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SF wastewater data shows unprecedented summer Covid surge

Rowan Zoltar and Nurse practitioner Mawayidna Tombegou prepare covid testing kits for passerbys out of the City Health mobile testing van, which parked at 16th and Mission streets on Wednesday, May 25, 2022. The DPH program aims to test everyone, especially uninsured community members. | Camille Cohen/The Standard

Data collected from San Francisco’s toilet water shows that the recent Covid surge may have topped the city’s former record high, illustrating how the city’s official case counts no longer give a complete picture of how the virus is spreading.

The wastewater data shows a peak that gathered steam throughout May, exceeding highs not seen since the first surge of the Omicron variant in January 2022. Cases spiked again in late June, according to the data, likely reflecting a rise in the highly infectious Omicron BA.5 variant, which is good at evading immune defenses. 

The data demonstrates how official case counts increasingly paint a limited picture as more Covid patients stick with at-home testing. Testing data shows a seven-day average of over 400 new cases per day versus more than 2,300 at the peak of the January surge. But the wastewater data, collected by a team of researchers at Stanford and Emory Universities, suggests a current true case count that is considerably higher. Los Angeles County, meanwhile, is considering going back to an indoor mask mandate amid rising cases and hospitalizations.  

However, San Francisco’s wastewater data also shows that the current surge could be on the downswing—at least on the west side of the city, which looks to be carrying a considerably higher viral load, according to calculations by Stanford researchers. 

“The higher concentrations in Oceanside vs Southeast suggests that, during the current Covid wave, the infection rates (number of infections divided by the number of people in the sewershed) are higher in the oceanside compared to southeast sewershed,” wrote Alexandria Boehm, a Stanford professor of civil and environmental engineering who helped develop the data, in an email. 

Despite the dramatic summer surge, current cases have fortunately not proven more lethal. Deaths in May and June numbered  29 and 26, respectively—far lower than the 165 people who died during the Omicron surge in January. People who are unvaccinated are catching Covid at more than twice the rate of unvaccinated residents, according to the San Francisco Department of Public Health.

David Sjostedt can be reached at