What makes the South Africa variant different?

There are emerging variants of COVID-19 – like in the U.K. and South Africa -  which the lab is now in the process of getting, to begin testing on those.
Posted at 5:57 PM, Feb 11, 2021

SAN DIEGO (KGTV) -- Scientists detected the first cases of the South Africa variant in California this week, a version of the coronavirus that appears to be more elusive to current vaccines and the natural immunity produced by previous infections.

The South Africa variant shares a mutation with the UK variant that scientists believe makes the virus stickier to cells and more transmissible. The South Africa variant, officially known as B.1.351, also has two other mutations in its spike proteins that scientists consider troubling.

Researchers pay close attention to the spike proteins on the virus because they allow the pathogen to latch onto cells. Spike is also the protein targeted by the current generation of COVID-19 vaccines.

All of the current vaccines train the immune system to build antibodies by introducing fake spike proteins. These harmless imposters are designed to look just like the spiky knobs on the surface of the actual coronavirus.

But the South Africa variant has tiny mutations in its spikes that make it more difficult for some antibodies to lock on, based on early research.

“The whole spike doesn't change shape. What happens is a little knob or piece -- we call it an epitope -- that specific antibodies bind to is changed so they no longer bind,” said UC San Diego virologist Dr. Doug Richman.

A study by Moderna using blood samples found antibodies produced by its vaccine were six times less effective against the South Africa variant.

There have also been several confirmed cases of COVID survivors getting reinfected with the variant. One vaccine study in South Africa found new infections in 2 percent of people who had been infected with an earlier version of the virus.

Generally, second infections tend to be more mild than the first, Richman noted.

He also stressed that the vaccines have shown promising results in their ability to prevent severe disease caused by the variant, even if they can’t prevent symptoms entirely.

“What's going to happen is someone who would have a life-threatening or hospitalization-required infection will have a milder infection,” he said.

The South Africa variant is distinct from the UK variant, which has been detected in about 1,000 people in the United States.

The UK variant, B.1.1.7, currently accounts for about 1 to 2 percent of infections in the United States but is spreading rapidly. A study from Scripps Research estimates it is doubling in cases every 10 days and will become the dominant strain in this country by the end of March.

The two variants share a mutation that makes the virus stickier, known as N501Y. That scientific shorthand means at the 501st amino acid position in the viral sequence, an “N” (the abbreviation for asparagine) was replaced by a “Y” (the abbreviation for tyrosine).

But the South Africa variant contains two other mutations, E484K and K417N, that seem to help it escape, said Scripps researcher Karthik Gangavarapu.

“These mutations put together, the end result is that it’s able to escape immunity,” he said.

Gangavarapu is part of the lab that detected the UK variant in San Diego. He said so far, they have not detected the South Africa variant in their samples.