What Bioinformatics Tells Us About the Omicron Variant

What Bioinformatics Tells Us About the Omicron Variant

By Jane Cook
December 7, 2021

How Was the Omicron Variant Identified?

A little over a week ago, the world heard about a new COVID-19 variant of concern, identified by the national genomic surveillance team in South Africa.

This variant, termed the ‘Omicron’ variant by the WHO, was first detected due to its unusual result via PCR that uses three genomic probes to identify COVID-19 infection. One of the three probes was consistently returning as negative, prompting a deeper dive into the genetics of the samples producing such results.

After genotyping over a hundred samples that produced the unusual PCR result, the Network for Genomic Surveillance in South Africa alerted the WHO that they had in fact identified a new, highly mutated SARS-CoV-2 variant that appeared to be spreading rapidly in South Africa.

What Does the Sequencing Data Tell Us?

The genomic sequencing data was rapidly shared by GISAID and analyzed by the COVID variant tracking group Nextstrain, who perform publicly available bioinformatic analyses of COVID sequencing data.

Analysis of the sequencing data highlights a high number of mutations in the virus’ spike protein, which it uses to enter host cells. Mutations to the spike protein in other variants like the Delta variant have increased transmissibility of the virus, which is a growing concern for this variant.

Proactive research groups have been modeling and analyzing mutations that may arise in future SARS-CoV-2 variants, and many of the mutations identified in the Omicron variant have been created in these virtual studies. Two predicted spike protein mutations have appeared in Omicron and appear to increase the virus’ ability to bind to ACE2, the receptor it interacts with to enter its host’s cells.

Can COVID Vaccines Keep Up?

It is unknown as of yet whether the Omicron variant can evade the immune protection provided by vaccination, and worrying reports from South African researchers indicate that Omicron may be especially good at reinfecting people who have recovered from a previous COVID infection or even vaccination.

There is cause for hope, however. Vaccine companies like Moderna can quickly and specifically alter the RNA sequences in their vaccines to make variant-specific booster shots, and these efforts are already well underway.

Without the quick work of bioinformaticians and high-quality sequencing data of viral samples, we would not be able to respond to new variants so rapidly.


Jane Cook, Journalist & Content Writer, Bridge Informatics

Jane is a Content Writer at Bridge Informatics, a professional services firm that helps biotech customers implement advanced techniques in management and analysis of genomic data. Bridge Informatics focuses on data mining, machine learning, and various bioinformatic techniques to discover biomarkers and companion diagnostics. If you’re interested in reaching out, please email daniel.dacey@old.bridgeinformatics.com or dan.ryder@old.bridgeinformatics.com.











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