COVID-19 B.1.1.529 Omicron Variant Causes Mild Disease


The WHO or World Health Organization has in the last few hours classified the B.1.1.529 variant as a Variant of Concern (VOC) and also renamed it as the Omicron variant.

JOHANNESBURG : Angelique Coetzee, the chairwoman of the South African Medical Association, has declared: The new Omicron variant of the coronavirus results in mild disease, without prominent syndromes.

“It presents mild disease with symptoms being sore muscles and tiredness for a day or two not feeling well. So far, we have detected that those infected do not suffer loss of taste or smell. They might have a slight cough. There are no prominent symptoms. Of those infected some are currently being treated at home”

The official noted that hospitals have not been overburdened by Omicron patients and that the new strain is not been detected in vaccinated persons.

At the same time, the situation might be different for the unvaccinated.

“We will only know this after two weeks. Yes, it is transmissible, but for now, as medical practitioners, we do not know why so much hype is being driven as we are still looking into it. We will only know after two to three weeks as there are some patients admitted and these are young people aged 40 and younger”.

The chairwoman also criticized the decision by some countries to ban flights from South Africa is premature as there is not enough information on how dangerous it is.

The fact that the variant is not detectable by many existing PCR platforms and also by ATK test and that many travelers initially do not exhibit symptoms till the viral load hits a certain threshold and the causes the whole body system to collapse, makes it extremely hard for early detection while the infected are in the infectious phases.

Many experts are warning that unless the world unitedly imposes a general shut down of borders for a period of time and ban all flights and also inter border travel via land or sea, the new Omicron variant will spread faster than Delta globally and change the whole course of the COVID-19 pandemic.

To date, the US, UK, EU states and Switzerland have halted travel to and from seven African nations and other countries including the UAE, Israel, Japan, Kenya and Singapore have also restricted travel but these measures will not suffice.

The South variant has already been confirmed in Malawi, Botswana, South Africa, Hong Kong, Israel and Belgium and is also believed to be already in France, Germany, Netherlands, UK, USA, Singapore, Philippines, Qatar, Egypt, UAE, Malaysia, Myanmar, Nigeria and other countries in Africa but genomic sequencings of suspected cases are needed to verify the presence of the variant.

It was reported that acting on advice from US health officials, US President Joe Biden will restrict travel from South Africa, Botswana, Zimbabwe, Namibia, Lesotho, Eswatini, Mozambique and Malawi soon.

Canada is also shutting its borders to foreign travelers who have recently been to South Africa, Namibia, Lesotho, Botswana, Eswatini, Zimbabwe and Mozambique. Foreign citizens will be banned from Canada if they have been to the seven nations in the past 14 days.

The World Health Organization’s Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE), an independent group of experts, met Friday to discuss the variant, a WHO statement said.

The experts recommended WHO designate the variant as “of concern,” referencing the variant’s large number of mutations, the possibility of increased risk of reinfection and other evidence.

Various studies are underway in the US, UK and South Africa, and WHO will update member states and the public as needed, the WHO statement said.

The World HealthOrganization called on countries to enhance their surveillance and sequencing efforts to better understand coronavirus variants.

Joe Phaahla, South Africa’s Minister of Health said stressing it is currently unclear where the variant first emerged, “Initially it looked like some cluster outbreaks, but from yesterday, the indication came from our scientists from the Network of Genomic Surveillance that they were observing a new variant.”

Initially South African officials said there was one confirmed case in a traveler from South Africa to Hong Kong. Then Hong Kong health authorities on Friday identified a second case of the B.1.1.529 variant among returning travelers on the same floor of a designated quarantine hotel.

Yesterday, the Belgian government said one individual who had recently arrived from abroad, and was not vaccinated, had tested positive for the new variant, marking the first case in Europe. Also a few hours before that, Israel also said that they had detected a case.

Dr Tulio de Oliveira, the director of South Africa’s Center for Epidemic Response and Innovation, said the variant has “many more mutations than we have expected,” adding it is “spreading very fast, and we expect to see pressure in the health system in the next few days and weeks.”

Dr Neil Ferguson, the director of the MRC Centre for Global Infectious Disease Analysis at Imperial College London, said that the number of mutations on the spike protein was “unprecedented.”

