On November 26, the World Health Organization designated the newly recognized SARS-CoV-2 lineage B.1.1.529 with a whooping 32 mutations in the spike protein alone a variant of concern and named it ‘Omicron’, making it the thirteenth lineage to obtain a Greek letter beneath its nomenclature system.
The Greek letter nomenclature of variants was launched by the WHO in 2021 as a uniform system of naming variants of curiosity and concern. This nomenclature system unifies the completely different methods of nomenclature which have existed because the starting of the COVID-19 pandemic. These largely embrace the scientific names assigned by GISAID, the most important open-access international database of genome sequences and associated knowledge of SARS-CoV-2, Nextstrain, which supplies a phylogenetic context of the genome sequences out there in the general public area, and Pango, a community of researchers for dynamically figuring out and naming lineages of SARS-CoV-2.
Bypassing phases
With the designation of Omicron as a variant beneath monitoring and additional as a vaariant of concern (VOC) inside a quick span of two days, the WHO bypassed the stage of initially designating it as a variant of curiosity (VOI), which is a important departure from the priority adopted for different variants of concern in the previous.
For context, whereas the designation of Delta took about six weeks from the reporting of the lineage to the Pango community to the designation of the lineage as a VOC, Omicron was designated inside a week of detection of the lineage (B.1.1.529). Delta, in distinction, was first designated a VOI in April this yr and was additional upgraded to a VOC on May 11, taking into account the rising proof on the transmissibility, epidemiological correlations from India in addition to experimental proof from throughout the globe. Omicron, in distinction, was designated as a variant beneath monitoring on November 24 and was labeled as a VOC two days later.
The fast tempo at which WHO designated Omicron a VOC was a resolution that didn’t come out of haste however was based mostly on concrete scientific proof which got here early from Africa, though additional efforts for evaluating the variant shall proceed to achieve extra proof. The well timed detection of Omicron is predominantly attributable to the routine genome sequencing efforts of Network for Genomic Surveillance in South Africa (NGS-SA), an elaborate genomic and epidemiological surveillance community in South Africa comprising over 10 laboratories and educational establishments having a wealthy expertise of having handled earlier waves of COVID-19, together with the detection of the VOC Beta late in 2020. The wider attain of sequencing applied sciences and open-access databases together with GISAID and NCBI, which make genome sequencing knowledge publicly out there for analysis and interpretation, has additionally created a close to real-time system for knowledge era, knowledge sharing and interpretation. Along with these components, the immediate detection of Omicron and lots of extra new lineages in current months can also be attributed to the massive quantity of researchers who collaborate on-line and sift by rising genome sequences of the virus and maintain a fixed lookout for clusters of curiosity.
Three components
Typically, a variant is designated a VOC if it has proof that helps one of the three potential components – improve in transmissibility or a detrimental change in COVID-19 epidemiology, improve in virulence or change in medical illness presentation, or lower in effectiveness of public well being and social measures together with vaccines, therapeutics and diagnostics.
The early proof for Omicron steered a detrimental change in COVID-19 epidemiology, together with potential improve in transmissibility and decreased effectiveness of vaccines. The detection of the variant epidemiologically coincided with an outbreak and a additional uptick in the quantity of COVID-19 circumstances in Gauteng, South Africa, which was beforehand affected by the Delta wave and was anticipated to have excessive neighborhood immunity. There have been a number of situations of absolutely vaccinated circumstances, together with the place a booster dose had been obtained. This steered that the variant poses a increased threat of reinfection and vaccination breakthrough.
In distinction with the earlier VOCs, a important corpus of datasets having purposeful annotations of mutations in the virus based mostly on proof gathered from in-depth experiments from the world over is now out there to assist achieve a deeper understanding of mutations in the context of transmission, immune escape and affect on present diagnostic instruments and therapeutics.
Of the 32 mutations recognized in the Spike protein, a important massive quantity have been related to immune escape, cell entry in addition to higher binding to the human receptor proteins. Early structural evaluation was additionally suggestive of higher binding to the host receptors, which offered added confidence in the preliminary assessments. The early stories of a quantity of Omicron circumstances from completely different international locations in Europe additionally steered that the variant was certainly spreading quick. Apart from this, scientific proof gathered, classes learnt and knowledge gained whereas coping with the beforehand designated VOCs – Alpha, Beta, Gamma and Delta additionally helped in the evaluation.
Convergence of proof
The fast designation of Omicron as a VOC is due to this fact the convergence of a quantity of components, scientific proof of all of the above-mentioned components. A cluster of genome sequencing originating from Botswana, South Africa, in addition to a traveller from Hong Kong, all met the eyes of researchers in South Africa, which led to the designation of the cluster because the lineage B.1.1.529 by the Pango community.
While a half of the world prepares itself to fight the brand new variant with booster doses of vaccines and augmented healthcare preparedness, it’s a grim actuality that a massive quantity in one other half of the world are but to obtain their first dose of vaccine. The emergence of Omicron is thus a reminder that the virus will proceed to evolve and prevail so long as a massive half of the inhabitants lacks vaccines. The world needs to be reminded of the researchers in Africa, the place beneath 7% of the inhabitants is at the moment vaccinated, who labored in not the perfect of infrastructure, funding and assist methods that the world can provide, however have faithfully contributed to presenting with proof that enables the world to be higher ready to deal with the subsequent wave.
It is thus a disgrace that the healthcare staff in Africa must grapple with an upcoming wave of an infection with out entry to vaccines, therapeutics and assist important for combating the brand new variant. With the emergence of Omicron as a variant of concern, that we could lose many of our courageous African frontline warriors, for need of vaccines to the very menace they helped alert the world ought to certainly be a concern.
(The authors are researchers at CSIR-IGIB, New Delhi.)
