Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Citywide serosurveillance of the initial SARS-CoV-2 outbreak in San Francisco.

ABSTRACT: Serosurveillance provides a unique opportunity to quantify the proportion of the population that has been exposed to pathogens. Here, we developed and piloted Serosurveillance for Continuous, ActionabLe Epidemiologic Intelligence of Transmission (SCALE-IT), a platform through which we systematically tested remnant samples from routine blood draws in two major hospital networks in San Francisco for SARS-CoV-2 antibodies during the early months of the pandemic. Importantly, SCALE-IT allows for algorithmic sample selection and rich data on covariates by leveraging electronic medical record data. We estimated overall seroprevalence at 4.2%, corresponding to a case ascertainment rate of only 4.9%, and identified important heterogeneities by neighborhood, homelessness status, and race/ethnicity. Neighborhood seroprevalence estimates from SCALE-IT were comparable to local community-based surveys, while providing results encompassing the entire city that have been previously unavailable. Leveraging this hybrid serosurveillance approach has strong potential for application beyond this local context and for diseases other than SARS-CoV-2.

SUBMITTER: Routledge I

PROVIDER: S-EPMC7872360 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Citywide serosurveillance of the initial SARS-CoV-2 outbreak in San Francisco using electronic health records.

Project description:Serosurveillance provides a unique opportunity to quantify the proportion of the population that has been exposed to pathogens. Here, we developed and piloted Serosurveillance for Continuous, ActionabLe Epidemiologic Intelligence of Transmission (SCALE-IT), a platform through which we systematically tested remnant samples from routine blood draws in two major hospital networks in San Francisco for SARS-CoV-2 antibodies during the early months of the pandemic. Importantly, SCALE-IT allows for algorithmic sample selection and rich data on covariates by leveraging electronic health record data. We estimated overall seroprevalence at 4.2%, corresponding to a case ascertainment rate of only 4.9%, and identified important heterogeneities by neighborhood, homelessness status, and race/ethnicity. Neighborhood seroprevalence estimates from SCALE-IT were comparable to local community-based surveys, while providing results encompassing the entire city that have been previously unavailable. Leveraging this hybrid serosurveillance approach has strong potential for application beyond this local context and for diseases other than SARS-CoV-2.

| S-EPMC8195995 | biostudies-literature

Community-Based Response to Fentanyl Overdose Outbreak, San Francisco, 2015.

Project description:This report documents a successful intervention by a community-based naloxone distribution program in San Francisco. The program and its partner organizations, working with participants who use drugs, first identified the appearance of illicitly made fentanyl and increased outreach and naloxone distribution. Distribution of naloxone and reported use of naloxone to reverse opioid-involved overdoses increased significantly while the number of opioid-involved and fentanyl-involved overdose deaths did not. Community-based programs that provide training and naloxone to people who use drugs can serve as an early warning system for overdose risk and adaptively respond to the rapidly changing overdose risk environment.

| S-EPMC6391290 | biostudies-literature

SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood from the San Francisco Bay Area.

Project description:We report very low SARS-CoV-2 seroprevalence in two San Francisco Bay Area populations. Seropositivity was 0.26% in 387 hospitalized patients admitted for non-respiratory indications and 0.1% in 1,000 blood donors. We additionally describe the longitudinal dynamics of immunoglobulin-G, immunoglobulin-M, and in vitro neutralizing antibody titers in COVID-19 patients. Neutralizing antibodies rise in tandem with immunoglobulin levels following symptom onset, exhibiting median time to seroconversion within one day of each other, and there is >93% positive percent agreement between detection of immunoglobulin-G and neutralizing titers.

| S-EPMC7273245 | biostudies-literature

Decreased Time From Human Immunodeficiency Virus Diagnosis to Care, Antiretroviral Therapy Initiation, and Virologic Suppression during the Citywide RAPID Initiative in San Francisco.

