There are now almost 1.3 million cases of the coronavirus across the United States. More than half of them have been traced back to one source.

A huge percentage of the United States' coronavirus infections can be traced back to people travelling from New York City before it went into lockdown, according to new research from the Yale School of Public Health.

The analysis, whose conclusions are outlined in The New York Times today, shows New York was the "primary gateway" through which the virus spread to the rest of the country.

Experts say it shows officials at all levels of government in the US "missed the boat" by waiting too long to halt domestic travel and impose social distancing rules.

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As the virus spreads, it gains mutations, which subtly change its genetic "signature". Scientists can use that signature to distinguish between different lines of the disease and, in this case, determine where they came from.

The two earliest known outbreaks in the United States were in the state of Washington, on the country's west coast, and then New York on the east coast. Cases linked to Washington have a slightly different signature than the ones connected to New York.

After analysing thousands of samples from infected people across the US, Yale found that a majority of the cases bore mutations that could be traced back to the New York outbreak.

That was even true in a number of western states geographically closer to Washington. In California, for example, 50 per cent of the samples analysed were linked to New York, compared to 32 per cent that were linked to Washington.

"We now have enough data to feel pretty confident that New York was the primary gateway for the rest of the country," epidemiologist Nathan Grubaugh told The Times.

Grubaugh estimated that the spread of infections from New York accounted for "60 to 65 per cent of the sequenced viruses" in the US.

People wear face masks to protect against the coronavirus as they stand on line to grocery shop in the New York borough of Queens. Photo / AP
People wear face masks to protect against the coronavirus as they stand on line to grocery shop in the New York borough of Queens. Photo / AP

"It looks like most of the domestic spread is basically people travelling out from New York," confirmed Kari Stefansson, who is the CEO and founder of a genome analysis company.

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There have been 1.29 million confirmed cases of the virus in the US, and 76,844 deaths.

According to immunology professor Kristian Andersen, Yale's research is proof that the scale of the problem is America's "own fault".

"It means that we missed the boat early on, and the vast majority in this country is coming from domestic spread," Andersen told The Times.

In other words, officials were too slow to implement measures to contain the virus.

Birdsong, blaring sirens: A pandemic in sound. Video / AP

President Donald Trump restricted some travel from China at the start of February, but waited until March 11 to ban travel from Europe. It turns out most of the infections in New York came via Europe, rather than straight from China.

Mid-March was also when the White House finally issued a set of social distancing guidelines as part of its plan to "slow the spread".

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By then, it was already too late. In the fortnight after Trump announced the Europe travel ban, the official tally of cases skyrocketed from fewer than 2000 infections, largely limited to Washington and New York, to more than 68,000, spread across the entire country.

But the federal government was not the only one at fault. Authorities in New York also failed to act swiftly.

The state's first confirmed case came on March 1, though research has suggested that by that point there were actually 10,000 undetected infections there.

Governor Andrew Cuomo declared a state of emergency on March 7. He did not implement a full lockdown until almost two weeks after that, on March 20.

Again, we now know that was too late. For weeks, thousands upon thousands of people continued to travel in and out of New York City, quietly spreading the virus to all corners of the US.

THE BLAME GAME

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In recent weeks, Trump has sought to shift blame for the pandemic onto China, where the virus originated.

An NYPD officer wears personal protective equipment while maintaining order along a line to enter a Covid-10 testing site. Photo / AP
An NYPD officer wears personal protective equipment while maintaining order along a line to enter a Covid-10 testing site. Photo / AP

Earlier this week, US Secretary of State Mike Pompeo publicly claimed there was "enormous evidence" the disease had come from a laboratory in the city of Wuhan.

Covid19.govt.nz: The Government's official Covid-19 advisory website

"There's enormous evidence that this is where this began," Pompeo told ABC News.

"China has a history of infecting the world. And they have a history of running substandard laboratories. These are not the first times that we've had a world exposed to viruses as the result of failures in a Chinese lab.

"So while the intelligence committee continues to do its work – they should continue to do that and verify so that we are certain – I can tell you that there is a significant amount of evidence that this came from that laboratory in Wuhan."

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He declined to describe the evidence in any more detail.

Pompeo tied the laboratory theory into a broader critique of China for initially seeking to cover up the outbreak.

The Chinese Communist Party had the opportunity to prevent all the calamity that has befallen the world," he said.

"This is an enormous crisis, created by the fact that the Chinese Communist Party reverted to form, reverted to the kinds of disinformation and concealment that authoritarian regimes do."

Yesterday Pompeo seemed to walk back his claims about the virus's origins, conceding "we don't have certainty" that it came from the lab.

And China hit back hard at the US, accusing it of spreading "lies".

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"Enormous evidence? Then show us," China's Foreign Ministry spokeswoman told reporters.

"Mr Pompeo cannot present any evidence because he hasn't got any. I think this matter should be handled by scientists and professionals instead of politicians."