A novel lineage of SARS-CoV-2, designated B.1.1.529, was 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.
What makes the Omicron variant unique?
The Omicron variant is intriguing since it has a substantial number of mutations when compared to other widely circulated variants across the globe. This covers 32 spike protein mutations. Many of these mutations are found in the spike protein’s receptor-binding domain, a crucial component of the protein that binds to human receptor proteins to allow entrance into the cell, and hence may have a role in antibody recognition by past infection or vaccinations.
The variant has been detected among travellers from South Africa, as well as other countries in the region, and has been epidemiologically connected to a recent surge in cases in the Gauteng province of South Africa.
What are the effects of spike mutations?
Many mutations in the spike protein have previously been linked to antibody resistance as well as enhanced transmission. As a result, this variety may be more likely to reinfect patients who have established immunity to prior viral strains. While the virus’s behaviour cannot be predicted precisely based on evidence from individual mutations, since the impact of a combination of mutations is not equal to the sum of individual mutations, such analysis might give helpful insights and pointers for further research. More research on the impact of these mutations on transmissibility and vaccine evasion is now underway.
Certain of the spike protein mutations cause primers used in some RT-PCR kits to not work as intended, which is a diagnostic issue. This is also known as spike gene target failure or spike gene dropout (SGTF). While most kits employ various primer sets to detect distinct genes in SARS-CoV-2 RNA, this should not compromise the diagnosis and may be used as a proxy for fast variant identification. However, this method is not exclusive to Omicron; other variants may have identical mutations that result in a surge in gene dropout.
Is there a risk of vaccine-related illnesses as a consequence of the variant?
Because some of the first people infected with the variant were also vaccinated against COVID-19, the variant has the potential to produce vaccine-breakthrough infections. This should not be of concern, since the most common variants of concern, such as Delta, have been demonstrated to cause breakthrough infections. It’s unclear if the variant produces more breakthrough infections than Delta.
What is the total number of nations that have reported Omicron?
Nine nations have verified the presence of Omicron yet. South Africa, Botswana, England, Hong Kong, Australia, Italy, Israel, the Czech Republic, and Belgium are among those countries.
Suspected instances are being investigated in many additional countries. Genomic monitoring programmes in many countries have detected the variant. Researchers in Botswana and South Africa, as well as nations that reported infection in incoming travellers, worked tirelessly to make the first reports of the variant possible.
Apart from independent research programmes, India has a nationwide genomic surveillance programme (INSACOG) as well as focused surveillance programmes in Kerala, Maharashtra, Delhi, and Karnataka. According to the latest INSACOG Bulletin, no sequenced samples in India carry the Omicron variant yet. The variation is being monitored more closely.
How can we prepare for the Omicron variant?
To discover and monitor the occurrence of the Omicron variant, more surveillance and genome sequencing efforts are required. Rapid sharing of the virus’s genomic sequences and epidemiological data to publically accessible databases will aid in the development of a deeper knowledge of the variant. To manage and prevent transmission, existing public health and social interventions must be improved.
To tackle the new variation, increasing vaccination coverage across diverse locations, as well as access to diagnostics, treatments, and support, will be critical. Controlling the Omicron variation and limiting the establishment of any subsequent variants would need equitable access to vaccinations.