Everything we know about the new Omicron B.1.1.529 COVID variant

Since early in the COVID pandemic, the Network for Genomics Surveillance in South Africa has been monitoring changes in SARS-CoV-2. This was a valuable tool to understand better how the virus spread. In late 2020, the network detected a new virus lineage, 501Y.V2, which later became known as the beta variant. Now a new SARS-CoV-2 variant has been identified, known as B.1.1.529.

Hunting for variants requires a concerted effort. South Africa and the UK were the first big countries to implement nationwide genomic surveillance efforts for SARS-CoV-2 as early as April 2020.

• Variant hunting, as exciting as that sounds, is performed through whole genome sequencing of samples that have tested positive for the virus.
• South Africa is well set up for this thanks to a central repository of public sector laboratory results, good linkages to private laboratories and advanced modelling expertise.
• South Africa also has several laboratories that can grow and study the actual virus and discover how far antibodies are able to neutralize it.

Omicron: Everything we know about the new COVID variant so far 

Seventy-seven samples collected in mid-November 2021 in South Africa's Gauteng province had the Omicron strain. It has also been reported in small numbers from neighbouring Botswana and Hong Kong.

B.1.1.529 carries certain mutations that are concerning. They have not been observed in this combination before, and the spike protein alone has over 30 mutations. This is important, because the spike protein is what makes up most of the vaccines.

B.1.1.529 has a genetic profile very different from other circulating variants of interest and concern. It does not appear to be a “daughter of delta” or “grandson of beta” but rather represents a new lineage of SARS-CoV-2.

Some of its genetic changes are known from other variants and we know they can affect transmissibility or allow immune evasion, but many are new and have not been studied as yet.

SA being ‘punished’ for ‘excellent science’

In a bid to stay abreast of rapidly developing information regarding the new Covid-19 Omicron variant, the Department of International Relations and Cooperation (Dirco) has assured that communication lines with countries opting to ban travel to and from South Africa are open and being pursued. 

Dirco said new variants had been detected in other countries as well, with these cases showing “no recent links with southern Africa”. 

The department emphasised the reaction to other variants “is starkly different to cases in southern Africa”. 

“This latest round of travel bans is akin to punishing South Africa for its advanced genomic sequencing and the ability to detect new variants quicker.

“Excellent science should be applauded and not punished.”

61 passengers from SA flights test positive for Covid-19, say Dutch authorities

Dutch health authorities said Saturday that 61 passengers from two flights from South Africa tested positive for Covid-19 and the results were being examined for the new Omicron variant.

“We now know that 61 of the results were positive and 531 negative,” the Dutch Health Authority (GGD) said in a statement. 

“The positive test results will be examined as soon as possible to determine whether this concerns the new worrisome variant, which has since been given the name Omicron variant.”

All passengers who tested positive must stay in quarantine at the hotel for seven days if they show symptoms and for five days if they do not, the GGD said.

Passengers who tested negative, but who are remaining in the Netherlands, are expected to isolate at home. 

“We understand that people are frustrated by this,” the statement added, “people have just made a long trip with the idea that they will shortly be home,” it said.

Those who do not live in the Netherlands can “continue their journey”

Omicron: Covid variant more transmissible, but maybe not deadlier

The new Covid-19 variant B.1.1.529 detected in South Africa is more transmissible and becoming dominant than the previous ones, but it is yet to be determined if it is deadlier.

This was revealed by the Minister of Health Dr Joe Phahlaa on Friday during a virtual question and answer session with journalists following a media briefing on Thursday.

South Africa currently has 22 cases of the variant, with up-to-date results due by the end of the week. 

The National Institute for Communicable Diseases reported no unusual symptoms have been reported on those infected with the B.1.1.529 variant, and as with other variants, some people infected with the variant are asymptomatic as well.

Variants are inevitable when a virus spreads and mutates, but wearing a mask, getting a vaccine and adhering to social distancing protocols are also excellent ways to minimise the chances of being infected.

Meanwhile, South Africa’s medical chief Dr. Angelique Coetzee described the panic as a “storm in a teacup,” adding that she had only seen “very very mild cases” of the variant so far.