Alongside the optimism of decreasing case counts, the progression of vaccine rollouts, and the promise of a new administration, new Covid-19 variants emerging across the globe are creating what Grand Rounds moderator Dr. Bob Wachter called “a remarkable time.”
With many questions materializing about the efficacy of vaccines against variants and the increased pressure to administer vaccines quickly, Wachter brought on several speakers to address the city’s vaccine rollout, the local and national covid situation, and new covid variants. He topped off the briefing with a look at how the United Kingdom is dealing with its surge.
San Francisco’s plan
SF Department of Public Health Acting Health Officer Dr. Susan Philip began her overview by discussing the biggest obstacle to vaccine rollout in the city: supply.
“The problem right now is supply, supply, supply. We don’t have adequate vaccine, and what we’re getting is very intermittent and erratic,” Philip said, noting that SFDPH has been working with healthcare partners to be ready to serve the public when the vaccine supply increases.
To achieve the city’s goal of vaccinating 10,000 people per day (San Franciscans and those who work in the city), SFDPH has three strategies once supplies are available: creating high volume vaccination sites, working with existing clinical sites, and using commercial pharmacy partners. The goal is to create a central point with registration and scheduling that is “agnostic” — meaning that, regardless of their primary-care provider, anyone can access a vaccination site once they meet eligibility criteria.
Already the city has launched a site at the City College of San Francisco where UCSF Health is vaccinating residents. Philip said the site has “gone very well, so far” and that new sites are planned for the Moscone Center and the produce market in Bayview because they are in parts of the city heavily hit by the pandemic.
Philip also promised that city agencies are working to offer vaccinations at “culturally and geographically appropriate and accessible sites with our city support.”
Philip added that California is slated to receive a 15 percent boost of Moderna vaccines in the next few weeks.
SFDPH launched a dashboard to track vaccine rollout, viewable here.
Regional and National Updates
Next up was UCSF Epidemiology and Biostatistics professor Dr. George Rutherford, whose updates on Grand Rounds are so popular that as Rutehrford came on, Wachter brandished a t-shirt with Rutherford’s face on it and the words “In George we trust.”
Cases continue to grow worldwide, though “you may be seeing a kind of an end of this wave,” Rutherford said. As of Jan. 24, there were almost 100 million cases worldwide with the U.S. leading the pack at an average of 160,000 cases per day.
However, both nationally and statewide, we are on the “downslope of this third wave,” Rutherford said. The statewide case rate has fallen by 33 percent and hospitalizations have fallen by 22 percent over the last week. Deaths have not started to decrease yet, as they typically lag three weeks behind; right now, they’re up 14 percent.
Most of the new activity in California is being driven by Southern California, and Los Angeles in particular, where 20 percent of the population has been infected.
Moving on to vaccines, Rutherford highlighted three vaccines that will likely be authorized by this summer: Astrazeneca, novavax, and Johnson & Johnson, which could have data available as early as the end of January.
Rutherford also presented vaccine efficacy data for single-dose vaccinations from the Moderna FDA filing to answer the question of efficacy after a single dose. After following a group that was not randomly sampled for a median of 28 days, protection went from 80.2 percent immediately after the dose, to 50.8 percent in the first two weeks following the vaccination, and back up to 92.1 percent from days 15 to 28 post-initial vaccination. The results only include data for up to 28 days after the initial dose of the vaccine.
Rutherford said that the state’s partial reopenings were “probably” the right call, stating that “you could let your foot off the brake a little bit, but understanding you’re going from a statewide stay-at-home order — except for the northern tier of counties — to up to the purple tier, which is almost as restrictive.”
Investigating new variants
Dr. Shane Crotty, professor at La Jolla Institute for Immunology’s Center for Infectious Diseases and Vaccine Research, provided some relief when he noted that the UK covid variant “is unlikely to be a concern for covid vaccines,” and that “the vaccines will still almost certainly protect from serious cases of Covid-19” caused by the South African and Brazilian variants.
However, he said, because “there’s some immunological reasons for concerns, it would be wise to develop updated vaccines that could better recognize these particular variants that are sort of different than what’s been seen in the past.” Modern and Pfizer have announced they are going to do exactly that.
Crotty discussed two studies of the South African variant that observed “more dramatic effects of mutations,” with half of the subjects experiencing undetectable neutralization. Two of the mutants have also improved the binding affinity of the viral spike to the ACE2 receptor, making these variants, like the UK variant, more infectious.
However, Crotty noted that immune responses are more than just antibodies, and that “your immune system has a lot of weapons, not just antibodies. There are memory B cells, but also two kinds of T cells. And all of these can work together for infections,” even if the virus is able to get past antibodies.
The UK variant and response
Sir Patrick Vallance, chief scientific adviser for the UK government, had much to share about the UK variant. The country is in the midst of a lockdown to slow rates (which, he noted, is working) and has vaccinated “well over” 10 percent of its population with a first dose. The country began a large sequencing effort last April to look at the origins and lineages of the virus and hopes to be sequencing 20,000 samples per week by the end of February.
These sequencing efforts have proven fruitful following a fast-moving outbreak the government observed near London in December, even as rates elsewhere were shrinking. Taking a closer look, scientists realized that a variant they had observed early on was the reason for the increased spread.
Today, this new variant makes up 75 percent of cases and can be detected in routine PCR testing. It is 30 to 70 percent more transmissible, but scientists are not sure why. Vallance said that, last week, hints emerged indicating increased mortality as well as severity, but noted that antibodies in the body from previous infection, monoclonal antibodies produced in labs, and antibodies produced in response to the vaccinate should fight off the virus.
Vallance believes there is no reason to change individual behavior regarding the increased efficacy of spread (i.e. wearing two masks or increasing physical distancing to nine feet), because these rules are based on droplet properties, not virus properties. However, he still emphasized the importance of not relaxing too much because of vaccines.
“Until you get to very high vaccination rates, of course, the rest of the population still remains vulnerable, and quite a big wave of infection could recur,” he said.
The UK has taken aggressive measures to get first doses out to individuals by pushing back second doses, a position Wachter advocated for but Crotty noted uncertainty around, both in terms of efficacy and the potential for increased vaccine hesitancy. Rutherford said a preferential single-dose strategy could be useful to stop transmission in areas where variants are occurring.
For his final question, Wachter asked the panelists if they were feeling pessimistic or hopeful about the state of things. Despite the difficulties posed by new variants, all three — even the Brit — were optimistic.
See our previous Grand Rounds coverage here.
Other counties like Santa Clara seem able to get the largest percentages of doses sent directly to them rather than health care providers. They have a great dashboard. In SF, the majority of the doses are not going to DPH. What is Santa Clara County doing the SF could learn from?