By the time June 15 rolled around and San Francisco and the rest of California emerged from the prolonged pandemic lockdown, Peter Johnston was fully vaccinated and ready to have one of the best summers of his life.
He hit bars and clubs in the Castro every Friday and Saturday, and a few weeknights in between. He rented a house in Carmel with some friends, then took a trip up to Guerneville with another group. “It was definitely a Roaring Twenties kind of thing,” said Johnston, 29, who said he found himself relating to the celebrations that followed the end of the 1918-19 pandemic and World War I.
But the party came to an abrupt halt two weeks ago, when Johnston woke up one Monday feeling ill. He developed a bad cough, then fever and chills and body aches. He tested positive for the coronavirus a week later.
“I would definitely say I thought the pandemic was over, or at least firmly in the rear view mirror,” Johnston said from his home in the Castro, where he’s still recuperating. “I knew there was a possibility of getting COVID after being vaccinated, but I didn’t think it would happen to me.”
Evidence is growing that post-vaccination breakthrough cases like Johnston’s are not as rare as once previously thought, or perhaps hoped for. And the culprit appears to be the highly infectious delta variant that’s now dominating San Francisco and pretty much everywhere else in the United States.
To be clear: The vaccines are holding up when it comes to preventing the most dire outcomes, in particular hospitalization, intensive care requiring ventilation, and death. They’re also still very good at preventing infection. Vaccines remain the best protection against COVID-19 and are key to ending the pandemic.
Peter Johnston, who lives in San Francisco’s Castro district, became infected with the delta variant after being fully vaccinated for COVID-19. “I knew there was a possibility of getting COVID after being vaccinated, but I didn’t think it would happen to me.”
Nick Otto/Special to The ChronicleBut delta is proving to be the first variant to test the strength of the vaccines, especially when it comes to stopping transmission. And that, in turn, has led to disheartening setbacks in the public health response as cases rise faster now than at any other time in the pandemic and health officials consider new mask mandates and other measures to stop the spread of disease.
“It is COVID on steroids. In many ways this is a different virus than the virus we were dealing with earlier this year,” said Dr. Grant Colfax, director of the San Francisco Department of Public Health, in a news briefing on Friday during which he implored people who are not vaccinated to get the shots now.
Experts in vaccines and immunology say the breakthrough infections, though disappointing, are not unexpected and do not mean the COVID vaccines are failing. Indeed, studies of post-vaccination cases, and better data on why they may be happening, underscore that the vaccine-induced immune response is robust and multilayered.
Mounting evidence suggests that delta is so easily transmissible in large part because it replicates much faster than previous variants and exposes people to a much higher viral load.
That larger viral dose may be overwhelming the first-strike antibody response in vaccinated people, who were better able to shake off earlier variants and remain symptom-free. It may also mean that they are infectious and able to spread the virus to others, perhaps as easily as those who are not vaccinated — an especially discouraging finding, health experts said.
But antibodies aren’t the only tool of the immune system to fend off the coronavirus. And so far it appears that the next-level response — namely the T cells and B cells that wipe out a virus that’s able to evade antibodies — is doing its job well and preventing severe illness.
“The vaccines have maintained full protection against severe and critical illness, even with delta,” said Dr. Catherine Blish, an infectious disease expert at Stanford. “Most of these (post-vaccination) cases we’re seeing are mild or sometimes moderate illness, and that means the vaccine is giving people a head start in clearing the virus but it’s not quite enough to prevent the infection in the first place. But at least it’s keeping them out of the hospital.”
When the vaccines initially were rolled out, although health experts noted that breakthrough infections would happen, the understanding was that they would be rare, and in most cases cause asymptomatic or very mild illness. And that seemed to hold up for awhile, as vaccination rates skyrocketed in the spring and cases plummeted. At the time, two variants were dominating California, both of them more infectious than the original strain of virus — but each, it’s now believed, half as infectious as delta.
In the delta phase of the pandemic, breakthrough infections remain uncommon, but they’re hardly rare. UCSF has reported 140 coronavirus cases among its staff of 35,000 since mid June — and 80% of those infections were among full vaccinated people. Similar scenarios have played out across the country, including at a homeless shelter in Santa Rosa.
