Dr. Dave Chokshi, the chief New York City health minister, oversees the publication of data about the Coronavirus pandemic. Mayor Bill de Blasio refuses to explain the plunge in sample sizes used for the weekly variant sequencing studies, raising questions about the unknown breakdown of COVID-19 variants in the major sources of Coronavirus testing. NYC Mayor's Office (YouTube/Fair Use)

Letter From New York : Drop in weekly New York City COIVD-19 sequencing sample sizes prompts questions about the reliability of the weekly studies

The appearance that the City of New York may now be undersampling COVID-19 specimens for its weekly variant sequencing studies raises a whole new set of questions.

By Progress New York Staff

For weeks, Progress New York has been drawing attention to the appearance of incompleteness to weekly variant sequencing studies, a key tool used by the City of New York to monitor for infectious strains of the Coronavirus. Last month, Progress New York raised questions when Mayor Bill de Blasio (WFP-New York City) began announcing plans to reopen the economy at a time when the weekly variant sequencing studies contained no traces of a new contagious strain of the Coronavirus wreaking havoc around the world. Progress New York has also raised questions about the delay in the publication of the studies and the quality of the data, amongst other issues.

After Progress New York began to follow a plunge in the sample sizes used for the weekly variant sequencing studies, a deeper look was warranted.

Many of Mayor de Blasio’s critics have seized on the drop in the sample size as evidence that something had gone awry in the Government’s data about the Coronavirus pandemic. Because this data involves the surveillance of infections strains of the Coronavirus, many critics and advocates for Government transparency became concerned that the Government was not adequately monitoring for the emergence or prevalence of variants in New York City, the former epicenter of the Coronavirus pandemic. But the focus on the drop in the sample sizes masked other questions.

To examine the issues provoked by the drop in the sample sizes used in the weekly variant sequencing studies, Progress New York received information from three experts in the field of statistics. The conversations took place on condition of anonymity, so that a robust exchange of ideas could take place. In one case, one expert disclosed that they were regulated by strict media guidelines by their employer. What follows is an examination of some of important issues raised by the state of the weekly variant sequencing studies.

For this report, the City Hall press office refused to answer multiple requests for information.

EDITORIAL : Mayor Bill de Blasio is obfuscating COVID-19 sequencing studies, masking the growth of the Delta variant, and the consequences could be deadly.

After Progress New York raised questions about the weekly variant sequencing studies, the de Blasio administration revamped the data — and made it more opaque. The only solution now is the formation of an independent, external panel of scientists to provide oversight. >> Read More

City Hall’s messaging to the public telegraphs that there is no more concern from the Coronavirus pandemic, even as other Nations, where this attitude was prevalent, have faced surges of a highly contagious Coronavirus variant.

Mayor de Blasio has been celebrating a trend of low positivity results from recent Coronavirus tests, and he has declared that a continued strategy of vaccinations will end the Coronavirus pandemic. But for weeks, Progress New York has been reporting that the City has not been transparent about its surveillance of Coronavirus variants. Throughout this time, Mayor de Blasio has appeared to be solely focused on reopening the economy to activities that were restricted last year. He repeatedly claims that the data shows that we are recovering from the pandemic. But all three experts with whom Progress New York spoke expressed reservations about the reliability of the City’s data.

One source informed Progress New York that the City Agency in charge of collecting information about positive COVID-19 cases was missing positive tests. It was also possible to miss diagnoses that were not reached from tests. According to information obtained by Progress New York, all large-scale testing centres report their testing findings to NYC Health, the City health ministry. However, many small testing centres are not reporting all of their Coronavirus test results to NYC Health, a source said. Furthermore, the source added that home tests taken by individuals, who can afford them, do not report their test outcomes to the NYC Health. Because of Mayor de Blasio’s refusal to answer media inquiries made by Progress New York, it was not possible to confirm these claims.

