Spikes of flu virus in wastewater raise questions about spread of bird flu

Spikes of influenza A virus seen in wastewater samples from 59 sewer systems across 18 different states this spring may point to the spread of the H5N1 avian influenza virus that is currently infecting dairy cattle, a new study suggests.

So far, the US Department of Agriculture has reported more than 30 herds of dairy cows infected with H5N1 influenza across nine states. But there are questions about how large the outbreak might be and whether the US can adequately track it.

In a news conference last week, USDA officials admitted that it’s been difficult to get milk producers to let them test for the infection. Recent tests of milk purchased at grocery stores found genetic material from the H5N1 virus in 1 out of 5 samples tested, though further testing showed the virus fragments detected in milk were not infectious.

Last week, in a multi-agency news conference on the government’s response to the spreading virus, Dr. Nirav Shah, principal deputy director of the US Centers for Disease Control and Prevention, said the agency was looking at whether it might be feasible to use wastewater to pinpoint areas where the virus is spreading. First, he said, scientists would need to develop a test that could distinguish H5 influenza from the larger soup of circulating A-strain flu viruses.

Now scientists at Emory, Stanford and Verily Life Sciences, a research organization affiliated with the WastewaterSCAN network that monitors a large network of wastewater treatment plants across the US, say they have done just that.

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Wastewater testing is a passive way of tracking the spread of infections.  It doesn’t depend on people or animals to be swabbed to test for pathogens.  Instead, evidence flows into the wastewater every time a toilet is flushed or someone dumps material down a drain.

Out of 190 wastewater treatment plants that currently monitor sludge samples for influenza A, 59 saw increases of the A-strain viruses this spring, just as human flu cases were flat or falling. Wastewater experts wondered if it might be from H5N1, the highly pathogenic avian influenza infections in dairy cattle or other animals.

The WastewaterSCAN team developed a test to check for the flu virus’ H5 gene and used it on stored samples from sewer systems near areas in Texas where dairy cattle had tested positive, but not including wastewater directly from the farms.

The team measured both a genetic marker for influenza A viruses and genetic markers specific to H5 viruses.

As levels of the marker for influenza A viruses began to rise in early March, the markers for the H5 viruses began to rise in tandem.  The concentration of the H5 gene in the samples was nearly as high as the concentration of the influenza A viruses overall, suggesting that a large fraction of the viruses in the samples were H5N1.

What’s more, the concentrations of influenza A viruses measured in these wastewater sludge samples from the Amarillo, Texas, area were “among the highest ever measured in wastewater,” the study noted.

The stored sludge samples tested for the study were taken between February 4 and April 16 at two treatment plants sites in the City of Amarillo watershed, and a third wastewater treatment plant in Dallas County. The researchers confirmed wastewater processing plants sampled in the Amarillo area permitted some producers to dispose of animal byproducts, including dumped milk from dairies, which may explain the high concentrations of influenza A viruses, and H5 viruses in their samples.

Just as wastewater testing has proven to be a harbinger of rising Covid-19 infections in the past, researchers say their study suggests it could be an early warning for bird flu outbreaks in farm animals, too.

“We detected the H5 marker right before there was confirmed highly pathogenic avian influenza in those counties,” said Dr. Alexandria Boehm, who is a professor of civil and environmental engineering at Stanford University.

“I think that is super interesting. It means that the wastewater in this particular case, with this particular pathogen, can reveal information about what was circulating in these cattle before there was information publicly available,” Boehm said.

The paper was posted as a preprint on the BioRxiv server, ahead of rigorous review by outside experts. The researchers say they are working to get it published in a scientific journal.

The study authors stress that no H5N1 outbreaks in cows have been reported in any of the sewersheds they tested.  Instead, they think that the permitted dumping of milk likely caused the big spikes in H5 virus they saw in early March.

The researchers note that they can’t rule out that the H5 genetic material they’re picking up in the wastewater is all from dairy cattle. It could also be from birds or even humans.

The researchers say they also don’t have enough information to know where the increases in influeza A virus are coming from across multiple states.

“We don’t know the answer to that question. It is something that I think needs to be followed up on,” Boehm said.

But if the spike in viruses is from dumped milk or other animal waste across the sewersheds they monitor — and that’s still a pretty big if — it means the outbreak is likely far more widespread than is currently known.

“If dairy industry activities in these sewersheds are a primary source of H5 in wastewater, this suggests that there may be additional, unidentified outbreaks among cattle with milk sent to these facilities since milk from infected animals is required to be diverted from the food supply,” the study authors note.

But the researchers also say their results should be interpreted carefully.  Without tracking down possible sources in the sewersheds they monitor, the source of the virus can’t be proven.

“However, multiple lines of evidence suggest animal sources,” the paper says.

The researchers say their testing method is very sensitive. It can detect even small amounts of the genetic material from the H5 viruses, but they can’t tell if the viruses would be able to infect people and make them sick. Boehm says they didn’t try to culture the virus to see if it could infect cells.

The US Food and Drug Administration said last week that it has been testing samples of pasteurized milk in which traces of the H5N1 virus have been detected and so far found the milk is not infectious and cannot make people sick.

The wastewater researchers acknowledge that it’s also possible that their tests are picking up other types of H5 viruses, including low-pathogenic H5 influenza viruses, but they say these are not expected to be circulating in these areas at this time.

“This is a situation where we really felt like we were ethically bound to share this information with colleagues through a preprint and get the conversation going, because there are unanswered questions that are really important to answer,” Boehm said.