The variant in November testing on the left and in January testing on the right as it appeared more often in sequencing. Source: Chan Zuckerberg BioHub. Presented to the Latino Task Force.

A Covid-19 variant increasingly found in other parts of California has grown more prevalent in San Francisco households, UCSF researchers and the Latino Task Force announced today. 

The variant, known as L452R, showed up in 53 percent of the positive samples collected at the 24th Street BART Plaza between Jan. 10 and 27. That compares to 16 percent during the November testing, according to Dr. Diane Havlir, co-founder of the Unidos en Salud initiative and chief of UCSF’s Division of HIV/AIDS, Infectious Disease, and Global Medicine.

While sequencing is the kind of drill-down data generally reported in research papers, the report on Monday was also indicative of the close relationship that Havlir and other UCSF researchers have established with the Latino Task Force. That collaboration — known as Unidos en Salud — means the community is treated as an equal partner, privy to research as it happens because it is also helping with that research.  

The Monday morning conference call with more than a dozen community leaders offered a window into how the community can inform the science. 

Indeed, Dr. Joe DeRisi, co-president of the Chan Zuckerberg BioHub, which sequenced the samples from the 24th Street BART Plaza, said that discovering how the L452R variant operated in households was only possible because of the community collaboration that allowed them to see the impact on households. 

“It’s actually hard to answer the question (of which variant is important) without having a community-based study like the one we have now,” DeRisi said. 

DeRisi, whose lab at the Chan Zuckerberg Biohub is doing 45 percent of the state’s sequencing, said that most samples come decoupled from households, but with the Mission study’s extension into household testing and checking up on positive residents, they can tell when a variant appears in the same household.  

The January campaign tested 8,846 people, and DeRisi sequenced the virus from more than 630 positive samples. The household infection rate showed that the L452R variant was slightly more transmissible within a household than other strains. That means he and others will be watching it closely here and in other counties where it is appearing. 

Measuring how aggressive the variant was in households followed by Unidos en Salud.

The 24th Street BART site, he said, has ended up being particularly effective because its walk-up ease and location near BART attracts vulnerable residents from across the Bay Area. 

A scattershot of where people come from to test at the 24th Street BART Plaza.

DeRisi also had some good news on Monday’s call to the community. Neither the U.K. nor the South African variant showed up in the January samples. They did identify one case of P.2., the Brazilian variant, but because rapid tests enable quick turn-around, they were also able to trace and test the individual’s contacts to determine no further transmission. 

Havlir also updated the community on the Capp Street vaccination site that opened on Feb 1. It has vaccinated 1,601 people — 60 percent Latinx. Havlir hopes for more than the 120 doses a day the site has been getting, but regardless, the team there has pivoted to act as a navigation site. 

Results from the Capp Street vaccination site.

Team members either help residents make an appointment for Capp Street, shuttle a person to nearby ZSFGH for a vaccination, or make an appointment at one of the city’s other sites.

Already, it has managed long lines that formed on Capp Street the day it opened, and it will be tested again on Wednesday as the city opens up vaccinations to new groups, including teachers and frontline workers. True to its mission to get the most vulnerable vaccinated and tested, the Unidos outreach team spent Friday and Saturday educating local residents on the expansion.

An expansion of testing on Feb 24.

Updates like the one on Monday allow researchers to dig into the science with the community, but also for community leaders to announce new initiatives. Susana Rojas, who has been key in the Wellness Teams and outreach efforts announced a new education campaign on Monday that will illustrate how vaccinations help build community immunity.

Lydia Chávez

I’ve been a Mission resident since 1998 and a professor emeritus at Berkeley’s J-school since 2019 when I retired. I got my start in newspapers at the Albuquerque Tribune in the city where I was born...

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4 Comments

  1. It seems like since coronavirus is the same family of viruses as the common cold we’ve got excellent opportunities to learn more about that disease we all take for granted. Doesn’t anymore find this lack of curiosity bizarre? It’s Twilight Zone. And all the coronavirus discoveries we keep making months after they were reported in EU and Chinese press. We can’t believe them? We can’t learn from other nations? Folks preaching against Trump’s ‘America First’ were still practicing it in their everyday lives- even though that policy has put us last.

    1. @RJ

      Most common colds are caused by rhinovirus, which is a different class than coronaviruses. Only about 15% of colds are from coronaviruses. Colds are soley upper respiratory infections, while SARS-CoV-2 (Covid-19) also goes into the lungs. And they have studied similar viruses, such as SARS and MERS.

  2. Thank you Lydia.

    Dr. Jonathan Fuchs, M.D., M.P.H. (SFDPH) Testing/Vaccination Tsar indicated last week that City would collect and analyze San Francisco sewage for earliest detection of emerging variants. UC Berkeley and Standford are currently sampling sewage as per Dr. Fuchs (Jonathan. fuchs@ sfdph. org).

    Fondly,

    RJ Sloan

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