The COVID-19 pandemic both started earlier than previously thought in New York City and Long Island and was fueled by dozens of people infected mostly with strains of the virus that originated from Europe. That is the finding of new research from investigators at NYU Langone Health, which also found that most of the spread was within the community as opposed to that coming into the area from recent overseas travel.
The new study, published online Oct. 22 in the journal Genome Research, is the largest effort to date to trace the COVID-19 pandemic using gene sequencing.
Led by researchers at the NYU Grossman School of Medicine, the new study used genetic testing to trace the origins of SARS-CoV-2, throughout the New York City region in the spring. It showed that the virus first took root in late February, seeded by at least 109 different sources that created chains of infection, and didn’t originate from a single “patient zero.”
Notably, more than 40% of people who tested positive had no known contact with another infected person before they contracted the virus.
“Our findings show that New York’s early screening test methods missed the onset and roots of the outbreak by several days at the minimum,” says study co-lead author Matthew Maurano, Ph.D., an assistant professor in the Department of Pathology at NYU Langone Health. “The work strongly suggests that to nip future outbreaks in the bud, we need a system of rapid, plentiful real-time genetic surveillance as well as traditional epidemiologic indicators.”
The investigators also found that more than 95% of New Yorkers with COVID-19 had a strain of the virus with a mutation that may make it easier to transmit to others, a finding, that explains why the virus spread so aggressively in the region.
For their research, the investigators compared small snips of genetic code to identify mutations that are only found in a particular strain of the virus. These “flags,” Maurano says, were then be used to track how the strain spread over time, much in the same way consumer genetic tests trace ancestry in people.
For this study, the researchers collected viral genetic information on 864 nasal swabs taken from New Yorkers who had tested positive for COVID-19 between March 12 and May 10. Most of the people were from Manhattan, Brooklyn, and Nassau County on Long Island. Then, the investigators compared the gene sequences of the virus from these samples to those seen in the original strain isolated last winter from patients in Wuhan, China, where the pandemic is believed to have begun.
The study revealed that the genetic codes of the virus in New York more closely matched those of strains from Europe or other U.S. states rather than those from China, where the virus originated. In addition, some of the early chains of infection from person to person ran at least 50 people long.
“Our gene sequencing techniques allowed us to evaluate the precision of our screening tests,” says senior study author Adriana Heguy, Ph.D., a professor in the Department of Pathology at NYU Langone. “Based on these results, it is clear that we need a system of plentiful testing that provides rapid results.”
She notes that the sequences analyzed in the study accounted for just 10 percent of COVID-19 patients within a single hospital system in New York. The true scale of the community infection was therefore likely much higher, and the original introduction of the virus to New York City was possibly earlier.
Heguy says the team next plans to investigate whether the mutations uncovered by genetic testing could affect the coronavirus in other ways, such as causing new or more severe symptoms of COVID-19.