Friday’s report from the Centers for Disease Control and Prevention focused on 469 cases associated with gatherings in one Massachusetts county; about three-quarters of the cases were in fully vaccinated people, and 79% of them had symptomatic illness. Especially concerning to health experts: The viral load was about the same between those who were vaccinated and those who were not, suggesting they may be equally able to spread the virus to others.
That report, along with other evidence worldwide, prompted the CDC to recommend even vaccinated people start wearing masks again.
“This does not bode well for the concept of herd immunity in the face of delta,” said Nadia Roan, an investigator at the Gladstone Institutes in San Francisco, about the CDC report. She said it’s possible that the vaccinated people may be carrying “dead” virus that isn’t able to infect others — which wouldn’t necessarily be apparent in the type of testing the CDC did. “Nonetheless, these data are concerning,” she said.
Scientists are still figuring out how much more infectious delta is, and why. Dr. Charles Chiu, who runs the UCSF-Abbott Viral Diagnostics and Discovery Center, said delta has several mutations that were already associated with increased infectiousness and resistance to vaccines — including the L452R mutation found in the so-called California variant that Chiu discovered in January.
“It’s like a super L452R because of the way it’s developed,” Chiu said. “It’s probably the combination of these mutations that’s conferring all these advantages on delta.”
Its primary advantages seem to be a fast replication cycle — how quickly it can take over cells and establish an infection — and the high viral payload it delivers on exposure. People are infectious over a longer period of time with delta than with other variants, and they have much more virus in their nose and the rest of their upper respiratory tract.
A preprint paper published last week by scientists at Helix — a San Carlos genomic sequencing company that has done coronavirus testing across the U.S. — found evidence that the viral load with delta may be three times higher than with alpha. Another study out of China found a thousand-fold increase in viral load with delta compared to the original strain of the coronavirus.
“The threefold difference in our data — that’s probably big enough that even if you are fully vaccinated, if you get infected you’re maybe not getting seriously ill, but you might still be transmitting to someone else,” said William Lee, vice president for science at Helix.
The COVID vaccines induce a large antibody response — in fact, far more than what’s needed to fend off infection from the original coronavirus strain and most of the variants. But antibodies wane, often within a few months of vaccination. Studies out of Israel have shown a drop in vaccine efficacy within six to 10 months, though some experts question that data.
The delta variant is probably able to overcome the antibody response to some degree. That’s why even vaccinated people may get infected and have mild to moderate illness. But vaccines also induce a cellular response, which takes longer to rally than antibodies but is more powerful. That response is probably what keeps the infection from spreading beyond the upper respiratory tract and into the lungs in vaccinated people.
“The vaccine, even if it can’t prevent every cell from getting infected, it can prevent the virus from getting deep and causing disease,” Blish said.
Johnston, who’s been battling symptoms of COVID for nearly two weeks, said this is the worst he’s felt since a bout of pneumonia when he was 13. But “I’m extremely grateful I had the vaccine, because I figure if I hadn’t, I’d be in the hospital right now,” he said.
“Overall I’m a very healthy person. I wasn’t really expecting to have a rough time with COVID were I to get it,” Johnston said. Two fully vaccinated friends he was with on the night he thinks he became infected also tested positive, but their symptoms were much milder, he said.
Johnston was so eager to get vaccinated that he drove four hours to Tulare County for his first shot in April, back when demand still far exceeded supply. Getting sick, even with a fairly troublesome illness, has made him more pro-vaccination.
“I’ve had some frustration, some anger, especially over the not-great uptake of vaccinations,” he said. “Vaccination is for the public good. Most of the benefit flows to other people and not yourself. But I guess In order to get people vaccinated, you basically have to mandate it.”
San Francisco Chronicle staff writers Catherine Ho and Danielle Echeverria contributed to this report.
Erin Allday is a San Francisco Chronicle staff writer. Email: eallday@sfchronicle.com Twitter: @erinallday
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