The study, published in the open-access journal PLOS Biology on Friday, is a collaboration between researchers in the UK, US, and Belgium. The lead authors are Prof, David L Robertson (at the MRC-University of Glasgow Centre for Virus Research, Scotland) and Prof Sergei Pond (at the Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia).
The scientists used their past experiences analyzing data from HIV and other viruses to SARS-CoV-2. Pond’s state-of-the-art analytical framework, HyPhy, was instrumental in teasing out the evolutionary signatures embedded in the virus genomes and rests on decades of theoretical knowledge on molecular evolutionary processes, according to Phys.org.
The researchers show that since December 2019, and for the first 11 months of the SARS-CoV-2 pandemic there has been very little ‘important’ genetic change observed in the hundreds of thousands of sequenced virus genomes. They point out that generally, with viruses, novel adaptations are often seen, but surprisingly, with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), little to no significant adaptation to humans was required.
First author Dr. Oscar MacLean explains, “This does not mean no changes have occurred, mutations of no evolutionary significance accumulate and ‘surf’ along the millions of transmission events like they do in all viruses.”
Dr. MacLean points to the Spike replacement D614G, which has been found to increase transmissibility, along with “certain other tweaks of virus biology scattered over its genome.” But he says that overall, ‘neutral’ evolutionary processes have dominated, per Science Daily.
“This stasis can be attributed to the highly susceptible nature of the human population to this new pathogen, with limited pressure from population immunity, and lack of containment, leading to exponential growth making almost every virus a winner.”
Pond comments, “what’s been so surprising is just how transmissible SARS-CoV-2 has been from the outset. Usually viruses that jump to a new host species take some time to acquire adaptations to be as capable as SARS-CoV-2 at spreading, and most never make it past that stage, resulting in dead-end spillovers or localized outbreaks.”
Little evidence of significant change
The researchers went back and studied the mutational processes of SARS-CoV-2 and related sarbecoviruses (the group of viruses SARS-CoV-2 belongs to that comes from bats and pangolins). What they found is really quite interesting. The authors found a fairly significant amount of change in earlier outbreaks of Sars-related viruses, but that was all before the emergence of SARS-CoV-2 in humans.
According to the study, this means that owing to the “generalist” nature of many coronaviruses and their apparent facility to jump between hosts, SARS-CoV-2 was embued with a ready-made ability to easily infect humans and other animals.
Joint first author and Ph.D. student Spyros Lytras adds, “Interestingly, one of the closer bat viruses, RmYN02, has an intriguing genome structure made up of both SARS-CoV-2-like and bat-virus-like segments. Its genetic material carries both distinct composition signatures (associated with the action of host anti-viral immunity), supporting this change of evolutionary pace occurred in bats without the need for an intermediate animal species.”
This evolutionary change of pace was evident in the latter part of 2020 when coronavirus variants began showing up. Robertson explains, “the reason for the ‘shifting of gears’ of SARS-CoV-2 in terms of its increased rate of evolution at the end of 2020, associated with more heavily mutated lineages, is because the immunological profile of the human population has changed.”
At the end of 2020, the virus was running into people with existing host immunity as the numbers of previously infected people around the world rose. The virus responded by selectively tweaking or creating mutants to get around the host immunity.
The authors say that SARS-CoV-2 still remains an acute virus, and very deadly. It is already moving away from the January 2020 variant used in all of the current vaccines to raise protective immunity. And the current vaccines in use right now will apparently cover most of the circulating variants.
But the authors also say that as more time passes, and the bigger the differential between vaccinated and not-vaccinated numbers of people, the more opportunity there will be for vaccine escape. Robertson adds, “The first race was to develop a vaccine. The race now is to get the global population vaccinated as quickly as possible.”
