New York City Hit a 3% Positive Test Rate. Or Did It?

Three percent.

It is the most important number in New York City right now, a critical threshold that triggers restrictions by state and local governments in response to the coronavirus. The mayor of New York shut down public schools at 3 percent. The governor says that a sustained 3 percent level in the city would result in banning indoor dining, closing gyms and hair salons, and placing a 25-person cap on attendance at houses of worship even as the holidays approach.

But as important as that number is, it seems the city and the state can’t agree on whether we’re there yet.

That’s the situation that has played out over the past week, with Mayor Bill de Blasio saying 3 percent has been reached, while Gov. Andrew M. Cuomo said it is well below that. Each relies on his own statistics, which are compiled and reported in different ways. And, it turns out, the state and city can’t agree on which tests to include in the calculation.

The discrepancy can be striking: On Saturday, for instance, the city said its seven-day average was 3.11 percent. Mr. Cuomo’s office, however, put the city’s rate a more than half a point lower, at 2.54 percent.

In one way, of course, not all numbers are equal, as Mr. Cuomo’s statistics from the state Department of Health govern a wider array of activities and businesses in regions all across New York. But Mr. Cuomo granted local school districts the right to set their own parameters for school shutdowns, and Mr. de Blasio, who controls the school system, set 3 percent as that level.

And so, in the end, it was the city’s numbers that caused the temporary pause of in-person learning in the nation’s largest school system.

Why can’t they agree on whether we are at 3 percent?

The cause of the discrepancy lies in both the tests that are included and the time frame in which statistics are reported, leading to the mayor and the governor giving different numbers each day.

It is the latest discordant message between two rivals that has played out over the entire pandemic, adding a level of dysfunction and confusion to the response.

The state and city health departments have different accounting rules for tracking the spread of the virus. The state treats a new case as arising on the day the test results came in. The city dates each new case to the day the sample was provided.

So if an infected person goes to a clinic to have his nose swabbed on Monday, that sample is often delivered to a laboratory where it is tested. If those results are reported to the health authorities on Wednesday, the state and city would record it differently. The state would include it with Wednesday’s tally of new cases, while the city would add it to Monday’s column.

The 3 percent threshold is based on a seven-day rolling average. It matters what day a new case is registered.

Another factor contributes to the discrepancy as well, which has received little attention so far: antigen tests. New York State includes the tests in its official metrics. But while they are generally faster, they are less likely to detect the infection in people with a low viral load.

New York City, however, does not include antigen tests, preferring a more sensitive one known as a polymerase chain reaction test. The city only includes P.C.R. tests performed in a laboratory in its count. That’s why the state — which is counting both antigen and P.C.R. tests — may have a higher tally for overall cases in New York City but a lower percentage of positives.

P.C.R. tests in a laboratory have long been considered the gold standard because they are so unlikely to miss any infections. But some public health experts say that much of the P.C.R. testing for coronavirus is too sensitive, resulting in coronavirus diagnoses for people who are carrying relatively insignificant amounts of the virus and are probably not contagious.

Antigen tests, which can be performed rapidly and cheaply, detect bits of coronavirus proteins. But they are more likely to miss cases, including people recently infected who have lower viral loads.

The difference in sensitivity between the two types of tests has contributed to a widening gap in the positivity rates between the city and state.

In fact, the positivity rate of the same group of people — in this case, New York City residents — can vary depending on how many receive antigen tests versus traditional P.C.R. tests. Antigen tests can miss some cases when the amount of virus is still low.

Say 1,000 people get tested. Let’s assume all have a P.C.R. test, and that 30 tests are positive, for a positivity rate of 3 percent. Now let’s assume half get an antigen test and half get a P.C.R. test. Maybe only 25 tests come back positive, for a positivity rate of 2.5 percent.

Bill Neidhardt, the mayor’s spokesman, noted that the city’s decision to exclude antigen tests from positivity rates mirrors the C.D.C.’s protocol.

“We believe in our number and our methodology,” he said, before alluding to the mayor’s decision on Wednesday to declare the 3 percent threshold breached, rather than adopting the state’s metric in a last-minute bid to keep schools open.

“Switching up a public health standard in the middle of the morning is not a good idea for clarity and public confidence,” he said.

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Words to Know About Testing

Confused by the terms about coronavirus testing? Let us help:

    • Antibody: A protein produced by the immune system that can recognize and attach precisely to specific kinds of viruses, bacteria, or other invaders.
    • Antibody test/serology test: A test that detects antibodies specific to the coronavirus. Antibodies begin to appear in the blood about a week after the coronavirus has infected the body. Because antibodies take so long to develop, an antibody test can’t reliably diagnose an ongoing infection. But it can identify people who have been exposed to the coronavirus in the past.
    • Antigen test: This test detects bits of coronavirus proteins called antigens. Antigen tests are fast, taking as little as five minutes, but are less accurate than tests that detect genetic material from the virus.
    • Coronavirus: Any virus that belongs to the Orthocoronavirinae family of viruses. The coronavirus that causes Covid-19 is known as SARS-CoV-2.
    • Covid-19: The disease caused by the new coronavirus. The name is short for coronavirus disease 2019.
    • Isolation and quarantine: Isolation is the separation of people who know they are sick with a contagious disease from those who are not sick. Quarantine refers to restricting the movement of people who have been exposed to a virus.
    • Nasopharyngeal swab: A long, flexible stick, tipped with a soft swab, that is inserted deep into the nose to get samples from the space where the nasal cavity meets the throat. Samples for coronavirus tests can also be collected with swabs that do not go as deep into the nose — sometimes called nasal swabs — or oral or throat swabs.
    • Polymerase Chain Reaction (PCR): Scientists use PCR to make millions of copies of genetic material in a sample. Tests that use PCR enable researchers to detect the coronavirus even when it is scarce.
    • Viral load: The amount of virus in a person’s body. In people infected by the coronavirus, the viral load may peak before they start to show symptoms, if symptoms appear at all.

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