*** The County of Santa Clara Public Health Department discontinued updates to the COVID-19 data tables effective June 30, 2025. The COVID-19 data tables will be removed from the Open Data Portal on December 30, 2025. For current information on COVID-19 in Santa Clara County, please visit the Respiratory Virus Dashboard [sccphd.org/respiratoryvirusdata]. For any questions, please contact phinternet@phd.sccgov.org ***

The datset summarizes counts and rates of cumulative COVID-19 cases by zip codes in Santa Clara County. Source: California Reportable Disease Information Exchange.

This dataset is updated every Thursday.

A. SUMMARY Medical provider confirmed COVID-19 cases and confirmed COVID-19 related deaths in San Francisco, CA aggregated by several different geographic areas and normalized by 2016-2020 American Community Survey (ACS) 5-year estimates for population data to calculate rate per 10,000 residents. On September 12, 2021, a new case definition of COVID-19 was introduced that includes criteria for enumerating new infections after previous probable or confirmed infections (also known as reinfections). A reinfection is defined as a confirmed positive PCR lab test more than 90 days after a positive PCR or antigen test. The first reinfection case was identified on December 7, 2021. Cases and deaths are both mapped to the residence of the individual, not to where they were infected or died. For example, if one was infected in San Francisco at work but lives in the East Bay, those are not counted as SF Cases or if one dies in Zuckerberg San Francisco General but is from another county, that is also not counted in this dataset. Dataset is cumulative and covers cases going back to 3/2/2020 when testing began. Geographic areas summarized are: 1. Analysis Neighborhoods 2. Census Tracts 3. Census Zip Code Tabulation Areas B. HOW THE DATASET IS CREATED Addresses from medical data are geocoded by the San Francisco Department of Public Health (SFDPH). Those addresses are spatially joined to the geographic areas. Counts are generated based on the number of address points that match each geographic area. The 2016-2020 American Community Survey (ACS) population estimates provided by the Census are used to create a rate which is equal to ([count] / [acs_population]) * 10000) representing the number of cases per 10,000 residents. C. UPDATE PROCESS Geographic analysis is scripted by SFDPH staff and synced to this dataset daily at 7:30 Pacific Time. D. HOW TO USE THIS DATASET San Francisco population estimates for geographic regions can be found in a view based on the San Francisco Population and Demographic Census dataset. These population estimates are from the 2016-2020 5-year American Community Survey (ACS). Privacy rules in effect To protect privacy, certain rules are in effect: 1. Case counts greater than 0 and less than 10 are dropped - these will be null (blank) values 2. Death counts greater than 0 and less than 10 are dropped - these will be null (blank) values 3. Cases and deaths dropped altogether for areas where acs_population < 1000 Rate suppression in effect where counts lower than 20 Rates are not calculated unless the case count is greater than or equal to 20. Rates are generally unstable at small numbers, so we avoid calculating them directly. We advise you to apply the same approach as this is best practice in epidemiology. A note on Census ZIP Code Tabulation Areas (ZCTAs) ZIP Code Tabulation Areas are special boundaries created by the U.S. Census based on ZIP Codes developed by the USPS. They are not, however, the same thing. ZCTAs are areal representations of routes. Read how the Census develops ZCTAs on their website. Row included for Citywide case counts, incidence rate, and deaths A single row is included that has the Citywide case counts and incidence rate. This can be used for comparisons. Citywide will capture all cases regardless of address quality. While some cases cannot be mapped to sub-areas like Census Tracts, ongo

Robustness check with marginal probabilities estimated from logit and probit models for respondents who were extremely worried about COVID-19 after versus before the San Francisco Bay Area shelter-in-place announcement 1.

On 6/28/2023, data on cases by vaccination status will be archived and will no longer update.

A. SUMMARY This dataset represents San Francisco COVID-19 positive confirmed cases by vaccination status over time, starting January 1, 2021. Cases are included on the date the positive test was collected (the specimen collection date). Cases are counted in three categories: (1) all cases; (2) unvaccinated cases; and (3) completed primary series cases.

