The Omicron variant: Rapid Spread to Over 40 Countries

By Suranjith L Seneviratne, Buddhika Samaraweera, Chamara Dalugama, Jayani Kariyawasam and Visula Abeysuriya | Published: 2:00 AM Dec 6 2021
Focus The Omicron variant: Rapid Spread to Over 40 Countries

By Suranjith L Seneviratne, Buddhika Samaraweera, Chamara Dalugama, Jayani Kariyawasam and Visula Abeysuriya

It has been just over a week since the WHO named the newest SARS-CoV-2 variant as Omicron. The information available on the new variant as at the end of last week has been previously published. Following this initial report, the Omicron variant has been spotted in many more countries and some additional information has been gathered. This article would build on the previous account and outline what is currently known about the Omicron SARS-CoV-2 variant.   

Omicron variant mutations

The Omicron variant has a large number of mutations. The COVID-19 Genomics UK Consortium (COG-UK) recently released an image mapping the different mutations and compared these to those found in the currently widespread Delta variant. In the spike protein, the Omicron variant is characterised by 30 amino acid changes, one small insertion and three small deletions compared with the original virus. Fifteen of these changes are found in the Receptor Binding Domain and there are a number of changes and deletions in other genomic regions. Many of the mutations have not been observed in other SARS-CoV-2 variants. 

The spike protein is the main target of antibodies generated by infections and the current COVID vaccines. The number of spike protein mutations in Omicron is nearly five times that of the Delta variant. The fur in cleavage site increases infectivity of SARS-CoV-2, and Omicron has three mutations (H655Y, N679K, and P681H) at this location. These three mutations were also found in the Delta variant and led to increased viral transmission. The E484A mutation is at a position that is also mutated in other variants. 

Mutations to other amino-acids at this position have been associated with immune-escape. The Q498R and N501Y mutations significantly increase the binding affinity to ACE2. The 69/70 deletion is also found in the Alpha variant. It causes a dropout of the S-gene target in some real-time reverse transcriptase polymerase chain reaction (RT-PCR) testing methods. Thus S-gene target failure (SGTF) may be used as marker for this variant, pending sequence confirmation. The ORF1a 3 amino-acid deletion (NSP6 deletion 105-107), may help in innate immune evasion, by compromising the cells ability to degrade viral components.

Global infection pattern

So far, the Omicron variant has been found in over 40 countries worldwide. In addition to Africa, it has reached Asia, Europe, the Middle East and the America’s. Newer data suggests this variant may have been spreading in several countries for several weeks, before South Africa first reported its presence. 

South Africa and other parts of Africa

Recently, there has been a large increase in daily COVID cases in South Africa. On 26 November, there were 2,828 new cases and by 3 December 2021, this had increased to 16,055. The National Institute for Communicable Diseases (NICD) reported that 183 (73 per cent) of the 249 cases that have been sequenced in South Africa were of the Omicron variant. One would notice that only a small number of positive samples are analysed for variants. For instance, the number of positive samples sequenced, is less than one per cent of positive cases for November 2021. In South Africa, five of the country's nine provinces have confirmed cases and it is believed the prevalence of the variant is high in the remaining four, where positive samples are still to be sequenced. 

The Gauteng province is the epicentre of the Omicron outbreak, with one third of all cases found there. The KwaZulu-Natal and Northern Cape provinces each have nearly twenty per cent of the cases. COVID hospital admissions have nearly tripled in a week. Generally there is a time gap of about two to three weeks between case number trends and the patterns of hospitalisation and death. At present, South Africa is still recording fewer overall COVID cases per population size than the UK and the US (63 cases per million people in South Africa, compared to 638 and 257 in the UK and the US). 

This is because although cases are rising sharply in South Africa, it started at a lower number of COVID cases in recent months. COVID vaccine uptake in South Africa is low with around one quarter of the population having received two vaccine doses. In comparison, 70 and 80 per cent of people in the UK and some European countries have received two vaccine doses. Transmission of the virus in low vaccinated areas has the potential to accelerate its evolution. By 04 December, some of the other countries in Africa with cases of the Omicron variant include: Zimbabwe, Ghana, Botswana, Nigeria and Reunion. Reports suggest Nigeria had found a case in a sample taken in October.

Europe and the United Kingdom 

The Netherlands has stated that a case was detected, one week before the first case was reported from Africa. Norway has announced that 60 people likely contracted the Omicron variant at a single Christmas party. On 20 November 2021, there were nine cases in Scotland. This has led to speculation that the Omicron variant was imported from the COP 26 climate conference or at an international rugby game. So far, 160 cases of the Omicron variant have been identified in the UK. An analysis of the first 22 Omicron cases in England, found that more than half of those infected were at least 14 days after their second COVID vaccine dose.  

The USA, Canada and South America

The Omicron variant has been found in several states of the United States of America (USA), Brazil and Canada. After the first known case of community transmission of Omicron was found in the USA, tougher coronavirus restrictions have been imposed. For instance, International passengers heading to the USA will have to be tested for COVID-19 within one day of travel regardless of their vaccination status. The requirement to wear masks on planes, trains and buses have been extended till March 2022.

