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New COVID-19 Variant C.1.2 Found In South Africa: Everything About This New ‘Variant Of Interest’

Recently, a new variant of COVID-19 has been identified by scientists in South Africa. It is known to be a potential 'Variant of Interest' and is assigned to the PANGO lineage C.1.2.

Scientists say that they are still unsure of the dangers related to this new variant, but according to the many older and new mutations it carries, there are chances of increased transmissibility of this variant. The virologists of South Africa's National Institute for Communicable Diseases say that they are keeping an eye on it and is investigating more on C.1.2.

Let's know about C.1.2 in detail.

When Was C.1.2 First Identified?

According to the study that is still a preprint in the server medRxic and has not been peer-reviewed yet, the C.1.2 variant was first identified in May 2021 in the two provinces of South Africa: Mpumalanga and Gauteng at the time when the third wave of COVID-19 was ongoing in the country.

The C.1.2 is known to have evolved from lineage C.1 that has dominated the first wave of COVID-19 in South Africa and was last detected in January 2021.

Later in June, this new variant was also detected in the Limpopo and KwaZulu-Natal provinces of South Africa and in countries like England and China.

Since then, it has been identified in a majority in many other provinces of South Africa, along with seven other countries spanning Europe, Asia, Africa and Oceania.

As of 13 August 2021, the C.1.2 variant of COVID-19 has been reported in six out of nine provinces of South Africa, including the Eastern Cape and Western Cape, Mauritius, the Democratic Republic of the Congo (DRC), New Zealand, Switzerland and Portugal.[1]

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Is C.1.2 Variant Concerning?

According to the researchers of the study, the emerging of the new variant C.1.2 is linked to a high substitution rate, similar to Alpha, Beta and Gamma variants (VOCs). The high substitution rate implies high mutation and short replication rates.

The C.1.2 has the following spike protein mutations: R190S, D215G, N484K, N501Y, H655Y and T859N, Y144del and L242-A243del.

These mutation types have been observed in many other 'Variant of Concerns' (VOCs) which are known for their increased transmissibility and low sensitivity to antibody neutralisation.

The reason why C.12 could be concerning is because of the presence of additional spike protein gene mutations C136F, Y449H and N679K. These additional genes could possibly lower antibody neutralisation sensitivity or furin cleavage and increase infectivity. [2]

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In the older mutated version of C.1.2 i.e C.1, only the D614G mutation was present. The D614G was previously known to be the dominant COVID-19 lineage with a high transmissibility rate.

However, with its new evolved version consisting of multiple older and new mutations, it is clear that C.1.2 can be concerning compared to any of its earlier versions and also, other VOCs and VOIs.

The study mentions "C.1.2 is highly mutated beyond C.1 and all other VOCs and VOIs globally with between 44-59 mutations away from the original Wuhan Hu-1 virus. While the VOI Lambda (C.37) is phylogenetically closest to C.1.2, the latter has distinct lineage-defining mutations".

When Has C.1.2 Caught Scientists' Attention?

Earlier, it was the Delta variant that was predominating other variants of COVID-19 globally, including South Africa. However, during the ongoing genomic surveillance in the country, it was found that the sequence assigned to C.1 is on the rise during the third wave (May 2021).

This was quite unexpected as C.1 variant was first identified in the country itself during the first wave and is also distinct from C.1.1 due to multiple mutation types. This has made scientists assign a new lineage to C.1 as C.1.2 on 22 July 2021.

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According to the preliminary molecular clock that indicates the mutation rate of different organisms, the overall rate of evolution of COVID-19 is 24 substitutions a year, with many of its variants of interest/concern to approx 25.2 substitutions a year, with C.1.2 as 26.6 substitutions a year.

This clearly indicates that the new C.1.2 variant is having an increased substitution rate compared to many other sequences to date. Also, it is suggested to be 1.7-fold faster than the current global rate while 1.8-fold faster compared to the initial COVID-19 lineages.

The study mentions "This short period of increased evolution compared to the overall viral evolutionary rate was also associated with the emergence of the Alpha, Beta and Gamma VOCs, suggesting a single event, followed by the amplification of cases, which drove faster viral evolution."

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Symptoms Of C.1.2

As of now, there are no reports of any distinctive symptoms of C.1.2. Some of the common symptoms of C.1.2 may include headache, fever, sore throat, runny nose and body ache, similar to other variant types of COVID-19.

As we will get updates on its varying symptoms, we will update you with them accordingly.

Impact Of C.1.2 On COVID-19 Vaccine Efficacy

To date, the scientists do not have adequate experimental data to confirm the impact of the C.1.2 variant on antibody neutralisation following vaccination against COVID-19 in South Africa.

Another study based on the topic "Sixteen novel lineages of SARS-CoV-2 in South Africa" says that if the pandemic is not controlled with time and the COVID-19 virus keeps on mutating, the efficacy of the current vaccines could potentially be affected. [3]

To Conclude

C.1.2 has many mutations, all those which has previously been identified in all four variants of concern and three variants of interest of COVID-19, along with some additional mutations. This new variant is continuing to grow and is yet to determine the impact of this mutation type on humans.