The supercomputer TACC Frontera (Texas Advanced Computing Center) has helped scientists figure out why and how why variants of the coronavirus in the UK and South Africa are more infectious and deadly.
All viruses mutate as they copy themselves in order to spread. SARS-CoV-2, the virus that causes COVID-19, is no exception. There are now more than 4,000 variants of COVID-19, from which more than 2.7 million people worldwide have already died during the pandemic.
The British variant, also known as B.1.1.7, was first discovered in September 2020 and now causes 98% of all COVID-19 cases in the United Kingdom. It has also spread to about 100 other countries, including France, Denmark and the United States.
The World Health Organization states that B.1.1.7 is one of several options of concern, along with others in South Africa and Brazil. “Variants of the virus in the United Kingdom, South Africa and Brazil are more infectious and easier to get rid of immunity than the original virus,” explains Victor Padilla-Sanchez, a research fellow at the Catholic University of America. “We need to understand why they are more infectious and in many cases more deadly.”
All three variants have undergone changes in their spike protein – the part of the virus that attaches to human cells. As a result, they better infect cells and spread.
In a research article for Research Ideas and Outcomes, Padilla-Sanchez discusses in detail the UK and South African mutation options. It presents a computational analysis of the structure of the spike glycoprotein associated with the ACE2 receptor that has mutated. His article outlines the reason why these variants bind better to human cells.
“I analyzed the recently published structure of the SARS-CoV-2 spine, associated with the ACE2 receptor, and found out why the new variants are more transmissible6,” he said. “These results were obtained using UC San Francisco’s Chimera software and molecular dynamics simulations using the Texas Advanced Computing Center (TACC) Frontera supercomputer.”
Padilla-Sanchez found that the British variant has many mutations in the spike glycoprotein. But most important is one mutation, N501Y, in the receptor-binding domain that interacts with the ACE2 receptor.
“The N501Y mutation provides much higher binding efficiency, which in turn makes the virus more infectious. This option is dominated by the United Kingdom and is spreading to other countries around the world, ”he said.
The South African variant of the coronavirus emerged in October 2020 and has more important changes in the spiked squirrel. This makes it more dangerous than the British version. It includes the key mutation E484K. It helps the virus evade antibodies and parts of the immune system that might fight the coronavirus, based on the experience of a previous infection or vaccine. As a result, the body cannot fight the virus.
Padilla-Sanchez performed a structural analysis by examining the crystal structure of the virus. Current vaccines may not necessarily be effective against the British and South African variants, he said. “They will need their own vaccines. We will need as many vaccines as there will be options, ”the scientist concludes.