Scientists believe that the Omicron super-mutant strain of Covid that is causing panic across the globe may have originated in rodents.

Since South African scientists discovered the existence of this mutation last week, experts have puzzled over the origin of it. 

Omicron contains 32 mutations of its spike proteins. This is nearly five times the number found in Delta. It’s also more infectious than Delta. Vaccines may be less effective because it has a divergent nature. 

In recent times, it has been revealed that Omicron, which was not observed by scientists, has evolved in the darkness. Omicron split from Delta and Alpha in evolutionary terms sometime around the middle last year.

Omicron was possibly found in an immune-compromised patient with undiagnosed AIDS. This would have provided Omicron with time to adapt to his immune system and resulted in multiple mutations.

However, Professor Kristian Andersen at Scripps Research Institute, California has suggested that Omicron could have originated in rodents, who are known to carry the coronavirus. This is after an infected person passed it to them. 

This is why the animal split with its evolutionary branch. It ‘vanished’ at some point in 2020.

Omicron would have been infected by an animal host’s ancestor, then it would have become highly mutated. The virus then spread rapidly to humans in reverse zoonosis. 

Professor Andersen’s theory was based on the observation that Omicron differed from other Covid variants at the end of last year but genomic testing suggested it had only begun circulating among people in October.  

Omicron is so unique because of what happened between the two periods. 

Could Omicron have evolved in rodents? One scientists says a widely popular theory of the new supermutant Covid variant evolving in an immunocompromised patient doesn't stack up

What if Omicron evolved from rodents? A scientist says that a popular theory about the supermutant Covid variant developing in immunocompromised patients doesn’t hold up. 

Omicron is nearly five times more mutated than Delta in terms of its spike proteins. Delta's mutations gave it an edge over Alpha allowing it to outcompete its predecessor and become the dominant strain. There are fears Omicron will do the same.

Omicron has nearly five times the number of spike proteins mutations as Delta. Delta’s mutations allowed it to beat Alpha and became the dominant strain. Omicron is also at risk. 

A week on from its discovery in Southern Africa, Omicron has spread to dozens of countries

Omicron is now spread across the globe, just a week after it was discovered in Southern Africa 

A total of 42 cases of Omicron have now been detected in the UK, 22 in England and 10 in Scotland, while the vaccination status of the infected individuals is unknown none have required hospitalisation 

Although stating that it is theoretical, Professor Andersen stated in a tweet that he favors a zoonic animal-based origin for Omicron because ‘the lineage in immunocompromised patients(s) is long and undetected circulation for that long seems unlikely’. Also, Covid was previously shown to move between species. 

Second, Omicron’s mutations were also found in rodent species like mice and hamsters. 


A group of mutations — including K417N, S477N, E484A and N501Y — are thought to help Omicron dodge antibodies that usually help fight off the virus.

N501Y was seen previously on Alpha. It helps the virus to bind more readily to cells in the body, making it easier for the virus to penetrate the body and reproduce more effectively.

It also has 26 mutations in its spike protein, which are new to this variant.

Three mutations found on the furin cleavage site may increase Omicron’s transmissibility. P681H (which was previously found in Alpha), as well H655Y, and N679K which were discovered in the Gamma-strain.

A series of mutations may help the virus bind to the human cell and help Omicron escape the body’s immune response. T478K was on Delta, Q498R and has never been on other variants of concern.

There are also missing mutations, from 105 to 107

Two mutations in the nucleocapsid — R203K and G204R, found on the Alpha and Gamma strains — may be associated with increased infectivity. 

Covid is believed to have originated from a species of bats. The virus was then transmitted from one animal species to another. Covid has been discovered in mink in Denmark fur farms and deer in Canada.  

Professor Andersen added that while many scientists have concluded Omicron came from an immunocompromised person, such as HIV patient, it was too early to call.  

While that is certainly possible, there are no data to support it. He wrote, “Let’s not close our eyes to any hypotheses.” 