1. All cases: Includes cases among all San Francisco residents regardless of vaccination status.

2. Unvaccinated cases: Cases are considered unvaccinated if their positive COVID-19 test was before receiving any vaccine. Cases that are not matched to a COVID-19 vaccination record are considered unvaccinated.

3. Completed primary series cases: Cases are considered completed primary series if their positive COVID-19 test was 14 days or more after they received their 2nd dose in a 2-dose COVID-19 series or the single dose of a 1-dose vaccine. These are also called “breakthrough cases.”

On September 12, 2021, a new case definition of COVID-19 was introduced that includes criteria for enumerating new infections after previous probable or confirmed infections (also known as reinfections). A reinfection is defined as a confirmed positive PCR lab test more than 90 days after a positive PCR or antigen test. The first reinfection case was identified on December 7, 2021.

Data is lagged by eight days, meaning the most recent specimen collection date included is eight days prior to today. All data updates daily as more information becomes available.

B. HOW THE DATASET IS CREATED Case information is based on confirmed positive laboratory tests reported to the City. The City then completes quality assurance and other data verification processes. Vaccination data comes from the California Immunization Registry (CAIR2). The California Department of Public Health runs CAIR2. Individual-level case and vaccination data are matched to identify cases by vaccination status in this dataset. Case records are matched to vaccine records using first name, last name, date of birth, phone number, and email address.

We include vaccination records from all nine Bay Area counties in order to improve matching rates. This allows us to identify breakthrough cases among people who moved to the City from other Bay Area counties after completing their vaccine series. Only cases among San Francisco residents are included.

C. UPDATE PROCESS Updates automatically at 08:00 AM Pacific Time each day.

D. HOW TO USE THIS DATASET Total San Francisco population estimates can be found in a view based on the San Francisco Population and Demographic Census dataset. These population estimates are from the 2016-2020 5-year American Community Survey (ACS). To identify total San Francisco population estimates, filter the view on “demographic_category_label” = “all ages”.

Population estimates by vaccination status are derived from our publicly reported vaccination counts, which can be found at COVID-19 Vaccinations Given to SF Residents Over Time.

The dataset includes new cases, 7-day average new cases, new case rates, 7-day average new case rates, percent of total cases, and 7-day average percent of total cases for each vaccination category.

New cases are the count of cases where the positive tests were collected on that specific specimen collection date. The 7-day rolling average shows the trend in new cases. The rolling average is calculated by averaging the new cases for a particular day with the prior 6 days.

New case rates are the count of new cases per 100,000 residents in each vaccination status group. The 7-day rolling average shows the trend in case rates. The rolling average is calculated by averaging the case rate for a part

Demographic characteristics for Bay Area and in the study population overall–N (%) 1.

Alternative characterization of DID groups for analysis of experienced difficulties after versus before the San Francisco Bay Area shelter-in-place announcement.

Changes in social distancing, difficulties, and concern after the shelter-in-place versus before in the Bay Area versus elsewhere in the U.S.

While most construction sites have been closed down in the greater San Francisco Bay Area, many construction works in Los Angeles County appear to be moving forward. Read More

*** The County of Santa Clara Public Health Department discontinued updates to the COVID-19 data tables effective June 30, 2025. The COVID-19 data tables will be removed from the Open Data Portal on December 30, 2025. For current information on COVID-19 in Santa Clara County, please visit the Respiratory Virus Dashboard [sccphd.org/respiratoryvirusdata]. For any questions, please contact phinternet@phd.sccgov.org ***

The dataset summarizes the average rate of COVID-19 tests completed by date among Santa Clara County residents by major healthcare systems in the county. The daily average rate of tests is the daily average number of tests completed over the past 7 days per 100,000 people served by the individual healthcare system. Each ‘test’ or ‘testing incident’ represents at least one specimen tested per person, per day. This does not represent the number of individuals tested, as some people are tested multiple times over time because of the risk of frequent exposure. Source: California Reportable Disease Information Exchange. Data notes: The State of California has defined an initial goal of at least 150 tests per day per 100,000 people. Bay Area County Health Officers set a goal of 200 tests per day per 100,000 people.

