Saudi Arabia has recorded the Gulf's first confirmed case of the Omicron variant of the coronavirus in a citizen returning from North Africa, a health ministry official said Wednesday.

The strain, which was first announced by South Africa but has since been discovered to have been present earlier in Europe, has prompted governments around the globe to reimpose travel restrictions, despite warnings from the World Health Organization this could do more harm than good.

"One case of the Omicron variant has been detected in the kingdom -- it was a citizen coming from a North African country," the ministry official told the state SPA news agency.

"He has been put in isolation, as have his contacts, and the necessary health measures have been taken."

Saudi Arabia last week halted flights from seven southern African countries, mirroring similar moves by other government, but travel links with North Africa have remained unaffected. 

The kingdom had been lifting some of the remaining restrictions it imposed early in the pandemic, allowing worshippers at the Muslim holy places to resume praying shoulder to shoulder from October.

Since the pandemic started, Saudi Arabia has recorded 549,000 cases of Covid-19, 8,836 of them fatal.

More than 47 million doses of Covid vaccine have been administered in the kingdom, which has a population of nearly 35 million.

Meanwhile, Nigeria, Africa's most populous country, on Wednesday confirmed its first cases of the new Covid-19 variant, among three passengers who had arrived from South Africa.

"Genomic surveillance has now identified and confirmed Nigeria's first cases of the B.1.1.529 SARS-CoV-2 lineage, now known as the Omicron variant," said the head of Nigeria's Centre for Disease Control, Ifedayo Adetifa.

Contact tracing and "follow up to ensure isolation... have commenced," Adetifa said.

"Omicron is widespread globally... Therefore, it is a matter of when, not if, we will identify more cases," he added.

The coronavirus outbreak has killed 2,976 people and infected 214,113 in Nigeria, according to official statistics, but the real figures are believed to be much higher, in part because of low testing rates.

Home to around 210 million people, the West African nation has launched vaccination campaigns and requires civil servants to show proof of vaccination or a negative test to enter public buildings. 

But vaccination rates remain low, with just over 6.5 million people given one shot and about 3.5 million people given two shots.

The government said it plans to inoculate 112 million or 70 percent of adults by the end of next year.

The emergence of Omicron, first reported to the World Health Organization in South Africa a week ago, has already spread rapidly across the globe with borders shutting and dozens of countries rolling out travel restrictions.

Nigeria had already reinforced some of its travel measures and imposed an additional test on day two.