When asked about theories, British experts replied that they preferred the immunocompromised patient theory.

Responding to this theory, Professor David Livermore from the University of East Anglia, who is a microbiologist, said that Omicron split with its ancestors sometime ago. However, he also suggested that Omicron’s mutation was probably the result of an immunocompromised patient theory. 

He stated that Omicron has a very long history with its ancestors. It also exhibits an extraordinary combination of many changes. 

“It’s more probable that it was selected under high selective pressure such as in chronically-infected patients with immunosuppression.

Professor Lawrence Young of Warwick Medical School, who is a virus expert, said that we are still in the early stages of understanding Omicron’s mutations. 

He stated that while these people can model as many things as they want, using it to try and predict the biology of the virus’ behaviour is at best very speculative.

‘It’s very difficult to predict what this combination of mutations really means for infectiousness and immune evasion.’

Professor Young added that previous research points still suggests an immunosuppressed Covid patient having the virus for months as the likely origin of Omicron.  

He stated that “Differential select pressure in immunocompromised hosts can serve as an incubator for the emergence variants associated with immune escape,” 

There are many reports that prolonged infections can occur in immunocompromised people (70-100 days). This includes transplant recipients as well as patients with autoimmune disease. The variants may be more transmissible and less immune evasive.

‘These variants could then spread to other people – especially those who are unvaccinated.’

Today, 42 Omicron cases have been reported in the UK. The cases do not require hospitalization and are mild. Health authorities have not yet disclosed whether the Omicron status has been confirmed.

This mutant strain quickly becomes the predominant variant of Covid South Africa.

Data in South Africa shows the R-rate has soared to over three per cent in recent weeks as Omicron took hold in Gauteng province

South Africa data shows that the R-rate rose to more than three percent in South Africa since Omicron was established in Gauteng.

As the Omicron epidemic has intensified, South African’s reproduction rates have jumped from below one percent to three percent in less than a month. The super-strain is outpacing Delta at a rapid pace.

In just one week, Omicron is South Africa’s dominant brand 

Johannesburg’s public health officer revealed the fact that 75 percent of the cases in the country were caused by this highly developed virus eight days after South Africa alerted them.

Dr Anne von Gottberg is a South African clinical microbiologist who told an urgent World Health Organization conference that it looked like Omicron was the predominant disease in South Africa.

Omicron has been confirmed in five of nine U.S. provinces. Officials expect Omicron to increase in four other areas, where there have yet not been any sequences.

Only 183 cases have been confirmed because there are only a handful positive samples that can be tested for variants. South Africa currently has 8,561 confirmed cases of the strain per day. This is six times more than it was 1,275 weeks ago.

In the meantime, hospitalisations more than doubled over the past week, going from an average 86 to 184 per day. Despite reports that the strain causes mild illness, the virus was initially circulating among young people — who are not usually hospitalised with the virus.

Prof. von Gottberg indicated that Omicron cases are increasing among those who were previously infected with Covid. These numbers are significantly higher than the reinfection rates during the Beta- and Delta-fueled waves.

However, she stated that while the virus could be transmitted to more people than Delta and is less severe, its effects are thought to be much less. Vaccines can be used to prevent it from spreading.

This comes amid conflicting reports regarding Omicron’s ability to cause mild or severe illnesses and its impact on vaccine efficacy. The experts warn that the current evidence is speculative and they will need to wait two weeks for laboratory testing.

While up to 80 percent of South Africa’s inhabitants are believed to be protected from natural infections, only a quarter of them have double-jabbed.

Public Health officials in Guateng province estimated the R value — a key measure used to gauge how fast a wave is growing — could be as high as 3.5. The R rate in the UK has been below 1.6 for comparison.   

Omicron virus has seen a dramatic rise in South Africa’s cases. Most of these cases are concentrated in Guateng. Guateng is the country that alerted the international community about this highly-evolved virus in November 24. 

