Wastewater surveillance is crucial for tracking new variants, BA.2.86 shows us

The CDC publishes data from about 400 wastewater testing sites that are sequencing their samples. Chart shows data from the week of August 17.

This week, the health department in New York City, where I live, announced that they’d identified new variant BA.2.86 in the city’s wastewater. (For more details about BA.2.86, see last week’s Q&A post.)

I covered the news for local outlet Gothamist/WNYC, and the story got me thinking about how important wastewater surveillance has become for tracking variants. With less clinical testing, sewage is now a crucial source for understanding how the coronavirus is mutating and what impacts those mutations have. But there are continued barriers to obtaining and interpreting wastewater data.

Quoting from the story:

The declaration of the end of the public health emergency in May made COVID-19 tests less available in health care settings, and sewage monitoring has since emerged as an important way to identify new variants.

“As the wastewater testing has gotten better, the patient surveillance has decreased,” [said Marc Johnson, a virologist at the University of Missouri]. Several variants have been found in sewage before cases were confirmed, he said.

That list now includes BA.2.86, in New York City as well as Ohio and other countries. The CDC publishes variant data from about 400 wastewater testing sites, including the city’s.

But wastewater data from New York City is reported unevenly, with significant delays between when samples are collected and when data is published on dashboards run by the CDC and New York state.

Wastewater surveillance has some distinct advantages, when it comes to variant monitoring:

  • It covers thousands of people—the entire population of a sewershed—with one sample. In big cities like NYC, one sample can include data from more than one million residents.
  • Through sewage samples, scientists can look for multiple variants at once, rather than compiling data over many PCR test results. They can also track population-level trends over time.
  • Unlike traditional case data, wastewater data don’t rely on how many people are getting tested or where. This lack of testing bias is important, as people typically use rapid tests—which are not reported to health systems—over PCR these days (rapid tests are easier to access, PCR sites have closed following the end of the federal public health emergency, etc.).

But there are also some problems, as the NYC detection this week demonstrated:

  • Public health officials are still getting used to using and sharing wastewater data, as this is a relatively novel source with novel pipelines for transmitting data. While the CDC and other organizations are working to compile these data in a standardized way, it’s still a work in progress.
  • Discrepancies and delays can sometimes occur as a result. For example, in New York, the governor’s office put out a press release on Tuesday morning claiming that BA.2.86 hadn’t been detected in the state yet—then, just hours later, the city health department announced they’d found it. State health officials weren’t aware of the detection before the city made its public announcement, I learned for my news story.
  • Health officials are also still learning how to interpret and act on wastewater data. The NYC health department failed to answer my questions about in which sewershed or from which sampling date they found BA.2.86; it’s unclear if they’re using the detection to take any specific actions, besides simply warning the public that this variant is present.
  • As wastewater surveillance captures such broad samples, it’s difficult to tie new variant detections to clinical data, such as whether an infected person went to the hospital due to their symptoms. Officials can’t contact trace from these detections, making it hard to answer questions like whether BA.2.86 causes more severe symptoms.

For more reading on this topic, I recommend my feature for Gothamist/WNYC and MuckRock last fall about NYC’s wastewater surveillance program, as well as other past posts at the COVID-19 Data Dispatch.

More about wastewater surveillance

Wastewater surveillance expands beyond COVID-19
I have a new story up this week at Science News, describing how the field of wastewater surveillance exploded during the COVID-19 pandemic and is now looking toward other public health threats.
National numbers, September 24
The COVID-19 plateau that I’ve described over the last couple of weeks continues, with wastewater and test positivity data showing that viral spread has slowed in much of the U.S. However, this is likely just a lull before respiratory virus …
COVID source shout-out: Wastewater surveillance in Wyoming
Wastewater surveillance is re-starting in some Wyoming sewersheds after an earlier iteration of the program ended in December 2021, according to local news reports. This monitoring is a good sign for expanded coverage across more rural parts of the U.S.
National numbers, August 27
This week, our limited COVID-19 data picture suggests that transmission may be starting to level off. But if BA.2.86 or another newer variant enters this high-spread environment, the outlook could get less rosy.
COVID source callout: Nebraska stops reporting wastewater data
The Nebraska state health department has discontinued its wastewater surveillance data page, depriving residents of important COVID-19 updates at a time when cases are rising.
National numbers, August 20
The summer COVID-19 surge continues. While wastewater surveillance data suggest that transmission trends may be turning around in some places, the virus is largely still increasing across the U.S. New variants are on the horizon, too.

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