Covid-19 Was Here Earlier Than Most Americans Thought. Now What?

For the past two months, the earliest known community spread of Covid-19—passed between people here in the United States, rather than a traveler bringing it home from abroad—was a case identified at the UC Davis medical center on February 26. Now we have confirmation the virus was circulating here far earlier than that. Last week, health officials in Santa Clara County, California, announced that a 57-year-old woman died of Covid-19 at her home in San Jose on February 6. Two others followed her in mid-February and early March. None of those people had recently traveled abroad. Their diagnoses were all confirmed posthumously from tissue samples taken by the county coroner and sent to the Centers for Disease Control for testing.

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Health officials are likely to turn up more cases like those. “They’re really like iceberg tips,” said Sara Cody, the public health officer for Santa Clara County, at a press conference last week. “When you have an outcome like death … that means there’s an iceberg of cases of unknown size.”

The findings have underlined the early failures of the US’s pandemic response. As federal officials, including President Donald Trump, downplayed the crisis and cast it as a foreign problem, the virus was already here, slipping through border checks and spreading undetected due to a lack of tests. They also left people wondering once again whether they might have already had the disease and hoping they are now immune. (The answer, still, is probably not.)

For scientists who have studied the early spread of Covid-19 in the US, the virus’s timeline did not need to be rewritten. “There’s nothing even vaguely surprising about this finding,” says Arthur Reingold, an epidemiologist at the University of California, Berkeley. “It’s easy to be smart in hindsight, but all the evidence we have has pointed to this.”

“This is in line with our projections,” says Kate Coronges, director of the Network Science Institute at Northeastern University. Using travel patterns and data about the virus’s transmission, a team there recently estimated that tens of thousands of invisible cases were already occurring in US cities prior to March 1. As the new cases confirm, fatalities from the virus were invisible, too, going unexplained or labeled with the wrong cause of death. But even with the new information, their models still point to a likely mid-January introduction in states like California and New York.

Even if the experts expected this result, the new cases highlight some of the challenges of precisely understanding the early stages of the virus’s spread in the US—a process that could have lessons for containment if the virus roars back later this year after social distancing measures are relaxed. That starts with what researchers have learned about how the virus arrived here in the first place.

Much of what we know about the early spread of Covid-19 has been learned from sleuthing through the virus’s genetic code. As a virus spreads, hijacking the cellular machinery of its host’s cells to replicate its RNA, it picks up mutations at a relatively predictable pace. That allows researchers to walk backwards through the virus’s evolutionary history, tracing when mutations occur and where the virus splits off into new strains. Researchers have used those genetic techniques to trace the origins of the virus back to strains circulating in China, and to draw various paths that brought it to the US.

In the US, an analysis by Trevor Bedford, a computational biologist at the Fred Hutchinson Research Center, put the virus’s introduction at some point in the middle of January. But the virus took multiple routes. Some strains came via travelers arriving directly from China. Other strains, especially on the East Coast, arrived by way of Europe. From there, the various strains began to bounce around the country, as Americans continued to jet about prior to the enactment of shelter-in-place rules.

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