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As COVID-19 levels continue to rise in Bay Area wastewater for summer 2024, what do you need to know? Beth La Berge/KQED
As COVID-19 levels continue to rise in Bay Area wastewater for summer 2024, what do you need to know? (Beth La Berge/KQED)

COVID Keeps Rising in Bay Area Wastewater. What to Know, From New Variants to Symptoms

COVID Keeps Rising in Bay Area Wastewater. What to Know, From New Variants to Symptoms

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Are you hearing about people in your circles once again getting COVID-19? It’s not just you.

Levels of COVID-19 in the Bay Area’s wastewater have been rising for the last few weeks — and this summer increase is happening earlier than it did in 2023.

Data from Stanford University’s WastewaterSCAN project, which monitors the presence of COVID-19 in human sewage across the U.S. and other viruses, indicates that COVID-19 levels are up across 73% of the sites monitored around the Bay Area.

WastewaterSCAN’s Amanda Bidwell told KQED by email that COVID-19 has been detected in 70% of Bay Area sewage samples they’ve collected over the last three weeks. (If you have COVID-19, the virus will show up in your feces soon after you’re infected.)

A graph showing WastewaterSCAN data from June 10 on COVID-19 levels in Bay Area wastewater, aggregated from across the region’s wastewater sites. (WastewaterSCAN)

Keep reading for what to know about this rise in Bay Area COVID-19 levels, or jump straight to:

What’s going on with COVID in the Bay Area’s wastewater right now?

The Bay Area’s own COVID-19 wastewater levels are “higher than where they were this time last year,” said WastewaterSCAN’s Bidwell, who noted that in 2023, “late June is when we started to see a summer increase.”

The Stanford team is observing a sharp rise in San Francisco’s wastewater in particular, said Bidwell, who last week told KQED that “we are seeing some [of the] highest concentrations we’ve ever measured” at the Oceanside SF and Southeast SF wastewater sites.

A graph showing WastewaterSCAN data from June 10 illustrating COVID-19 levels in San Francisco wastewater, aggregated from the city’s two wastewater sites. (WastewaterSCAN)

The San Francisco Department of Public Health told KQED in a June 11 email that it’s “difficult to determine an exact cause of why COVID-19 detections have increased” locally, noting that “it can be the result of various factors, including waning immunity, the increase in travel and gatherings associated with the summer season, and the emergence of new subvariants.”

The agency also pointed to the seasonal behavior of the virus in previous years, notably the “increase in COVID-19 activity around late spring to late summer, followed by another increase during the winter.”

In addition to these two San Francisco sites, wastewater locations in Mill Valley, Novato, Palo Alto, Richmond, San Jose, Las Gallinas, Sausalito, Sunnyvale and Vallejo are also currently all in the “High” category for COVID-19 levels.

Nationally, COVID-19 wastewater levels have also been rising across the country — although levels of the virus are currently back in the “Medium” category on WastewaterSCAN’s dashboard of all its sites around the United States after being classified as “High” for the last few weeks.

You can check the COVID-19 levels in your own county’s wastewater according to WastewaterSCAN’s monitoring:

San Francisco | Alameda | San Mateo | Santa Clara | Contra Costa | Solano | Marin | SonomaNapa

Why is COVID back earlier this summer?

It’s undoubtedly become harder in 2024 to materially track COVID-19 levels in a certain area. As of May 1, the Centers for Disease Control and Prevention (CDC) no longer requires hospitals nationwide to report the number of patients admitted with COVID-19. This had been one of the remaining indicators of rising COVID-19 levels in an area, along with PCR tests. Now, health officials must rely on a combination of wastewater data and hospital deaths of patients with COVID-19.

According to the California Department of Public Health (CDPH), the state’s seven-day test positivity rate — the average percentage of people each week who get a positive diagnostic test result from a lab after taking a PCR test — has steadily risen since April 27 (from 1.9% to 4.8%, with the last available data from May 27.)

However, since this data doesn’t include at-home antigen testing, it doesn’t represent the full picture of COVID-19 positivity around the state.

