Uncommon test solved a Mission medical mystery
Metagenomic sequencing can be a cutting edge strategy to diagnose patients
Annika Hom | March 6, 2023 for Mission Local
A mystery disease wound its way through the Mission this January, wreaking runny noses and headaches upon its victims. But when doctors had patients test for likely diseases — Covid-19, flu, respiratory syncytial virus (RSV) — results turned up negative for all three.
What was ailing them? Chan Zuckerberg Biohub scientists used metagenomic sequencing to find out.
“It’s hard to guess, right? There’s a lot of things it could be,” said Genay Pilarowski, a scientist with Chan Zuckerberg Biohub. “That’s where metagenomics come into play. You don’t have to know what you’re looking for to find it, which is unique.”
The results revealed that 44 percent of the patients had a form of rhinovirus, the untreatable source of the common cold, and 44 percent had seasonal coronavirus, which is endemic and generally more mild than Covid-19, according to the U.S. Centers for Disease Control and Prevention. About 7 percent had adenovirus, which can cause sore throats or bronchitis; 5 percent had metapneumovirus, a common respiratory virus like a common cold.
Gov. Gavin Newsom updates state’s Covid-19 strategy from the Mission
Press conference highlighted Unidos en Salud collaboration, the imperative of equity, community partnerships, and boosters for the holidays
Anlan Cheney | November 22, 2021 for Mission Local
Gov. Gavin Newsom arrived at the corner of 24th and Capp streets Monday morning to prioritize boosters and celebrate community-based partnerships.
The spot was chosen with purpose: the Mission-grown collaboration with the University of California, San Francisco, and the Latino Task Force, known as Unidos en Salud/United in Health, has become a model for testing, vaccination and resource sites guided by science and community service.
“I had the privilege of being all over the state of California, visiting sites large and small, and you know when sites are distinctive with their excellence,” said Newsom. “This is one of those sites doing the important work that we’re here to promote.”
Community-Based Strategy Succeeds in Vaccinating Latinx San Franciscans
Newly Vaccinated People Become Ambassadors to Overcome Hesitancy of Friends and Family
Laura Kurtzman | September 21, 2021
A community-based effort to overcome vaccine hesitancy designed by UC San Francisco scientists working together with San Francisco’s Latino Task Force is succeeding in the Mission District of San Francisco, where many Latinx people live and work.
The Unidos en Salud/San Francisco Department of Public Health neighborhood vaccination and testing site is housed in a collection of white tents pitched in a parking lot behind a McDonald’s. There, newly vaccinated people are learning how to spread the word among family and friends about the benefits of vaccination. They are coached to calm people’s fears of unpleasant or long-term side effects and counter the conspiracy theories they read online.
More than 90 percent said they reached out to at least one person, according to a study published Sept. 20, 2021, in PLOS, and almost 20 percent said they persuaded at least six other people to get vaccinated.
How Inequities Fueled the COVID-19 Pandemic – And What We Can Do About It
Partnerships Were One Key to the Health Response, Public Health Experts Say During Panel Discussion
Brandon R. Reynolds | March 22, 2021
An early UCSF partner was the Latino Task Force. Marquez said that UCSF brought testing and data collection, while the Task Force designed and led community outreach. “We have all learned to dance together,” said Jon Jacobo, the Task Forces’ Health Committee Chair. “At first there was a lot of stubbing of toes, but I think at this point, we can waltz, we can do some bachata, we can do a little bit of salsa, we can do it all.”
Jacobo said that community partnerships often start not with organizations meeting, but with individual health care workers reaching into communities with harm-reduction goals. “When you have those relationships, it allows the bridge of trust to be expanded a little bit,” he said. “Every time they’ve said they’re going to do A, B, and C, they deliver.”
COVID-19 Study Finds Increase of Coronavirus Variants in San Francisco’s Mission District
Laura Kurtzman | February 22, 2021
New results from an ongoing collaborative effort to slow the spread of COVID-19 in San Francisco’s Mission District, a predominantly Latinx community, shows that the prevalence of a coronavirus lineage, characterized by the L452R substitution and two other mutations in the virus’s spike protein, has significantly increased in recent months. This lineage has previously been detected in other U.S. locations, including California, and is now increasingly being found in multiple counties throughout 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 for COVID-19, and the San Francisco Department of Public Health, provides rapid, low-barrier, walk-up COVID-19 testing and response services to San Francisco’s Mission District community.
In January, Unidos en Salud conducted a COVID-19 study using the BinaxNOW rapid antigen test to collect and analyze positive results. A total of 8,846 people were tested as part of the month-long study. Genomic sequencing of the virus from over 630 positive samples was used to monitor for the emergence of new variants or introduction of new viral strains, providing an accurate view of which viruses are circulating in this community.
