Nigeria uncovers Omicron case in October, changing timeline of variant

Omicron Covid appeared in Nigeria in OCTOBER – weeks before South Africa announced discovery of variant, new tests reveal

  • Nigeria found first cases of Omicron Covid today in travellers from South Africa 
  • But health chief said retroactive testing had found an earlier case in October 
  • If confirmed it would be the earliest-known Omicron infection, meaning the virus was in circulation undetected for weeks before South Africa identified it
  • Comes after Dutch scientists also found case that pre-dates Omicron’s discovery

Nigeria has confirmed its first cases of Omicron Covid and revealed it was in the country in October, weeks before South Africa alerted the world to its existence.

Three Omicron cases were detected in travellers who arrived in Nigeria from South Africa within the past week, the Nigerian Centre for Disease Control said today.

But Dr Ifedayo Adetifa, the agency’s director, added that retroactive testing of Covid samples collected in recent weeks had identified another case of Omicron dating back to October.

It means that Omicron – designated a ‘variant of concern’ by the WHO and believed to be the most-infectious form of Covid yet found – was likely circulating undetected for weeks before first being identified. 

The discovery comes just a day after after Dutch health authorities said they also found a case of Omicron in a sample collected on November 19, four days before South Africa sounded the alarm. 

Nigeria has reported its first official cases of Omicron in passengers arriving from South Africa (pictured), but said retroactive testing also picked up a case dating back to October

If confirmed, the Nigerian case would be the earliest-known Omicron infection – rewriting the timeline of the variant’s origins.

However, it does not necessarily mean the variant emerged in Nigeria because it is unclear how or why the sample was collected and Dr Adetifa did not give details.

Nigeria  – in western Africa – extensively tests travellers into and out of the country, meaning it is possible the case was imported from overseas. 

Until now, it had been assumed the variant first emerged in southern Africa where it was detected on November 23 by South African scientists in a sample collected from Botswana on November 9.  

Nigeria’s three recent cases were all in travellers from South Africa who had taken a Day 2 PCR test, with samples collected within the last week.

It is unclear when exactly the samples were collected. Nigeria said efforts are underway to track and isolate the individuals.

Analysts had suspected the virus was already circulating in Nigeria, after two Canadians returning from the country had tested positive for the variant last week.

The pair were Canada’s first confirmed cases of the variant, though experts warned at the time that Omicron has probably already circulated widely.

‘I think it’s fair to say that this variant probably emerged weeks or even months ago,’ infectious disease expert Dr. Isaac Bogoch said last week.

‘And by the time you start identifying it, it’s usually pretty widespread, especially for a very contagious respiratory viral infection like this.’

In the Netherlands, scientists from the RIVM health institute said their first cases were found in samples dated November 19 and November 23, without disclosing how or why either sample was collected.

It adds further evidence that Omicron was circulating widely before first being reported, and adds credence to the theory that the original version of Covid could have circulated unnoticed for weeks or months before China first reported it.   

Much is still not known about the variant, which is the most-mutated form of Covid yet uncovered by scientists.

Several of the mutations suggest the variant will be more infectious than the previously-dominant Delta strain, even in vaccinated people. 

Data from South Africa, where cases have ballooned 400 per cent in a week, also seems to suggest Omicron is more infectious.

But huge question marks remain, including whether Omicron causes more or less severe forms of infection.

Prominent health figures, including the man in the running to be Germany’s next health minister, have suggested that Omicron could end up being a blessing in disguise if it turns out it causes less severe infections.

This is because it would out-compete and replace the deadly Delta strain, while landing fewer people in hospital.

So-far, the WHO has not reported any deaths from Omicron – though information is still in the very early stages and the UN body has urged caution. 

Authorities in the eastern German city of Leipzig said Tuesday they had confirmed an infection with the omicron variant in a 39-year-old man who had neither been abroad nor had contact with anyone who had been, news agency dpa reported. 

Leipzig is in the eastern state of Saxony, which currently has Germany’s highest overall coronavirus infection rates.

Meanwhile, Japan and France announced their first cases of the new variant on Tuesday.

French authorities confirmed its presence in the French island territory of Reunion in the Indian Ocean. 

Patrick Mavingui, a microbiologist at the island’s research clinic for infectious diseases, said the person who has tested positive for the new variant is a 53-year-old man who had traveled to Mozambique and stopped in South Africa before returning to Reunion.

The man was placed in quarantine. He has ‘muscle pain and fatigue,’ Mavingui said, according to public television Reunion 1ere.

Dr Angelique Coetzee, chair of the South African Medical Association and the first person to spot the new variant in a patient, said her patients infected with Omicron reported different and much milder symptoms, including tiredness, muscle aches, a sore head and a dry cough. But none reported the tell-tale symptoms of a loss of smell or taste or breathing difficulties 

A day after banning all foreign visitors as an emergency precaution against the variant, Japan also confirmed its first case, in a visitor who had traveled from Namibia. 

A government spokesperson said the patient, a man in his 30s, tested positive upon arrival at Narita airport on Sunday and was isolated and is being treated at a hospital.

Travel bans also continued to fall Tuesday.

Cambodia barred entry to travelers from 10 African countries, citing the threat from the variant. 

The move came just two weeks after Cambodia reopened its borders to fully vaccinated travelers.

While it has urged against border closures, the WHO has stressed that while scientists are hunting evidence to better understand this variant, countries should accelerate vaccinations as quickly as possible.

WHO said there are ‘considerable uncertainties’ about the omicron variant. But it said preliminary evidence raises the possibility that the variant has mutations that could help it both evade an immune-system response and boost its ability to spread from one person to another.

Despite the global worry, doctors in South Africa are reporting patients are suffering mostly mild symptoms so far. 

But they warn that it is early and most of the new cases are in people in their 20s and 30s, who generally do not get as sick from Covid-19 as older patients.

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