He said there was no evidence the new variant was contributing to increased transmission in Nigeria, but cautioned the country does less genomic surveillance than Britain.
The Nigeria CDC and the African Centre of Excellence for Genomics of Infectious Diseases in Nigeria will study more samples, Nkengasong said.
“Give us some time ... it's still very early”, he said, in response to questions about the variant.
Nigeria's principal Covid-19 investigator has just released publicly the genomic sequences of the new variant, he added.
Nigeria's CDC did not immediately respond to a request for say on Nkengasong's remarks.
“Over recent weeks, we've had a huge increase in number of samples to (the Nigerian CDC's) reference lab,” the Nigeria CDC's director-general Chikwe Ihekweazu tweeted on Thursday.
“This has led to an unusual delay with testing, but we're working round the clock.”
Nigeria, Africa's most populous country with more than 200 million people, has seen fewer coronavirus cases than many others on the continent. Total cases crept past 80,000 on Wednesday. Daily recorded cases exceeded 1,000 for the first time this month.
Africa has reported more than 2.5 million coronavirus cases, making up 3.3% of global cases, according to the Africa CDC.
The new, faster-spreading variant that SA detected on Dec. 18 is now the predominant one there, Nkengasong said, though — as with the new variant in Britain — there is no evidence that it leads to a more severe disease.
The rate of coronavirus infections in SA will soon surpass the peak hit in the first wave earlier in the year, its health ministry said on Wednesday.
Nkengasong said the Africa CDC did not believe the mutation in SA would affect the deployment of the Covid-19 vaccines on the continent.