More work needed to identify risk from Nigeria variant, says researcher

A researcher who identified a novel coronavirus variant in Nigeria has cautioned against automatic assumptions that it poses similar risks to strains that have emerged elsewhere.

The new strain was uncovered last week by scientists at the African Centre of Excellence for Genomics of Infectious Diseases (ACEGID) in southeastern Nigeria.

ACEGID director Christian Happi said the variant was found in two out of 200 samples of virus collected from patients between August 3 and October 9.

The two samples were taken from the same state in Nigeria at different times.

They show a variant "different to the one that has been circulating in Nigeria, different from the one in South Africa and different from the one in the U.K.," he said in an interview with AFP.

Britain tightened restrictions after finding a new strain there that it said was more contagious than initial forms of the virus.

South Africa says a new strain detected there could explain the rapid spread of a second wave that has especially affected younger people.

Happi stressed that scientists were racing to unlock knowledge about the Nigeria strain and urged people not to "extrapolate."

"We have no idea, no evidence to say that this variant is linked to the spike we are seeing in Nigeria or not," said Happi, explaining that samples from the latest cases were being analysed for an answer.

Nigeria has recorded more than 82,000 cases of COVID-19, of which 1,246 were fatal.

Compared to the country's population of some 200 million people, this number is tiny.

However, the tally of cases has been rising by several hundred a day since the start of December. There has been a major increase in Lagos, Nigeria's economic capital, prompting the authorities there to reinstate a curfew and gatherings of more than 50 people.

But the number of deaths in Nigeria has not experienced a proportionate surge.
 

VIRUS MUTATION

Happi, a Cameroon-raised, Harvard-trained professor of molecular biology, works in a state-of-the-art lab in Ede, southeastern Nigeria.

It is one of only 12 in Africa designed to sequence viral genetic code and track mutations -- telltale changes that can be used to build a family tree of the microbe.

From this, the scientists at Ede believe the variant evolved "within Nigeria, I don’t think it was imported from anywhere," said Happi.

"When changes occur, what matters most, what we’re focusing on, is the spike protein," he said, referring to the prong-like protein by which coronavirus latches onto a cell and infects it.

Happi said there was a "tendency to extrapolate" after a discovery of this kind.

But he cautioned strongly against automatically assuming that what happened in one population setting would also happen elsewhere.
 

AFRICAN DIFFERENCE?

"A lot of the models drawn at the onset of the pandemic, all got it wrong," he said.

"They were saying by now that a third of the African population would be dead. So people need to think," he said.

"It is very wrong to assume models based on knowledge that are not accurate or on assumptions that are dependent on data obtained from Europe or the U.S. and transpose it to a continent like Africa -- we are genetically different, we are immunologically different."

All of Africa has recorded 2.4 million cases, according to an AFP tally -- just 3.6 per cent of the global tally, although testing is also far less widespread. The continent's death toll of 57,000 is less than a fifth of that of the United States.

John Nkengasong, head of the Africa Centres for Disease Control and Prevention, the African Union's health agency, also urged patience as scientists worked to understand the Nigerian variant.

"Give us some time," he said in a videoconference from Addis Ababa. "It's still very early."

Nkengasong appealed to Africans not to let down their guard, warning of the danger of a second wave of infection.

By Louise Dewast

CTV News

New virus variant appears to emerge in Nigeria

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 Britain 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.

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 Aug. 3 and on Oct. 9 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% of global cases. Infections across the continent have risen 10.9% over the past four weeks, Nkengasong said, including a 52% increase in Nigeria and 40% 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.

By Cara Anna

AP

Video - Nigeria's students return to school amid COVID-19 crisis

Millions of students across twelve African countries have headed back to class as schools reopened after a six-month coronavirus lockdown. In Nigeria, nearly 40 million of them will now have to try to catch-up on missed schoolwork. But they will also return to a new set of rules as the government continues the struggle to stop the spread. Al Jazeera's Ahmed Idris reports from the capital, Abuja.