Sarah Zhang writes:

In the beginning, there was one.

The first genome for the virus causing a mysterious illness we had not yet named COVID-19 was shared by scientists on January 10, 2020. That single genome alerted the world to the danger of a novel coronavirus. It was the basis of new tests as countries scrambled to find the virus within their own borders. And it became the template for vaccines, the same ones now making their way to millions of people every day. That first coronavirus genome may have been the most important 30,000 letters published in all of 2020.

Since then, the number of sequenced genomes has simply exploded, to 700,000. In just over a year, the virus that causes COVID-19 has become the most sequenced virus of all time—soaring past such longtime contenders as HIV and influenza. Thousands of coronavirus genomes are sequenced around the world every day; several were generated in just the minute it’s taken for you to read these three paragraphs. “It’s been a revolution,” says Judith Breuer, a virologist at University College London.

We are now living through the first pandemic in human history where scientists can sequence fast and furiously enough to track a novel virus’s evolution in real time—and to act decisively on that information. Viruses constantly acquire mutations—genetic typos—and occasionally they mutate into a variant of interest. It was sequencing that identified a distinct and more transmissible variant in the UK. It was sequencing that prompted stricter lockdowns in response. And it’s now sequencing that is tracking the spread of variants, including those first found in South Africa and Brazil, that have mutations blunting immunity from vaccines and previous infections.

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. [Continue reading…]