This table was updated for the last time on May 20, 2021.

*Authors contributed equally to the work

** Corresponding authors

Robustness check with marginal probabilities estimated from logit and probit models for respondents who were sheltering-in-place all of the time after versus before the San Francisco Bay Area shelter-in-place announcement 1.

Long COVID (LC) occurs after at least 10% of SARS-CoV-2 infections, yet its etiology remains poorly understood. We used “omic†assays and serology to deeply characterize the global and SARS-CoV-2-specific immunity in the blood of individuals with clear LC and non-LC clinical trajectories, 8 months post-infection. We found that LC individuals exhibited systemic inflammation and immune dysregulation. This was evidenced by global differences in T cell subset distribution implying ongoing immune responses, as well as by sex-specific perturbations in cytolytic subsets. LC individuals displayed increased frequencies of CD4+ T cells poised to migrate to inflamed tissues and exhausted SARS-CoV-2-specific CD8+ T cells, higher levels of SARS-CoV-2 antibodies and a mis-coordination between their SARS-CoV-2-specific T and B cell responses. Our analysis suggested an improper crosstalk between the cellular and humoral adaptive immunity in LC, which can lead to the immune dysregulation, inflammation a..., , , READ ME FILE

General Information

Title: Long COVID manifests with T cell dysregulation, inflammation, and an uncoordinated adaptive immune response to SARS-CoV-2

Contact:

Nadia Roan, PhD

Gladstone Institutes

University of California, San Francisco

Dates of collection:

12/23/21 -- 2/16/22

Information about geographic location of data collection:

San Francisco Bay Area

Key Words:

COVID-19, SARS-CoV-2, Long Covid, LC, CyTOF, T cells

Data and File Overview

Included are 172 FCS files total from 86 different CyTOF specimens total. Each file name begins with the de-identified patient ID (PID), followed by whether the individual was classified as LC or Recovered (R) individual. Next, the file name indicates CD4+ or CD8+ T cells were analyzed. Finally, the file name indicates "Atlas" for samples that were analyzed at baseline, and "resp" for responding cells that were identified after spike peptide stimulation. The table at the end of this ReadMe file includes addit...

Note: The cumulative case count for some counties (with small population) is higher than expected due to the inclusion of non-permanent residents in COVID-19 case counts.

Reporting of Aggregate Case and Death Count data was discontinued on May 11, 2023, with the expiration of the COVID-19 public health emergency declaration. Although these data will continue to be publicly available, this dataset will no longer be updated.

Aggregate Data Collection Process Since the beginning of the COVID-19 pandemic, data were reported through a robust process with the following steps:

• Aggregate county-level counts were obtained indirectly, via automated overnight web collection, or directly, via a data submission process.
• If more than one official county data source existed, CDC used a comprehensive data selection process comparing each official county data source to retrieve the highest case and death counts, unless otherwise specified by the state.
• A CDC data team reviewed counts for congruency prior to integration. CDC routinely compiled these data and post the finalized information on COVID Data Tracker.
• Cases and deaths are based on date of report and not on the date of symptom onset. CDC calculates rates in this data by using population estimates provided by the US Census Bureau Population Estimates Program (2019 Vintage).
• COVID-19 aggregate case and death data were organized in a time series that includes cumulative number of cases and deaths as reported by a jurisdiction on a given date. New case and death counts were calculated as the week-to-week change in reported cumulative cases and deaths (i.e., newly reported cases and deaths = cumulative number of cases/deaths reported this week minus the cumulative total reported the week before.

This process was collaborative, with CDC and jurisdictions working together to ensure the accuracy of COVID-19 case and death numbers. County counts provided the most up-to-date numbers on cases and deaths by report date. Throughout data collection, CDC retrospectively updated counts to correct known data quality issues. CDC also worked with jurisdictions after the end of the public health emergency declaration to finalize county data.

