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A new study of unreported coronavirus variants is a reminder that early detection and frequent genome sequencing are among the most powerful arrows in public health officials’ quiver.
But that is precisely what is not happening in many countries, putting their own people – as well as the rest of the world – at greater risk.
Researchers in the United States and Nigeria studied an interesting variant, Eta, which was circulating in Nigeria in early 2021, as well as a rare delta sublineage in the region that differed from the delta variant circulating in the rest of the world.
Eta might have warranted classification as a “variant of concern” if its growth potential had been recognized earlier, the researchers from Northwestern University’s Feinberg School of Medicine and the University of Ibadan in Nigeria wrote. your research was released this month in Nature Communications.
“We were just lucky that this variant didn’t spread worldwide,” said Dr. Oyewale Tomori, a virologist who heads a Nigerian government committee on Covid-19.
Judd Hultquist, co-author of the report and associate director of Northwestern’s Center for Pathogen Genomics and Microbial Evolution, said variant tracking is “incredibly uneven” around the world.
“Less than 1 percent of the sequences come from the African continent and less than 3 percent come from South America,” he said in an interview.
On Thursday, the World Health Organization‘s Africa director, Dr. Matshidiso Moeti, the wider use of genome sequencing technology in Africa to speed up the detection of new variants. The technology is only available in a few middle-income countries in the region, such as South Africa and Botswana.
Researchers from all over the world use it GISAIDthe online global repository of coronavirus sequences to share new genomes and look for mutations in its hundreds of thousands of viral genetic sequences.
With a population of 220 million people, Nigeria is the seventh most populous country in the world and the largest black majority nation. It is also one of the least vaccinated, with less than 3 percent of its population fully vaccinated Our world in data Project at the University of Oxford.
The World Health Organization labeled Eta an interesting variant, meaning it’s worth investigating, but not as dangerous as a variant of concern. But after Eta supplanted the Alpha variant in Nigeria and the surrounding region early last year, researchers found that it went largely unnoticed while Alpha remained the focus of much of the world.
“Eta had all the hallmarks of a variant of concern and was able to crowd out the Alpha variant in the region prior to Delta’s arrival,” said Dr. Hultquist.
And after the rise and fall of Eta, a rare delta subline (AY.36) appeared in the region, distinct from the delta variant that circulated in most parts of the world.
The study highlights the urgent need to improve surveillance and surveillance of coronavirus infections to ensure early detection of new variants in Nigeria and the West Africa region, said Dr. Moses Adewumi from Ibadan University, one of the collaborators.
Even now, the researchers said, only a little over 1,400 coronavirus sequences from Nigeria are available in public repositories. The United States is in comparison sequencing Tens of thousands of copies per week.
The variants scrutinized by researchers are no longer a threat. But at that time, variants of Alpha and Eta produced the highest spike in new infections; and the rare delta line, according to Dr. Ramon Lorenzo-Redondo of Northwestern, one of the study’s authors, the second peak. The spikes brought the highest death rates of the pandemic, he said.
“Inadequate sequencing is happening in Africa because many African governments have failed to recognize the usefulness of such facilities in providing data for better epidemic control,” he said. “There is also a lack of collaboration between African researchers, some of whom prefer to work with their former ‘colonial’ colleagues.”
One lesson is clear: it’s never too early to try to predict what impact a variant might have. Researchers are already observing a new subvariant of Omicron, BA.2.
Alex Sigal, a virologist at the Africa Health Research Institute in Durban, South Africa who helped identify the beta and omicron variants, said: “The more important message here is that we are not seeing everything and that some of these locations may not be the ones have control over Covid-19.”