Why the US may not see the next dangerous coronavirus variant coming

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There’s a reason why a new, more contagious variant of SARS-CoV-2 appeared first in the UK: The country does a lot of viral genetic sequencing. Since the start of the pandemic, researchers in the UK have uploaded 151,859 individual SARS-CoV-2 sequences to GISAID, an international platform for sharing viral genomic data. That’s the highest number of sequences shared by any country in the world.

If a more contagious strain of SARS-CoV-2 first evolved in the United States, scientists likely would not have noticed so quickly. Despite having a larger population than the UK, a sophisticated biomedical research industry, and tens of millions more cases of Covid-19, to date US labs have only uploaded 69,111 sequences, according to GISAID.

“It’s embarrassing, is all I can say,” Diane Griffin, a microbiologist and immunologist at Johns Hopkins, told Vox.

The US has lagged behind on so many aspects of pandemic response — from an initial lack of testing, to the current strained and clumsy rollout of the Covid-19 vaccines. Lack of genetic surveillance is just another. Without it, we’re kept in the dark: Scientists can’t see, clearly or quickly, how and if the virus is mutating in concerning ways. It also leaves us without another useful tool to deploy in contact tracing studies.

And it’s one this country ought to invest in, and get right, scientists say — at least before the next pandemic strikes.

How the US fails on testing viral genomes

Earlier this year, Griffin was on a committee making recommendations for a recent National Academies of Science report on the state of genomic surveillance in the US. Genomic surveillance is used, routinely, around the world to track flu, and to try to predict which flu vaccine strains will be most effective in a given season. Genetic sequencing tools are not a new technology, and the Academies wanted a report to survey how they were being deployed in the pandemic in the US. Genetic sequencing is of particular import when it comes to coronaviruses because they use RNA as their genetic code, and RNA viruses are known to mutate frequently.

The report, when it was published in July, outlined a bleak landscape of SARS-CoV-2 mutation tracking. It’s not just that the US isn’t collecting enough genome samples of the virus. It’s doing so in an unsystematic, patchwork way.

“Current sources of SARS-CoV-2 genome sequence data … are patchy, typically passive, reactive, uncoordinated, and underfunded in the United States,” the report concluded. And the data that did exist? The report found it was “inadequate to answer many of the pressing questions about the evolution and transmission of the virus.”

Early on in the pandemic — way back in March — the UK government invested £20 million ($27 million) to launch the COVID-19 Genomics UK (COG-UK) consortium, which coordinates the collection of this data from public health labs. The consortium also tracks viral genetic samples…



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