• Source: The weekly archived dataset is based on county-level aggregate count data
• Confirmed/Probable Cases/Death breakdown: Cumulative cases and deaths for each county are included. Total reported cases include probable and confirmed cases.
• Time Series Frequency: The weekly archived dataset contains weekly time series data (i.e., one record per week per county)

Important note: The counts reflected during a given time period in this dataset may not match the counts reflected for the same time period in the daily archived dataset noted above. Discrepancies may exist due to differences between county and state COVID-19 case surveillance and reconciliation efforts.

The surveillance case definition for COVID-19, a nationally notifiable disease, was first described in a position statement from the Council for State and Territorial Epidemiologists, which was later revised. However, there is some variation in how jurisdictions implement these case classifications. More information on how CDC collects COVID-19 case surveillance data can be found at FAQ: COVID-19 Data and Surveillance.

Confirmed and Probable Counts In this dataset, counts by jurisdiction are not displayed by confirmed or probable status. Instead, counts of confirmed and probable cases and deaths are included in the Total Cases and Total Deaths columns, when available. Not all jurisdictions reported probable cases and deaths to CDC. Confirmed and probable case definition criteria are described here: "https://ndc.services.cdc.gov/case-definitions/coronavirus-disease-2019-covid-19/">Coronavirus Disease 2019 (COVID-19) 2023 Case Definition | CDC Council of State and Territorial Epidemiologists (ymaws.com).

Deaths COVID-19 deaths were reported to CDC from several sources since the beginning of the pandemic including aggregate death data and NCHS Provisional Death Counts. Historic information presented on the COVID Data Tracker pages were based on the same source (Aggregate Data) as the present dataset until the expiration of the public health emergency declaration on May 11, 2023; however, the NCHS Death Counts are based on death certificate data that use information reported by physicians, medical examiners, or coroners in the cause-of-death section of each certificate. Counts from previous weeks were continually revised as more records were received and processed.

Number of Jurisdictions Reporting There were 60 public health jurisdictions that reported cases and deaths of COVID-19. This included the 50 states, the District of Columbia, New York City, the U.S. territories of American Samoa, Guam, the Commonwealth of the Northern Mariana Islands, Puerto Rico, and the U.S Virgin Islands as well as three independent countries in compacts of free association with the United States, Federated States of Micronesia, Republic of the Marshall Islands, and Republic of Palau. In total there were 3,222 counties for which counts were tracked within the 60 public health jurisdictions.

Additional COVID-19 public use datasets, include line-level (patient-level) data, are available at: https://data.cdc.gov/browse?tags=covid-19.

Note: In early 2020, Alaska enacted changes to their counties/boroughs due to low populations in certain areas:

Case and death counts for Yakutat City and Borough, Alaska, are shown as 0 by default. Case and death counts for Hoonah-Angoon Census Area, Alaska, represent total cases and deaths in residents of Hoonah-Angoon Census Area, Alaska, and Yakutat City and Borough, Alaska. Case and death counts for Bristol Bay Borough, Alaska, are shown as 0 by default. Case and death counts for Lake and Peninsula Borough, Alaska, represent total cases and deaths in residents of Lake and Peninsula Borough, Alaska, and Bristol Bay Borough, Alaska.

Historical cases and deaths are not tracked separately in the county level datasets, and differences in weekly new cases and deaths could exist when county-level data are aggregated to the state-level (i.e., when compared to this dataset: https://data.cdc.gov/Case-Surveillance/United-States-COVID-19-Cases-and-Deaths-by-State-o/9mfq-cb36).

Context

Bay Area Rapid Transit or BART is a public rail system that connects much of California's San Francisco Bay Area. The transport system "connects the San Francisco Peninsula with Berkeley, Oakland, Fremont, Walnut Creek, Dublin/Pleasanton and other cities in the East Bay".

Content

This dataset is the most detailed information of trip information for BART and was provided by BART directly. Specifically, this data was pulled from the provided source http://64.111.127.166/origin-destination/. The data are automatically updated on the site and BART says they "are usually available by the 5th of the next month".

