Without sequencing, we might have seen mysterious new surges or reinfections, only to speculate wildly and retrospectively about why; now scientists can trace these epidemiological trends to letter-by-letter changes in the coronavirus’s genetic code—and do it fast enough to influence policy, potentially slowing the variants before they take over. This systematic sequencing of positive COVID-19 tests is called genomic surveillance.
The rise of genomic surveillance has caught even scientists a bit by surprise. If they had known that variants would become front-page news, they might have come up with better names than B.1.1.7, 20I/501Y.V1, and VOC 202012/01, which are, confusingly, all names for the same U.K. variant. (No wonder the public has continued to simply call it “the U.K. variant,” despite official admonitions to avoid geographic names.) The WHO is just now discussing a new variant-naming scheme. Such a scheme does not exist, because we’d never had to talk about variants in public before—because we’d never identified variants quickly enough to matter for pandemic response before.
The inscrutable variant names are a small, if illustrative, example of the challenges that come with yanking genomic surveillance out of academic labs and thrusting it into public health. Sequencing is easy these days, scientists told me over and over. Analysis is hard. And, with a few notable exceptions, persuading the public to make real sacrifices based on some changing letters in a viral genome is harder still. The pandemic has shown the power of genomic surveillance but also exposed the challenges of wielding it. In the future, when we have learned the lessons of COVID-19, genomic surveillance of diseases might become routine and bureaucratic. That could be the pandemic’s biggest scientific legacy.
But this time, in this pandemic, the successes of genomic surveillance have depended on human intuition and human foresight and an occasional lucky break.
The story of the linked discoveries of the U.K. and South Africa variants is one such example. Last winter, Tulio de Oliveira, a bioinformatician at the University of KwaZulu-Natal in South Africa, began watching a cluster of mysterious pneumonia cases in China. And when that first viral genome hit the internet in January, he began preparing his lab to sequence the coronavirus in South Africa.
De Oliveira was one of a small cadre of scientists worldwide who already had significant experience with this sort of thing. He had previously sequenced the genomes of viruses, such as Zika, dengue, chikungunya, and yellow fever, that circulate in South America. (De Oliveira is originally from Brazil.) Others have done similar work on influenza, Ebola, West Nile, and Lassa fever. But for the most part, these studies tended to be small and retrospective—and they went at the leisurely pace of academia. By the time the results were published, the outbreak was typically long over.