South Africa Reports Emergence Of New Worrisome SARS-CoV-2 Variant C.1.2 That Has Enhanced Transmissibility And Immune Evasion!
South African researchers from the National Institute for Communicable Diseases (NICD), University of the Witwatersrand, University of Cape Town, University of Pretoria, University of KwaZulu-Natal and the Charlotte Maxeke Johannesburg Academic Hospital have discovered a new emerged SARS-CoV-2 variant called C.1.2 that is currently gaining dominance in circulation and could change the course of the COVID-19 pandemic as it is far more transmissible and also immune evasive due to enhancement by newer mutations found on its genome.
Both the WHO and also the U.S. CDC has been informed of the development and from the GSAID platforms it can be seen that C.1.2 variants has since been detected across the majority of the provinces in South Africa and alarmingly also in seven other countries spanning Africa, Europe, Asia and Oceania!
The report from study findings were published on a preprint server and are currently being peer reviewed. https://www.medrxiv.org/content/10.1101/2021.08.20.21262342v1
Various emerging SARS-CoV-2 variants of interest have been associated with increased transmissibility, neutralization resistance and disease severity.
Fortunately ongoing SARS-CoV-2 genomic surveillance world-wide has improved researcher’s ability to rapidly identify such variants.
The South African study team reports the identification of a potential variant of interest assigned to the PANGO lineage C.1.2. This lineage was first identified in May 2021 and evolved from C.1, one of the lineages that dominated the first wave of SARS-CoV-2 infections in South Africa and was last detected in January 2021.
Alarmingly, the emergence of C.1.2 variant
was associated with an increased substitution rate, as was previously observed with the emergence of the Alpha, Beta and Gamma variants of concern (VOCs).
While the VOI Lambda (C.37) is phylogenetically closest to C.1.2, the latter has distinct lineage-defining mutations.
The new C.1.2 variant contains multiple substitutions (R190S, D215G, N484K, N501Y, H655Y and T859N) and deletions (Y144del, L242-A243del) within the spike protein, which have been observed in other VOCs and are associated with increased transmissibility and reduced neutralization sensitivity.
However, of greater concern is the accumulation of additional mutations (C136F, Y449H and N679K) which are also likely to impact neutralization sensitivity or furin cleavage and therefore replicative fitness.
Though these mutations occur in the majority of C.1.2 viruses, there is additional variation within the spike region of this lineage, suggesting ongoing intralineage evolution.
Approximately 44% of the viruses also contain a P25L mutation in the NTD, ~19% have L585F in S1, ~16% have T478K in the RBM, ~11% contain P681H adjacent to the furin cleavage site, 8% have D936H, and a further ~8% have H1101Q in S2. The majority of these mutations (P9L, C136F, R190S, D215G, L242del, A243del, Y449H, E484K, N501Y, H655Y, and T716I) appeared together early in the lineage evolution (Fig. 3a). Thereafter, the majority of sequences have also accumulated the mutations Y144del, N679K and T859N. The mutations P25L, W152R, R
346K, T478K, L585F, N440K, P681H, A879T, D936H and H1101Q can be seen in some of the smaller clusters from more recent sequences, further highlighting continued evolution within the lineage.
Researchers are worried that continued evolution of this lineage could result in the much anticipated deadly ‘Omega’ variant.
The C.1.2 lineage was first detected in the Mpumalanga and Gauteng provinces of South Africa, in May 2021. In June 2021, it was also detected in the KwaZulu-Natal and Limpopo provinces of South Africa as well as in England and China.
As of August 13, 2021 the C.1.2 lineage has been detected in 6/9 South African provinces (including the Eastern Cape and Western Cape), the Democratic Republic of the Congo (DRC), Mauritius, New Zealand, Portugal and Switzerland
The study team warns that while the phenotypic characteristics and epidemiology of C.1.2 are being defined, it is important to highlight this lineage given its concerning constellations of mutations.
: The C.1.2 according to latest study findings have a mutation rate that is almost twice of the Delta variant.It means that the C.1.2 variant has somehow mutated so fast and far that it is now the Furthest Mutated
variant found to date! It has mutated the greatest genetic distance from the original Wuhan 1.0 strain and implies potential troubles for 1.0 vaccines.
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