CONNECT THE DOTS— It’s been two weeks since South African scientists alerted the world of a new Covid variant on Friday, Nov. 26. Two weeks is also the amount of timethe president’s top health adviser, Anthony Fauci, said it would take to get a better ideaof what we’re dealing with when it comes to Omicron.

On cue, new info has been trickling out of South Africa this week, suggesting that while the variant is spreading like wildfire in the country, it’s possible the disease it causes is less severe — though it’s still way too early to really tell.

As for how Omicron will affect the U.S., figuring that out in two weeks was a “little optimistic,” Charles Chiu, an infectious diseases researcher at the University of California San Francisco, told Nightly.

Wehave the genomic sequencing data and capabilities, Chiu said. The problem is the U.S. lacks the infrastructure to quickly turn this information into action.

Unlike South Africa, the U.S. has a fractured virus surveillance system, with some states sequencing Covid cases at high percentages and others just examining a small number of samples. There’s no national standard for genomic virus sequencing, he said, and the result is an incomplete and biased picture of the current state of the virus — one that tends to ignore rural and minority populations.

It took U.S. health officials an extra five days — until Dec. 1—to detect Omicron, meaning we’re about a week behind South Africa, which has one of the world’s most robust national surveillance systems, Chiu pointed out. Once a country has access to a variant, it can take scientists up to two weeks to grow enough of a virus like Omicron for widespread distribution to labs, Chiu said. After that, scientists can conduct studies on the variant’s transmissibility, severity and ability to evade vaccines. Results from these studies in the U.S. will continue to roll out in the coming days and weeks.

There are a few reasons the U.S. was slow to identify a case fromthe new variant. Factors like population size and Omicron’s origin across the Atlantic Ocean, either in Europe or Africa, put us behind. But so did the U.S. system of public health, Chiu said.

Time is important — many U.S. labs don’t sequence a sample until two weeks after it’s collected,he said. This means the data is almost useless for contact tracing and other public health measures.

And U.S. labs are also not sharing the right data. The genome itself is virtually useless, Chiu said. You also need metadata attached to the sample, which would include valuable information such as the demographics of the person infected, whether they had symptoms, the severity of disease, and vaccination status. “We don’t have this sort of sample-to-answer-to-action pipeline that’s really needed to provide information as soon as possible,” Chiu said.

In the U.K., sequencing labs are processing hundreds to thousands of samples a day, Chiu said, tagging and annotating them with clinical metadata that’s then fed to hospitals and the country’s public health agency, so the information can immediately be applied in both clinical and public health decision making. Nothing like that happens in the U.S.

States like California have set goals to sequence 20 percent of Covid cases. But these samples aren’t linked to any clinical metadata, which Chiu blames on the lack of a national health care system in the U.S., as well as privacy and confidentiality concerns.

“On a national level, in some cases, we were unable to even release the ZIP code of where the sequence came from. Much less identifying information like potentially age or sex, or gender,” he said.

Finding a way to address this information-sharing blockade will be key to preventing future pandemics, he said. The U.S. can’t necessarily overhaul its entire health care system, Chiu said, but he thinks it should be possible toset new standards for how we collect and share public health data.

“We know that it’s only a matter of time before we’re going to see another virus or even a relative of this virus emerge and become the next pandemic,” Chiu said. “The next critical step that needs to be made is that we need to more tightly integrate our national surveillance system.”

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