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A passenger being tested for COVID-19 at Johannesburg’s international airport in January. A coronavirus variant of concern that arose in South Africa has spread around the world.

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Scientists tracking coronavirus variants struggle with global blind spots

Science’s COVID-19 reporting is supported by the Heising-Simons Foundation.

Last month, Gytis Dudas was tracking a concerning new coronavirus variant that had triggered an outbreak of COVID-19 in his native Lithuania and appeared sporadically elsewhere in Europe and in the United States. Exploring an international database of coronavirus genomes, Dudas found a crucial clue: One sample of the new variant came from a person who had recently flown to France from Cameroon. A collaborator, Guy Baele of KU Leuven, soon identified six more sequences from people in Europe who had traveled in Cameroon. But then their quest to pinpoint the variant’s origins hit a wall: Cameroon had uploaded a total of only 48 genomes to the global sequence repository, called GISAID. None included the variant.

With dogged legwork, Baele and Dudas, an evolutionary biologist at the Gothenburg Global Biodiversity Centre, learned another team had gathered as-yet-unpublished sequences from a COVID-19 outbreak among staff at a great ape program in the Central African Republic—near the Cameroonian border. Six people there carried the new variant.

Baele, Dudas, and their colleagues reconstructed the variant’s evolutionary tree and geographic spread, and concluded that the new variant most likely arose in Cameroon, as they reported in a preprint on 8 May. They note that the variant carries a suite of mutations seen in other “variants of concern” that are more infectious or dangerous.

“It looked like the typical thing that should raise all red flags,” says Sebastien Calvignac-Spencer, an evolutionary biologist at the Robert Koch Institute whose team sequenced samples from the ape station. But Cameroon and neighboring countries, where the team inferred the variant might already be prevalent, had been blind to it.

The researchers say the story of this variant, designated B.1.620, holds a warning for the world: “The sequencing effort in Cameroon and other African countries is not enough,” says co-author Ahidjo Ayouba, a biologist at the French National Research Institute for Sustainable Development at the University of Montpellier. He is traveling to his native Cameroon next month to set up the country’s first next-generation sequencer. The emergence of new variants with deleterious mutations in countries with no regular sequencing “may become an alarming norm,” the researchers caution in the paper.

It is not just Africa. Of 152 countries for which data were available as of 10 May, 100 had uploaded sequence data for less than 1% of their reported cases to GISAID (see map, below). Among those, 51 countries, including large nations such as India, Indonesia, Russia, and Brazil, had uploaded sequences for less than 0.1% of cases. Ten wealthy nations accounted for 82% of the more than 1.4 million sequences in GISAID’s database. “We are working to change that,” says Frank Konings, leader of the World Health Organization’s (WHO’s) Virus Evolution Working Group. 

Most countries with scarce sequencing also currently have little or no access to vaccines, and some have severe outbreaks. As the virus replicates unchecked, those regions can become breeding grounds for new mutants, which can then spread around the world. India, for example, is coping with a world-leading surge of cases. On 11 May, WHO labeled the new variant B.1.617, which arose in India and has spread to dozens of countries, a variant of concern. “Where the pandemic is currently unchecked is where we can expect that variants are on the rise,” Dudas says. “It would be much more interesting to sequence the last 1000 cases in the Central African Republic than the next 100,000 cases in Germany.”

A patchy picture

Sequencing of the pandemic coronavirus is minimal in most countries around the world, so scientists often have little insight into emerging new variants.