The evolution of the virus behind the COVID-19 pandemic has slowed markedly in recent months, new research has found, buoying hopes a vaccine will work against all strains of the disease.
But it also shows the virus has figured out the best way to infect people, for now at least, "honing the tactics that may make it more successful". And there are worrying signs it's trying other mutations out which could give it more options, should scientists figure out how to stop the current version.
Scientists in the US looked at 15,300 different SARS-CoV-2 genomes - from the first released by Chinese scientists in January, to some collected in May.
They found sometime in April the rate of mutation started to slow down - that's when the infamous D614G mutation of the spike protein virtually took over "the entire virus population".
"The spike was a completely different protein at the very beginning than it is now. You can barely find that initial version now," said study co-author Tre Tomaszewski, a doctoral student in the University of Illinois College of Agricultural, Consumer and Environmental Sciences.
The D614G mutation makes the virus more infectious, and in some studies, more deadly. This latest study picked up two other mutations around the same time which the virus appears to have kept - one which duplicates the virus' RNA, and another which proofreads the duplicated RNA strands.
"All three mutations seem to be coordinated with each other," said Gustavo Caetano-Anolles, professor of bioinformatics and senior author. "They are in different molecules, but they are following the same evolutionary process."
He said this is "bad news".
"The virus is changing and changing, but it is keeping the things that are most useful."
The research also uncovered another part of the virus which appears to be mutating more frequently than before - suggesting while natural selection has pretty much nailed the spike protein, other parts of the virus are now being selected for survival, including two proteins which can mess with our immune system.
Dr Caetano-Anolles says it will be vital to track future mutations to stay one step ahead, or at least not too far behind.
"Considering this virus will be in our midst for some time, we hope the exploration of mutational pathways can anticipate moving targets for speedy therapeutics and vaccine development as we prepare for the next wave."
Early in the pandemic, scientists quickly noted COVID-19 wasn't mutating as fast as some other viruses, like influenza. While it's not good the virus evolved to become more infectious so early, the fact virtually all strains of the virus now have the same spike protein means scientists working on vaccines have obvious clear targets to aim at.
"In vaccine development, for example, you need to know what the antibodies are attaching to," said Tomaszewski.
"New mutations could change everything, including the way proteins are constructed, their shape. An antibody target could go from the surface of a protein to being folded inside of it, and you can't get to it anymore. Knowing which proteins and structures are sticking around will provide important insights for vaccines and other therapies."
The research was published on Tuesday (NZ time) in journal Evolutionary Bioinformatics.
