As we recover from a hot week, the focus today is once again on infectious diseases. We will start with Covid, one of our most familiar viruses, and end with the plague, a rare but serious disease. (Spoiler: the risk to you is currently practically zero.)
We continue to see high but declining Covid-19 activity across the state. The peak in wastewater levels in 2026 occurred about three weeks ago, consistent with last year’s trend.
High Covid-19 activity should be expected for a few weeks. Which matters more in light of the recent arrival of the flu.
On the flu front, transmission rates are increasing by the day. The season started almost two months before our usual end of November date. This chart shows that emergency room visits for Covid-19 decrease as flu increases. You can also see here that RSV, which is the third main respiratory virus that we’re focusing on in California, remains stable. It generally increases at the end of October or November.
I expect these upper lines to cross over the next few weeks and the flu to assume its usual role as the primary contributor to serious respiratory illness in California during the fall and winter.
Combined risk: Since Covid-19 will also remain active for a few weeks, our risk of being exposed to both viruses while out and about is high. If you are at higher risk of severe illness, consider masking in indoor public spaces.
Uptake of the flu vaccine: The most important thing we can do to protect ourselves from the flu is to get vaccinated, and preliminary data shows that many of us know this. Nearly 3 million Californians have already received the flu vaccine this fall, about 400,000 more than this time last year. So I hope everyone understands that this is the game against the flu. Vaccines are available in pharmacies and clinics across the state.
We continue to see unusually high levels of West Nile Virus (WNV) across the state. Remember that we are only infected by mosquito bites. Our risk therefore depends on the virus load present in the mosquitoes around us and our probability of being bitten.
Record temperatures in winter, spring and summer encouraged a larger mosquito population and also allowed the virus to reproduce more quickly.
Currently, we are at 252 human cases, about five times more than this time last year, with 19 deaths.
Almost every region of the state is affected. Thirty-eight counties have reported WNV activity and 23 have human cases. Adjacent Los Angeles and Orange counties have the highest regional burden, with a total of 143 cases and 8 deaths.
There is no vaccine or treatment, so it is mainly about bite prevention.
Remember the four Ds:
Use an insect repellent containing Deet or picaridin.
Cover your arms and legs dawn and to duskwhen West Nile-carrying mosquitoes are most active.
Drain any standing or stagnant water around your property.
Finally, the plague. You’ve probably heard about a death from the plague of a researcher working in a laboratory in Russia. (To keep you up to date, see YLE National FAQ from earlier this week.) This is definitely making headlines, but we need more information before we know what to make of it.
In the meantime, it’s a good time to recall what we know about the plague. For Californians, plague is no stranger: the bacterial disease is actually endemic in our state. Here’s a reminder.
Is this THE Plague? Yes, it’s the same bacteria (Yersinia pestis) at the origin of the Black Death which killed around a third of the population of medieval Europe. But our situation is very different today.
This is extremely rare. In 2025, El Dorado County reported a case of human plague. The patient was likely infected by a flea bite while camping in South Lake Tahoe. Two people were infected in 2015 after exposure in Yosemite National Park. Nationally, we see on average about seven cases per year.
We know how to diagnose and treat it. Antibiotics can treat it, and doctors and nurses in endemic areas are trained to spot and manage it. Without treatment, about two out of three people with the plague die. With treatment, mortality drops to around one in ten people.
It is usually spread by fleas after contact with infected rodents, such as chipmunks, prairie dogs, mice, rats or squirrels. Pets, especially cats, can also bring infection into homes if they wander outside. Person-to-person spread, even in the pneumonic (respiratory) form of plague (the form from which the Russian lab worker is suspected of having died), is very rare. Transmission of plague between people requires close, prolonged contact.
It’s regional. In the United States plague is present in rural areas of the Westparticularly in California, where the bacteria circulates naturally among wild rodents. Urban rats have not been found to carry plague in California.
Note: All cases reported in the East recently came from the West.
Note to self: When I was at the Indian Health Service in Arizona, I cared for a woman with pneumonic plague who had been infected by her cat. A smart doctor I worked with recognized the signs and immediately started antibiotics. She survived and the source was traced to a colony of infected prairie dogs near her home.
THE California Department of Public Health tests rodents to monitor the risk of plague. This map shows where rodents carry antibodies against the bacteria that causes plague, a sign that they have been exposed.
Let’s return to the case of Russia… The most important thing I’m looking for at the moment in Russia is additional cases, because the most worrying scenario is that the bacteria was modified in the laboratory to give it a more contagious form – which I doubt. If human-to-human contagiousness has changed, then we could see real outbreaks with more cases and we will need to prepare over time. But that’s theoretical and Californians needn’t worry until we know more. I will monitor this and keep you posted.
Preventing the plague in California. Plague prevention is most relevant when we are in an endemic area and practicing outdoor activities.
Never touch or feed wild animals.
Keep pets on a leash to avoid contact with rodents.
Use insect repellent on socks and clothing to prevent flea bites.
Keep fleas away from your pets by applying flea control products year-round.
The plague exists in our rural areas, but the risk remains extremely low. Continue to enjoy our great outdoors (and let me know about your great campsites!) and take simple precautions to stay healthy.
I will monitor the situation overseas and provide relevant updates.
I recently joined a Stanford forum on trust and safety in the use of AI in healthcare, and came away keenly aware that the rapid evolution and adoption of AI is in part a matter of public health. As we seek to determine where the public health voice fits into this conversation, I’d like to know what you think are some of the most pressing concerns. Please put others in the comments.
This is your summary of this week! Remember, your up-to-date Covid-19 and flu vaccines can now be found in pharmacies and clinics.
Love,
Mast
Dr. Matt Willis is the author of Your Local Epidemiologist in California. A California native, he served as a primary care physician, CDC epidemiologist and public health officer for Marin County, where he guided the pandemic response. He lives in Marin with his family and their dogs, Teddy and Ramona.
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