To better understand the weekly variant sequencing studies, Progress New York constructed a data model to calculate for a period of seven weeks the sample sizes used for the weekly sequencing reports based on the number of the prior week’s seven-day moving average of confirmed and probable cases of COVID-19. Over the course of the studied period, the actual sample sizes used by the City of New York to sequence COVID-19 specimens plunged from a peak of 1,831 at the start of the period to just 211 by the end. Over the corresponding period, the sample size calculated by the model created by Progress New York began at 514, and it dropped to just 310. At the beginning of the study period, the model was showing that the City was oversampling specimens, and, by the end of the study period, the model was showing that the City was undersampling specimens for its weekly variant sequencing studies.

The model was premised on a 95 per cent. confidence level, a population proportion set to 0.5, and a margin of error of 4 per cent. Had Progress New York premised its data model on more conservative figures, like a 99 per cent. confidence level with a margin of error of just 1 per cent., then the City of New York would have severely undersampled throughout the entire studied period.

When Progress New York showed the model and shared some of the analysis and information to another expert, the expert said that the issue more pressing than the drop in the sample sizes was the fact that the Government was not sharing information about the subjects of the weekly variant sequencing studies. The expert said that it would be important to know :  Of all people with COVID-19, what percentage of people with variants came from three sources of testing data — large testing centres, small testing centres, and home testing. Without knowing that information, it would be difficult for the public to have confidence in the weekly variant sequencing studies. If the City health ministry was not managing the proportions of the populations in its studies, there would be very little the public could infer from the studies, because failing to manage the proportions could lead to bias in the study results.

In statistical analysis, whenever samples are not proportionate to the underlying populations, they can be adjusted, sometimes by simple weighted average, if the sample size had been randomly selected. One expert told Progress New York that adjustments to data may miss the emergence of new variants. But nothing is known about how the City of New York selects the samples for the weekly variant sequencing studies. The Mayor’s Office has refused to answer information requests made by Progress New York. As repeatedly reported by Progress New York, Mayor de Blasio has politicised the release of Government data.

The celebration of the drop in cases of COVID-19 is masking concerns over variants, and those concerns are focused on the weekly variant sequencing studies.

The sample sizes calculated by the statistical model created by Progress New York held relatively steady in the face of a plunge in positive cases of COVID-19, unlike the actual sample sizes used for the weekly variant sequencing studies.

There is no doubt that the number of COVID-19 cases has been plunging. However, Mayor de Blasio has been increasingly telegraphing to the public that there is no major concern from the Coronavirus pandemic. The change in messaging has permitted the public to return to normal behaviour, including foregoing each of facial coverings, social distancing, and confinement. This permissive messaging was once shared by other Governments, like in India, Singapore, the U.K.Australia, and others, but they have each faced recent surges of a highly contagious strain of the Coronavirus. The strain, referred to as the Delta variant, was identified by scientists as B.1.617.2 and was first detected in India. (The first time that the Delta variant was reported in New York City was in a retroactive disclosure in an overdue study.) New variants of the Coronavirus continue to emerge.

Another expert told Progress New York that one way the City of New York could overcome questions about its methods would be to test the entire population of positive COVID-19 specimens. However, such an approach may trigger issues of compliance, rights to privacy, and the limitations of Government budgets, the expert said. (The budgetary claims by that expert appeared to contradict an April report that President Joseph Biden (D) planned on spending an additional $1,7 billion to track Coronavirus variants.)

Notwithstanding any restrictions, the expert said that testing for the Coronavirus should continue to go up, in order to monitor emerging outbreaks in order to monitor its spread and to deploy resources. But Mayor de Blasio’s messaging about testing has changed, with health officials in his administration, including Dr. Dave Chokshi, the City’s chief health minister, saying that testing should be focused on individuals, who had yet to receive their vaccinations. As a result, testing has gone down in New York City. The drop in testing, and the changes in population subjected to testing, can also affect the randomness of the specimens available for sampling for the weekly variant sequencing studies. According to critics, the Mayor’s message of a “return to normal” ignores the possible threats posed by variants, the Delta variant, in particular.

