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Supercomputer analysis reveals why coronavirus mutants in the UK and South Africa are more contagious and deadly

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COVID-19 variant

TACC’s Frontera supercomputer COVID-19 (new coronavirus infection) (# If there is no character limit, add parentheses when it first appears variant.

All viruses mutate as they make copies of themselves, spread, and propagate. SARS-CoV-2The virus that causes COVID-19 has proven to make no difference. Currently, there are more than 4,000 COVID-19 variants, and more than 2.7 million people have already died worldwide during the pandemic.

The UK variant, also known as B.1.1.7, was first detected in September 2020 and currently causes 98% of all COVID-19 cases in the UK. It also seems to be well-understood in about 100 other countries that have expanded in the last few months, such as France, Denmark and the United States.

According to the World Health Organization, B.1.1.7 is one of several variants of concern, as are other viruses that have emerged in South Africa and Brazil.

“The British, South African and Brazilian variants are more contagious and easier to evade immunity than the original virus,” said Victor Padilla Sanchez, a research scientist at The Catholic University of America. “We need to understand why they are more infectious and often more deadly.”

All three variants have modified spike proteins, some of the viruses that attach to human cells. As a result, they are excellent at infecting and spreading cells.

In a research treatise published in January 2021 Research ideas and results, Padilla-Sanchez details the British and South African variants. He presents a computational analysis of the structure of spiked glycoproteins bound to the mutated ACE2 receptor. His treatise outlines why these mutants bind better to human cells.

“I was analyzing the structure of the recently published SARS-CoV-2 spike bound to the ACE2 receptor and discovered why the new mutant was more contagious,” he said. “These findings were obtained using molecular dynamics simulations using the UC San Francisco Chimera software and the Texas Advanced Computing Center (TACC) Frontera supercomputer.”

Padilla-Sanchez found that the UK variant has many mutations in spiked glycoproteins, but most importantly is the mutation N501Y, one of the receptor-binding domains that interacts with the ACE2 receptor.

Victor Padilla Sanchez

Victor Padilla Sanchez, a research scientist at the Catholic University of America.Credit: Catholic University

“This N501Y mutation provides much higher binding efficiency, resulting in increased virus infectivity. This variant replaces the previous British virus and has spread to many other parts of the world. “He said.

The South African variant emerged in October 2020 and is more dangerous than the UK variant due to significant changes to the peplomer protein. This includes an important mutation called E484K that helps the virus evade antibodies and parts of the immune system that can fight the coronavirus, based on previous infection or vaccine experience. The mutant escapes immunity, preventing the body from fighting the virus. “South African variants are beginning to be seen here in the United States,” he said.

Padilla-Sanchez performed a structural analysis to study the crystal structure of the virus. Molecular dynamics to get these discoveries.

“The main computational challenge in doing this study was finding a computer that was powerful enough to perform molecular dynamics tasks. It generated very large files and required a lot of memory. This study would not have been possible without the Frontera supercomputer, “says Padilla-Sanchez.

According to Padilla-Sanchez, current vaccines do not always treat mutants. “Subspecies require their own specific vaccine. The mutants that emerge need as many vaccines as possible.”

Going forward, Padilla-Sanchez will continue to investigate the changes taking place in SARS-CoV-2.

“This was a very quick project. The computational research lasted for a month,” he said. “There are many other labs doing wet lab experiments, but not so many computational studies, so I decided to do this important job now.”

This study, called “SARS-CoV-2 Structural Analysis of New Mutants of Receptor Binding Domains from the United Kingdom and South Africa,” Research ideas and results The researcher who worked on this research is Victor Padilla Sanchez of the Catholic University of America.

See: SARS-CoV-2 Structural Analysis of New Mutants of Receptor Binding Domains from the United Kingdom and South Africa, Victor Padilla-Sanchez, January 15, 2021 Research ideas and results..
DOI: 10.3897 /rio.7.e62936

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