Large-scale supercomputer simulations at the atomic level, described in a new study published in Science Advances, show that the dominant ‘G form’ variant of the Covid-19-causing virus, SARS-CoV-2, is more infectious partly because of its greater ability to readily bind to its target host receptor in the body, compared to other variants.
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Researchers knew that the G variant, also known as D614G, was more infectious and could be neutralised by antibodies, but they didn’t know how. Simulating more than a million individual atoms and requiring about 24 million CPU hours of supercomputer time, the new work provides molecular-level detail about the behaviour of this variant’s spike protein.
Current vaccines for SARS-CoV-2 are based on the original D614 form of the virus. This new understanding of the G variant could mean it offers a backbone for future vaccines.
The research team, led by Los Alamos National Laboratory of the US Department of Energy, discovered the D614G variant in early 2020. Within weeks, this D614G mutation prevailed globally.
The new research shows that interactions among the building blocks of the spike are more symmetrical in the G variant than those in the original D strain. On its website, Los Alamos National Laboratory quoted Gnana Gnanakaran, corresponding author of the paper, as saying: “We found that the interactions among the basic building blocks of the spike protein become more symmetrical in the G form, and that gives it more opportunities to bind to the receptors in the host… But at the same time, that means antibodies can more easily neutralise it. In essence, the variant puts its head up to bind to the receptor, which gives antibodies the chance to attack it.”
—Source: LANL, US DoE