US researchers have identified how multiple mutations on the SARS-CoV-2 spike protein independently create variants that are more transmissible and potentially resistant to antibodies.
By acquiring mutations on the spike protein, one such variant gained the ability to leap from humans to minks and back to humans. Other variants — including Alpha, which first appeared in the UK; Beta, which was first identified in South Africa; and Gamma, first identified in Brazil — independently developed spike mutations that enhanced their ability to spread rapidly in human populations and resist some antibodies.
The researchers have published their findings in Science.
“The spike on the surface of the virus helps SARS-CoV-2 enter into host cells,” said senior author Priyamvada Acharya, from Duke University’s Human Vaccine Institute.
“Changes on the spike protein determine the transmissibility of the virus — how far and quickly it spreads. Some variations of the SARS-CoV-2 spike are occurring at different times and different places throughout the world, but have similar results, and it’s important to understand the mechanics of these spike mutations as we work to fight this pandemic,” Acharya said.
The team developed structural models to identify changes in the virus’s spike protein. Cryo-electron microscopy allowed atomic level visualisation, while binding assays enabled the team to create mimics of the live virus that directly correlated with its function in host cells. From there, the team used computational analysis to build models that showed the structural mechanisms at work.
“By building a skeleton of the spike, we could see how the spike is moving, and how this movement changes with mutations,” said Rory Henderson from the varsity.
“The different variant spikes are not moving the same way, but they accomplish the same task. The variants first appearing in South Africa and Brazil use one mechanism, while the UK and the mink variants use another mechanism,” he added.
All the variants showed increased ability to bind to the host, notably via the ACE2 receptor. The changes also created viruses that were less susceptible to antibodies, raising concerns that continued accumulation of spike mutations may reduce the efficiency of current vaccines.