“The research findings indicate that the L452R variant represents 53 percent of the positive test samples collected between January 10th and the 27th. That is a significant increase from November when our sequencing indicated that this variant comprised only 16 percent of the positive tests,” said UCSF infectious disease expert Diane Havlir, MD, co-founder of the Unidos en Salud initiative and professor of medicine at UCSF.
UCSF Partnership with San Francisco Brings COVID-19 Vaccinations to the Mission District
Latino Task Force Collaboration Builds on Testing Sites Set up in the Community
Laura Kurtzman | February 2, 2021
When UC San Francisco researchers and their community partners in the Unidos en Salud collaboration asked people coming to their COVID-19 testing site in San Francisco’s Mission District if they wanted to be vaccinated, a whopping 86 percent said yes.
That is a higher number of people willing to be vaccinated than several national, statewide or even Bay Area surveys have shown – and a testament to the trust that UCSF’s Diane Havlir, MD, and colleagues have built over many months of working side by side with the Latino Task Force to help a community that has been hit especially hard by the coronavirus.
Now, with the help of the San Francisco Department of Public Health, Unidos en Salud is bringing vaccines to the people of the Mission District. With limited supply, the first doses are going to community health workers and those who are 65 years and up.
“The data are quite overwhelming in dispelling the myth that the entire Latinx community is vaccine hesitant,” said Havlir, a UCSF professor of medicine who collaborated with the leaders of the Latino Task Force to create Unidos en Salud, which provides rapid “test and respond” services at the BART plaza at 24th and Mission.
Latinx Low-Income Workers Hardest Hit by SF COVID-19 Surge
Nicholas Weiler | December 10, 2020
COVID-19 infections are once again rising at an alarming rate in San Francisco’s Latinx community, predominantly among low-income essential workers, according to results of a massive community-based testing blitz conducted before and after the Thanksgiving holiday by Unidos En Salud – a volunteer-led partnership between the Latino Task Force for COVID-19 (LTF), UC San Francisco, the Chan Zuckerberg Biohub (CZ Biohub), and the San Francisco Department of Public Health (SFDPH).
Unidos En Salud launched their “Healthy Holidays” initiative the weekend before Thanksgiving (Nov. 22-24) in San Francisco’s Mission District, where they have been perfecting their community-based surveillance testing and response program and solidifying relationships with community members through the LTF since April. The initiative then expanded testing after the holiday (Nov. 29-Dec. 1) to three additional highly impacted neighborhoods – the Bayview, Excelsior, and Tenderloin.
“Cases have been surging for weeks, and it was clear that the holiday season this year was going to present a high risk for accelerating the spread of the virus,” said UCSF infectious disease expert Diane Havlir, MD, co-Founder of the Unidos En Salud initiative, who presented initial findings to LTF community partners on December 7, 2020. “Rather than wait and see what would happen, UCSF and the Latino Task Force decided to respond proactively with a surge of our own, in partnership with DPH, focused on the communities where we knew the hammer was going to fall hardest.”
“As the region enters a renewed phase of lockdown, these results are a reminder the brunt of this disease is still being felt by Latinos and people without the economic privilege to easily shelter in place. Because existing disparities, it is often those with the least who are being hurt the most, people who are often working multiple jobs just to make rent and keep food on the table for themselves and family,” said LTF Health Committee Chair, Jon Jacobo, one of the initiative’s organizers. “If we truly want to turn this pandemic around, we need to fundamentally change how we are addressing the pandemic and how we are supporting the most vulnerable among us.”
Rapid COVID-19 Test Shows Promise in Community Test Setting
Test Can ID Infectious Individuals in 15 Minutes, Could Help Quell Continued High Transmission Among Mission Latinx Population
Nicholas Weiler | October 15, 2020
Preliminary data from a study by UC San Francisco and Chan Zuckerberg Biohub scientists suggests that new rapid COVID-19 tests now being distributed to public health departments nationwide could be a valuable tool to accelerate the COVID-19 public health response. The new tests — if used correctly and as a complement to existing gold-standard PCR testing — show promise for use in community settings to rapidly and affordably identify individuals with and without symptoms who are most likely to be actively infectious, individuals who should be the highest priority for isolation to prevent further transmission, the researchers say.
Since the beginning of the COVID-19 pandemic, governments, businesses, and healthcare providers have relied on PCR-based tests to identify people infected with the SARS-CoV-2 virus. These tests are highly sensitive, but are also expensive, require specialized equipment, and can take days to return results — often too slow for effective infection control.
Recently, so-called rapid tests — less sensitive than PCR but able to provide results in 15 to 30 minutes — have been emerging as a potential complement to PCR testing. On Aug. 27, the U.S. Department of Health and Human Services (HHS) announced that the Federal government had purchased 150 million BinaxNOW rapid COVID-19 tests, designed and manufactured by Abbott, and these are currently being sent to public health departments across the country to accelerate COVID-19 testing.
