Flu spikes A virus found this spring in wastewater samples from 59 sewage systems in 18 different states may indicate the spread of the H5N1 bird flu virus currently infecting dairy cattle, a new study suggests.
So far, the U.S. Department of Agriculture has reported that more than 30 herds of dairy cows in nine states have been infected with the H5N1 flu. But there are questions about how big the outbreak could be and whether the U.S. can adequately monitor it.
At the press conference last week, USDA officials admitted that it was difficult to get milk producers to let them be tested for the infection. Recent tests on milk bought in supermarkets found genetic material from the H5N1 virus in 1 in 5 samples tested, although further testing showed that the virus fragments found in milk were not infectious.
Last week Dr. Nirav Shah, deputy director of the U.S. Centers for Disease Control and Prevention, said at a multi-agency news conference on the government’s response to the spreading virus that the agency was looking at whether it would be feasible to divert wastewater to areas locate where the virus is spreading. First, he said, scientists should develop a test that could distinguish H5 flu from the larger soup of circulating A flu viruses.
Now scientists from Emory, Stanford and Verily Life Sciences, a research organization affiliated with the WastewaterSCAN network that monitors a large network of wastewater treatment plants in the US, say they have done just that.
Wastewater testing is a passive way to monitor the spread of infections. It does not rely on humans or animals to be sampled to test for pathogens. Instead, evidence flows into the wastewater every time a toilet is flushed or someone dumps material down the drain.
Of the 190 wastewater treatment plants currently monitoring sludge samples for influenza A, 59 saw an increase in A strain viruses this spring, just as the number of human influenza cases remained stable or decreased. Wastewater experts wondered whether this could come from H5N1, the highly pathogenic bird flu infections in dairy cattle or other animals.
The WastewaterSCAN team developed a test to check for the H5 gene of the influenza virus and used it on stored samples from sewage systems near areas in Texas where dairy cattle had tested positive, but excluding wastewater directly from the farms.
The team measured both a genetic marker for influenza A viruses and genetic markers specific to H5 viruses.
When the levels of the markers for influenza A viruses started to rise in early March, the markers for the H5 viruses started to rise at the same time. The concentration of the H5 gene in the samples was almost as high as the concentration of influenza A viruses in general, indicating that a large proportion of the viruses in the samples were H5N1.
In addition, 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 said.
The stored sludge samples tested for the study were collected between February 4 and April 16 at two treatment plants in the city of Amarillo watershed and a third wastewater treatment plant in Dallas County. The researchers confirmed that wastewater treatment plants sampled in the Amarillo area allowed some producers to dispose of animal byproducts, including dumped milk from dairies, which could explain the high concentrations of influenza A viruses and H5 viruses in their samples.
Just as wastewater testing has historically been a harbinger of rising Covid-19 infections, researchers say their research suggests it could also be an early warning of bird flu outbreaks in farm animals.
“We discovered the H5 marker just before highly pathogenic bird flu was confirmed in those counties,” said Dr. Alexandria Boehm, professor of civil and environmental engineering at Stanford University.
“I find that super interesting. It means that the wastewater in this specific case, with this specific pathogen, can reveal information about what was circulating in these cattle before any information was publicly available,” Boehm said.
The article was posted to the BioRxiv server as a preprint prior to rigorous review by external experts. The researchers say they are working to publish it in a scientific journal.
The authors of the study emphasize that no H5N1 outbreak in cows has been reported in any of the sewage sheds they tested. Instead, they think the permitted dumping of milk likely caused the large spikes in the H5 virus they saw in early March.
The researchers note that they cannot rule out that the H5 genetic material they pick up in the wastewater all comes from dairy cattle. It could also be from birds or even people.
The researchers say they also don’t have enough information to know where the increase in influenza A virus in multiple states is coming from.
“We don’t know the answer to that question. It’s something that I think needs to be followed up on,” Boehm said.
But if the spike in viruses comes from dumped milk or other animal waste in the sewage sheds they monitor — and that’s still a pretty big if — it means the outbreak is likely much more widespread than currently known.
“If dairy industry activities in these sewage sheds are a primary source of H5 in wastewater, this suggests that there may be additional, unidentified outbreaks among livestock whose milk is sent to these facilities because milk from infected animals must be derived from the food supply. ” note the study authors.
But the researchers also say their results should be interpreted carefully. Without detecting possible sources in the sewers they monitor, the source of the virus cannot be proven.
“However, there are several lines of evidence pointing to animal sources,” the paper says.
The researchers say their testing method is very sensitive. It can detect even small amounts of genetic material from the H5 viruses, but they cannot tell whether the viruses can infect people and make them sick. Boehm says they haven’t tried growing the virus to see if it could infect cells.
The U.S. Food and Drug Administration said last week that it tested samples of pasteurized milk that found traces of the H5N1 virus. So far it has been shown that the milk is not contagious and cannot make people sick.
The wastewater researchers acknowledge that it is also possible that their tests may pick up other types of H5 viruses, including low pathogenic H5 flu 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 had an ethical obligation 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 .
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