As the SARS-CoV-2 omicron variant (B.1.1.529) rapidly became the dominant strain in South Africa in late 2021, public health officials around the globe recognized that a new, highly transmissible form of the virus was likely emerging.1,2 However, understanding the specifics of what was different about omicron remained to be seen. Beyond higher transmissibility, questions around disease severity, vaccine effectiveness, and the time course of the disease were yet to be uncovered.
Now, in just a few short months since omicron was initially identified, a clearer picture of the variant is coming into focus. And with that clearer picture of omicron’s complex biology, we have a better understanding of how our testing practices need to adjust. In this article, we’ll provide a quick summary of what we now know about omicron, how that affects testing strategies, and what we can learn to be prepared for future variants.
What we know about omicron so far
Omicron carries many mutations1
Compared to the original SARS-CoV-2 alpha strain (B.1.1.7), the genome of the omicron variant carries over 60 different mutations.1 More than half of omicron’s mutations are in the spike protein,1 which mediates cell attachment and entry.3 Interestingly, as with all of the SARS-CoV-2 variants of concern, the omicron spike protein carries the D614G mutation that is associated with higher viral loads in the upper respiratory tract and a younger patient age range.1 Other mutations in the spike protein are associated with functionality that is expected to enhance infectivity.1
Omicron is likely capable of at least partial immune evasion4–6
Evidence reported in preprints suggests that omicron can evade immunity from previous infections4–6 and vaccinations,5 leading to reinfection, as well as infection of vaccinated individuals. However, one of the studies is reporting that prior infection and vaccination do protect against hospitalization and death.6
Omicron is likely to cause less severe disease7
An analysis of COVID-19 patients in Southern California, including 52,297 cases infected with the omicron variant and 16,982 cases with the delta variant, suggests that omicron causes less severe disease than delta, even when you take into account vaccination status or previous SARS-CoV-2 infection.7 The caveat to this study is that it is still in the preprint stage and has yet to be peer-reviewed.
Omicron likely reproduces faster8,9 and may have a shorter incubation period10,11
Faster reproducibility is one of the critical features of omicron that may help explain its ability to out-compete other variants, such as delta, to become the dominant strain in a region.8,9 Two studies still in the preprint stage report that the mean serial interval for omicron is 2.2 days8 and between 1.5 and 3.2 days.9 In contrast, reports of the mean generation time for delta spans a range of 3.3 – 4.24.8,12,13
Early indications suggest that omicron also has a shorter incubation period than other variants. One early study in Denmark found a median incubation period of 3 days for omicron10, compared with 4.3 and 5.0 days for delta and other variants11, respectively.
What this means for testing
Given omicron’s large mutational burden1 and the early indications that it can evade prior immunity,4–6 likely reproduces faster,8,9 and may have shorter incubation times,10,11 some public health agencies and healthcare systems are already rethinking their testing strategies.14,15
Can PCR and antigen tests sensitively and accurately detect omicron?
The first thing to consider about testing is whether the large mutational burden carried by omicron affects the sensitivity and accuracy of either nucleic acid amplification tests (NAATs) like PCR or rapid antigen tests that rely on lateral flow technology.
A January 22, 2022, technical brief from the World Health Organization (WHO) observes that the diagnostic accuracy of the PCR and rapid antigen tests listed in their emergency use list (EUL) is not significantly affected by the omicron variant,15 although one of the deletions in the gene encoding the spike protein, the S gene ?69-70, can cause S gene target failure (SGTF) in some NAATs.
In addition, the Infectious Diseases Society of America (IDSA) is reporting that preliminary evidence suggests no loss in accuracy of currently available NAATs16 and that antigen tests are mostly based on detecting the nucleocapsid protein and should therefore be unaffected by the mutations in omicron.16
Does omicron affect testing frequency?
While the CDC has not made any updates to their testing recommendations in response to omicron,17,18 the shorter generation and incubation times are leading some physicians to recommend frequent serial testing with rapid tests.19
What can we learn from omicron?
Emerging just as much of the world was beginning to relax COVID-19 protection measures, the omicron variant drove huge surges in infection rates, especially in the United States.20 The good news is that, as the CDC notes, “we have the tools to fight omicron”.18 Vaccines, masks, and testing are all effective tools that remain highly effective against omicron.18 What’s critical is that we keep on the lookout for the emergence of new variants and adjust our practices as quickly as we can based on initial and evolving evidence.