Dr Ferguson told :”The spike protein gene is the protein which is the target of most vaccines. There is therefore a concern that this variant may have a greater potential to escape prior immunity than previous variants.”

Despite a total of 59 mutations on the genome of the new variant with 32 just on the spike protein(note that the Delta only has 17 mutations on its spike protein), the virus is still exhibiting that it is very stable, dispelling and contradicting comments from certain virologists that if a virus has too many mutations, it will be unstable and gradually die off.

Typically, viruses, including the one that causes Covid-19, mutate regularly and most new mutations do not have significant impact on the virus’s behavior and the illness they cause.

However, from the case reports so far of those that were found infected with the new Omicron variant, there are may unusual clinical manifestations that are worrying researchers not just in terms of both immune and vaccine evasiveness.

The dean of Brown University’s School of Public Health, Dr Ashish Jha, told media that the variant was “acting differently,” however, and it “looks like it’s much more contagious than even the Delta variant.”

Dr Sharon Peacock, a professor of Public Health and Microbiology at the University of Cambridge, said while the overall number of Covid-19 cases is relatively low in South Africa, there has been a rapid increase in just the past seven days.

Dr Peacock said while 273 new infections were recorded on November 16, the figure had risen to more than 1,200 cases by November 25, with more than 80% coming from Gauteng province in South Africa alone.

She said, “The epidemiological picture suggests that this variant may be more transmissible, and several mutations are consistent with enhanced transmissibility.”


Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern

The Technical Advisory Group on SARS-CoV-2 Virus Evolution (TAG-VE) is an independent group of experts that periodically monitors and evaluates the evolution of SARS-CoV-2 and assesses if specific mutations and combinations of mutations alter the behaviour of the virus. The TAG-VE was convened on 26 November 2021 to assess the SARS-CoV-2 variant: B.1.1.529.

The B.1.1.529 variant was first reported to WHO from South Africa on 24 November 2021. The epidemiological situation in South Africa has been characterized by three distinct peaks in reported cases, the latest of which was predominantly the Delta variant. In recent weeks, infections have increased steeply, coinciding with the detection of B.1.1.529 variant. The first known confirmed B.1.1.529 infection was from a specimen collected on 9 November 2021.

This variant has a large number of mutations, some of which are concerning. Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other VOCs. The number of cases of this variant appears to be increasing in almost all provinces in South Africa. 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.

There are a number of studies underway and the TAG-VE will continue to evaluate this variant. WHO will communicate new findings with Member States and to the public as needed.

Based on the evidence presented indicative of a detrimental change in COVID-19 epidemiology, the TAG-VE has advised WHO that this variant should be designated as a VOC, and the WHO has designated B.1.1.529 as a VOC, named Omicron.

As such, countries are asked to do the following:

  • enhance surveillance and sequencing efforts to better understand circulating SARS-CoV-2 variants.
  • submit complete genome sequences and associated metadata to a publicly available database, such as GISAID.
  • report initial cases/clusters associated with VOC infection to WHO through the IHR mechanism.
  • 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.

Individuals are reminded to take measures to reduce their risk of COVID-19, including proven public health and social measures such as wearing well-fitting masks, hand hygiene, physical distancing, improving ventilation of indoor spaces, avoiding crowded spaces, and getting vaccinated.

For reference, WHO has working definitions for SARS-CoV-2 Variant of Interest (VOI) and Variant of Concern (VOC).

A SARS-CoV-2 VOI is a SARS-CoV-2 variant:

  • with genetic changes that are predicted or known to affect virus characteristics such as transmissibility, disease severity, immune escape, diagnostic or therapeutic escape; AND
  • that has been identified as causing significant community transmission or multiple COVID-19 clusters, in multiple countries with increasing relative prevalence alongside increasing number of cases over time, or other apparent epidemiological impacts to suggest an emerging risk to global public health. 

A SARS-CoV-2 VOC is a SARS-CoV-2 variant that meets the definition of a VOI (see above) and, through a comparative assessment, has been demonstrated to be associated with one or more of the following changes at a degree of global public health significance:

  • increase in transmissibility or detrimental change in COVID-19 epidemiology; OR
  • increase in virulence or change in clinical disease presentation; OR
  • decrease in effectiveness of public health and social measures or available diagnostics, vaccines, therapeutics


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