As has been widely reported, the Delta variant is highly infectious. Its transmissability is estimated to be between 30 to 100 per cent. greater than the previously dominant variant in the U.K., according a report published by the Guardian. It is also capable of vaccine escape. If the weekly variant sequencing studies were meant to be used as a tool to identify the emergence of new variants, then the sudden, and unexplained, collapse in sample sizes appears to contradict that intention. One expert explained that it wouldn’t be feasible to rely solely on studies that were conducted based on samples for new variant surveillance, because it could be possible for samples to miss a new emergence. As a result, the Government should instead rely on sentinels, or other indicators, for signs of upticks in infections. Whereas the City of New York already does some of that, by monitoring hospitalisations, for example, another expert raised other questions about the weekly variant sequencing studies. Without knowing the geographical and demographic make-up of the sources of specimens used in the studies, it would be difficult to know if the specimens were good representations of the population.

Politicians complain about untruths and conspiracy theories, but they create the conditions that sow the seeds of doubt.

One expert said that if the weekly variant sequencing studies failed to serve as a tool for surveillance of emerging variants, then it was incumbent on the City of New York to stop travel from Nations with outbreaks of dangerous variants. Absent a travel ban, the expert agreed that testing should be made mandatory for all travelers, with obvious contact tracing for individuals testing positive for COVID-19, and the creation of models to predict outbreaks of variants already detected in New York. But Mayor de Blasio had not been transparent about such models that they City may use, if any. Without this Government information, the public are left with questions, and doubt.

Because the modeled undersampling revealed by the Progress New York data analysis has been taking place as the Delta variant has been ravaging other Nations, it’s not known why City health officials could not revert to the oversampling of earlier weeks, based on the assumptions of the Progress New York data model. In the face of so many questions, one expert accused the de Blasio administration of not really engaging in sampling ; instead, the expert concluded that the City was just carrying out mandatory reporting — that the weekly variant sequencing studies were not tantamount to a real form variant surveillance. Indeed, the weekly variant sequencing studies include a disclaimer in one of its footnotes : “The rate of variants in these samples may not be generalizable to all NYC COVID infections.”

The Coronavirus pandemic revealed racial disparities in the healthcare system. Many people of colour and people earning low incomes are unable to access full-service healthcare. As a result, Coronavirus testing and the vaccination campaign may not reach large segments of a population that is at-risk for comorbidities. The disparities in access to healthcare only add to the gaps in the method in which the City identifies and collects specimens of positive cases of COVID-19, affecting, in turn, the specimens available for sampling by the weekly variant sequencing studies.

As reported by Progress New York, the U.K. has an advantage in the vaccination rate over New York State, but this superiority was no match for the Delta variant, as the U.K. is on the precipice of succumbing to a new wave of Coronavirus infections. And the disadvantages New York faces is growing : The rate of new vaccinations being administered in New York City is falling. When critics of Mayor de Blasio look at this data, they feel like the public is vulnerable.

Of particular concern to one expert with whom Progress New York spoke was the growing issue of the public’s loss of confidence in the Government that is now at the reported root of untruths and conspiracy theories about the Coronavirus pandemic and the Government’s response.

In the U.K., Independent SAGE, a panel of scientists and doctors untethered to the Government, was formed to provide advice to the Government and the public about the Coronavirus pandemic. There has been no similar formation of a group of scientists or doctors to provide independent analyses to Government leaders and the public in New York, leaving Mayor de Blasio and Gov. Andrew Cuomo (D-NY) to almost solely determine public health policy.

At the outset of the Coronavirus pandemic, it was reported by the New Yorker magazine that Mayor de Blasio and Gov. Cuomo allowed politics to guide the Government’s response to the pandemic, not science.

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A very awakening article. Cuomo’s lies about cases earlier and the mistrust of anything deBlasio says should worry everyone.