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What Do We Know About the New SARS-CoV-2 Variant?

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A new SARS-CoV-2 variant – currently referred to as B.1.1.529 – has been detected in South Africa after a rapid increase in cases over the last seven days. Here's what we know so far.

B.1.1.529 emerged in South Africa


Over 80% of the newly reported COVID-19 cases in South Africa occurred in the Gauteng province, which led the Ministry of Health and scientists to conduct rapid genome sequencing analysis of samples collected from individuals that tested COVID-19 positive in the region.

The sequencing identified a SARS-CoV-2 variant of the B.1.1.529 lineage that, as Professor Sharon Peacock, director of COG-UK Genomics UK Consortium told the UK Science Media Centre (SMC), has a "very unusual constellation of mutation: "[It has] a mutation profile that is different to known variants of concern (VOCs)," she said. "The B1.1.259 variant genome has around 50 mutations, but more than 30 of these are in the spike protein, the region of the protein that interacts with human cells prior to cell entry. The receptor binding motif (the part that binds to our cell receptor called hACE2) has 10 mutations." This is a higher number of mutations than previous variants of concern.

Approximately 100 genome sequences have now been analyzed that were obtained from the Gauteng province. However, scientists are concerned that the variant could be present across the wider geographic area of South Africa.

Scientists hypothesize that the variant could have emerged in an individual that is immunocompromised, who became infected with the virus but was unable to clear it. This provides the virus with an opportunity to evolve. "The same hypothesis was proposed for the Alpha variant, and studies have been done in individual immunocompromised patients that show changes occur in the virus over time, and in response to antibody therapy," said Peacock. She added that, in the context of aiding a pandemic response, looking to pinpoint the index case of a VOC could be counterproductive.

What do we know so far about the impact of these mutations?

The large number of mutations that B.1.1.529 carries has sparked concerns that it could be more transmissible, or more likely to cause severe illness, than the original strain of the virus and previous VOCs. “From the suite of mutations, we can expect that B.1.1.529 is less well recognized by neutralizing antibodies, (i.e., the antibodies that bind to the spike protein and thus precluding attachment to host cells and hence infection). As such, we anticipate B.1.1.529 is more likely to (re-) infect people who acquired immunization from vaccination and previous infection," Francois Balloux, professor of computational systems biology and director of the UCL Genetics Institute, told the SMC.

He emphasized that, at present, it is not possible to make any robust predictions based on the genetic analysis from the Gauteng province alone. Thus far, B.1.1.529 has been detected in Botswana and South Africa, and in one incoming traveler from South Africa in Hong Kong, Balloux added.

What happens now?

The World Health Organization (WHO) will be meeting to discuss the new variant. "Right now, researchers are getting together to understand where these mutations are and what that potentially may mean for our diagnostics or therapeutics or vaccines. It's good that they [variants] are being detected, it means that we have a system in place, and it will take a few weeks," Dr. Maria Van Kerkhove, infectious disease epidemiologist at University College London and COVID-19 technical lead at the WHO said. "There's a lot of work that is underway."

Speaking on Twitter, the UK Health Secretary Sajid Javid said that the UK Health Security Agency is investigating the new variant.  

Will B1.1.529 become a VOC?

At this stage, the new variant has not been declared a variant of concern (VOC), but that could soon change. "Based on the limited evidence available so far, B.1.1.529 probably qualifies as a VOC. It will likely be elevated to that status before the end of the week," Balloux said.

If B.1.1.529 is determined to be a VOC, it will be assigned a Greek letter – like the other SARS-CoV-2 variants – which will most likely be Nu (v).