OMICRON VARIANT OF SARS-COV-2
By ¹Kwakye Sylvester, ²Darko Obiri Stella, and ³Lyanne Sackey
The omicron variant is the latest variant of the COVID-19 virus first identified in South Africa on November 24, 2021. It has been classified by WHO as a Variant of Concern (VoC) as cases have been recorded in about two dozen countries across all continents except Antarctica.
In Africa, the Omicron variant has now been detected in four countries, with Ghana (34 cases) and Nigeria (3 cases) becoming the first West African countries and the latest on the continent to report the new variant. So far, Botswana and South Africa have reported 19 and 172 Omicron variant cases, respectively. Globally, more than 20 countries have detected the variant to date. The two southern African countries account for 62% of cases reported globally.
The European Center for Disease Prevention and Control has also classified this variant as a variant of concern due to concerns of increased transmissibility compared to other variants.
The omicron variant has been found to contain many spike protein substitutions, some of which are known to be associated with reduced susceptibility to available monoclonal antibodies. The variant has been characterized by at least 30 amino acid substitutions, three deletions, and one insertion.
Among the mutations are E484A which is known to make the virus less recognizable to some antibodies. There is also the N501Y mutation which is known to give the alpha and gamma variants their increased transmissibility as well as the D614G Miata ion that helps the virus to better attach to cells it infects.
These mutations in the spike protein have raised concerns as to whether the vaccines already produced would be effective against this variant since the vaccines were designed using bits of the previous spike proteins to elicit immunity. Therefore a change in the spike protein has the potential to make it less recognizable to the immune system.
It is currently unclear how the omicron variant is transmitted and if it is associated with the more severe disease since a relatively low number of cases have been recorded.
Omicron (B.1.1.529) Characteristics
WHO (World Health Organization) Label: Omicron
Pango (Phylogenetic Assignment of Named Global Outbreak) Lineage: B.1.1.529
Next strain clade: 21K
The spike protein of the Omicron variant is characterized by at least 30 amino acid substitutions, three small deletions, and one small insertion. Notably, 15 of the 30 amino acid substitutions are in the Receptor Binding Domain (RBD). There are also several changes and deletions in other genomic regions.
Key Amino Acid Substitutions in Spike Protein (RBD substitutions in bold type): A67V, del69–70, T95I, del142–144, Y145D, del211, L212I, ins214EPE, G339D, S371L, S373P, S375F, K417N, N440K, G446S, S477N, T478K, E484A, Q493R, G496S, Q498R, N501Y, Y505H, T547K, D614G, H655Y, N679K, P681H, N764K, D796Y, N856K, Q954H, N969K, L981F
What Can We Do To Stay Safe
We must use all the prevention strategies available, including masking, improving ventilation, social distancing, handwashing, and testing to slow SARS-COV-2 transmission and stop the COVID-19 pandemic. The CDC recommends that everyone ages 2 years or older, including those who are fully vaccinated, wear masks in public indoor places in areas of substantial or high transmission.
For the most up-to-date information and guidance on diagnostic assays, which will be updated to reflect the impact of the Omicron variant, please refer to the U.S. Food and Drug Administration web page on SARS-CoV-2 Viral Mutations: Impact on COVID-19 Tests.
The CDC 2019-Novel Coronavirus (2019-nCoV) Real-Time RT-PCR Diagnostic Panel and the Multiplex Assay for Flu and SARS-CoV-2 are expected to detect the Omicron variant.
The Thermo Fisher TaqPath COVID-19 Combo Kit (3 total targets) has significantly reduced S-gene target sensitivity due to the deletion at H69 and V70 in the B.1.1.529 (Omicron) spike protein. Specimens being tested using the TaqPath COVID-19 Combo Kit that yield an S gene target failure (SGTF) could be Omicron. Importantly, any possible Omicron specimen must be confirmed by sequencing. Since the TaqPath COVID-19 Combo Kit is designed to detect multiple genetic targets, the overall test sensitivity should not be impacted.
“The world should not panic about the new Omicron variant of Covid-19 but it should prepare.
We’re in a different situation today than we were at the beginning of 2020, we have tools, we know what to do, we know what works. This was something we had expected, that new variants would emerge, we’ve been through rounds of other variants.
It is something to worry about, we didn’t want to see another variant emerge and spread around the world at this stage of the pandemic, certainly not what we wanted, but we’re not entirely surprised and I think we’re much better prepared to handle it.” — WHO’s Chief Scientist, Soumya Swaminathan told Reuters
Centers for Disease Control and Prevention