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New York City has been closing PCR testing sites, even as the city faced a major Omicron resurgence this spring. This was the main finding from a story I wrote for Gothamist and WNYC (New York Public Radio), based on my analysis of public information on city-run testing sites.

While this was a local story, I think the trends I found—and the pushback that the piece received from city health officials—are pretty indicative of the national state of COVID-19 testing right now. Since the federal government ran out of funding to cover testing for Americans without health insurance in late March, private testing companies have started requiring insurance information and, in many cases, raising their prices.

At the same time, state and local health departments have closed their public PCR testing sites and directed people to use at-home rapid tests instead. New York City still has more accessible testing than most of the country, but my story showed how even here, getting tested is becoming more difficult—and less popular.

NYC has faced a major COVID-19 surge this spring — yet the city closed public testing sites and made it harder to get PCR results.

I crunched the numbers for @Gothamist/@WNYC: https://t.co/MKsv8UYHaO (1/10) pic.twitter.com/tRm9eFgYVd

— betsy ladyzhets 📊 (@betsyladyzhets) July 5, 2022

Here are a few key statistics from the piece:

• The number of public PCR testing sites run by NYC Health + Hospitals was cut in half between mid-February and mid-April.
• The total hours that public testing sites were open decreased from over 10,000 during a week in February, to 8,500 during a week in April, to 7,500 in the last week of June.
• Manhattan testing hours remained relatively constant (about 1,500 in each of the weeks I analyzed), while hours were cut in other boroughs.
• The numbers of New Yorkers getting tested on a daily basis were similar in June 2021 and June 2022—even though reported case rates were about ten times higher this year.
• New York City’s test positivity rate recently shot above 10%, and is now over 15%. It was closer to 1% at this time last year.

The NYC health department had some issues with my story. In fact, city health commissioner Dr. Ashwin Vasan posted a Twitter thread stating that it was “missing key information” and that the city actually has “more testing resources than ever.” But the “testing resources” he cites here are mostly at-home tests; PCR testing in NYC is both less accessible and less popular. A follow-up story that I coauthored with Nsikan Akpan, my editor at Gothamist/WNYC, further explains the situation in the city.

The decline in PCR testing is making it harder to understand where and how fast the coronavirus is spreading, both in the city and around the U.S. To explain the implications of this trend, here’s a short FAQ on how to think about testing during our current surge.

Why is PCR testing still important for individuals?

One of the city officials’ main responses to my story was that NYC has made it easy for people to get free at-home rapid tests, in place of PCR testing. The city has distributed more than 35 million at-home tests at hundreds of libraries and other community sites.

At-home tests certainly have advantages: they’re more convenient, with results back in 15 minutes. Turnaround times for PCR tests are generally pretty fast right now thanks to limited demand (usually under 48 hours, if not under 24 hours, in NYC), but that’s still a long wait compared to a rapid test. Rapid, at-home tests also provide a better indicator of contagiousness.

Still, PCR tests have continued utility because they remain the gold standard of accuracy: they’re able to identify a COVID-19 case with much smaller amounts of coronavirus present in someone’s respiratory tract than a rapid test. As a result, if you were recently exposed or are showing some mild symptoms—but testing negative on rapid tests—a PCR test could be valuable to provide a more reliable COVID-19 status.

PCR tests can also be helpful for documenting a COVID-19 case. While many doctors will take a rapid test positive as a clear indicator of an infection, some settings may require a PCR test—in which results are verified by the lab that processes the test. This can be particularly true for Long COVID clinics, health advocate JD Davids told me. So, if you tested positive on a rapid test but are concerned about Long COVID symptoms, a PCR test may be a helpful verification step.

Why is PCR testing still important for communities?

Rapid, at-home test results generally do not travel further than your trashcan, or maybe your phone camera. They don’t get reported to testing companies, or local public health departments, or the CDC—unlike PCR tests, which have established data pipelines for such reporting. Some jurisdictions do have options for residents to self-report rapid test results, but this self-reporting is generally a small fraction of the total tests conducted.