So far, these tests are only approved for clinical use by healthcare providers to diagnose people who are suspected of having COVID-19 and are within their first seven days since symptom onset. But the UCSF/Biohub researchers, who have been conducting community-based COVID-19 testing since April, set out to evaluate how the rapid tests perform in an open-air community testing environment. The researchers aimed to assess whether these tests are accurate enough to quickly identify individuals at highest priority for isolation.
“Our results suggest this test is likely to be a valuable addition to our arsenal in the fight against COVID-19. They are inexpensive and fast enough that we could test much more frequently to help stem the tide of infection in the locations and populations that need it the most,” said CZ Biohub Co-President Joe DeRisi, PhD, a professor in the Department of Biochemistry and Biophysics at UCSF, whose team led the analysis of the BinaxNOW tests at the CLIAhub, a joint UCSF/Biohub COVID diagnostic laboratory. “We are happy to be able to provide this data to our long-time partners at the California Department of Public Health to inform their deployment of the hundreds of thousands of test kits currently being supplied by HHS.”
COVID-19 Testing at Transit Hub Finds Ongoing High Transmission in Latinx Essential Workers
Study Highlights Urgent Need for Access to Rapid Testing to Shorten Delays Between Infection, Test Results and Isolation, Researchers Say
Nicholas Weiler | September 2, 2020
Low-income Latinx essential workers affected by San Francisco’s housing crunch continue to be disproportionately impacted by COVID-19, according to data from a three-week testing initiative conducted in San Francisco’s Mission District at the beginning of August.
The initiative was led by Unidos En Salud, a collaboration between UC San Francisco and the Latino Task Force on COVID-19. In an April study. Unidos En Salud identified the outsized exposure risk facing Latinx essential workers and their families in the Mission, driven in part by inequalities in economic and housing security. Their new study shows continued unmet demand for access to testing and the value of locating low-barrier testing at a central transit hub – believed to be the first such program in the nation.
The initiative tested 2,622 people at the busy 24th Street Mission BART Plaza in six half-day sessions – at an average rate of 100 tests per hour. Overall, 9 percent (235) of the PCR-based tests came back positive for SARS-CoV-2 infection, with a test positivity rate of 11 percent among Latinx participants. San Francisco’s overall test positivity rate is currently 2.61 percent, according to the Department of Public Health. The vast majority of those who tested positive at the transit hub site are Latinx (93 percent), speak Spanish as their preferred language (85 percent), earn incomes of less than 50,000 a year (87 percent), and live in high-density households (79 percent). People from across the Bay Area were tested at the plaza, but most positive results were seen in residents of the Mission or southeast San Francisco.
Analysis of the amount of virus being shed by individuals who tested positive – conducted by collaborators at the Chan Zuckerberg Biohub – showed that about half (48 percent) had the high levels of virus indicative of the most infectious stage of the disease. However, virtually all reported regularly wearing a mask when in public (98 percent) and using hand sanitizer (92 percent).
Transit-Based COVID-19 Monitoring Pilot Launched in Mission District
‘Low-Barrier’ Model for State-Wide Disease Monitoring in Vulnerable Populations to be Tested at Mission District Hub
Nicholas Weiler | July 28, 2020
In San Francisco’s Mission District, UC San Francisco infectious disease specialists and community partners are launching what is believed to be a first-in-the-nation pilot program to provide low-barrier COVID-19 testing – free, simple, and convenient – at a central transit hub. The project aims to enhance the ability of San Francisco public health officials to detect and contain the spread of the disease among the heavily impacted Latinx community and essential workers in the Mission.
The project is led by Unidos En Salud – a collaboration between UCSF and the Latino Task Force on COVID-19 – in partnership with the San Francisco Bay Area Rapid Transit (BART) District, the office of San Francisco Supervisor Hillary Ronen, the San Francisco Department of Public Health (SFDPH), and the Chan Zuckerberg BioHub. Along with recent initiatives to provide testing in the town of Bolinas and for housed and unhoused people in the Bayview, Sunnydale and Visitacion Valley neighborhoods in southeast San Francisco, the collaboration is part of UCSF’s tightly coordinated work with the City and County of San Francisco, the state of California, and affected communities to respond to the public health crisis presented by COVID-19.
In a late April study, Unidos En Salud identified the outsized exposure risk facing Latinx essential workers and their families in the Mission, driven in part by inequalities in economic and housing security. Despite San Francisco’s efforts to provide free testing to all essential workers, this same high-risk population continues to experience significant barriers to testing, including inability to take time off work to get tested, lack of access to medical systems, and fear of potential consequences of a positive test, including the need to go into isolation, potentially putting income and job security at risk.
