SARS-CoV-2: How Serious is B.1.1.529 variant, now named Omicron

The B.1.1.529 variant was first reported to WHO from South Africa on 24^th November 2021. The first known confirmed B.1.1.529 infection was from a specimen collected on 9^th November 2021¹. Another source² indicates that this variant was first detected in samples collected on 11^th November 2021 in Botswana and on 14^th November 2021 in South Africa. Since then, the number of COVID-19 cases has steeply increased in almost all provinces in South Africa. As on 27^th November 2021, new cases of this variant have also been reported in Belgium, Hong Kong, Israel, United Kingdom³, Germany, Italy and Czech Republic which are all travel related in origin.  

Thanks to the South African authorities for taking no time in communicating and sharing relevant information with the global scientific community so that WHO’s expert group could meet on 26^th November 2021 and swiftly designate this variant as a Variant of concern (VOC). Seriousness of the matter could be gauged from the fact that B.1.1.529 was designated a variant under monitoring (VUM) only two days ago on 24^th November 2021 before being designated as VOC on 26^th November 2021 without being designated first as variant under investigation (VOI).  

Table: SARS-CoV-2 Variants of concern (VOC) as on 26 November 2021 

The urgency in designating B.1.1.529 as a variant of concern (VOC) was warranted because it was found that this variant is the most divergent variant of SARS-CoV-2 so far. Compared to the SARS-CoV-2 virus originally detected in Wuhan, China, this has as many as 30 amino acid changes, 3 small deletions and 1 small insertion in the spike protein. Out of these changes, 15 are located in the receptor binding domain (RBD), the part of virus that allows it to gain entry into human cells, leading to infection. This variant also has a number of changes and deletions in other genomic regions². The mutations are so extensive that one could call it a new strain, instead of a variant. The incredibly high amount of spike mutations means an increased possibility of escape from known antibodies which make this variant a matter of grave concern⁵.  

Changing to new variants is common to coronaviruses. It has always been nature of things for the coronaviruses to undergo mutation in their genomes at extremely high rates, due to lack of proofreading nuclease activity of their polymerases; more the transmission, more the replication errors and hence more mutations accumulate in the genome, leading to new variants. Human coronaviruses have been building up mutations to create new variants in the recent history. There were several variants responsible for epidemics since 1966, when the first episode was recorded⁶. But, why such an extensive mutation in a single burst? May be, because B.1.1.529 variant evolved during a chronic infection of immunocompromised person, possibly an untreated HIV/AIDS patient⁷.  

Whatever may be the cause of extensive mutations, if the rapid rate at which it has spread in South Africa is any indication, evolution of this variant may have tremendous bearing on immunity, transmissibility & virulence and effectiveness of existing vaccines, currently in use.  

Whether the existing vaccines will remain effective against this new variant or if there will be more instances of vaccine breakthrough infections, there is little data currently available to draw any conclusion. However, in a recent study, a synthetic variant with 20 mutations in the spike protein had shown almost complete escape from antibodies⁷. This indicates that the new variant B.1.1.529 with far more increased mutations, may show significantly reduced neutralisation by antibodies. The new variant, however, does seem to be more transmissible going by the rapid rate at which it has replaced the Delta variant in South Africa, though the current data is not adequate enough to draw any reliable estimate. Similarly, it is not possible to comment on the severity of symptoms at this stage.  

In view of the fact that Europe is already reeling with an unusually high number of COVID 19 cases (due to highly transmissible delta variant) for the past few weeks and the rapid rate at which Omicron (B.1.1.529) variant has spread in South Africa recently replacing delta variant, several countries in Europe including UK, Germany and Italy have imposed travel restrictions on arrivals from South Africa and from neighbouring countries like Botswana, Malawi, Mozambique, Zambia and Angola. Fearing the worst, Israel is to ban the entry of visitors from all countries.  

The world has invested so much in developing and administering COVID-19 vaccines to protect people from the pandemic. The question that is topmost in the mind of scientists and authorities alike is whether the main COVID-19 vaccines like Pfizer–BioNTech, Oxford–AstraZeneca, Moderna, Johnson & Johnson will remain effective against Omicron (B.1.1.529) variant as well. This is fuelled by the fact that breakthrough infections have been reported in South Africa. The two Hong Kong cases too had received vaccine doses⁹. 

Development of ‘’pan-coronavirus” vaccines¹⁰ (multivalent vaccine platforms¹¹) seem to be the need of the hour. But, more quickly, it may be possible to quickly manufacture booster doses of mRNA and DNA vaccines covering the mutations. In addition, the recently approved antivirals (Merck’s Molnupiravir and Pfizer’s Paxlovid) should come handy in protecting people from hospitalisation and deaths.   

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References:  

1. WHO 2021. News – Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern. Published 26 November 2021. Available online at https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern  

2. European Centre for Disease Prevention and Control. Implications of the emergence and spread of the SARSCoV-2 B.1.1. 529 variant of concern (Omicron), for the EU/EEA. 26 November 2021. ECDC: Stockholm; 2021. Available online at https://www.ecdc.europa.eu/en/publications-data/threat-assessment-brief-emergence-sars-cov-2-variant-b.1.1.529  

3. UK Govt 2021. Press release – First UK cases of Omicron variant identified. Published 27 November 2021. Available at https://www.gov.uk/government/news/first-uk-cases-of-omicron-variant-identified   

4. WHO, 2021. Tracking SARS-CoV-2 variants. Available online at https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/ 

5. GitHub, 2021. Thomas Peacock: B.1.1 decendant associated with Southern Africa with high number of Spike mutations #343. Available online at https://github.com/cov-lineages/pango-designation/issues/343 

6. Prasad U.2021. Variants of Coronavirus: What We Know So Far. Scientific European. Posted 12 July 2021. Available online at http://scientificeuropean.co.uk/covid-19/variants-of-coronavirus-what-we-know-so-far/ 

7. GAVI 2021. Vaccine work – What do we know about the new B.1.1.529 coronavirus variant and should we be worried? Available at https://www.gavi.org/vaccineswork/what-we-know-about-new-b11529-coronavirus-variant-so-far 

8. Schmidt, F., Weisblum, Y., Rutkowska, M. et al. High genetic barrier to SARS-CoV-2 polyclonal neutralizing antibody escape. Nature (2021). https://doi.org/10.1038/s41586-021-04005-0 

9. Heavily mutated coronavirus variant puts scientists on alert. Nature News. Updated 27 November 2021. DOI: https://doi.org/10.1038/d41586-021-03552-w  

10. Soni R. 2021. “Pan-coronavirus” vaccines: RNA Polymerase Emerges as a Vaccine Target. Scientific European. Published 16 November 2021. Available at http://scientificeuropean.co.uk/covid-19/pan-coronavirus-vaccines-rna-polymerase-emerges-as-a-vaccine-target/  

11. NIH 2021. News release – NIAID issues new awards to fund “pan-coronavirus” vaccines. Posted 28 September 2021. Available at https://www.nih.gov/news-events/news-releases/niaid-issues-new-awards-fund-pan-coronavirus-vaccines  

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