What is the risk associated with the new variant of SARS-Cov-2, the Omicron?

Yusuf Akhter


The Omicron variant of SARS-Cov-2 was recently reported. What distinguishes it from other variants? Where has this coronavirus variant been discovered thus far?

A new lineage of SARS-CoV-2, designated as B.1.1.529, was recently discovered in samples sequenced and released in the public domain from Botswana, South Africa, and Hong Kong. The World Health Organization (WHO) has identified the variant as a Variant of Concern (VoC), and it has been given the name ‘Omicron’.

The Omicron variant is intriguing since it contains more number of mutations when compared to other widely circulated variants around the world. This covers 32 spike protein mutations. Many of these mutations are found in the receptor-binding domain of the spike protein, which is a crucial component of the protein that binds to human receptor proteins to allow the entry of the coronavirus into the cells, and hence may have a role in antibody recognition by past infection or vaccinations. In India, this variant has been detected among tourists from South Africa, and other countries from the same region, and has been epidemiologically connected to a recent surge in cases in the Gauteng province of South Africa.

Many mutations in the spike protein have previously been linked to antibody resistance as well as enhanced transmission. As a result, this variant may be more likely to re-infect patients who have established immunity to previous viral strains. While the behavior of the coronavirus cannot be predicted precisely based on evidence generated from individual mutations, because the effect of a combination of mutations is not equal to the sum of individual mutations, such analysis might provide useful insights and pointers for further research. More research into the effects of these mutations on transmissibility and vaccine escape should be conducted.

Some of the spike protein mutations fail primers used in available RT-PCR kits, which makes them undetectable yielding a pseudo negative result. This is also known as spike gene target failure or spike gene dropout. While most of the kits use various primer sets to detect distinct genes in SARS-CoV-2 RNA, this should not compromise the diagnosis and can be used as an alternative for fast variant identification.

However, this mutation is not unique to Omicron; other variants may have identical mutations that result in a surge in pseudo negative results. Because some of the first people infected with this variant were also vaccinated against COVID-19, it is not thought that this variant has the potential to produce vaccine-breakthrough infections. But, it is not new since the most common VoC, such as Delta, has been demonstrated to cause breakthrough infections. It is still not known whether this variant is capable of causing more breakthrough infections than Delta. Nine countries have confirmed the presence of Omicron so far – South Africa, Botswana, England, Hong Kong, Australia, Italy, Israel, the Czech Republic, and Belgium. Genomic surveillance programmes in many countries have detected the presence of Omicron. Researchers in Botswana and South Africa are the first to have detected this variant for the first time in the world.

No sequenced samples from India have revealed the existence of Omicron yet. Increased surveillance and genome sequencing efforts are needed to detect and track the spread of Omicron. Augmented efforts for rapid sharing of genomic sequence and epidemiological data to publicly available databases are urgently needed. This will contribute to the development of a better understanding of coronavirus variants.

Existing public health and social measures must be strengthened in order to manage and prevent transmission. Bigger vaccine coverage across the diverse locations of the country, as well as access to diagnostics, therapies, and medical support will be important in combating the new emerging and re-emerging variants. Controlling the Omicron variant and controlling the spread of future variants will necessitate inclusive immunization for all the citizens of the country.


[Dr. Yusuf Akhter is a faculty member at Department of Biotechnology, Babasaheb Bhimrao Ambedkar  University, Lucknow. He is editorial board member of several reputed journals like Scientific Reports (Nature), Frontiers in Genetics, etc.]