Live poultry markets may be source of bird flu virus in San Francisco wastewater

Federal officials suspect that live bird markets in San Francisco may be the source of bird flu virus in area wastewater samples.

Days after health monitors reported the discovery of suspected avian flu viral particles in wastewater treatment plants, federal officials announced that they were looking at poultry markets near the treatment facilities.

Last month, San Francisco Public Health Department officials reported that state investigators had detected H5N1 — the avian flu subtype making its way through U.S. cattle, domestic poultry and wild birds — in two chickens at a live market in May. They also noted they had discovered the virus in city wastewater samples collected during that period.

Two new “hits” of the virus were recorded from wastewater samples collected June 18 and June 26 by WastewaterSCAN, an infectious-disease monitoring network run by researchers at Stanford, Emory University and Verily, Alphabet Inc.’s life sciences organization.

Nirav Shah, principal deputy director of the U.S. Centers for Disease Control and Prevention, said that although the source of the virus in those samples has not been determined, live poultry markets were a potential culprit.

Hits of the virus were also discovered in wastewater samples from the Bay Area cities of Palo Alto and Richmond. It is unclear if those cities host live bird markets, stores where customers can take a live bird home or have it processed on-site for food.

Steve Lyle, a spokesman for the state’s Department of Food and Agriculture, said live bird markets undergo regular testing for avian influenza.

He said that aside from the May 9 detection in San Francisco, there have been no “other positives in Live Bird Markets throughout the state during this present outbreak of highly-pathogenic avian flu.”

San Francisco’s health department referred all questions to the state.

Even if the state or city had missed a few infected birds, John Korslund, a retired U.S. Department of Agriculture veterinarian epidemiologist, seemed incredulous that a few birds could cause a positive hit in the city’s wastewater.

“Unless you’ve got huge amounts of infected birds — in which case you ought to have some dead birds, too — it’d take a lot of bird poop” to become detectable in a city’s wastewater system, he said.

“But the question still remains: Has anyone done sequencing?” he said. “It makes me want to tear my hair out.”

He said genetic sequencing would help health officials determine the origin of viral particles — whether they came from dairy milk, or from wild birds. Some epidemiologists have voiced concerns about the spread of H5N1 among dairy cows, because the animals could act as a vessel in which bird and human viruses could interact.

However, Alexandria Boehm, professor of civil and environmental engineering at Stanford University and principal investigator and program director for WastewaterSCAN, said her organization is not yet “able to reliably sequence H5 influenza in wastewater. We are working on it, but the methods are not good enough for prime time yet.”

A review of businesses around San Francisco’s southeast wastewater treatment facility indicates a dairy processing plant as well as a warehouse store for a “member-supported community of people that feed raw or cooked fresh food diets to their pets.”