Why COVID demands genetic surveillance

Driving the news: New variants of SARS-CoV-2 — including the B.1.1.7 variant that appears to be helping to drive a tremendous spike in infections in the U.K. and Ireland — are being identified by scientists around the world, my Axios colleague Marisa Fernandez reports today.

• The B.1.1.7 variant is particularly worrying — Public Health England estimates it may be 30–50% more transmissible than other forms of the virus.
• While a few state health departments in the U.S. have identified a handful of B.1.1.7 cases, the CDC said on Friday that "neither researchers nor analysts at CDC have seen the emergence of a particular variant in the United States."

Yes, but: Genetic surveillance of coronavirus variants in the U.S. lags well behind dozens of other countries, which means we lack a clear picture of exactly how the novel coronavirus currently infecting more than 200,000 people a day is mutating here.

• To identify whether coronavirus variants are emerging in the U.S., scientists need to genetically sequence infections.
• But according to the nonprofit GISAID initiative, the U.S. has only sequenced a little more than 60,000 cases since the start of the pandemic, or roughly 0.3% of all cases.
• That's a little more than half the cases sequenced by the U.K., the world's leader in genetic surveillance, and the median time it takes to post a sequence of the virus on GISAID in the U.S. is 85 days, slower than far poorer countries like Bangladesh and Sri Lanka.

Be smart: The bottleneck here isn't scientific. Genetic sequencing has gotten faster and cheaper, and every state in the U.S. has the technical capacity to decode viral genomes.

• Rather, the U.S. lacks the kind of unified, national genetic surveillance program adopted by the U.K., which in the spring invested £20 million ($27 million) to launch a scientific consortium that standardized the sequencing and reporting of coronavirus variants.
• While the CDC in May brought together dozens of labs in an effort to accelerate sequencing, a report by the National Academies of Science, Engineering and Medicine in July concluded current efforts are "typically passive, reactive, uncoordinated, and underfunded."
• As a result, "currently available data are unrepresentative of many important population features, biased, and inadequate to answer many of the pressing questions about the evolution and transmission of the virus."

What they're saying: "You’ll never find what you aren’t actively looking for," as Michal Tal, a biologist at Stanford University, told the New Republic last month.

• If the U.S. had a strong national genetic surveillance system in place, it could see evidence of more transmissible variants and amp up vaccination or lockdown procedures before outbreaks got even more out of control.
• That's precisely what the U.K. government did in December, and in recent days new cases have begun to decline.

What's next: The incoming Biden administration may be open to the idea of a national genetic surveillance program, which would likely cost several hundred million dollars, according to the New York Times.

• Another option is to accelerate efforts to sequence variant strains from wastewater samples in community sewage systems.
• A more systematic genetic surveillance program could also pay dividends beyond the COVID-19 pandemic, by helping scientists identify emerging pathogens as soon as possible.

What to watch: If the weak U.S. genetic surveillance system begins to pick up signs that a variant like B.1.1.7 is beginning to dominate cases here, it would indicate a very bad pandemic is about to get much worse.

• And — since the coronavirus is constantly mutating — entirely new variants could show up, like those identified in Ohio today.

The bottom line: The pandemic has always been a race against time, and without a better genetic surveillance system, the U.S. will be perpetually slow out of the blocks.