Is C.1.2 the South African Variant More Dangerous?

While it’s now finally been shown Delta is twice as dangerous for hospitalizations, there may be yet another VOC on the horizon.

South African scientists have detected a new coronavirus variant with multiple mutations but are yet to establish whether it is more contagious or able to overcome the immunity provided by vaccines or prior infection, the National Institute for Communicable Diseases (NICD) has said.

The variant, known as C.1.2, was flagged last week by the KwaZulu-Natal Research and Innovation and Sequencing Platform in a preprint study that has yet to be peer reviewed.

Even as Delta is so contagious that China’s service sector has contracted, and the U.S. struggles with inflation and wage gains (and a service labor shortage) that certainly aren’t transitory, eventually a variant will come along that could displace Delta.

C.1.2 caught scientists’ attention because its mutation is almost twice as fast as observed in other global variants. C.1.2 has popped up across South Africa as well as in seven other countries in Africa, Asia and the Pacific, the researchers report.

They’re not sure whether its constellation of mutations will make it more dangerous, but it carries changes that have given other variants increased transmissibility and the ability to evade the immune system’s response to some degree.

  • C.1.2 was first detected in May and has spread to a majority of South Africa’s provinces as well as seven other countries, including China, Portugal and the U.K.
  • C.1.2. has been identified in South Africa, the Democratic Republic of the Congo, Mauritius, China, New Zealand, England, Switzerland and Portugal. It seems to have an unusually high mutation rate and more mutations than other variants of concern (VOCs) or variants of interest (VOIs).

Suddenly, at the end of August 2021, there’s a slew of news reports about C.1.2 and, we have to admit, there hadn’t been a new variant on the radar for a while and we were due.

The fear is that the transmissibility of Delta combines with a more vaccine resistant mutation. Researchers at South Africa’s National Institute for Communicable Diseases and the KwaZulu-Natal Research Innovation and Sequencing Platform found C.1.2 has a mutation rate of about 41.8 mutations per year, nearly double the current global mutation rate observed in other VOCs.

It is however not frequent enough to qualify as a “variant of interest” or a “variant of concern” such as the highly transmissible Delta and Beta variants, which emerged in South Africa late last year. At least, not yet. Lambda or C.37 never seemed to evolve as transmissible enough to compete with Delta, at least much outside of Peru.

C.1.2. evolved from C.1., a lineage of the virus that dominated infections in the first wave of the virus in South Africa in mid 2020. South Africa has been the hardest his country in Africa thus far. Genomic sequencing data from South Africa show the C.1.2 variant was still nowhere near displacing the dominant Delta variant in July, the latest month for which a large number of samples was available. C.1.2 is only from 3% to 5% of total cases in South Africa.

As for global economic recoveries we have to keep in mind we are entering flu season now. Delta is the fastest and fittest variant the world has encountered, and it is upending assumptions about COVID-19 even as nations loosen restrictions and reopen their economies.

However scientists worry that a more deadly variant could trigger the pandemic to hit health care systems (with ICU nurse churn) even harder in 2022 and 2023.

According to the yet-to-be peer reviewed study posted on the preprint repository MedRxiv on August 24, C.1.2 has mutated substantially compared to C.1, one of the lineages which dominated the SARS-CoV-2 infections in the first wave in South Africa.

South African scientists also discovered the beta variant in 2020, but have been keen to stress that the country’s advanced ability to sequence the genomes of the virus means that while new strains may be identified in the country, they could have originated elsewhere. We don’t know much about the new variant, but it’s one to watch as some countries have their fourth or fifth waves.

Delta hit China maybe harder than we were told. The official non-manufacturing PMI for August came in at 47.5, the lowest reading since the height of the pandemic in China in early 2020.

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