How the COVID-19 variant was found in South Africa

Biomedical scientists at the University of California, Riverside were part of an international team that determined the strain of the coronavirus

Credit: Stan Lim, University of California Riverside.

Riverside, California. Different forms of the Coronavirus appear in different parts of the world, many of which are spreading with alarming speed. One infectious variant is the South African variant, or SA, which has been identified by an international team of researchers, including biomedical scientists from the University of California, Riverside.

“The new variants of COVID-19 are the next new frontier,” said Adam Godzick, professor of biomedical sciences at the University of California, Riverside School of Medicine and a member of the research team that made the discovery. “Of these strains, the South Australian and Brazil strains are the most worrisome. They have mutations that make them resistant to the antibodies that we produce with existing vaccines. It is common to think that we are in a tight race: Unless we quickly vaccinate people and crush the epidemic, the new variants will dominate to the point that all Our COVID-19 vaccines will be ineffective. ”

Godzik and Arghavan Alisoltani-Dehkordi, a postdoctoral researcher who joined his lab two years ago, helped characterize the new SA variant by providing the protein spiky structure using computer simulations.

The results of the study appear today at Temperate nature.

Alisultani-Decordi, who was a postdoctoral fellow at the University of Cape Town in South Africa before joining UCR, reported that research teams at the University of KwaZulu-Natal in South Africa and the University of Cape Town have discovered the new – or alternative – lineage. SARS-CoV-2, the virus that causes COVID-19, is from samples collected between October 15 and November 25, 2020, in three provinces in South Africa. By early November, this variant quickly became the predominant variant in samples from two counties.

“Each type of SARS-CoV-2 has specific mutations that determine it,” said Alisultani-Decordi. “Professor Godzic and I used computer modeling to suggest the potential structural and functional consequences of elevated protein mutations in the SA strain. Our analysis, which was also confirmed by several other research groups, shows that some of the mutations are likely to lead to increased virus transmission and a weaker immune response.”

The SA variant has been detected in at least 40 countries, including the United States.

“It is likely that this species will be widespread in areas that have not been sequenced, and therefore cannot be identified,” Godzik said. “In the United States, sequencing is still a slow process. In many parts of the country, including Riverside, we have no information whatsoever on the variants.”

Preliminary research on the SA variant suggested that it could be resistant to antibodies, which might reduce the effectiveness of vaccines.

“That’s when I got a high degree of attention,” Godzik said. “Subsequent research has confirmed that it is vaccine-resistant and is spreading. Nevertheless, South Africa is doing a good job in controlling the variant through quarantines and other measures.”

All new variants of SARS-CoV-2 of concern in the UK, South Africa, Brazil and California show common mutational signatures. But each of these variants also has a unique set of mutations. For example, the SA and Brazil variants contain two unique mutations on the K417N and E484K spike proteins, respectively.

“Our preliminary results indicate that some sudden mutations may be associated with increased transmissibility of the SA variant,” said Alizultani-Decordi. However, the full significance of gene and other genome mutations in this new strain has yet to be determined. It should be emphasized that we do not have sufficient evidence to confirm a higher rate of disease progression, severity, or mortality associated with SA rates compared to other strains. But the high transmissibility and unusual variation of SA and other recently emerging strains compared to the wild type creates a significant demand for systematic monitoring of SARS-CoV-2 strains and early detection of variants before they turn into an outbreak.

Godzik explained that there is not a single virus for COVID-19. Instead, an ever-evolving family of viruses exists. The variants, which also evolve, acquire mutations and can undergo viral escape at any time.

“It is difficult to say that there is only one variable of self-attack,” he said. “One way to understand this is to imagine that this alternative is the main branch of a tree with many smaller branches. Some of these smaller ones may grow faster than others and take on more significance. It is difficult to predict this dynamic process.”

Godzik expects COVID-19 to be a constant presence in our lives, much like the flu.

“It takes six months to develop a flu vaccine,” he said. Models predict evolution of the influenza virus and vaccines are produced before variants emerge. If the outlook is good, vaccines work. If they miss them, a torrential flu season follows. This is how COVID-19 is likely to behave. A lot of effort will be invested in predicting what will happen in the next year, vaccines will then be updated, and people will need to get a booster shot. ”


The title of the paper is “The emergence of a disturbing SARS-CoV-2 variant with mutations in elevated glycoprotein”.

University of California, Riverside (http: // www.ucr.Edo) Is a doctoral research university, and a living laboratory for pioneering exploration of critical issues in Inland Southern California, state, and societies around the world. Reflecting the diverse California culture, UCR has an enrollment of more than 25,000 students. The campus opened the School of Medicine in 2013 and reached the heart of the Coachella Valley via the UCR Palm Desert Center. The campus has an annual statewide economic impact of approximately $ 2 billion. To find out more, send an email [email protected]

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