As nationwide wastewater testing ramps up, Texas researchers identify bird flu in nine cities

As health officials increasingly turn to wastewater testing as a way to track the spread of H5N1 bird flu among US dairy herds, some researchers are questioning the effectiveness of sewage tests.

Although the US Centers for Disease Control and Prevention says the current test is standardized and will detect bird flu, some researchers have expressed skepticism.

“Right now we’re using these broad tests” to test for influenza A viruses in wastewater, said epidemiologist Denis Nash, referring to a category of viruses that includes the common human flu and the bird flu that circulates in dairy cattle. wild birds. , and poultry.

“There may be some places around the country where the primers that are being used in these tests … may not work for H5N1,” said Nash, distinguished professor of epidemiology and executive director of the Institute for Applied Population Science City University of New York. Health.

Read more: What you need to know about the bird flu outbreak, raw milk concerns, and more

This is because the most commonly used tests – polymerase chain reaction, or PCR tests – are designed to detect genetic material from a specific organism, such as an influenza virus.

But in order for them to identify the virus, they must be “primed” to know what they are looking for. Depending on the part of the virus researchers are looking for, they may not be able to identify the bird flu subtype.

There are two common viruses against human influenza A: H1N1 and H3N2. The “H” stands for hemagglutinin, which is a recognizable protein in the virus. The “N” stands for neuraminidase.

On the other hand, bird flu is also an influenza A virus. But it has the H5N1 subtype.

This means that although the human and avian influenza viruses share the N1 signal, they do not share H.

If a test is designed to look at the H1 and H3 only as indicators of influenza A virus, they will miss the bird flu.

Marc Johnson, a professor of molecular microbiology and immunology at the University of Missouri, said he doesn’t think that’s too likely. He said the generic panels used by most laboratories will cover H1, H3 and H5.

He said that while his lab looks specifically for H1 and H3, “I think that might just be us.”

It is only in the last few years that health officials have begun to use wastewater as a public health watchdog.

Alexandria Boehm, professor of civil and environmental engineering at Stanford University and principal investigator and program director for WastewaterSCAN, said wastewater surveillance has been very successful during the pandemic. It is a common way to look for hundreds or thousands of viruses and other pathogens in municipal wastewater.

“Three or four years ago, no one was doing it,” said Boehm, who collaborates with a network of researchers in laboratories at Stanford, Emory University and life sciences research organization Alphabet Inc. “It evolved in response to the pandemic and continues to evolve.”

Since late March, when bird flu was first reported in Texas dairy cattle, researchers and public health officials have been combing through wastewater samples. Most are using the flu A tests they already have in their systems – most of which were designed to detect human flu viruses, not bird flu.

Read more: Flu season is over, but there’s a viral surge in California’s wastewater. Is it bird flu?

On Tuesday, the CDC released its own dashboard showing wastewater sites where it has detected influenza A over the past two weeks.

Showing a network of more than 650 sites across the country, there were only three sites — in Florida, Illinois and Kansas — where influenza A levels were deemed high enough to warrant further agency investigation. There were more than 400 for which there was insufficient data to make a decision.

Jonathan Yoder, deputy director of the CDC’s Division of Infectious Disease Preparedness and Innovation, said those sites were deemed to have insufficient data because the test hasn’t been in place long enough, or perhaps there weren’t enough influenza A positive samples. to be taken into account.

Asked if some of the tests being used could have missed bird flu because of the way they were designed, he said: “We have no evidence of that. It looks like we’re at a fairly broad level that we don’t have “We have no evidence that we won’t get H5.”

He added that the tests were standardized across the network.

“I’m pretty sure it’s the same assessment that all the sites are using,” he said. “They’re all based on … what the CDC has published as a clinical assessment for influenza A, so it’s based on clinical tests.”

But there are discrepancies between the CDC’s findings and those of others.

Earlier this week, a team of scientists from Baylor College of Medicine, the University of Texas Health Science Center at Houston, the Texas Epidemic Health Institute and the El Paso Water Utility, published a report showing high levels of bird flu from wastewater in nine Texas. cities. Their data shows that H5N1 is the predominant strain of influenza A swirling in the wastewater of these Texas towns.

But unlike other research teams, including the CDC, they used an “agnostic” approach called hybrid-capture sequencing.

“So it’s only targeting one virus or one of several viruses,” as one does with a PCR test, said Eric Boerwinkle, dean of the UTHealth Houston School of Public Health and a member of the Texas team. “We’re really in a very complex mix, which is wastewater, pulling down viruses and sequencing them.”

“The key thing here is that it’s very specific for H5N1,” he said, noting that they had been doing this kind of testing for about two years, and had never seen H5N1 before mid the month of March.

Blake Hanson, an assistant professor at the University of Texas Health Science Center at Houston School of Public Health and a member of the Texas wastewater team, agreed, saying that PCR-based methods are “exquisite” and “very accurate.”

“But we have the ability to look at the expression of the whole genome, not just a marker component of it. And so that allowed us to look at H5N1, to differentiate it from some of our seasonal fluids like H1N1 and H3N2,” he added. said. “What gave us a lot of confidence is that it’s completely H5N1, but the other papers are using part of the H5 gene as a marker for H5.”

Boerwinkle and Hanson pointed out that while they were able to identify H5N1 in the wastewater, they cannot say where it came from.

“Texas is really a confluence of a few different flyways for migratory birds, and Texas is also an agricultural state, despite having some pretty big cities,” Boerwinkle said. “It’s probably right, if you had to bet your dime and gamble on what was happening, it’s likely to come from not just one source but multiple sources. We have no reason to think that a more likely source just any of those things.”

But they are pretty confident that it is not coming from humans.

“Because we’re looking at the genome as a whole, when we look at the individual human H5N1 case, the genomic sequence … there’s a hallmark amino acid change … compared to all the cattle from the same point in time,” A Hanson said. “We don’t see that hallmark amino acid in any of our sequencing data. And we looked very carefully at that, which gives us confidence that we’re not seeing human-to-human transmission.”

The Texas team’s approach was very exciting, said Devabhaktuni Srikrishna, CEO and founder of, noting that it demonstrated “proof of principle” for using this type of metagenomic testing protocol for wastewater and air.

He said government agencies, private companies and academics are searching for a reliable way to test thousands of microscopic organisms – such as pathogens – quickly, reliably and at low cost.

“They showed it can be done,” he said.

This story originally appeared in the Los Angeles Times.

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