COVID-19 Examine Finds Improve of Coronavirus Variants in San Francisco’s Mission District 

Mission district residents will be swabbed for COVID-19 at a pop-up test site in front of the 24th Bart Station Mission in early December. Continued testing in this area shows that a new variant is much more widespread. Photo by Mike Kai Chen

New results from an ongoing collaboration to slow the spread of COVID-19 in the Mission District of San Francisco, a predominantly Latin American community, show that the prevalence of a line of coronavirus caused by the L452R substitution and two other mutations in the spike protein of the Virus has increased significantly in recent months. This line was previously discovered in other locations in the United States, including California, and is now increasingly being found in several counties across California.

Unidos en Salud, a volunteer-led collaboration between UC San Francisco, the nonprofit Chan Zuckerberg Biohub (CZ Biohub), the Chan Zuckerberg Initiative, the Latino Task Force on COVID-19, and the San Francisco Department of Health, offers fast walk-in COVID 19 low barrier test and response services for the Mission District community in San Francisco.

In January, Unidos en Salud carried out a COVID-19 study using the BinaxNOW rapid antigen test to collect and analyze positive results. A total of 8,846 people were tested in the one-month study. Genomic sequencing of the virus from over 630 positive samples has been used to monitor the appearance of new variants or the introduction of new virus strains and to get an accurate view of which viruses are circulating in this community.

“Research shows that the L452R variant represented 53 percent of the positive test samples collected between January 10 and January 27. This is a significant increase from November, when our sequencing revealed that this variant only comprised 16 percent of positive tests, ”said Dr. Diane Havlir, co-founder of the Unidos en Salud initiative and professor of medicine at UCSF.

With the help of the Mission District Community, staff were also able to investigate key questions about household transmission, symptoms, and infections in children. According to the research, the L452R variant has an increased rate of secondary attack in the household (the obvious intra-household transmission), suggesting that it is more transmissible than other strains.

“The study shows that the secondary attack rate of the L452R variant identified in the mission district in the household appears to be higher than other rates measured in the US and worldwide. However, more work needs to be done to confirm these results. There is an urgent need for research to better understand the implications for portability and continued genome sequencing and monitoring to understand the prevalence, range and distribution of the variants, ”said Joe DeRisi, Co-President of CZ Biohub, PhD.

The study also identified a case of P.2 – a variant line containing the spike E484K mutation that was first identified in Brazil in a person who was re-infected with the virus – although contact tracing suggests this Variant was not forwarded. Other variants associated with the spike protein were also identified by the study, confirming the need for ongoing surveillance to understand and track its spread, as well as laboratory experiments to understand its significance.

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

Outside of Mission District collaboration, efforts are being made to track variants of the virus nationwide in California. The California COVID Tracker, a joint initiative of the Chan Zuckerberg Initiative, CZ Biohub, and the US state of California, has since provided free sequencing and analysis of the SARS-CoV-2 virus for the entire genome to all California health departments and local health authorities Provided July 2020 to allow officials to better map the virus. To date, that partnership has performed approximately 45 percent of all sequencing in California and 5 percent of the country’s sequencing effort.

Unidos en Salud recently announced a partnership with the San Francisco Department of Health to bring vaccines to the people in the mission district. The efforts of the Latino Task Force in the mission district are backed by the Chan Zuckerberg Initiative and aim to strengthen resources in a community hard hit by the spread of COVID-19.

About UCSF: The University of California at San Francisco (UCSF) is entirely focused on health sciences and is dedicated to promoting health worldwide through advanced biomedical research, higher education in life sciences and health professions, and excellent patient care. UCSF Health, which serves as the UCSF’s primary academic medical center, comprises world-class specialty hospitals and other clinical programs and has offices across the Bay Area. Find out more at ucsf.edu or read our fact sheet.

About CZ Biohub: The Chan Zuckerberg Biohub is a not-for-profit research center bringing together doctors, scientists, and engineers from Stanford University, UC San Francisco, and UC Berkeley. CZ Biohub seeks to understand the underlying mechanisms of the disease and develop new technologies that lead to actionable diagnoses and effective therapies. His ultimate vision is to cure, prevent, or treat all diseases by the end of the century. To learn more, visit CZBiohub.org.