“In order to reduce community transmission of COVID-19 to a level where we can start opening up society again, there is an urgent need to deploy testing to persons most at-risk for infection,” said Diane Havlir, MD, chief of the UCSF Division of HIV, Infectious Diseases and Global Medicine and director of Ward 86 at Zuckerberg San Francisco General Hospital and Trauma Center (ZSFG). “With the idea that public transit is heavily utilized by frontline workers, we’ve partnered with BART to test the feasibility of setting up disease monitoring at a central transit hub in the Mission. If successful, we hope that this can become a model for low-barrier disease monitoring for Latinx and other at-risk communities across California.”
Inequality Fueled COVID-19 Transmission in San Francisco’s Mission District, Says New Study
Test Results Show Economic Factors Drove Increased Transmission in Latinx Essential Workers and Families Despite Shelter-in-Place
Nicholas Weiler | June 18, 2020
In the first six weeks of San Francisco’s shelter-in-place ordinance, continued spread of COVID-19 was increasingly concentrated among low-income Latinx people who were unable to work from home, according to results of a community-based screening initiative conducted in San Francisco’s Mission District in late April.
A report of the results, from both nasal swab (PCR) and serological (antibody) tests, has been submitted to a peer-reviewed journal, and was also posted publicly on the medRxiv preprint server on June 17, 2020, due to the results’ importance for public health policy and affected communities.
The testing initiative, called Unidos En Salud, was spearheaded by UC San Francisco infectious disease experts and community organizers from the Latino Task Force for COVID-19. Along with recent initiatives to provide testing in the town of Bolinas and for housed and unhoused people in the Bayview, Sunnydale and Visitacion Valley neighborhoods in southeast San Francisco, the collaboration is part of UCSF’s tightly coordinated work with the San Francisco Department of Public Health, the state of California, and affected communities to respond to the public health crisis presented by COVID-19.
In partnership with the City and County of San Francisco, Unidos En Salud offered free PCR and antibody testing, regardless of symptoms, to all residents and workers in US census tract 229.01, a densely populated 16-square-block section of the Mission District, which has a large Latinx population. Including initial walk-up testing conducted April 25–28, and additional testing of home-bound residents in early May, the initiative ultimately reached 3,953 individuals.
UCSF Brings COVID-19 Testing to San Francisco’s Bayview, Sunnydale and Visitacion Valley
Tests to be Made Available to All Who ‘Live, Work, Play or Pray’ in Three City Neighborhoods Hard-Hit by Pandemic
Pete Farley | May 28, 2020
UC San Francisco epidemiologists and infectious disease specialists are partnering with several community organizations and the San Francisco Department of Public Health (SFDPH) to offer comprehensive, voluntary COVID-19 testing to residents of the Bayview, Sunnydale and Visitacion Valley, three medically underserved neighborhoods in the southeast region of the City with significant African-American, Pacific Islander, Chinese and Latinx populations.
The collaboration is the latest example of UCSF’s tightly coordinated work with the City and County of San Francisco, the state of California, and affected communities to respond to the public health crisis presented by COVID-19.
Under the banner “United in Health D10” (a reference to San Francisco’s Supervisory District 10, where the neighborhoods are located), testing for the Bayview will take place on May 30 and 31, 2020, from 9 a.m. to 5 p.m. at Havard Early Education School, 1520 Oakdale Ave; testing for Sunnydale and Visitacion Valley will take place June 1 and 2, 2020, from 9 a.m. to 7 p.m. at Herz Playground, 1701 Visitacion Ave.
Initial Results of Mission District COVID-19 Testing Announced
Latinx Community, Men and Economically Vulnerable Are at Highest Risk
Elizabeth Fernandez and Nicholas Weiler | May 4, 2020
Of nearly 3,000 residents and workers in a Mission District census tract who were tested in late April for active infection with the novel coronavirus, 62 individuals (2.1 percent) have tested positive, according to initial results of the community-led screening project, called Unidos En Salud.
Overall, 1.4 percent of the participants who lived in the eligible area tested positive for COVID-19. More than half of those who tested positive (53 percent) reported experiencing no symptoms of COVID-19. Three quarters were men and an overwhelming number (95 percent) were Hispanic or Latinx. The majority of those who tested positive (82 percent) reported having been financially affected by economic fallout of the pandemic and only 10 percent reported being able to work from home.
The testing was conducted by Unidos En Salud, a unique partnership between Mission community organizers in the Latino Task Force for COVID-19, UC San Francisco researchers, the City and County of San Francisco, and the San Francisco Department of Public Health (DPH), which have come together to inform and mobilize a population that was not being reached by current testing and care systems.