New York City’s first COVID-19 surge was fueled by cases circulating in Queens, and to some extent north Brooklyn, before then spreading into Manhattan, according to a new study from an international team of scientists.

The report, published Thursday in the journal PLOS Pathogens, analyzed tiny genetic differences in coronavirus samples to trace lineages of the germ that had infected patients around the city. This process is called phylogeographic analysis.

The findings confirm the understanding that the virus was circulating early in Queens at high rates—made evident by the elevated hospitalization burden in the borough.

“The reality is that there was likely a lot more virus circulating in Queens than it was in Manhattan, for example,” said Adriana Heguy, co-author and the head of New York University Langone’s Genome Technology Center.

Until we have these neighborhoods really included in disease surveillance and prevention programs, we will not be able to get ahead of these problems.

Bruce Y. Lee, CUNY public health policy expert and executive director of PHICOR

To conduct the study, Heguy and researchers from NYU’s Grossman School of Medicine drew from the genetic material of more than 828 COVID-positive nose swabs, collected between March and May of last year across the state of New York. They included another 1,899 samples from elsewhere in North America as reference points.

The team then used these genetic sequences to build coronavirus family trees, called clades. By doing so, they could chart the various times that a new version of coronavirus arrived in the state because remember, the germ is constantly mutating. The study revealed that most importations—83%—happened in the second half of March, despite earlier research from Heguy's team showing that the city's outbreak started by at least mid-February. Many of the families spotted elsewhere in New York state had ancestors that sprouted in New York City.

Thick arrows on map shows how the coronavirus spread between boroughs in the spring of 2020 with Queens and Brooklyn serving as the major hubs of infection.

Thick arrows on map shows how the coronavirus spread between boroughs in the spring of 2020 with Queens and Brooklyn serving as the major hubs of infection.

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Thick arrows on map shows how the coronavirus spread between boroughs in the spring of 2020 with Queens and Brooklyn serving as the major hubs of infection.
Courtesy of Adriana Heguy, NYU Langone Genome Technology Center

Next, they divided the collection into ten randomized subsets and then ran computer simulations to map out where members of these coronavirus families appeared in New York City and when. They could then trace the most likely flow of the germs through the city after these introductions. Eight of those simulations found Queens and Brooklyn as key transmission boroughs, particularly northern parts of Brooklyn. Two simulations found the Bronx was a third hub.

The study’s authors speculate the high number of essential workers commuting into Manhattan every day played a role in how the virus spread.

“People who continue commuting are the essential workers, and they're most likely commuting from the outer boroughs into Manhattan, and not the other way around,” she said. Some 35% of Queens and Brooklyn residents commute daily into Manhattan, according to their study. A March 2020 report from the city comptroller’s office shows half of frontline workers live in Brooklyn (28%) and Queens (22%).

Points and lines on map show how COVID-19 infections traveled across New York City and Long Island in the spring of 2020.

Points and lines on map show how COVID-19 infections traveled across New York City and Long Island in the spring of 2020.

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Points and lines on map show how COVID-19 infections traveled across New York City and Long Island in the spring of 2020.
Courtesy of Adriana Heguy, NYU Langone Genome Technology Center

Examining commuting patterns could further confirm this trend and inform future disease preparations, Heguy said. She noted that JFK and LaGuardia airports are also located in Queens—another potential source of transmission.

Queens and Brooklyn, both with over 2 million people, are home to a higher proportion of Black and Hispanic city residents than Manhattan as well. Those racial groups have experienced higher death rates from COVID-19 in New York City and across the nation, which is linked to systemic social, economic, and healthcare inequities.

The study faced one constraint: Its data was limited due to inadequate coronavirus testing early in the pandemic. But the findings are helpful evidence to build on what was already suspected, said Bruce Y. Lee, a public health policy expert at the City University of New York who was not involved in the study. At the peak of the outbreak in early April, Queens saw the highest numbers of hospitalizations as sick patients flooded hospitals, like Elmhurst Hospital.

“This study reaffirms the fact that we’re all really connected,” said Lee, who is also the executive director of Public Health Informatics, Computational, and Operations Research. The report reiterates that health care and pathogen surveillance need to be more equitable, he added.

“Until we have all these neighborhoods really included in disease surveillance and prevention programs, we really will not be able to get ahead of these problems,” he said. “We should treat the pandemic and these findings from the pandemic as a map to show where our deficiencies are when it comes to public health.”

Genomic sequencing—the lengthy process of untangling the genes of virus samples—was a critical aspect of the study’s process. For NYU genome biologist Neville Sanjana, it indicates why tying genetics into medicine “can be so powerful.”

“Just based on the mutations in the virus, we can understand: Where is something introduced into a population?” added Sanjana, who was also uninvolved in the research. “I’m hopeful that we can take the lessons that we’ve learned through here and think, ‘Ok, how do we find viruses before they explode through New York?”

The NYU researchers plan to analyze how the second wave spread throughout New York City—which should show the pathways of new coronavirus variants. Over the winter, the B.1.117 variant that originated in the United Kingdom and the homegrown B.1.526 mutant from New York skyrocketed among COVID samples sequenced through the city’s surveillance program.

With higher testing rates, Heguy hopes the second tranche of data will paint an even more precise picture.

“What is very clear,” Heguy said, “is that, if you determine that a particular geographical place is a major hub for transmission, whenever you have an infectious disease epidemic going on, then you need to focus on that borough in terms of testing and in terms of any other mitigation strategies.”