One of the first cases Heguy’s team sequenced, collected in early March, came from a Long Island resident with no travel history whose viral genome correlated with a strain circulating in England. That suggested the patient had contact with someone who had brought the virus over from the U.K.

The findings suggest that even after the Trump administration imposed travel restrictions from China, the virus continued to infiltrate the most populous U.S. city via daily flights from Europe.

Not all the New York virus samples have European origins. Some appear to have come from the U.S. West Coast, while others appear to link directly to Asia. That indicates that there are numerous chains of transmission in the metro area, as would be expected in such a large outbreak.

The NYU genome center had previously previously had been focused on sequencing for common diseases such as cancer and heart conditions. But in early March it switched to working almost exclusively on Covid-19.

“We basically turned our labs into Covid-19 labs overnight,” said Heguy. “That is all we are doing right now.”