Variant News: Yet Another New Antibody-Resistant SARS-CoV-2 Variant Emerges In Colombia But WHO Still Classifying It As A VOI and Not VOC!
Source: Variant News Mar 17, 2021 3 years, 8 months, 4 days, 7 hours, 28 minutes ago
Variant News: Researchers from Instituto Nacional de Salud-Bogotá and Universidad Cooperativa de Colombia have alarmingly discovered yet another SARS-CoV-2 variant in Colombia that is antibody resistant and bears the L249S and E484K spike substitutions. Despite the same mutations having convergently appeared in other mutant strains of the virus, most notably in variants of concern, the WHO is still classifying the variant as a VOI or variant under investigation. There are speculations that the WHO is under pressure from vaccine manufacturers and also the Biden led American administration to downplay the seriousness of these emerging variants and also their ability to escape the vaccines.
The COVID-19 pandemic has led to genetic diversification of SARS-CoV-2 and the appearance of variants with potential impact in transmissibility and viral escape from acquired immunity. The Colombian study team reports a new lineage containing ten amino acid changes across the genome. Further studies are currently underway to assess its epidemiologic impact.
The discovery and study findings were published on a preprint server and are currently being peer reviewed.
https://www.medrxiv.org/content/10.1101/2021.03.12.21253000v1
The study team identified the new highly divergent SARS-CoV-2 lineage with spike substitutions L249S and E484K.
It is believed that the rapid spread and RNA nature of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have allowed it to give rise to mutant strains.
Despite only a few current variants are of real concern above the base virus, so far, over 800 lineages have been described, many of them evolving the same mutations independently of each other.
Lead researcher Dr Katherine Laiton-Donato and the rest of the study team in Colombia have now sequenced a new highly divergent variant, with mutations including Spike substitutions L249S and E484K.
Importantly these two substitutions are thought to be associated with immune escape. The presence of E484K is especially believed to be responsible for resisting antibodies from convalescent blood plasma. These two mutations are associated with the B.1.1.28 and B.1.351 lineages (the Brazilian and South African variants, respectively), two variants of concern.
The study team used the Pangolin algorithm ie a database of recorded SARS-CoV-2 genomes, to determine an origin for the new Colombian sequence. The algorithm assigned the lineage as belonging to the B.1.111 lineage, first identified in the USA in early March 2020. This variant is currently circulating in Colombia, USA, Aruba, and Belgium. A Maximum Likelihood phylogenetic tree was also used to estimate the parental lineage. The results of this also supported B.1.111 parentage. Other mutations within the sequence are also consistent with this hypothesis.
Interestingly despite this consensus, there are still many distinct mutations present in the newly identified strain that are divergent from B.1.111.
The study team posits that a larger sample size may well continue to support B.1.111 parentage. However, an alternative explanation is that these mutations may have convergently arisen from intense, presently unknown, ecological pressures.
To date, the L249S and
E484K substitutions have appeared convergently in nearly 70 identified strains, and this is not wholly unsurprising considering these are both thought to be associated with provided antibody resistance.
Alarmingly the rapid emergence of convergent antibody-resistant viral strains will challenge the current global vaccination program, as mutations such as L249S and E484K may be able to arise in any local population within any country sporadically.
The study team concludes, “In the context of pandemic spread of the virus, an enormous virus population size is expected, as it is also the emergence of virus variants that could also make possible the emergence of antibody-resistant mutants in the context of natural infection in immunocompetent people. It is necessary to evaluate the impact of this genetic background in the neutralization efficacy of convalescent sera/plasma from acquired immunity.”
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