Vinod Scaria
In the point of view of evolution, the variant seems to have a short and initial spurt of accelerated evolution signifying an event followed by rapid transmission as seen in previous variants of concern Alpha, beta and Gamma variants.
At this point in time, we do not know whether the variant is more transmissible or causes immune escape from the available data, though the mutations have been independently associated with these properties. Research is underway to better characterize and understand the properties of the virus.
While the variant has been consistently present in the light of the surge in delta in the recent months in South Africa, there is not yet any evidence suggesting the variant is more transmissible than delta. The variant is not yet annotated as a variant of concern by the World Health Organisation.
The Genome Surveillance Dashboard does not yet report any instances of C.1.2 in India.
The continuous evolution of SARS-CoV-2 in South Africa: a new lineage with rapid accumulation of mutations of concern and global detection
31 August 2021
Recently there has been a lot of discussion on a new variant of SARS-CoV-2 identified in South Africa. This variant has been named C.1.2. Variants of SARS-CoV-2 are created as part of natural evolution and the virus continuously accumulates mutations as continued infection and transmission of the virus occurs across the world. C.1.2 emerged from the C.1 lineage which dominated the first wave in South Africa in 2020. The closely related C.1.1 was found in Mozambique with a spike mutation S477N and A688S.
C.1.2 is a variant recently discovered in South Africa. The initial discovery seems to have come from the Mpumalanga and Gauteng provinces of South Africa and as of August the variant has been found in six of the nine South African provinces.
The variant has been widely discussed, since it has 14 mutations in Spike. This includes three mutations (Y449H, E484K, and N501Y) in the Receptor Binding Motif of the spike protein which is important for binding to the Human ACE2 receptors. The significance being E484K and N501Y have been previously found in three of the four variants of concern (Alpha, Beta, and Gamma).
Recently there has been a lot of discussion on a new variant of SARS-CoV-2 identified in South Africa. This variant has been named C.1.2. Variants of SARS-CoV-2 are created as part of natural evolution and the virus continuously accumulates mutations as continued infection and transmission of the virus occurs across the world. C.1.2 emerged from the C.1 lineage which dominated the first wave in South Africa in 2020. The closely related C.1.1 was found in Mozambique with a spike mutation S477N and A688S.
C.1.2 is a variant recently discovered in South Africa. The initial discovery seems to have come from the Mpumalanga and Gauteng provinces of South Africa and as of August the variant has been found in six of the nine South African provinces.
The variant has been widely discussed, since it has 14 mutations in Spike. This includes three mutations (Y449H, E484K, and N501Y) in the Receptor Binding Motif of the spike protein which is important for binding to the Human ACE2 receptors. The significance being E484K and N501Y have been previously found in three of the four variants of concern (Alpha, Beta, and Gamma).
Apart from this, the virus also has deletions at amino acid positions 144 and 242-243 in the spike protein. The deletion at position 144 has been previously seen in Alpha and the 242-243 in the Beta lineages. The E484K and the deletion at amino acid position 144 in the spike protein has been previously independently associated with immune escape.
Additional mutations around the furin cleavage site of the spike protein associated with replication of the virus have also been noted, similar to other variants of concern.
There are over 100 sequences of C.1.2 in public domain databases at this moment and represented in at least eight additional countries including Mauritius, Zimbabwe, Botswana, China, New Zealand, Portugal, Switzerland and the United Kingdom.
Additional mutations around the furin cleavage site of the spike protein associated with replication of the virus have also been noted, similar to other variants of concern.
There are over 100 sequences of C.1.2 in public domain databases at this moment and represented in at least eight additional countries including Mauritius, Zimbabwe, Botswana, China, New Zealand, Portugal, Switzerland and the United Kingdom.
In the point of view of evolution, the variant seems to have a short and initial spurt of accelerated evolution signifying an event followed by rapid transmission as seen in previous variants of concern Alpha, beta and Gamma variants.
At this point in time, we do not know whether the variant is more transmissible or causes immune escape from the available data, though the mutations have been independently associated with these properties. Research is underway to better characterize and understand the properties of the virus.
While the variant has been consistently present in the light of the surge in delta in the recent months in South Africa, there is not yet any evidence suggesting the variant is more transmissible than delta. The variant is not yet annotated as a variant of concern by the World Health Organisation.
The Genome Surveillance Dashboard does not yet report any instances of C.1.2 in India.
What we need to keep in mind is that effective control of the spread of the virus through public heath measures and vaccination would indeed go a big way in preventing the emergence of new and dangerous variants.
About the Author
Vinod Scaria is a scientist at the CSIR Institute of Genomics and Integrative Biology and can be reached at @vinodscaria on Twitter
All opinions expressed are personal and do not reflect the opinion of their employers or organizations associated.
About the Author
Vinod Scaria is a scientist at the CSIR Institute of Genomics and Integrative Biology and can be reached at @vinodscaria on Twitter
All opinions expressed are personal and do not reflect the opinion of their employers or organizations associated.
References
Cathrine Scheepers, Josie Everatt, Daniel G. Amoako, Anele Mnguni, Arshad Ismail, Boitshoko Mahlangu, Constantinos Kurt Wibmer, Eduan Wilkinson, Houriiyah Tegally, James Emmanuel San, Jennifer Giandhari, Noxolo Ntuli, Sureshnee Pillay, Thabo Mohale, Yeshnee Naidoo, Zamantungwa T. Khumalo, Zinhle Makatini, NGS-SA, Alex Sigal, Carolyn Williamson, Florette Treurnicht, Koleka Mlisana, Marietjie Venter, Nei-yuan Hsiao, Nicole Wolter, Nokukhanya Msomi, Richard Lessells, Tongai Maponga, Wolfgang Preiser, Penny L. Moore, Anne von Gottberg, Tulio de Oliveira, Jinal N. BhimanThe continuous evolution of SARS-CoV-2 in South Africa: a new lineage with rapid accumulation of mutations of concern and global detection
medRxiv 2021.08.20.21262342; doi: https://doi.org/10.1101/2021.08.20.21262342
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