Yet another new COVID variant called JN.1 is fueling yet another surge in COVID transmission according to wastewater data, while flu and RSV cases are also showing a sharp rise in the wake of holiday gatherings.

We’ve become used to post-holiday, early January surges in COVID-19 infection rates over the last three years, as people mobbed airports and gathered in groups in winter months where there is rarely as much ventilation. And thus far, the end-of-2023 COVID infection rates are not as high as they were for 2020, 2021, or 2022. But the new JN.1 COVID variant could change that in a hurry, and the CDC estimates that more than 40% of new COVID cases are JN.1 variant cases, which is up sharply from just about 20% two weeks ago. So yes, that’s a surge.

KGO has taken a look at the data and found several Bay Area cities, including San Francisco, are seeing higher levels of infection in wastewater not just for COVID, but perhaps even more so for the flu and respiratory syncytial virus (RSV).

But how much higher? The Chronicle charted COVID wastewater levels in 12 Bay Area regions, and the general trend is that the infection rates are the highest we’ve seen since the tail-end of the last holiday surge, that is, February 2023 levels.

"What we've seen over the past few years is a typical pattern of a 'one-two-three-punch' with Thanksgiving, Christmas, Hanukkah and then New Year, followed by increased cases in the community and spillover in the hospital," UCSF Infectious Diseases Specialist Dr. Peter Chin-Hong told KGO.


As seen above, COVID hospitalizations are not that bad right now compared to the previous two holiday seasons. But NBC News has the national data on COVID hospitalizations, and right now we are again seeing the highest national hospitalization rates since February 2023.

The issue is not confined to the Bay Area, but the Chronicle reported last week that nationwide COVID hospitalizations had increased by about 16,000 over the last month. More troublingly, influenza hospitalizations had increased by more than 55,000 over that same month, and we may see more of both surging in January.

"There are substantial increases in respiratory syncytial virus cases and hospitalizations in adults and substantial increases in influenza, in hospitalization, cases and tests in adults and children," UCSF epidemiologist George Rutherford explained to KGO.

So this would be an excellent time to get the updated COVID, RSV, and flu vaccines, all of which are available in SF and around the Bay Area. COVID and flu shots are generally free even for the uninsured, RSV vaccines generally require insurance or a paid fee.

Related: New COVID Variant Spikes Cases in the Bay Area (Again) [SFist]

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