Concerning constellations of mutations’: What to know about the C.1.2 variant of the coronavirus

Scientists identified a new variant of COVID-19 in South Africa and said in a recently pre-print paper that it displays “concerning constellations of mutations.”

There are only about 100 documented cases of the C.1.2 variant, first identified in May, in South Africa, according to the KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), which has been sequencing and tracking variants during the pandemic.

In the paper, which is preprint and has yet to be peer reviewed, researchers from KRISP outlined the various mutations that may one day make C.1.2. a variant of concern across the world. The Centers for Disease Control and Prevention has a “designated alert for further monitoring” on the variant, as of Wednesday, but it has yet to be listed as a variant of concern or interest.

Dr. Richard Lessells, an infectious disease specialist and a co-author of the paper, said he suspects, by extrapolation, that C.1.2 accounts for just 1% to 2% of cases in South Africa, but there is reason to suspect that it could become a dominant variant, such as delta. It has already been identified in eight of the nine South African provinces.

“I think really based on this mutation pattern, what we’re worried about is this combination of significant immune evasion and enhanced transmissibility,” Lessells said of C.1.2. “We just don’t know how that plays out, whether it may have increased transmissibility on a similar level to delta or not; we only know that by seeing how it plays out in the population.”

Lessells said there’s no need to sound significant alarms yet. He noted that it’s “quite plausible” that the variant will “fizzle out” and never reach the level of becoming a variant of concern.


“But it’s also plausible that we could start to see increasing cases,” he said. “It’s very difficult to predict, and unfortunately, we have to wait to see how it plays out.”

While there are only 100 cases reported thus far, that number can be misleading, Lessells said, as it only accounts for the samples obtained by the laboratory. It is likely that there are many cases that have yet to be documented or sequenced.

“But we’ve seen distribution can change quite rapidly,” Lessells said. “That’s where we are at the moment, actively monitoring that to see if distribution starts to change in the next weeks.”

In many cases, scientists have seen variants become the dominant strain of COVID-19 in a matter of weeks, Lessells said. That was the case for the beta variant,which first emerged in South Africa, as well as the highly transmissible delta variant first identified in India, so it’s important for scientists to continue monitoring the variant’s spread and evolution.

What is especially intriguing about C.1.2 is that it possibly evolved in immunocompromised individuals carrying an earlier strain of the virus in a process called “accelerated intra-host evolution,” Lessells said.

During intra-host evolution, people who are immunocompromised “and are unable to clear the virus in the short-term may have a more prolonged chronic infection,” so the virus evolves inside the body because of increased pressure from the immune system, Lessells said.

“So you get these variants emerging that, if they spread, they have an evolutionary advantage and it can start spreading more widely,” he added.

Lessells stressed that the research thus far on C.1.2 is “very preliminary,” but its many mutations make it likely that it will evade immunity, whether from the vaccine or previous infection. Further studies will be needed to determine whether this hypothesis will become an actuality.