Omicron: A variant of concern

The authors discuss the emergence of Omicron along with its epidemiology, structural variation, diagnosis, and the current regional strategic plans to combat the virus spread.

In December 2019 in Wuhan city of China, a cluster of patients presented to local hospitals with symptoms of cough, fever, and malaise. The causative virus was identified as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). On Jan 7, 2020, the suspect virus was identified as novel CoV-2019. The epidemic doubling time of COVID-19 was 1.8 days, and this forced the WHO to announce COVID-19 as a global pandemic and provide frequent updates on disease statistics, case definitions, and preventive strategies through their news briefings and websites [1,2].

The emergence of the pandemic led to the race to discover a vaccine to achieve herd immunity and curtail the damaging effects of COVID-19. Many vaccine candidates have shown worthy results with the vaccination coverage and is at positive levels among developed countries. The emergency of vaccines into the pandemic population started on 31 December 2020, the Pfizer COVID-19 vaccine (BNT162b2) was issued for emergency use listing by WHO. This was followed by the AstraZeneca/Oxford COVID-19 vaccine, manufactured by the Serum Institute of India and SKBio on 15 February 2021, on 12 March 2021, the Ad26.COV2.S, developed by Janssen (Johnson & Johnson) and Moderna on 30 April 2021. COVAX, coordinated by WHO, Gavi: The Vaccine Alliance, the Coalition for Epidemic Preparedness Innovations (CEPI), acts as a programme that supports the development of COVID-19 vaccine candidates and negotiates their pricing to ensure low-and-middle-income countries have a fair shot at receiving vaccines [3,4].

During the virus evolution, the virus undergoes replication resulting in a natural by-product, termed as mutation. In SARS-CoV-2, the variants are largely focused on its spike glycoprotein. The mutated SARS-CoV-2 variants are responsible for demonstrating variation in modes of transmission, disease severity, diagnosis, and therapeutic options. With a consistent circulation and emergence of frequent variants of SARS-CoV-2, the World Health organization (WHO) established a Virus Evolution Expert Working Group (VEWG) to specifically assess SARS-CoV-2 evolution, mutations, and variants. The independent scientists and virologists formalized with the name Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE). The TAG-VE group meets regularly to discuss and analyze the effects of SARS-CoV-2 variants on the high-risk population relating the modes of transmission, clinical manifestations, disease severity, diagnosis, treatment and to categorize them as either variant of concern (VOC) or a variant of interest (VOI). The TAG-VE group recommendations are informed to the WHO, and this alerts the COVID-19 prevention, control, and advisory groups to formalize a regional and national control plan to combat the emerging variants [5].

The B.1.1.529 variant was first reported to WHO from South Africa on 24 November 2021 and the WHO categorized it as a VOC and named it as Omicron. The epidemiological situation in South Africa has been characterized by three distinct peaks in reported cases due to Beta variant, and the latest of which was predominantly the Delta variant [5]. In recent weeks, infections have increased steeply, coinciding with the detection of Omicron variant. The first known confirmed Omicron infection was from a specimen collected on 9 November 2021 in South Africa. Ever since then the Omicron variant has been detected in over 30 countries around the world. The emergence of Omicron in South Africa is mainly due to its poor vaccine acceptance rate with only 24.6% of South Africa been fully vaccinated compared to the global rate of 42.7%. However, the rest of Africa has much lower vaccination rate than South Africa with fully vaccination rate as low as <0.1% in the Democratic Republic of the Congo [6].

The Omicron has been of concern due to its large number of mutations, an increased risk of reinfection and the occurrence of the virus in fully vaccinated individuals. Current SARS-CoV-2 PCR diagnostics continue to detect this variant. Several labs have indicated that for one widely used PCR test, one of the three target genes is not detected (called S gene dropout or S gene target failure) and this test can therefore be used as marker for this variant, pending sequencing confirmation. Using this approach, this variant has been detected at faster rates than previous surges in infection, suggesting that this variant may have a growth advantage [5,7].

