Nigeria detects first cases of omicron coronavirus variant

Nigeria has confirmed three omicron cases among travellers who had spent time in South Africa

A man receives a vaccine card from a health official in Lagos, Nigeria (AFP via Getty Images)

Nigeria has confirmed its first cases of the omicron coronavirus variant among three travellers who arrived in the country last week, the Nigeria Centre for Disease Control (NCDC) said.

The NCDC initially said on Wednesday that it had identified the variant among a sample collected from arrivals in October, weeks before South Africa raised the alarm.

In an amended statement later on Wednesday, it backtracked and said that sample contained the delta variant, not omicron.

The NCDC said the new variant was detected in “three persons with a history of travel to South Africa”.

Nigeria was the first West African country to record the omicron variant, although Ghana followed suit later on Wednesday.

About 20 countries have so far identified cases of the new variant, triggering travel bans across the world.

Data from other countries already shows the omicron variant was circulating before it was officially identified in southern Africa. Work to establish if it is more infectious, deadly or evades vaccines will take weeks.

Across Nigeria, the news of the omicron variant — which the World Health Organization has warned poses "very high" risk — has triggered concerns and renewed fears over the Covid-19 pandemic.

The NCDC urged the country’s states and the general public to be on alert and called for improved testing amid concerns that Nigeria’s low testing capacity might become its biggest challenge in the face of the new variant.

Testing for the virus is low in many states and even in the nation’s capital, Abuja. For instance, in parts of Kuje, a suburb of Abuja, Musa Ahmed, a public health official, said that no one has been tested for the virus for weeks.

The detection of the variant in Africa’s most populous nation, with 206 million people, coincides with Nigeria’s new requirement that all federal government employees must be inoculated or present a negative Covid-19 test result done in the last 72 hours.

With the vaccine mandate taking effect on Wednesday, there were chaotic scenes at several offices in the nation’s capital as civil servants without a vaccination card or a negative PCR test were turned away by security agents.

Nigeria — with 214,218 confirmed infections including nearly 3,000 deaths — has updated its travel advisory, ordering incoming international travelers to have a PCR test 48 hours before embarking on their trip to the country and two more tests, two days and seven days after arrival. Incoming international arrivals must also isolate for seven days.

Amid global concern over the omicron variant, the Nigeria CDC director-general told reporters that the country remains at alert in the face of the emerging crisis.

"We are working very hard to enhance ongoing surveillance, especially for inbound travelers, and also trying to ramp up testing (including) at the land borders," he said.

South African President Cyril Rampahosa and his Nigerian counterpart, Muhammadu Buhari are meeting in Abuja on Wednesday, when omicron is likely to be discussed.

Ghana on Wednesday also recorded its its first cases of the omicron variant on passengers who arrived at Accra international airport. Officials declined to specify how many positive cases were detected when the samples were sequenced on 21 November.

This article was amended on 1 December 2021. It originally said that the NCDC had stated it had detected its first cases of the omicron variant in a sample collected in October. However, it subsequently said it had been mistaken and that the variant detected in the October sample was delta. The omicron variant was detected among three travellers who arrived in Nigeria in the last week.