Acknowledgements

This obviously wouldn't be available without BART collecting and providing the data. It's great that the data is publicly available to this essential transportation to those living in the Bay Area!

Inspiration

This data was originally pulled in July 2020 during the COVID-19 pandemic. As counties in the Bay Area begin relaxing quarantine/lockdown restrictions yet an increase of COVID-19 cases continues, it could be important to see how public transportation has changed. It's possible to see the travel habits of different areas in the Bay.

A quick note

This is the maintained iteration from the first Kaggle dataset (which is no longer mainted): https://www.kaggle.com/mrgeislinger/bart-ridership

Alternative characterizations of DID groups for analysis of respondents who were sheltering-in-place all of the time after versus before the San Francisco Bay Area shelter-in-place announcement.

Codebooks for analyzing property (house, condo, flat, etc.) listing data for each of the 10 select regions in the bay area megaregion of California, USA (SAN JOSE, MODESTO, FRESNO, TURLOCK, LIVINGSTON, ATWATER, MERCED, MADERA, MARIPOSA, OAKHURST) were obtained from Zillow Inc. on a monthly basis between March 2018 and May 2019 (denoted as the period before 2020) and May 2020 and September 2021 (after 2020). Combined, the total number of observations (unique listed properties) is N = 57,414. For each month, we obtained a set of unique listing identifiers (ZPID) by manually scanning across the entire Zillow.com directory for a given region and property type ("For Sale" and "Rent"). Read the enclosed document DataDryad_DataDescription_Petersen_Zillow.pdf for a description of the data and output of provided supporting code. Contact the corresponding author for the raw property-level data files, which are anonymized [property address and property identifier (ZPID) fields].

Data used for analysis in paper. Includes concentrations of SARS-CoV-2 N and PMMoV genes in wastewater solids in three wastewater treatment plants in the greater Bay Area of California, USA

The widespread uptake of COVID-19 vaccines by women provided a unique opportunity to study the effects of pregnancy and lactation on immune responses to vaccination. Leveraging a cohort with well-defined SARS-CoV-2 exposure history, we found that the magnitude of humoral and cellular immune responses to vaccine-delivered SARS-CoV-2 spike was not affected by pregnancy or lactation status. However, vaccination during pregnancy elicited more stem-like SARS-CoV-2-specific CD4+ T cells. Moreover, breakthrough infection promoted spike-specific IgG in pregnant individuals in contrast to IgA in those lactating, suggesting that the pregnancy-to-lactation transition favors mucosal antibody responses. Breakthrough infection also reduced peripheral cytolytic SARS-CoV-2-specific CD8+ T cell frequencies during lactation but not pregnancy, which may reflect trafficking of the cells to mammary glands. Our study also uncovered an impact of pregnancy and lactation on global T cell phenotypes. In particul..., , , # Pregnancy and lactation induce distinct immune responses to COVID-19 booster vaccination and SARS-CoV-2 breakthrough infection

Contact: Nadia Roan, PhD Gladstone Institutes University of California, San Francisco nadia.roan@gladstone.ucsf.edu nadia.roan@ucsf.edu

Dates of collection: December 2020 to February 2022

Information about the geographic location of data collection: San Francisco Bay Area

Key words: SARS-CoV-2, CyTOF, T cells, pregnant, lactating

Data and file overview:

Included are 348 FCS files from 174 different CyTOF specimens. Each file name begins with a de-identified study participant identifier (ID). The Group category corresponds to whether the participant was non pregnant (Nonpreg), pregnant, or lactating at the time of specimen collection. The Status category indicates whether the sample was obtained prior (Pre) or subsequent (Post) to receiving a 3rd dose of a COVID-19 m..., This study was approved by the institutional review board of University of California, San Francisco (UCSF, IRB #20-32077 and IRB #19-29713) and written informed consent was obtained from all study participants, to publish de-identified data in the public domain.

Population-adjusted prevalence of antibodies from COVID-19 vaccination in Round 3 within race/ethnicity and age groups and prevalence differences between non-White and White individuals.

Characteristics of participants at each round of the study compared to study region population.