A registered nurse prepares a dose of the Moderna vaccine at St. Rose Hospital in Hayward, Alameda County, on Friday, Jan. 8, 2021. (Jessica Christian/The San Francisco Chronicle via Getty Images)

“Of course, it’s hard to use wastewater to tell you how many people that represents,” said Dr. Peter Chin-Hong, an infectious disease expert at the University of California, San Francisco (UCSF), of the recent observed rise in sewage. “But nevertheless, the trend is important. And I think we might see a [COVID] swell in the summer.”

As for why the Bay Area could now be seeing a summer rise in COVID-19 wastewater levels over a month earlier than it did in 2024, Chin-Hong said a big factor is our collective waning immunity against the virus.

“One year ago, last year, many more people had gotten additional vaccines,” he said. “They had additional immunity that was more recent.”

But in 2024, “we only have about 22% or so of Americans vaccinated” nationally, Chin-Hong said. In California, only 14.7% of people statewide are up-to-date on their COVID-19 vaccines. So if someone hasn’t been infected with COVID-19 recently and they haven’t gotten the latest vaccine, they’re left extra-vulnerable to rising COVID-19 levels in their community.

How much are new COVID variants driving this rise?

You might hear about new COVID-19 variants informally called “FLiRT”: KP.1.1,  KP.2 and now KP.3.

These latest omicron descendants, nicknamed for the letters used for their mutations, have risen in prominence recently around the country, overtaking the previous leading variant, JN.1 — the one that “was ruling the roost for a lot of the winter and spring,” Chin-Hong said. Now, KP.3 has become the most dominant strain nationwide.

In the CDC’s “Region 9” group of western states that encompasses California, KP.2 is still dominant, according to the most recent data. In the Bay Area, WastewaterSCAN’s Bidwell said that KP.1 and KP.2 are still the dominant variants in the three Bay Area wastewater sites where the Stanford team sequenced this data on specific variants.

The new variants matter because each new one brought increased transmissibility during the pandemic. This means that although much of the general population will not get particularly sick with these new COVID-19 variants when they become dominant, there will still be higher-risk groups that will get seriously ill, Chin-Hong said.

“Maybe that’s the fact of life, but my point is: It shouldn’t be the fact of life because we have so many tools” to reduce COVID-19 spread and treat infectious people, Chin-Hong said.

The CDC has also stated that based on current data, “there are no indicators that KP.2 would cause more severe illness than other strains.”

As for the reformulated seasonal COVID-19 vaccine, the Food and Drug Administration (FDA) recommended on June 5 that the new, updated COVID-19 vaccine that will be offered in the fall should in fact be based on the JN.1 variant.


Who is the most at risk for COVID right now?

“I’m not worried about the general population because people have seen it so many times already,” Chin-Hong said. “The majority of folks [are] going to be OK.”

But “I’m worried about the most vulnerable,” he said, pointing to low vaccination rates among people age 65 and older — despite an extra COVID-19 vaccine dose being made available to this age group back in February because of their heightened risk levels. Read more about finding an additional COVID-19 vaccine if you’re 65 or older.

While it may feel confusing and frustrating — or like a personal step backward — to still think about COVID-19 precautions in 2024, that’s understandable. But there are actions you can take in response to a rise in COVID-19 numbers to protect the health of you and your loved ones, stop community spread among the most high-risk people and reduce the disruption that a COVID-19 infection in your household can bring to your lives, your work and much-anticipated summer travel plans.

During a rise in COVID-19 levels locally, this might include bringing a well-fitting N95 mask along to indoor spaces that you know could be crowded, like the grocery store or BART during rush hour. Or, if you’re hosting people indoors in your home, ensure the space has good ventilation by taking measures like opening windows. If the weather allows, you might also consider favoring outdoor hangouts and meetups with friends and family at this current time.

And if you’re at higher risk for serious illness or hospitalization from COVID-19, it’s an especially good idea to take extra precautions against the virus during a rise in COVID-19 locally. These groups can include older people, immunocompromised and disabled folks.

