Omicron was first reported on November 25, 2021. Even after several waves of the pandemic, at a time when a considerable proportion of the population was vaccinated or had natural immunity, omicron still had a worldwide effect. It was first sequenced on a case from Botswana and, soon after, cases were found in people travelling from South Africa. The concerns around omicron are centered on four topics: the number of mutations; its transmissibility; its detection through lab tests; and the effectiveness of vaccines against it.
Omicron has a total of 18261 mutations in the genome [1] and around thirty of those mutations are related to the spike protein*. Based on our previous post, we know that viruses can change over time. They are continuously mutating and, if a certain mutation allows it to “survive” or spread faster, then that mutated virus is more likely to continue being transmitted. Some mutations in omicron’s genome are also present in other SARS-CoV-2 variants, like alpha, beta, gamma, or delta (please check this post for more information about the different COVID-19 variants). A few mutations already have a known effect but other mutations should be studied further [2].
Some of the mutations allowed omicron to have high transmissibility, which explains how fast omicron’s cases rose and spread around the world.
Moreover, one specific RT-PCR test (Thermo Fischer TaqPath COVID-19 assay) had trouble detecting omicron due to a “S-gene target failure” [3]. This means that the RT-PCR test had trouble recognizing the presence of the virus due to the differences in the S gene. However, it should be noted that many other RT-PCR test platforms were not affected because they targeted other genes or they targeted more than one gene of SARS-CoV-2. Therefore, even if the S gene was not detected, the N gene or the ORF1ab gene could still be identified [4].
Another problem is that the effectiveness of the mRNA vaccine decreased possibly due to waning immunity and/or omicron’s mutations helping it “escape” our immune system (more information on the post: “COVID-19 vaccine: do we need a third dose or booster shot?”). Indeed, the mRNA vaccines train our immune system to recognize and fight the spike protein, but this new omicron spike looks a bit different. Thus, if the spike changes, our body is less equipped to identify and combat the virus. This would partially compromise our efforts to fight this new variant. For more information about how our immune system recognizes pathogens, you can read this post or watch this video.
Despite the bad news, there is good news as well. Preliminary evidence has indicated that omicron may cause less severe symptoms – partially because it has trouble infecting lung tissue cells [5]. Moreover, the booster could help prevent moderate and severe COVID-19 cases. Overall, although the two-dose vaccine may have lower effectiveness against omicron, a booster dose can significantly increase the effectiveness and help prevent hospitalization [6].
In the context of the pandemic, receiving news of a third dose can be discouraging. People were told that two doses were helping to protect them against SARS-CoV-2… And they still do! The necessity of a booster for omicron is proof that vaccines are working; otherwise, a third dose of the same compound would not make a difference. The problem is that we are continuously facing new pressures and challenges in the form of mutated viruses. The same way that the influenza virus mutates every year (so we need new flu vaccine shots yearly), SARS-CoV-2 continues to evolve and our response to COVID-19 also needs to change accordingly.
*Protein - a molecule that forms the structure and gives function to organisms at the most basic level. Proteins consist of amino acids, which can be combined in different sequences to form different protein structures with different functions in cells.
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Written by: Nicole
Edited by: María and Natasha
BioDecoded is a volunteer group committed to sharing accurate scientific information. For more information about vaccines and their safety profile, please see previous posts or consult with your personal physician. If you have any questions about this topic, please comment or send them to our email.
References:
Araf, Y., et al. (2022) “Omicron variant of SARS-CoV-2: Genomics, transmissibility, and responses to current COVID-19 vaccines”, Journal of Medical Virology, pp. 1-8. Available at: https://onlinelibrary.wiley.com/doi/10.1002/jmv.27588
Salim, S., et al. (2021) “Omicron SARS-CoV-2 variant: a new chapter in the COVID-19 pandemic”, Lancet (398), pp. 2126-2128. Available at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8640673/
Ferré, V. et al. (2022) “Omicron SARS-CoV-2 variant: What we know and what we don’t”, Anesthesia Critical Care & Pain Medicine, 41(1), p. 100998. Available at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8660660/
Brown, K. et al. (2021) “S-Gene Target Failure as a Marker of Variant B.1.1.7 Among SARS-CoV-2 Isolates in the Greater Toronto Area, December 2020 to March 2021”, JAMA, 325(20), p. 2115. Available at: https://jamanetwork.com/journals/jama/fullarticle/2778599
U. et al. (2022) Omicron’s feeble attack on the lungs could make it less dangerous, Nature.com. Available at: https://www.nature.com/articles/d41586-022-00007-8 (Accessed: 2 March 2022).
Thompson, M. et al. (2022) “Effectiveness of a Third Dose of mRNA Vaccines Against COVID-19–Associated Emergency Department and Urgent Care Encounters and Hospitalizations Among Adults During Periods of Delta and Omicron Variant Predominance — VISION Network, 10 States, August 2021–January 2022”, MMWR. Morbidity and Mortality Weekly Report, 71(4), pp. 139-145. Available at: https://www.cdc.gov/mmwr/volumes/71/wr/mm7104e3.htm (Accessed: 2 March 2022).
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