SARS-CoV-2 was in NYC a good month before it was first identified, researchers say

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Researchers at the Icahn School of Medicine at Mount Sinai in New York have provided evidence suggesting that coronavirus 2 (SARS-CoV-2) was a very serious respiratory syndrome – the causative agent for coronavirus disease 2019 (COVID-19) – infecting people in New York. City (NYC) at least a month before the first case was officially filed in the city.

The team’s molecular screening study, which included samples from more than 3,000 patients, found SARS-CoV-2 RNA in samples collected during the week ending 25th January.

The samples of the respiratory-negative pathogens (RPN) -specimens were taken from patients diagnosed for flu-like illness and respiratory symptoms in the first ten weeks of 2020.

Emilia Sordillo and colleagues say the findings indicate that SARS-CoV-2 infections were present among a small number of people seeking care at the Mount Sinai Health System (MSHS) several weeks before there has been an increase in cases that have flooded the NYC health system.

The researchers advise that regular screening of people with undiagnosed respiratory illness for emerging viruses must be an essential part of approaches aimed at preventing local infections from occurring. going out of control.

A pre-printed version of the research paper can be found on the medRxiv* server, while the article is subject to peer review.

NYC quickly emerged as the main messenger of COVID-19

Following the first outbreak of SARS-CoV-2 in Wuhan, China, in December 2019, the virus spread to other Asian countries, Europe and North America, within a few weeks.

In the United States, the first disease was identified on 20th January 2020 was followed by sporadic outbreaks of disease across the country.

After the first SARS-CoV-2 diagnosis in NYC on 29th In February, the city quickly emerged as a major hub of COVID-19.

“However, by mid-March, 2020, detection of the COVID-19 case was limited by the availability of diagnostic tests and involved in the display of symptoms with other respiratory and viral illnesses,” wrote Sordillo and colleagues. “Therefore, direct molecular evidence of SARS-CoV-2 in NYC is not required prior to the first reported case.”

What did the researchers do?

To systematically explain the emergence of SARS-CoV-2 in NYC, the researchers implemented a sample collection strategy to screen nasopharyngeal RPN samples from 3,040 people who presented with respiratory symptoms or flu-like illness. at the MSHS in the first ten weeks of 2020.

This resulted in 304 RPN pools that were then screened for SARS-CoV-2 RNA using a nucleic-acid amplification test (NAAT).

This assay tested for the presence of the SARS-CoV-2-specific ORF1ab gene (target 1) and the pan-Sarbecovirus (E) -gene envelope (target 2).

Outcomes were classified as positive for SARS-CoV-2 RNA if target 1 or both targets were detected, “presumptive positive” if only target 2 was detected, and negative if none of the targets were detected.

Detection of SARS-CoV-2 nuclear acid in nasopharyngeal samples collected in the first ten weeks of 2020. (A) Decorative representation of the study design. Nasopharyngeal swab samples that tested negative for respiratory pathogens (RPN) were combined. Each pool contained 10 samples from the same week from one of five hospital sites. Nuclear acid amplification test (NAAT) was performed and RNA was processed for SARS-CoV-2 genome synthesis. (B) Selected events and responses to the SARS-CoV-2 pandemic are identified over the study period. Confirmed cases have been noted in NYC for the past two weeks. Total counts of baths that tested positive, positive, and negative with RT-PCR are shown according to the week collected. (C) Circulation of positive (solid) and positive (hatched) baths across the five different hospital sites in NYC.

Detection of SARS-CoV-2 nuclear acid in nasopharyngeal samples collected in the first ten weeks of 2020. (A) Decorative representation of the study design. Nasopharyngeal swab samples that tested negative for respiratory pathogens (RPN) were combined. Each pool contained 10 samples from the same week from one of five hospital sites. Nuclear acid amplification test (NAAT) was performed and RNA was processed for SARS-CoV-2 genome synthesis. (B) Selected events and responses to the SARS-CoV-2 pandemic are identified over the study period. Confirmed cases have been noted in NYC for the past two weeks. Total counts of baths that tested positive, positive, and negative with RT-PCR are shown according to the week collected. (C) Circulation of positive (solid) and positive (hatched) baths across the five different hospital sites in NYC.

What did the study find?

Of the 304 RPN pools screened, nine (3%) tested positive for SARS-CoV-2 RNA, eight (2.6%) tested positive and 287 (94.4%) tested negative.

Five of the positive positive pools included samples collected in the weeks ending 18th January, 25th January, and 1st February.

None of the RPN pools containing samples collected over the next three weeks produced visible SARS-CoV-2 RNA.

Viral RNA was detected in 5.4% of RPN pools in which samples collected during the week ended 29th February and in 33.3% of baths in which samples collected during the week ended 7th March.

To validate NAAT results, the team performed a genome sequence of viral RNA extracted from all positive and presumptive-positive RPN pools.

Three baths containing samples collected in the weeks ending 25th January and 1st February brought SARS-CoV-2 readings scattered throughout the viral genome, thus confirming the presence of SARS-CoV-2 RNA.

What is the impact of the study?

“Taken together, we provide clear evidence that SARS-CoV-2 infections were present in NYC at least 6 to 8 weeks before issues arose that flooded NYC’s health system,” he wrote. Sordillo and colleagues.

The team says the high number of SARS-CoV-2 positive RPN pools in the first week of March explains the “sudden” abstract increase in the number of COVID-19 cases of admitted to MSHS hospitals from mid-March 2020.

“Systematic, impartial study of clinical samples obtained from individuals presenting with unclear or abnormal clinical manifestations of respiratory illness for the presence of emerging viral pathogens must be a key consideration. part of early warning sentinel programs in the future, ”say the researchers.

“These systematic measures must be an integral part of our new routine to prevent local diseases and transmissions from escalating into an uncontrolled outbreak,” they conclude.

* Important message

medRxiv publish preliminary scientific reports that are not peer-reviewed and, therefore, should not be seen as final, guiding health-related clinical practice / behavior, or be treated as information established.

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