Press reports indicate that New York City "missed" the emergence of the Omicron variant. However, newly released wastewater surveillance records indicate that New York City first detected an "Omicron overlap" from samples dated 15 November 2021. NYC Dept. of Environmental Protection/Public Domain

Newly released New York City wastewater SARS-CoV-2 sequencing records confirmed early, never before admitted detection of the Omicron variant

Wastewater variant sequencing records showed that Omicron was detected in New York City prior to the Minnesota revelation of a COVID-19 case of an anime convention attendee.

By LOUIS FLORES

Coronavirus sequencing records of New York City wastewater show that the Omicron variant was being detected in samples drawn from the Newtown Creek wastewater treatment plan in Greenpoint, Brooklyn, as of 22 November 2021, contradicting information reportedly later shared by the de Blasio administration over a week later with then Councilmember Stephen Levin (D-Brooklyn) that there was no detection being made of Omicron at the same wastewater treatment plant.

As reported by Progress New York, then Councilmember Levin said that New York City health officials told him that they did not believe that the Omicron variant was responsible for a spike in COVID-19 cases in his Council District at the end of November. The City’s misrepresentation was made firm when City health officials affirmatively denied that Omicron was being detected in wastewater samples as of 30 November, according to a social media post shared on Twitter by then Councilmember Levin.

Before the end of December, then Councilmember Levin promised to release records about Coronavirus sequencing data, but he left office without following-through with the release. A message left at Mr. Levin’s new office was not answered.

The New York City Department of Environmental Protection takes three days to process wastewater samples and shares the information with the City’s health department on a daily basis, according to a page on its Web site.

At the end of November, as Europe became worried about the spread of the contagious new variant, some nations began to close their borders, leading to new restrictions and, ultimately, confinement orders. By seemingly withholding information about the timing of the Omicron’s detection, New York City Hall appeared to continue on its no more economic closures maneuvering — from former Mayor Bill de Blasio (WFP-New York City) to Mayor Eric Adams (D-New York City) — despite endless promises to “follow the science.”

An unexplained “Omicron overlap” dated back to 15 November 2021.

The wastewater records were released to Progress New York by the New York City Department of Health and Mental Hygiene in response to an open records request filed in December. However, only one spreadsheet was produced, for a limited range of 2021 dates, even though the open records request described four categories of records being sought, and a media report showed that the City’s wastewater surveillance dated back to at least 2020.

In notations that deviated from the normal tracking of variants, the spreadsheet indicated that an “Omicron overlap” existed as early as 15 November 2021 at the Tallman Island wastewater treatment plant in College Point, Queens, and on 22 November at both the Bowery Bay wastewater treatment plant in Queens and at Newtown Creek.

The first reported case of Omicron in New York City was announced on 2 December by Minnesota health officials of an individual, who attended the now-infamous anime convention at the Javits convention centre in November. 

Following the Minnesota revelation, Mayor de Blasio said on 2 December that the public “should assume there is community spread of the variant in our city.” But, in keeping with his propensity to prevent the release of pandemic data, he stopped short of providing actual data available to him, such as the wastewater variant sequencing results, to inform and demonstrate to the public the areas of outbreak.

Less than three weeks later, the U.S. Centers for Disease Control and Prevention estimated that 90 per cent. of all COVID-19 cases in the New York region were being caused by Omicron, shocking the public, who were uninformed about, and unprepared for, the dramatic rise of the Omicron variant outbreak.

Variant surveillance of wastewater samples could guide the public response to emerging outbreaks.

In the immediate aftermath of the first reported case of the Omicron variant, the media noted that New York City health officials had missed the emergence of the new variant. The Coronavirus pandemic was “outpacing a public health response” that was “simply unable to keep up,” a team of New York Times reporters wrote. But the wastewater sequencing records that were provided to Progress New York revealed that the City was capable of being aware of the Omicron outbreak before the Minnesota announcement.

The role of variant sequencing from wastewater samples have grown in importance over the course of the Coronavirus pandemic. The CDC notes that, “Wastewater surveillance can be an early indicator that the number of people with COVID-19 in a community is increasing or decreasing.”

“It’s impossible to test people every day. But that’s what sampling wastewater allows us to do,” said Dr. Kartik Chandran, an environmental engineer with experience in Coronavirus variant surveillance and research in wastewater.

Dr. Chandran added that, because of several limitations of tested individuals that result in COVID-19 samples used for sequencing, “The wastewater numbers are always going to give us a more complete picture,” because the wastewater samples don’t face the same restrictions as testing of individuals. 

Limitations on individual COVID-19 test results would make wastewater surveillance more important, but the Government doesn’t appear to be interested in allowing surveillance to determine the pandemic response.

In a report published by The City news Web site, some of those limitations were identified as clinical samples being drawn from seriously-ill patients (and not those, who may be asymptomatic or less-severely ill) ; COVID-19 test samples not reflecting all cases of COVID-19, since not all cases are diagnosed or trigger the taking of tests ; the failure to sequence all positive test samples ; and the lack of regular testing of vaccinated individuals.

The reliance on testing of individuals raised additional issues, such as the failure of many small testing centres and individuals using home test kits to report all of their Coronavirus test results to City health officials, according to a prior report published by Progress New York. 

Furthermore, a data model constructed by Progress New York showed that the City was under-sampling specimens for its weekly variant sequencing studies, raising the spectre that as sampled data was being adjusted to meet statistical analysis reliability standards, the process was at risk of missing the emergence of new variants, one expert told Progress New York for a prior report.

The detection of the Omicron variant in wastewater samples drawn on dates before the Minnesota revelation took place after the de Blasio administration began raising concerns about a trimming in pandemic surveillance, as noted in a July 2021 report published by the Times, which claimed that the cutbacks would put New York City in a position to be “ill prepared should more contagious forms of the virus cause new outbreaks.”

Even though tools, like wastewater surveillance exist, to augment possibly biased human test variant surveillance, New York City Hall made no use of such tools, particularly to inform and prepare the public for the Omicron variant outbreak. In The City report, when scientists approached New York City health officials about the possibility that Coronavirus variants were being shed by animals in their waste, the Government appeared to have “zero willingness to help explore this potential public health risk.” It was almost as if the Government has been setting its pandemic response without relying on the scientific outcomes of early-detection methods, like wastewater surveillance.

For this report, a media request made to New York City Hall was not answered.

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