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A new study on underreported coronavirus variants is a reminder that early detection and frequent genomic sequencing are among the most effective arrows in the quiver of public health officials.
But that is precisely what is not happening in many countries, putting their own populations – as well as the rest of the world – at risk.
Researchers in the United States and Nigeria examined a variant of interest, Eta, which circulated in Nigeria in early 2021, as well as a regionally rare Delta sublineage that was different from the Delta variant that circulated around the world.
Eta might have warranted the “variant of concern” designation if its growth potential had been recognized earlier, the researchers from the Feinberg School of Medicine at Northwestern University and the University of Ibadan in Nigeria wrote. Their research was published this month in Nature Communications.
“We were just lucky that this variant didn’t spread globally,” 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 was “incredibly uneven” across the world.
“Less than 1% of footage is from the African continent and less than 3% is from South America,” he said in an interview.
On Thursday, the World Health Organization’s Africa director, Dr Matshidiso Moeti, urged wider use of genomic sequencing technology in Africa to help 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 around the world use GISAID, the global online repository of coronavirus sequences, to share new genomes and search for mutations in its hundreds of thousands of viral genetic sequences.
Nigeria, with a population of 220 million, is the seventh most populous country in the world and the largest majority black country. It is also one of the least vaccinated: less than 3% of its population is fully inoculated, according to the Our World in Data project at the University of Oxford.
The World Health Organization has labeled Eta a variant of concern, which means it was worth studying but not as dangerous as a variant of concern. But after Eta moved the Alpha variant to Nigeria and the surrounding region early last year, researchers found it went largely unnoticed while Alpha remained at the center of much of the world. .
“Eta had all the hallmarks of a variant of concern and was able to outmatch the Alpha variant in the region before Delta arrived,” Dr Hultquist said.
And after the rise and fall of Eta, a rare Delta sub-lineage (AY.36) appeared in the region that was different from the Delta variant that circulated most of the world.
The study underscores the critical need for improved surveillance and tracking of coronavirus infections to ensure early detection of new variants in Nigeria and the West African region, said Dr Moses Adewumi of the ‘University of Ibadan, one of the collaborators.
Even now, the researchers said, there are just over 1,400 Nigerian coronavirus sequences available in public repositories. The United States, by comparison, sequences tens of thousands of specimens each week.
The variants that have been examined by researchers are no longer a threat. But at the time, the Alpha and Eta variants produced the highest spike in new infections; and the rare Delta lineage caused the second spike, according to Northwestern’s Dr. Ramon Lorenzo-Redondo, one of the study’s authors. The spikes resulted in the highest death rates of the pandemic, he said.
Africa is not fully utilizing available laboratory resources, Dr Tomori said. He said mainland labs had sequenced 70,000 viral genomes by the end of 2021.
“Sequencing is inadequate in Africa because many African governments have not appreciated the usefulness of such facilities to provide data for better epidemic control,” he said. “Furthermore, there is a lack of collaboration among African scholars, some of whom prefer to work with their former ‘colonial’ colleagues.”
One lesson is clear: it’s never too early to try to say what the impact of a variation might be. Researchers are already keeping a close eye on a new Omicron sub-variant, BA.2.
Alex Sigal, a virologist at the Africa Health Research Institute in Durban, South Africa, who helped identify Beta and Omicron variants, said: “The most important message here is that we don’t see everything, and that some of these places may not have Covid-19 control.