It also includes people who aren’t up-to-date on their COVID-19 vaccines, so if you haven’t already gotten the latest vaccine, you can still find a free COVID-19 shot near you. Remember, people 65 and older are also eligible for an extra COVID-19 vaccine dose.

One more reason you might consider being extra cautious about COVID-19 right now is if you’ve got upcoming travel plans. Even if your symptoms are mild, a COVID-19 infection can require isolation from other people for well over a week. And you can double that timeline if you get a rebound (i.e., second) infection, which is surprisingly common even in people who don’t take the antiviral treatment Paxlovid.

I’m worried I might have COVID. What should I do?

Know the 2024 symptoms of COVID-19

Chin-Hong confirms that there don’t appear to be any surprising “wild card” symptoms expected for a COVID-19 infection in 2024, either for JN.1 or the FLiRT variants. Rather, they seem to largely be the same COVID-19 symptoms you’re used to hearing about from previous variants.

According to the CDC, possible symptoms of COVID-19 include, but aren’t limited to, fever or chills, cough, shortness of breath or difficulty breathing, fatigue, muscle or body aches, headache, new loss of taste or smell, sore throat and congestion or runny nose.

They can also include gastrointestinal symptoms like nausea, vomiting and diarrhea, which Chin-Hong told the New York Times can often confuse people experiencing them, who initially assume they have a condition like norovirus rather than COVID-19.

During a rise in COVID-19 levels locally, protect the health of yourself and your loved ones by bringing a well-fitting N95 mask to spaces that could be crowded, like the ballpark, grocery store or BART during rush hour. (Ezra Shaw/Getty Images)

Find a reliable test (and keep testing)

Incubation periods for COVID-19 — the time between exposure and testing positive — have shortened during the pandemic. It went from a five-day average in 2020 to as soon as a few days in 2024. So, if you’re having symptoms even two days after an exposure, it makes sense to test.

But if your first test is negative, you should absolutely test again in the next 48 hours if symptoms persist — and again after that if you’re still negative. It’s been suggested that COVID-19 symptoms can start much earlier in 2024. This is due to the average immune system being more primed to detect and react to a COVID-19 infection as we navigate the fifth year of this pandemic.

So don’t assume a negative result means you don’t actually have COVID-19: If you’re feeling sick, play it safe, stay home as much as you can and wear a well-fitted mask if you can’t. Also, be sure to take another antigen test soon. You could also seek out a more sensitive PCR test.

Remember, if you’ve been stockpiling COVID-19 tests in the last year, make sure the one you’re using hasn’t expired. And if it has, you can still check the list of manufacturers who’ve had their test expiration dates extended by the Food and Drug Administration (FDA).

If you have health insurance, you can still request reimbursement from your health insurer for up to eight at-home tests per month. You can also read more about how to find free COVID-19 tests near you.

And if you test positive for COVID …

In March, the CDC officially revised their national COVID-19 isolation guidance, saying that COVID-positive people could now return to work or regular activities once “symptoms are improving overall” and they’ve been fever-free for at least 24 hours without use of a fever-reducing medication.

The CDC’s new guidelines now mostly resemble California’s own updated COVID-19 isolation recommendations, which the state revised back in January. Read more about current isolation guidance for COVID-19.

If you’ve been infected, consider asking your health provider for the COVID-19 medication Paxlovid, an antiviral treatment in pill form that is still available free by prescription in California. Read more on requesting a prescription for Paxlovid, with or without health insurance.

Tell us: What else do you need to know about COVID right now?

At KQED News, we know that it can sometimes be hard to track down the answers to navigate life in the Bay Area in 2024. We’ve published clear, practical explainers and guides about COVID, but also how to cope with intense winter weather and how to exercise your right to protest safely.

So tell us: What do you need to know more about when it comes to COVID — or anything else? Tell us, and you could see your question answered online or on social media. What you submit will make our reporting stronger, and help us decide what to cover here on our site, and on KQED Public Radio, too.

Earlier versions of this story were originally published on May 23 and June 5.


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