Asia Pacific and the Middle East 

Two persons in the Karnataka State of India initially tested positive for the Omicron variant, and since then other cases have been detected. One of the earliest cases had no travel history, pointing to the possibility of community transmission. Currently, the authorities are discussing about giving a booster vaccine dose to at least some persons and commencing a child (12 – 17 years) COVID vaccination program. On 03 December, the Omicron variant was identified in a previously unvaccinated lady who had returned to Sri Lanka from Nigeria. Australia has reported community transmission of the Omicron variant. Cases have also been reported from Hong Kong, South Korea and Malaysia. In the Middle East, cases have been noted in Israel, Saudi Arabia and the United Arab Emirates.


The Omicron variant is more transmissible than the other variants of concern. It is estimated to be around 3 – 6 times as transmissible as the Delta variant. Furthermore, unlike with Delta, a larger pool of persons may be susceptible to Omicron. This is because in general,a previous SARS-CoV-2 infection provided sufficient protection against Delta. 

Reinfection rates 

Reports from the Gauteng province in South Africa suggest reinfections have been occurring. The reinfections were defined as a positive test from an individual, 90 days after they first tested positive. The Omicron variant is at least 2.4 times more likely to re-infect a person compared to the original strain. Such increases in reinfections were not seen with the Beta or Delta waves. When the Beta and Delta variants were predominant, the risk of reinfection was 0.7 compared to the first wave of infection. It appears that previous infection does not provide protection from infection due to Omicron. This has important public health implications, especially in countries with high rates of prior infection. The hope is that it provides protection against severe disease, hospital admissions and death. An important question that needs to be answered is whether the Omicron variant is able to evade vaccine induced immune protection. Recently, the Netherlands stated that all 14 air travellers from South Africa with confirmed Omicron infection had been previously vaccinated. 

Disease severity

Currently, there are differing perspectives on whether the Omicron variant produces mild or more severe illness. A reduced incubation period for the Omicron variant has been identified by the UK Health and Security Agency (UKHSA). Some of the symptoms reported in the patients include: tiredness and muscle aches, headache, dry cough, sore throat, fever and sneezing. There have been reports of Omicron-infected children being admitted to hospital in South Africa. However, it appears these children have an uncomplicated clinical course and were soon discharged. 

Vaccine effectiveness against Omicron

Currently, there is uncertainty about vaccine effectiveness against the Omicron variant. It would take around two weeks to assess how effective anti-viral antibodies would be in neutralising the Omicron variant in a laboratory setting. With some previous SARS-CoV-2 variants,a reduction in neutralisation by vaccine induced antibodies was seen, but the vaccines were still able to prevent severe disease, admission to hospital and deaths. T cell and NK cell protection may also be less affected by the Omicron variant mutations than effects on antibody neutralisation. Initial observations from Israel, appear to show that existing vaccines protect against severe illness. A recent report indicated the Pfizer vaccine is 90 per cent effective at preventing symptomatic infection by the Omicron variant. If these findings are confirmed, protection obtained from some of the COVID vaccines would only be slightly lower than seen against Delta. Very recently, the UK Government accelerated the rollout of Covid vaccine boosters, recommending them for all adults (18 years and over) and reducing the time interval between the second and booster doses to three months. Booster vaccine doses have been found to supercharge neutralising antibody levels.  

Effectiveness of Covid monoclonal antibodies against Omicron 

Early reports suggest the Regeneron COVID monoclonal antibody cocktail, may be less effective against the Omicron variant. Of the two monoclonal antibodies that are in the cocktail, the effect of one of them is expected to be significantly reduced whilst the other would be less affected. On the other hand,  Sotrovimab, a neutralising monoclonal antibody that binds an epitope on SARS-CoV-2 that is shared with SARS-CoV-1 (that is it is a highly conserved epitope), has recently been found in pre-clinical studies to retain activity against key mutations of the Omicron variant including those found in the binding site of sotrovimab. The data was generated through pseudo-virus testing of specific individual mutations found in Omicron.

Effectiveness of COVID treatments 

Antiviral medications such as molnupiravir, paxlovid and remdesivir are likely to work as well against the Omicron variant as they do against other variants. Medications that dampen down overactive immune responses during Covid (such as dexamethasone) or block a targeted inflammatory molecule (such as tocilizumab) would still be effective in treating hospitalised patients with severe Covid. 

Other measures to mitigate the rate of spread 

Several countries have stopped air travel from specific regions and countries. There has been a re-introduction of compulsory mask wearing in some settings. The ECDC put forward a model that indicated that strict travel restriction would delay the novel variants impact on European countries by two weeks and that this would allow countries to prepare for this variant. It needs to be remembered that travel curbs could buy time, but this alone would not be the complete answer. The WHO has called for a reassessment of the protocols that are to be followed, as the current system disincentives countries from alerting others. With the current system, countries that are heavily dependent on tourism may take steps to delay the release or supress information regarding the discovery of new variants of concern.     


One week since the Omicron variant was reported, certain aspects have become better defined. However, as yet important information regarding the severity of illness caused by the variant and if effective vaccine immunity is present, is still to be determined. The WHO has urged countries to boost healthcare capacity and rapidly increase vaccine coverage to mitigate the effects of the Omicron variant.   

By Suranjith L Seneviratne, Buddhika Samaraweera, Chamara Dalugama, Jayani Kariyawasam and Visula Abeysuriya | Published: 2:00 AM Dec 6 2021

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