The so-called South African variant was identified by an international team of researchers, including biomedical scientists from the University of California, Riverside. They explain the process behind discovering the variants, why they are so concerning, and what the future holds.
“The new COVID variants are the next new frontier,” said Adam Godzik, a professor of biomedical sciences in the UC Riverside School of Medicine. “Of these, the SA and Brazil strains are most worrying. They have mutations that make them resistant to antibodies we generate with existing vaccines. It is commonly believed we are in a tight race: Unless we vaccinate people quickly and squash the pandemic, new variants would dominate to the point that all our COVID vaccines would be ineffective.”
Prof Godzik and Arghavan Alisoltani-Dehkordi, a postdoctoral researcher who joined his lab two years ago, helped characterise the new SA variant by providing its spike protein structure using computer simulations.
Dr Alisoltani-Dehkordi, who was a postdoctoral fellow at the University of Cape Town before she joined UCR, mentioned that research teams at the University of KwaZulu-Natal and UCT discovered the new SARS-CoV-2 variant from samples collected between October 15 and November 25, 2020, in three provinces. By early November, this variant rapidly became the dominant variant in samples from two provinces. The researchers suggested that this may be due to increased transmissibility or immune escape.
“Each SARS-CoV-2 variant has specific mutations defining it,” Dr Alisoltani-Dehkordi said. “Professor Godzik and I used computer modeling to suggest possible structural and functional consequences of spike protein mutations in the SA lineage. Our analysis, confirmed also by several other research groups, shows that some of the mutations potentially result in a higher transmissibility of the virus and a weaker immune response.”
The SA variant has been detected in 40 countries, and is quite likely present in more still.
“This variant is probably spreading in areas where it has not been sequenced and is, therefore, not identifiable,” Prof Godzik said. “In the US, sequencing is still a slow process. In many parts of the country, including Riverside, we have no information whatsoever about variants.”
The SA variant prompted concern among scientists because its mutations allowed it to evade antibody protection, and potentially, vaccines. Indeed, the AstraZeneca vaccine rollout was halted in South Africa due to the low level of protection against this new variant.
“That’s when it received a high level of interest,” Prof Godzik said. “Subsequent research confirmed it is resistant to vaccines and is spreading. South Africa is doing a good job, however, at controlling the variant through quarantining and other measures.”
Common mutational signatures can be seen in each of the newly emerged SARS-CoV-2 variants of concern in the UK, SA, Brazil, and California. But each of these variants also has a unique set of mutations; for example, the SA and Brazil variants have two unique mutations on spike proteins K417N and E484K, respectively. But, as Prof Godzik explains, there is no single “SA variant”, rather a branch on an evolutionary tree. And viruses can acquire mutations and escape at any time.
Prof Godzik thinks COVID will become a permanent feature of our lives. “It takes six months to develop a flu vaccine,” he said. “Models predict the evolution of the flu virus and vaccines are produced before the variants show up. If the predictions are good, the vaccines work. If they miss, a heavy flu season follows. This is how COVID will likely behave. A lot of effort will be invested in predicting what will happen the following year, vaccines would then be updated, and people will need to get a booster shot.”
