New Covid-19 variant in SA mutates 1.7 times faster

The new Covid-19 variant discovered in South Africa, and assigned to the PANGO lineage C.1.2, was first detected in Mpumalanga and Gauteng back in May 2021.

By June 2021, it had spread to KwaZulu-Natal and Limpopo, as well as England and China. As of 13 August, the Pango variant was detected in six of the nine South African provinces.

UPDATE: The Network of Genomic Surveillance in South Africa (NGS-SA) on Monday confirmed the C.1.2 lineage has now been detected in seven provinces.

“The majority of samples have been detected in Gauteng, followed by Limpopo and KwaZulu-Natal. […] Mpumalanga, the Eastern Cape and the Western Cape have two C.1.2 detections each”.

PANGO lineage C.1.2

Where was the new variant detected?

As per the study, the “variant has been detected throughout the third wave of infections in SA from May 2021 onwards and has been detected in seven other countries within Europe, Asia, Africa and Oceania”.

ALSO READ: Gauteng reaches 3 million mark for Covid-19 vaccines

Locally, the variant is in Gauteng, Mpumalanga, KwaZulu-Natal, Limpopo, Eastern Cape and Western Cape. Internationally, it has been detected in Congo, Mauritius, New Zealand, Portugal and Switzerland as well.

Researches say the PANGO lineage C.1.2 “contains many mutations that have been identified in all four variants of concern (Alpha, Beta, Delta and Gamma), as well as three variants of interest (Kappa, Eta, Lambda)”.

“The C.1.2 lineage is continuing to grow [As of 20 August], there were 80 C.1.2 sequences”.

PANGO lineage C.1.2 mutates 1.7 faster

In addition, the emergence of C.1.2 resulted from a rate of 41.8 mutations per year, meaning it mutates approximately 1.7 times faster than the current global rate.

“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 VOCs2,3,12,” the researchers say.

The variant is also highly mutated when compared to all other “variants of concern (VOC)” and “variants of interest (VOI)”, and is close to the evolutionary development of the Lambda variant.

Impact yet to be determined

The impact of the new Covid-19 variant on neutralisation antibodies (NAb), following natural infection or vaccine­induced immune response in South Africa, is yet to be determined.

Speaking to New Frame, one of the lead authors Catherine Scheepers said C.1.2 likely emerged after “a prolonged Covid-19 infection and accumulated additional mutations”.

She said it is still unclear whether the new linage is more transmissible than previous Covid-19 mutations. The research team will continue to monitor the C.1.2 variant.

The study – titled, ‘The continuous evolution of SARS-CoV-2 in South Africa: a new lineage with rapid accumulation of mutations of concern and global detection’ – is available in the medRxiv while the article undergoes peer review.

NOW READ: New C.1.2 variant: Vaccines needed ‘more than ever’

Evolution of the C.1 lineage in South Africa with multiple Spike mutations – pre-print at: https://t.co/kJ906bKfe6 – In this tweet thread, I highlight this lineage (assigned as C.1.2), the potential impact of the mutations, and the likelihood that this become a variant of concern

— Tulio de Oliveira (@Tuliodna) August 27, 2021