As a result, public health experts generally rely upon PCR testing data to understand patterns in COVID-19 spread. When less PCR testing takes place, these patterns become more difficult to interpret. For example, in the U.S. as a whole, around 100,000 new cases a day have been reported for the last several weeks; but we know that the true trend would likely be a lot more variable if we had data from rapid tests.

Also, as Brown University epidemiologist Dr. Jennifer Nuzzo pointed out when my editor Nsikan interviewed her for our follow-up story, PCR tests are necessary for tracking variants. A selection of PCR test samples get genetically sequenced; this doesn’t happen for rapid tests.

“It’s really important for us to stay ahead of what variants are circulating in our communities,” Nuzzo said, citing what society has already learned about different variants to date. “Some are more transmissible. Some have been more severe. We need to stay ahead of the virus, so that we can know when and how and if to change our strategy about how to control it.”

What’s the value of abundant local testing sites?

If PCR testing is less popular in this current phase of the pandemic, you might ask, why not just have a few central testing hubs in a place like NYC, and maintain testing capacity in a more efficient way? This seems to be the city’s response, to some extent: officials explained that some brick-and-mortar testing sites (mostly at NYC hospitals) are staying open, while the city’s fleet of mobile testing vans can move around as needed.

But for a lot of people, traveling outside their neighborhood to get a test or tracking down the right mobile van can be a major barrier to getting tested. This is especially true for essential workers and low-income New Yorkers—who are the people most in need of testing. Maintaining public testing throughout the city is a health equity issue.

To quote again from the follow-up story:

And even if the testing capacity is technically maintained, location is important. Consider a region like South Brooklyn: Four brick-and-mortar testing sites scheduled to close in mid-July are all located in this area: 4002 Fort Hamilton, Bay Ridge, Bensonhurst and Midwood Pre-K.

It’s unclear whether mobile sites will move to South Brooklyn in response. Shrier said each closing site has “dedicated at-home test distribution sites” within one mile. But residents of Bay Ridge, Bensonhurst and other nearby neighborhoods may need to travel further to get a PCR test — or face high costs at private sites.

What data sources could replace information from PCR tests?

Dr. Denis Nash, an epidemiologist at the City University of New York whom I interviewed for the first NYC story, talked about two types of data that may be collected by a health agency tracking disease spread.

“There’s active surveillance and passive surveillance,” he said. “In active surveillance, the health department staff are actively going out and trying to ascertain how many cases there might be. They’re going to hospitals and to homes, looking for cases. And when you do that, you’re more likely to exhaustively find a high proportion of cases.” One example of active surveillance: a survey conducted by Nash and his team at CUNY in April and May, which indicated about 20% of New Yorkers may have had COVID-19 within a two-week period.

Meanwhile, passive surveillance “relies on healthcare providers and laboratories to voluntarily report their tests and cases to the health department,” Nash said. NYC and other health departments which receive much of their COVID-19 data—PCR test results, hospital admissions, etc.—from healthcare providers are exemplifying this passive approach.

As COVID-19 becomes less of a public concern and testing is less popular, health agencies should step up their active surveillance, Nash said. Wastewater can be another source of data that’s more active than PCR test results, since it reflects COVID-19 spread across a large population. (Unfortunately, in NYC, wastewater data is pretty inaccessible; that’s a topic for another time.)

What’s the best way to use at-home rapid tests?

Rapid test use can fall into three different categories. First, if you are trying to determine whether you’re actively contagious right before a gathering or seeing a high-risk person: take one test, as close in time to the event as possible. (For example, if I’m going to a large march in NYC, I plan to test myself a few minutes before heading to the subway.)

Second, if you had a recent COVID-19 exposure (or attended a high-risk event), test multiple times in succession—ideally at least twice in 48 hours. This testing process should start a couple of days after the exposure, because rapid tests aren’t accurate enough to pick up the infection right away. You could also use a single PCR test to serve the same purpose as multiple rapid tests.

And third, if you are isolating after a positive COVID-19 test, rapid tests can help identify when you’re no longer contagious and able to return to society. As I wrote in an earlier post, the CDC’s five-day isolation guidance is not actually backed up by data; testing out of isolation is much safer.

As always, if you have questions about testing or any other COVID-19 topic, my inbox is open.

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