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- He X, Hong W, Pan X, Lu G, Wei X. SARS-CoV-2 Omicron variant: Characteristics and prevention. MedComm. 2021;2(4):838-845. doi:10.1002/mco2.110
- Viana R, Moyo S, Amoako DG, et al. Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Nature. Published online January 7, 2022:1-10. doi:10.1038/s41586-022-04411-y
- Shang J, Wan Y, Luo C, et al. Cell entry mechanisms of SARS-CoV-2. Proc Natl Acad Sci. 2020;117(21):11727-11734. doi:10.1073/pnas.2003138117
- Altarawneh H, Chemaitelly H, Tang P, et al. Protection afforded by prior infection against SARS-CoV-2 reinfection with the Omicron variant. medRxiv. Published online January 1, 2022:2022.01.05.22268782. doi:10.1101/2022.01.05.22268782
- Yang W, Shaman J. SARS-CoV-2 transmission dynamics in South Africa and epidemiological characteristics of the Omicron variant. medRxiv. Published online January 1, 2021:2021.12.19.21268073. doi:10.1101/2021.12.19.21268073
- Pulliam JRC, van Schalkwyk C, Govender N, et al. Increased risk of SARS-CoV-2 reinfection associated with emergence of the Omicron variant in South Africa. medRxiv. Published online January 1, 2021:2021.11.11.21266068. doi:10.1101/2021.11.11.21266068
- Lewnard JA, Hong VX, Patel MM, Kahn R, Lipsitch M, Tartof SY. Clinical outcomes among patients infected with Omicron (B.1.1.529) SARS-CoV-2 variant in southern California. medRxiv. Published online January 1, 2022:2022.01.11.22269045. doi:10.1101/2022.01.11.22269045
- Kim D, Jo J, Lim JS, Ryu S. Serial interval and basic reproduction number of SARS-CoV-2 Omicron variant in South Korea. medRxiv. Published online January 1, 2021:2021.12.25.21268301. doi:10.1101/2021.12.25.21268301
- Abbott S, Sherratt K, Gerstung M, Funk S. Estimation of the test to test distribution as a proxy for generation interval distribution for the Omicron variant in England. medRxiv. Published online January 1, 2022:2022.01.08.22268920. doi:10.1101/2022.01.08.22268920
- Brandal LT, MacDonald E, Veneti L, et al. Outbreak caused by the SARS-CoV-2 Omicron variant in Norway, November to December 2021. Eurosurveillance. 2021;26(50):2101147. doi:10.2807/1560-7917.ES.2021.26.50.2101147
- Grant R, Charmet T, Schaeffer L, et al. Impact of SARS-CoV-2 Delta variant on incubation, transmission settings and vaccine effectiveness: Results from a nationwide case-control study in France. Lancet Reg Health – Eur. 2021;0(0). doi:10.1016/j.lanepe.2021.100278
- Hwang H, Lim JS, Song SA, et al. Transmission Dynamics of the Delta Variant of SARS-CoV-2 Infections in South Korea. J Infect Dis. Published online December 2, 2021:jiab586. doi:10.1093/infdis/jiab586
- Li L, Han ZG, Qin PZ, et al. Transmission and containment of the SARS-CoV-2 Delta variant of concern in Guangzhou, China: A population-based study. PLoS Negl Trop Dis. 2022;16(1):e0010048. doi:10.1371/journal.pntd.0010048
- Omicron Guidance Updates | Nebraska Medicine Omaha, NE. Accessed January 26, 2022.
- Enhancing response to Omicron SARS-CoV-2 variant. Accessed January 26, 2022.
- Vaccines FAQ. Accessed January 26, 2022.
- CDC. Healthcare Workers. Centers for Disease Control and Prevention. Published February 11, 2020. Accessed January 26, 2022.
- CDC. Omicron Variant: What You Need to Know. Centers for Disease Control and Prevention. Published December 20, 2021. Accessed January 27, 2022.
- Godoy M. Why rapid COVID tests aren’t more accurate and how scientists hope to improve them. NPR. Published January 23, 2022. Accessed January 26, 2022.
- CDC. COVID Data Tracker. Centers for Disease Control and Prevention. Published March 28, 2020. Accessed September 24, 2021.
*Internal test data on file and available upon request.