many of us with regards to revealing the things we do not understand about the ways viruses infect, spread, and how evolution works within viruses.”
He emphasizes the need for evolutionary biology to partner with other fields – including information theory and biophysics – to help unlock viral mysteries: “We need to think very, very carefully about the way those fields intersect.”
Dr. Nelson also pointed to the need for better, more centralized data gathering in the United States.
The sheer volume of information scientists have collected about SARS-CoV-2 will aid in the study of virus evolution for years to come, said Dr. Koonin.