Led by researchers at NYU Grossman School of Medicine, the new study used genetic testing to trace the origins of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the pandemic virus, across the New York area. York in the spring. It showed that the virus first took root at the end of February, seeded by at least 109 different sources who broke into chains of infection, rather than a single “patient zero”.
Notably, the study authors say, more than 40% of people who tested positive had no known contact with another infected person before contracting the virus.
“Our results show that New York’s early testing methods missed the onset and roots of the epidemic by at least several days,” says study lead co-author Matthew T. Maurano, PhD, Assistant Professor in the Department of Pathology, NYU. Langone health. “The work strongly suggests that to nip future epidemics in the bud, we need a rapid and abundant real-time genetic surveillance system as well as traditional epidemiological indicators.
Investigators also found that more than 95% of New Yorkers with COVID-19 had a strain of the virus with a mutation that could facilitate transmission to others. This finding, says Dr Maurano, helps explain why the virus has spread so aggressively in New York City, even given the city’s high population density.
In gene sequencing, researchers compare small fragments of genetic code to identify mutations that are only found in a particular strain of the virus. These “flags,” says Dr. Maurano, can then be used to track the spread of the strain over time, much like the tests used to trace ancestry in people. Experts have already used this technique to track methicillin-resistant influenza outbreaks Staphylococcus aureus (MRSA) and Ebola, among other infections.
The new study, published online Oct. 22 in the journal Genomic research, is the largest effort to date to trace the COVID-19 pandemic using gene sequencing, according to Dr. Maurano.
For the study, the researchers collected viral genetic information on 864 nasal swabs taken from New Yorkers who 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. Next, investigators compared the genetic sequences of the virus from those samples to those seen in the original strain isolated last winter from patients in Wuhan, China, where the pandemic is believed to have started.
The study found that the genetic codes of the virus in New York City matched those of strains from Europe or other US states more closely than those in China, the country of origin of the virus. In addition, some of the first strings of infection from person to person lasted for at least 50 people.
“Our gene sequencing techniques allowed us to assess the accuracy of our screening tests,” says Adriana Heguy, PhD, lead author of the study, professor in the Department of Pathology at NYU Langone. “Based on these results, it is clear that we need a system of abundant tests that provide rapid results. ”
She notes that the sequences analyzed in the study represented only 10% of COVID-19 patients in a single hospital system in New York. The actual extent of the community infection was therefore likely much higher, and the initial introduction of the virus into New York City may have been earlier.
Dr Heguy says the team next plans to study whether the mutations found by genetic testing could affect the coronavirus in other ways, such as causing new or more severe symptoms of COVID-19.
Funding for the study was provided by grants from the National Institutes of Health R35 GM119703, P50 CA016087, P30 CA016087, and UM1 AI148574. Additional support was provided by grant MR / R015600 / 1 from the MRC Center for Global Infectious Disease Analysis.
Besides Dr Maurano and Dr Heguy, other researchers from NYU Langone involved in the study are Sitharam Ramaswami, PhD; Paul Zappile; Dacia Dimartino, PhD; Ludovic Boytard, PhD; André Ribeiro-dos-Santos, PhD; Nicholas Vulpescu; Gael Westby; Guomiao Shen; Xiaojun Feng, PhD; Megan Hogan, PhD; Christian Marier; Peter Meyn; Yutong Zhang; John Cadley; Raquel Ordoñez, PhD; Raven Luther; Emily Huang; Emily Guzman; Carolina Arguelles-Grande; Kimon Argyropoulos, MD; Margaret Black, MD; Antonio Serrano, MD; Melissa Call; Min Jae Kim; Brendan Belovarac, MD; Tatyana Gindin, MD; Andrew Lytle, MD, PhD; Jared Pinnell; Theodore Vougiouklakis, MD; John Chen, PhD; Lawrence Lin, MD, PhD; Amy V. Rapkiewicz, MD; Vanessa N. Raabe, MD; Marie I. Samanovic, PhD; George Jour, MD; Iman Osman, MD; Maria Aguero-Rosenfeld, MD; Mark J. Mulligan, MD; and Paolo Cotzia, MD. Matija Snuderl, MD, was a co-lead author of the study. Further research support was provided by Manon Ragonnet-Cronin, PhD; Lily Geidelberg; and Erik Volz, PhD, at Imperial College London.