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Increase of coronavirus variants in Mission District, according to UCSF study

Increase of coronavirus variants in Mission District, according to UCSF study

The latest study, conducted in late January by UCSF researchers and collaborators, found that 53 percent of positive samples at the 24th BART Plaza “rapid test and response” site have been that of a coronavirus variant, L452R, most recently coined by some as the “California variant.” 

On Monday, Feb.22, Unidos en Salud researchers and the Latino Task Force shared the study with local community-based organizers during a webconference. 

“That is a significant increase from November when our sequencing indicated that this variant comprised only 16 percent of the positive tests,” said Diane Havlir, MD, UCSF infectious disease expert and professor of medicine, co-founder of the Unidos en Salud initiative.

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Between Jan. 10-29, the 24th Street site tested 8,798 people; 6,421 were from the Latinx population. Of the total people tested, 883 resulted positive for coronavirus. 630 positive samples were then sequenced, and 53 percent were of a new variant.

San Francisco residents receive their COVID-19 vaccinations on Feb. 3 at a neighborhood vaccination center located on the corner of 24th St and Capp St in the Mission. In partnership with UCSF, The Latino Task Force organized accessible COVID-19 testing and vaccination centers for San Francisco residents. Photo: Benjamin Fanjoy

The collaboration with the Mission District community has proven to be a vital scientific resource in studies for understanding how “aggressive” a virus might be.

Similar to research found in other cities and counties throughout California and the U.S., genome sequencing has shown an increased prevalence of a coronavirus lineage characterized by the L452R substitution and two other mutations in the virus’s spike protein. Such mutations have begun to raise concerns surrounding the “aggressive” potential of new variants.

“When we see mutations in the protein cell, we instantly want to know: does that make the virus better at getting into cells or does it not matter…is it random or something biological,” said Joe DeRisi, PhD and Chan Zuckerberg Biohub co-president.

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Using household information data, researchers can calculate a key epidemiological parameter that is called a “secondary household attack rate,” which measures, for those who are infected, the proportion of household members who also get sick. 


By asking key questions, researchers are able to monitor the “attack rate” in San Francisco households, and data shows “modestly higher” numbers compared to other California counties and globally. This supports the notion that the new variants found might have a slight advantage in spreading. 

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The collaboration with the Mission District community has proven to be a vital scientific resource in studies for understanding how “aggressive” a virus might be. With just the one site at 24th Mission BART Plaza, researchers are able to sample from over eight Bay Area counties.

“The beauty of having community participation/collaboration, like we have here with LTF and the City, is that we’re able to ask deeper questions,” said DeRisi. 

Viviana Pacho receives a free COVID-19 test provided by Unidos en Salud and the Latino Task Force. Photo: Benjamin Fanjoy


DeRisi was quick to note that, at this time, researchers did not detect any variants that share the same key mutations of those more aggressive forms found in South Africa and the United Kingdom; not to say that those variants aren’t here, but if so, they are at a lower frequency not detected by researchers.


“The Latinx community continues to be disproportionately impacted by COVID-19 and the uptick of the L452R variant among our community is concerning,” said Jon Jacobo, health committee chair with the Latino Task Force. “Unidos en Salud is an important partnership to help track and contain the virus. It’s a model that I believe should be adapted in communities across the country.”

Encouraging data revealed by researchers during the same web conference, showed that 86 percent of surveyed people tested at the site desired to get vaccinated. 


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