The national rate of cases rose by 37% to 11,535 last Thursday. This is a significant increase from the 8,500 reported yesterday. Within a matter of weeks, the strain has overtaken all other varieties in the country. It now accounts for 75% of the sequenced samples. 

Yesterday’s preprint published in South Africa found that this strain has at least two-and a half times the ability to re-infect people as compared with all others. 

This may explain why the disease is rapidly spreading in Guateng province where 80 per cent of residents have natural immunity. It has not spread in countries that it was detected, such as the UK which took weeks to detect it. Only 25% of South Africans have been vaccinated, as opposed to 70% in Europe, the US, and UK.

Omicron’s infectiousness is undisputed, but there are growing concerns about its ability to evade vaccinations and the severity of the disease it will cause. According to the World Health Organization (WHO), the latest variant has not caused any deaths anywhere in the world.

South African public health professionals and WHO insist that cases of the disease are not severe and that vaccines against it should be effective despite the lack of data. 

But UK Health Security Agency (UKHSA) epidemiologist Meaghan Kall warned that data currently suggests Omicron may be ‘worse’ than Delta — although the picture is still emerging. 

She stated that she is ‘highly skeptical’ about the possibility of milder symptoms. However, infections might only seem less severe if people are immune to other strains. 

Doctors in Norway say that Omicron was contracted by 60 people at a Christmas party. They report mild symptoms like headaches, sore throats, and fatigue. All of those infected, however, are young. They are likely to have had their vaccines.

Although optimism is evident, South African hospitals are seeing an increase in admissions, with Thursday’s 274 being up 180% on last week. This despite the fact that they have been rising steadily from a low baseline.  

Researchers are at an all-time high speed trying to determine if Omicron has a higher transmissibility and death rate than other mutant strains. They say that reliable estimates could take up to a week.

Early reports in South Africa suggest that many cases are either completely or mildly symptomatic. It is not clear if this could be because of the spread of the strain to older individuals. 

According to the WHO, it’s a mild strain. Christian Lindmeier, a spokesperson for WHO, told journalists in Geneva today: “I haven’t seen any reports about Omicron-related deaths.” 

“We are collecting all evidence, and will continue to find more evidence.

Are animals able to catch Covid? 

Numerous times has covid been found in animals.

The virus has been shown to be transmissible from person to animal in studies that have already been done. This includes pets and pests such as cats, dogs, mice, etc. 

It is known as reverse zoonosis. An animal is infected by a human disease.

This is the reverse of zoonosis where an animal transmits a disease to a human.

One theory behind the origin of Covid is Zoonosis.

Examples of Covid reverse Zoonosis that have been reported recently include cases in which mink from Denmark’s fur farms were killed after contracting the virus late 2020.

Just yesterday, Covid was reported in Canada as having been discovered in deer populations. 

“The more people we test, the more places… We will find more cases, more data, and hopefully, not only deaths, but more.”

Dr Kall however said that the claim of a new strain being less dangerous is not true.

On Twitter, she wrote: ‘I am extremely skeptical that it could be more mild. It’s best to assume it is similar in severity as Delta… however, you will see milder symptoms than Delta because more people are immune now.

Pre-prints published yesterday indicated that Omicron had three times the chance of re-infecting people who’d had Covid previously.

South African scientists reported that there were 35,670 cases of reinfections in South Africa since the outbreak of the pandemic. The risk of reinfection increased by 0.7 percent during last summer’s Delta-fuelled second winter wave and Delta wave this summer.

However, the likelihood of getting the virus has increased to at most 2.4.

Researchers from Stellenbosch University near Cape Town said that Omicron is more able than others to overcome immunity.

The preprint means that the paper hasn’t been reviewed by any other scientists. These scientists then verify its conclusions.

Simon Clarke, a microbiologist from Reading University said that the data were the first indication Omicron might be immune to previous Covid infections.