Variant Hunters Race to Find New Strains Where Testing Lags

In mid-February, three travelers were stopped at the airport in Luanda, Angola. Even during the pandemic, the country, a hub for the oil industry, had seen plenty of passengers from Europe and South Africa, where two concerning variants of the virus that causes Covid-19 hold sway. But the strains weren’t yet circulating widely in Angola, so this winter, health officials battened down the hatches. Before any passports get stamped, travelers receive a rapid antigen test and wait 30 minutes for a result. A negative test means self-quarantine, followed by another test a few days later. A positive test means a two-week stay at a quarantine hotel. For the three travelers, it was option two.

A few weeks later, samples taken from their noses arrived 2,000 miles south in South Africa, at the lab of Tulio de Oliveira, a geneticist at the University of KwaZulu-Natal. He was in for a surprise. The virus that had infected these three travelers didn’t resemble the strains circulating in most other places, including those labeled as “variants of concern” for their ability to spread faster and evade certain types of immunity. If those variants are like siblings, this one was more like a forgotten second cousin. It came from a lineage of the virus that emerged in the early days of the pandemic but had disappeared soon thereafter, apparently outcompeted by other variants. And yet here it was, a year later. And it had been busy. The virus had since accumulated dozens of mutations, including many of the same ones that made those other strains worrisome because of increased transmissibility and immune evasion. It had arrived at a similar genetic conclusion all on its own.

The new variant seemed to have stepped out of an epidemiological void. Which, in a way, it had, because the travelers had arrived from a country where the pandemic did not officially exist. Last June, the president of Tanzania, John Magufuli, declared the country Covid-free, having rid itself of the virus through three days of national prayer. Since then, reports from doctors and nonprofits within the country told of a “hidden epidemic” raging as fiercely as it was anywhere. But the government’s data had evaporated: no tests or case numbers or genome sequences. With so little information—just three genomes—it was hard to say what this new variant meant. Where had it come from, and where were its closer relatives? Was it spreading widely, or were these cases just a fluke? Were its mutations as worrisome in practice as on paper? De Oliveira and his colleagues are now racing to answer those questions.

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Such surprises are somewhat common in de Oliveira’s line of work. Since the pandemic began, African labs have uploaded fewer than 12,000 genomes to GISAID, the leading database for viral sequences, compared with 280,000 from North America, a continent with less than half the population. About half of those African genomes come from South Africa, where de Oliveira’s lab is the centerpiece of a national sequencing effort. That means there are plenty of gaps to be explored. “It’s concerning,” says Emma Hodcroft, a molecular epidemiologist at the University of Bern. “It’s a huge continent, and we know that there are Covid outbreaks happening. But, apart from South Africa, we don’t have a good idea of what’s happening anywhere else.”

In recent months, De Oliveira has been working to change that. In early December, the lab’s genomic sleuthing amidst a surge of cases in South Africa led to the identification of a strain now known as B.1.351. That variant is now spreading globally, causing headaches because it is more resistant to the protection of some vaccines. It was also a wake-up call for South Africa’s neighbors. So earlier this year, de Oliveira’s lab, in partnership with the Africa Centres for Disease Control and Prevention, began receiving weekly or biweekly samples from 10 countries in southern Africa, part of an effort to track the newly uncovered variant and others around the continent. A second lab, Nigeria’s Africa Centre of Excellence for Genomics of Infectious Diseases, or ACEGIP, handles the northern half of the continent. The research from Angola, which was co-led by the country’s health minister, Silvia Lutucuta, appeared as a preprint Monday and has not yet been peer reviewed.

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