A new study of underreported coronavirus variants is serving as 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 greater risk.
Researchers in the United States and Nigeria examined a variant of interest, Eta, that circulated in Nigeria in early 2021, as well as a rare Delta sublineage in the region that was different from the Delta variant that circulated in the rest of the world.
Eta may have warranted designation as a “variant of concern” had its growth potential been recognized earlier, wrote the researchers from Northwestern University’s Feinberg School of Medicine and the University of Ibadan in Nigeria. Their research was published this month in Nature Communications.
“We were just lucky that this variant did not spread globally,” said Dr. Oyewale Tomori, a virologist who leads a Nigerian government committee on Covid-19.
Judd Hultquist, a co-author of the report and the associate director of the Center for Pathogen Genomics and Microbial Evolution at Northwestern, said tracking of variants was “incredibly uneven” across the world.
“Less than 1 percent of sequences are from the continent of Africa, and less than 3 percent are coming from South America,” he said in an interview.
On Thursday, the World Health Organization’s Africa director, Dr. Matshidiso Moeti, encouraged wider use of genomic-sequencing technology in Africa to help speed up the detection of new variants. The technology is available only in a few of the region’s middle-income countries, like South Africa and Botswana.
Researchers from around the world use GISAID, the online global repository of coronavirus sequences, to share new genomes and scan for mutations in its hundreds of thousands of viral genetic sequences.
Nigeria, with a population of 220 million people, is the world’s seventh most populous country and the largest Black-majority nation. It is also one of the least vaccinated: Less than 3 percent of its population is fully inoculated, according to the Our World in Data project at the University of Oxford.
The World Health Organization labeled Eta a variant of interest, meaning it was worth studying but not as dangerous as a variant of concern. But after Eta displaced the Alpha variant in Nigeria and the surrounding region early last year, the researchers found that it went largely unnoticed while Alpha remained the focus of much of the world.
“Eta had all the characteristics of a variant of concern, and it was able to outcompete the Alpha variant in the region before the arrival of Delta,” Dr. Hultquist said.
And after Eta’s rise and fall, a rare Delta sublineage (AY.36) appeared in the region that was different from the Delta variant that circulated in most of the world.
The study emphasizes the critical need to improve surveillance and monitoring coronavirus infections to ensure early detection of new variants in Nigeria and the West Africa region, said Dr. Moses Adewumi of the University of Ibadan, one of the collaborators.
Even now, the researchers said, there are only just over 1,400 coronavirus sequences from Nigeria available in public repositories. The United States, by comparison, is sequencing tens of thousands of specimens each week.
The variants that were scrutinized by researchers are no longer a threat. But at the time variants of Alpha and Eta produced the highest peak of new infections; and the rare Delta lineage caused the second peak, according to Dr. Ramon Lorenzo-Redondo of Northwestern, one of the study’s authors. The peaks brought the highest death rates of the pandemic, he said.
Africa is not fully utilizing available lab resources, Dr. Tomori said. He said the continent’s labs had sequenced 70,000 viral genomes by the end of 2021.
“There is inadequate sequencing going on in Africa, because many African governments have not appreciated the usefulness of such facilities in providing data for better control of epidemics,” he said. “Also, there is a lack of collaboration among African researchers, some of whom prefer to work with their past ‘colonial’ colleagues.”
One lesson is clear: It’s never too early to try to tell what the impact of a variant 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 the Beta and Omicron variants, said: “The bigger message here is that we’re not seeing everything, and that some of these places may not have control of Covid-19.”