The ongoing research is mainly concentrated towards identifying the ability of Omicron to cause global spread. The genome sequencing data obtained from laboratory in Botswana revealed Omicron contained over 30 mutations in its spike protein. The spike protein is the major protein of SARS-CoV-2 virus that allows the virus to recognize the host cell receptor. Genome sequencing and other genetic analysis from a team at the University of KwaZulu-Natal, found that the Omicron variant was responsible for all 77 of the virus samples the team analyzed from Gauteng, the smallest province in South Africa collected between 12 and 20 November 2021. The Omicron positive patients in South Africa were mainly of young age and manifested mild illness consisting of only mild cough [6,8].

The WHO immediately sent out guidelines and strategic plans to regional and at risk countries to deter the spread of Omicron by: a) enhancing surveillance and sequencing efforts to better understand circulating SARS-CoV-2 variants, b) submit complete genome sequences and associated metadata to a publicly available database, c) report initial cases/clusters associated with VOC infection to WHO through the IHR mechanism, and d) where capacity exists and in coordination with the international community, perform field investigations and laboratory assessments to improve understanding of the potential impacts of the VOC on COVID-19 epidemiology, severity, effectiveness of public health and social measures, diagnostic methods, immune responses, antibody neutralization, or other relevant characteristics. The effectiveness of vaccines and current treatments are still under assessment by the global researchers. However, the classical approach to combat SARS-CoV-2 is still recommended by the WHO to the pandemic population [9,10].



  1. Umakanthan S, Sahu P, Ranade AV, et al. Origin, transmission, diagnosis and management of coronavirus disease 2019 (COVID-19). Postgrad Med J. 2020;96(1142):753-758. doi:10.1136/postgradmedj-2020-138234
  2. Umakanthan S, Chattu VK, Ranade AV, Das D, Basavarajegowda A, Bukelo M. A rapid review of recent advances in diagnosis, treatment and vaccination for COVID-19. AIMS Public Health. 2021;8(1):137-153. Published 2021 Feb 1. doi:10.3934/publichealth.2021011
  3. Francis AI, Ghany S, Gilkes T, Umakanthan S. Review of COVID-19 vaccine subtypes, efficacy and geographical distributions [published online ahead of print, 2021 Aug 6]. Postgrad Med J. 2021;postgradmedj-2021-140654. doi:10.1136/postgradmedj-2021-140654
  4. Umakanthan S, Patil S, Subramaniam N, Sharma R. COVID-19 Vaccine Hesitancy and Resistance in India Explored through a Population-Based Longitudinal Survey. Vaccines. 2021; 9(10):1064.
  5. Terms of Reference for the Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE). WHO. COVID-19: Surveillance, case investigation and epidemiological protocols [Internet]. Available: [Accessed 1 Dec 2021].
  6. Callaway E. Heavily mutated Omicron variant puts scientists on alert. Nature. 2021;600(7887):21. doi:10.1038/d41586-021-03552-w.
  7. Update on Omicron. WHO. Regional Office for Africa [Internet]. Available: [Accessed 1 Dec 2021].
  8. Covid: South Africa new cases surge as Omicron spreads. BBC News [Internet], 2021. Available: [Accessed 1 Dec 2021].
  9. How South African scientists spotted the Omicron COVID-19 variant. Alarabiya News [Internet], [Accessed 2 Dec 2021].
  10. Callaway E. Ledford H. How bad is Omicron? What scientists know so far. Nature [Internet], 2021. Available: [Accessed 2 Dec 2021]



Dr. Srikanth Umakanthan

Department of Para-clinical sciences

Faculty of Medical Sciences,

The University of the West Indies

Saint Augustine



Dr. Maryann M Bukelo

Department of Anatomical Pathology

Eric Williams Medical Sciences Complex,

North Central Regional Health Authority



Dr. Mario J Bukelo

Department of Paediatrics

Father Muller Medical College

Mangalore, Karnataka,



Dr. Shashidhar Gangappa

Department Of Critical Care

Vikram Hospital

Bangalore, Karnataka



Dr. Kingsley Akaba

Department of Haematology and Blood Transfusion,

University of CalabarTeaching Hospital,

Calabar, Nigeria

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