New Covid variant has emerged in Nigeria, says Africa CDC

Another new variant of the coronavirus appears to have emerged in Nigeria, Africa's top public health official said Thursday, but he added that further investigation was needed.

The discovery could add to new alarm in the pandemic after similar variants were announced in the UK and South Africa, leading to the swift return of international travel restrictions and other measures just as the world enters a major holiday season.

"It's a separate lineage from the UK and South Africa," the head of the Africa Centers for Disease Control and Prevention, John Nkengasong, told reporters. 

He said the Nigeria CDC and the African Center of Excellence for Genomics of Infectious Diseases in that country — Africa's most populous — will be analyzing more samples.

"Give us some time ... it's still very early," he said.

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The alert about the apparent new variant was based on two or three genetic sequences, he said, but that and South Africa's alert late last week were enough to prompt an emergency meeting of the Africa CDC this week.

The variant was found in two patient samples collected on 3 August and on 9 October in Nigeria's Osun state, according to a working research paper seen by The Associated Press.

Unlike the variant seen in the UK, "we haven't observed such rapid rise of the lineage in Nigeria and do not have evidence to indicate that the P681H variant is contributing to increased transmission of the virus in Nigeria. However, the relative difference in scale of genomic surveillance in Nigeria vs the U.K. may imply a reduced power to detect such changes," the paper says.

The news comes as infections surge again in parts of the African continent.

The new variant in South Africa is now the predominant one there, Nkengasong said, as confirmed infections in the country approach 1 million. While the variant transmits quickly and viral loads are higher, it is not yet clear whether it leads to a more severe disease, he said.

"We believe this mutation will not have an effect" on the deployment of COVID-19 vaccines to the continent, he said of the South Africa variant.

South Africa's health minister late Wednesday announced an "alarming rate of spread" in that country, with more than 14,000 new cases confirmed in the past day, including more than 400 deaths. It was the largest single-day increase in cases.

The country has more than 950,000 infections and COVID-19 is "unrelenting," Health Minister Zwelini Mkhize said.

The African continent now has more than 2.5 million confirmed cases, or 3.3 per cent of global cases. Infections across the continent have risen 10.9 per cent over the past four weeks, Nkengasong said, including a 52 per cent increase in Nigeria and 40 per cent increase in South Africa.

For the first time since confirming sub-Saharan Africa's first virus case in February, Nigeria is in the spotlight during this pandemic as infections surge.

"Over recent weeks, we've had a huge increase in number of samples to (Nigeria CDC) reference lab," the CDC director-general Chikwe Ihekweazu tweeted on Thursday. "This has led to an unusual delay with testing, but we're working around the clock," with many colleagues cutting short their holidays and returning to work.

Nigeria now has more than 80,000 confirmed coronavirus cases.