When the pandemic began accelerating in spring 2020, the lab leak hypothesis – which suggests that COVID-19 may have emerged from a virology lab, rather than originating purely zoonotically – was broadly viewed as a fringe conspiracy theory. Over the past six months, however, that perception has changed, thanks in large part to revelations that a group of workers from the Wuhan Institute of Virology fell ill in early November 2019 and renewed credibility and attention from government officials, including President Biden. Now, HPC cloud-powered research delving into the origins of the pandemic – first reported by HPCwire in May – has been published in Scientific Reports.
The work, led by David Winkler (a professor at La Trobe University, Monash University and the University of Nottingham), sought to identify animal vectors that could have helped transfer the SARS-CoV-2 virus to humans. Beginning in early 2020, the research team used models of the SARS-CoV-2 spike protein and the ACE2 receptors of various host organisms to study how likely it was that the virus could infect those organisms and, in turn, infect a human. To conduct this research, they used a state-of-the-art protein docking package (HDOCK) and GROMACS, a molecular dynamics package, running on Oracle Cloud HPC resources.
After a series of simulations, they came to some surprising conclusions. “Surprisingly, we found that humans had the highest affinity,” Winkler said. “You would expect the virus – like the flu virus or a coronavirus – to adapt to its host over time and become more tightly bound, but this was a structure that we had from the very, very early part of the pandemic before the virus would have had time to adapt to a human host.”
“Pangolins were a little bit lower,” he continued. “Bat was quite a long way down. That was where people considered the virus originated, and it needed to pass through an intermediate animal, which at this stage most likely to be a pangolin based on these calculations. But there are other things, like [the] snake, which was also considered a potential source of the coronavirus, and it was way, way down on the binding energy – so it seems very unlikely.”
“We didn’t really expect the human to come out on top,” he added. “Because we would have thought that if the virus had come from a bat, probably that would come out to be the top – possibly a pangolin. So based on this information, you can’t really exclude the possibility that the virus could have escaped from a lab. I’m not saying it did, but those calculations suggest that it could have come from a lab.”
When HPCwire first reported on Winkler’s research, it had not yet been published. Now, that’s changed: the research has been published in the June 2021 issue of Scientific Reports. The article, titled “In silico comparison of SARS-CoV-2 spike protein-ACE2 binding affinities across species and implications for virus origin,” was written by Sakshi Piplani, Puneet Kumar Singh, David Winkler and Nikolai Petrovsky. It can be accessed here.
To read HPCwire‘s original reporting on this research, click here.