Impact of the rapid spread of the SARS-CoV-2 Omicron variant in Southern Africa

The emergence and rapid spread of a novel coronavirus, namely, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has resulted in the coronavirus disease-2019 (COVID-19) pandemic.

Study: Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. Image Credit: natatravel/Shutterstock

Since its onset in 2019, this virus has continuously evolved via mutations and resulted in the emergence of many variants. These variants are different than the original strain, which was first reported in Wuhan, China, in terms of, virulence, transmission, evasion of immune responses, and some other aspects.

These variants have been classified as variants of concern (VOC) and variants of interest (VOI).


The very first VOCs were the Alpha, Beta, and Gamma variants that increased the number of SARS-CoV-2 infections globally. These VOCs were replaced by the Delta variant which was reported to be more virulent than the preceding VOCs. Scientists found that the Delta variant evolved in multiple sub-lineages and some of the mutations were reported to be very specific to a certain location. These observations bolstered the belief that the next variants would be derived from the Delta variant. Although the Delta variant was continuing to dominate in the Northern hemisphere, it was reported to subside in Southern Africa. However, scientists reported the simultaneous emergence of a variant, named, Omicron, which was deemed to be the fifth VOC of SARS-CoV-2 by the World Health Organization.

Scientists are working extensively to characterize this new variant and elucidate its transmission trajectory. A new study, published on medRxiv* preprint server, has focused on the genomic profile and early transmission dynamics of Omicron. This study revealed the dominance of the Omicron variant in regions with high levels of population immunity. 

The study

As part of weekly genomic surveillance, four samples were collected, from Gaborone, Botswana, and sequenced on 11th November 2021. On the 22nd of November 2021, the Botswana Ministry of Health and Wellness was informed about the unusual sequence, and these sequences were subsequently uploaded to GISAID. A similar lineage outbreak was also reported from South Africa. Further genomic studies confirmed the emergence of a new VOC, which was named Omicron. By late November, both South Africa and Botswana experienced a sharp increase in SARS-CoV-2 cases in all provinces.

To understand when and where this variant originated, the authors analyzed all available Omicron genomes present in GISAID and the genomic sequence of the original strain that emerged in 2019 was used as the reference sequence. Preliminary studies showed that the BA.1/Omicron sequences were a monophyletic clade rooted within the B.1.1 lineage (Nextstrain clade 20B) without a clear basal progenitor. This variant’s cluster was found to be phylogenetically distinct from other existing VOCs or VOIs. Recently, two related lineages have emerged that have been designated as BA.2 and BA.3. Interestingly, these two lineages share many but not all characteristic mutations and possess many unique mutations of their own.

This study has primarily focussed on BA.,1 as this lineage is rapidly spreading in many countries and has been designated as the Omicron VOC. Time-calibrated Bayesian phylogenetic analysis showed that the BA.1 genome from Southern Africa most likely prevailed from 9th October 2021 with an exponential growth rate of 0.136, reflecting a doubling time of 5.1 days. Spatio-temporal phylogeographic analysis suggested that the Omicron variant had transmitted from the Gauteng province of South Africa to seven of the eight other provinces and to two regions of Botswana, starting late October. 

Compared to the reference strain, Omicron carries fifteen mutations in the receptor-binding domain (RBD) of the spike region. Five of the mutations, i.e., G339D, N440K, S477N, T478K, N501Y, are associated with an increase in the binding to the ACE2 receptor of the host. Seven of the RBD mutations are associated with moderate to strong impacts on the binding of RBD-targeted neutralizing antibodies (NAbs). 

The authors found no evidence, based on phylogenetic or statistical studies, on ancestors of either the BA.1 or BA.2 lineages having been derived through recombination. Scientists revealed that the branch separating BA.1/Omicron, from its most recent B.1.1 ancestor, strongly supported the hypothesis that adaptive evolution played a pivotal role in the mutational divergence of Omicron from other B.1.1 SARS-CoV-2 lineages. Additionally, in regards to the intensity of selection, this study shows that three genes have possibly intensified in the ancestral Omicron lineage. These are S-gene, exonuclease, and nsp6. Scientists indicated that these selective patterns show that during its current exponential spread, there is a high chance for the Omicron variant to evolve and modify its neutralization profile. This study believes that partial evasion of immune protection is the reason for the rapid spread of this variant.


This study has some limitations. The estimation of Omicron replication has been based on the early sequence data and such data could be biased due to stochastic effects in a low incidence setting. Also, due to the lack of reliable data on the level of immune protection against the Delta variant, researchers could not estimate the transmissibility or immune evasion of Omicron. Scientists suggested that close monitoring of the transmission of this variant in other countries could help establish the transmission pattern of this variant.

*Important notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:
  • Viana, R. et al. (2021). Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa. medRxiv. Doi:

Posted in: Medical Science News | Medical Research News | Disease/Infection News

Tags: ACE2, Antibodies, Coronavirus, Coronavirus Disease COVID-19, Evolution, Exonuclease, Gene, Genes, Genome, Genomic, immunity, Pandemic, Receptor, Respiratory, SARS, SARS-CoV-2, Severe Acute Respiratory, Severe Acute Respiratory Syndrome, Syndrome, Virus

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Written by

Dr. Priyom Bose

Priyom holds a Ph.D. in Plant Biology and Biotechnology from the University of Madras, India. She is an active researcher and an experienced science writer. Priyom has also co-authored several original research articles that have been published in reputed peer-reviewed journals. She is also an avid reader and an amateur photographer.

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