Northeastern model suggests Boston’s coronavirus outbreak began much earlier than previously thought

While the city was still bracing for the pandemic’s arrival, COVID-19 may have already been spreading undetected.

An electron microscope image from the US National Institutes of Health in February shows the virus that causes COVID-19. The sample was isolated from a patient.Associated Press/file

When the Boston Public Health Commission broke news of the city’s second, third, and fourth coronavirus infections on March 6, the department took a cautiously reassuring tone: “There is currently no evidence of community transmission in Boston,” the online announcement read. “The risk remains low, but this situation is evolving rapidly and changes day to day."

But unbeknownst to public health officials, thousands in Boston may already have been infected, according to a new model of the early days of the pandemic. Long before lockdowns proliferated and official case counts skyrocketed, the virus was rampaging through parts of the unsuspecting city, researchers at Northeastern University now believe. The time for calm reassurance already had passed.

Boston was one of the first cities in the country to detect a case of the virus. On Feb. 1, a student at the University of Massachusetts Boston who had recently traveled from Wuhan, China, tested positive. For over a month, his was the only confirmed case in the city. But according to the Northeastern projections, more than 100 people in Boston had likely been exposed to the virus by mid-February. By March 1, five days before the city changed its official count to four coronavirus cases, the virus may have been transmitted 2,335 times.

A March 24 state order shuttering nonessential businesses and advising people to stay at home was still weeks away.

“Between the second half of January and the first half of February,” there were likely enough infected people in Boston “to generate local transmission,” said Alessandro Vespignani, the principal investigator behind the Northeastern model.

The model Vespignani and his team developed uses real-world data on commuting and national and international flight patterns to estimate how far people infected with COVID-19 traveled, and how many other people they might have interacted with and infected in turn. To account for how preventive measures such as social distancing effect the pace of the outbreak, the researchers tested and fine-tuned the model using data from China. The group published its preliminary findings in the journal Science on April 24. The estimates reflect the model’s median projections and could change as the team continues to incorporate information.

"From my perspective, [the model] really fits with what we’re seeing on the ground,“ said Samuel Scarpino, a Northeastern mathematical epidemiologist who is not a member of Vespignani’s team.

“The peak of cases in the Boston area happened much earlier than we would have expected given the reported cases,” Scarpino explained. But, “there was a much larger outbreak here than we realized earlier, and that really explains the peak timing, the early surge in deaths and cases.”

In a press conference on Monday, Mayor Martin J. Walsh said the new model reinforces the need for more testing. “I haven’t reviewed this research yet, but any data that shows more widespread infection again just shows the continued need for more testing."

Walsh added that the city is committed to increasing testing and cited a plan to screen 1,000 Boston residents for antibodies that would indicate whether they already have built some immunity to COVID-19. The state Department of Public Health referred questions to the city.

Health care workers perform a COVID-19 test on a patient in a drive-through testing site set up in the parking lot of the Bowdoin Street Health Center in Dorchester.John Tlumacki/Globe Staff

“Of course, if we had seen the positive results earlier in March, we would have acted earlier," said Walsh. “Every step we have taken has been guided by public health since day one.”

To some extent, outbreaks of novel diseases are, by their very nature, difficult to track accurately early on.

“Initial recognition of a new pathogen that is transmitting in a community is hard and requires people to be willing to make mistakes many times,” said Dr. Sarah Fortune, chair of the department of immunology and infectious diseases at Harvard T.H. Chan School of Public Health.

Predicting when the illness will spread to new communities is also difficult. “It’s like projecting the path of a hurricane,” Vespignani said. “You have uncertainty about when it will touch down.”

In the case of COVID-19, the timing of the outbreak made early detection even harder. “We were dealing with a few things in the US that made it very complicated," said Scarpino. “Because it was flu season, there were a lot of respiratory cases. It’s much harder to notice a handful of unusual cases when there’s just so many people that are ill.”

Still, Scarpino believed the federal response could have been stronger and come sooner. “We knew by mid to late January that this disease was spreading rapidly through China,” he said. "We should’ve been ready. We should’ve had things in place building into February, certainly by the beginning of March, to have really high testing capacity.”

Lack of testing led to a wide gap between what local public health officials thought they knew, and the true scope of the pandemic. In this, Boston was far from alone.

According to New York Times reporting on the national implications of the Northeastern model, there had likely been 28,000 infections across five major United States cities by March 1. The official tally at the time was 23.

EMTs hurry a patient into the emergency room at Massachusetts General Hospital.Stan Grossfeld/ Globe Staff

Throughout the country, “There was incredible resistance to doing the kind of surveillance testing that would have been necessary,” Fortune said. Even as the virus wreaked havoc around the world, she said, “The United States seemed to suffer from a failure of imagination.”

Vespignani said “there are two major implications” of his research that should inform how officials respond to the pandemic moving forward.

The first is that a more accurate timeline of the pandemic could better predict its future spread. “We need to learn from that invisible spreading so we are not finding ourselves in that situation again when we begin lifting social distancing,” he said.

The second lesson: We still need to do a better job of tracking new cases of COVID-19. “Now we know we need to do testing, and we need to do massive testing," Vespignani added.

For Fortune, the Northeastern model’s greatest lesson goes beyond the current pandemic. “We need proactive public health," she said. Stronger infrastructure will be key to detecting and addressing the nation’s next public health crisis. ”We need to remember this moment and invest in surveillance, not just reactive public health."

The Northeastern model does bring good news for the future: The worst may soon be over. “We are flattening the curve . . . We are going in the right direction,” said Vespignani, who estimates that Boston is a few weeks away from being able to safely consider gradually reopening nonessential businesses.

"However, we need to be patient with reopening,” he added. And in the meantime, “We need to throw everything we have at this disease.”