Project description:BackgroundEarly virologic suppression (VS) after human immunodeficiency virus (HIV) infection improves individual health outcomes and decreases onward transmission. In San Francisco, immediate antiretroviral therapy (ART) at HIV diagnosis was piloted in 2013-2014 and expanded citywide in 2015 in a rapid start initiative to link all new diagnoses to care within 5 days and start ART at the first care visit.MethodsHIV providers and linkage navigators were trained on a rapid start protocol with sites caring for vulnerable populations prioritized. Dates of HIV diagnosis, first care visit, ART initiation, and VS were abstracted from the San Francisco Department of Public Health HIV surveillance registry.ResultsDuring 2013-2017, among 1354 new HIV diagnoses in San Francisco, median days from diagnosis to first VS decreased from 145 to 76 (48%; P < .0001) and from first care visit to ART initiation decreased from 28 to 1 (96%; P < .0001). By 2017, 28% of new diagnoses had a rapid start, which was independently associated with Latinx ethnicity (AOR, 1.73; 95% CI, 1.15-2.60) and recent year of diagnosis (2017; AOR, 16.84; 95% CI, 8.03-35.33). Persons with a rapid ART start were more likely to be virologically suppressed within 12 months of diagnosis than those with a non-rapid start (RR, 1.17; 95% CI, 1.10-1.24).ConclusionsDuring a multisector initiative to optimize ART initiation, median time from diagnosis to VS decreased by nearly half. Immediate ART at care initiation was achieved across many, but not all, populations, and was associated with improved suppression rates.

| S-EPMC8561247 | biostudies-literature

Performance characteristics of a rapid SARS-CoV-2 antigen detection assay at a public plaza testing site in San Francisco.

Project description:We evaluated the performance of the Abbott BinaxNOW™ Covid-19 rapid antigen test to detect virus among persons, regardless of symptoms, at a public plaza site of ongoing community transmission. Titration with cultured clinical SARS-CoV-2 yielded a human observable threshold between 1.6×104-4.3×104 viral RNA copies (cycle threshold (Ct) of 30.3-28.8 in this assay). Among 878 subjects tested, 3% (26/878) were positive by RT-PCR, of which 15/26 had a Ct<30, indicating high viral load. 40% (6/15) of Ct<30 were asymptomatic. Using this Ct<30 threshold for Binax-CoV2 evaluation, the sensitivity of the Binax-CoV2 was 93.3% (14/15), 95% CI: 68.1-99.8%, and the specificity was 99.9% (855/856), 95% CI: 99.4-99.9%.

| S-EPMC7654907 | biostudies-literature

Diverse SARS-CoV-2 variants preceded the initial COVID-19 outbreak in Croatia.

Project description:We developed a next-generation SARS-CoV-2 sequencing platform and obtained the first SARS-CoV-2 sequences from patients in Croatia at the beginning of the COVID-19 outbreak in the spring of 2020. Integrating the sequencing and the epidemiological data, we show that patients were infected with different SARS-CoV-2 variants belonging to different clades (mostly G and GH). This result confirms that there was widespread virus transmission early in 2020. Interestingly, we identified a unique mutation resulting in a V13I substitution in Nsp5A, the main viral protease, in a patient who had not received antiviral therapy.

| S-EPMC7988246 | biostudies-literature

Allocating Resources for Cancer Care in Times of the Sars-CoV-2 Outbreak. Health Care Research

Project description:The focus on treatment of COVID19 patients during the Sars-CoV-2 outbreak has most likely implications for the extent and quality of diagnosis and treatment of non-COVID19 patients. Medical care of cancer patients is a particularly sensitive area. To draw holistic conclusions, it is necessary to analyze the provision of healthcare as broadly as possible with regard to the dimensions of access, processes and outcome during the Sars-CoV-2 pandemic. This will be implemented exemplarily for the early detection, diagnosis and treatment of colorectal cancer (CRC) and pancreatic cancer (PaCa) in Saxony. Patients with diagnosis, treatment or early detection measures for type 2 diabetes (T2D), coronary heart disease (CHD) and multiple sclerosis (MS) serve as comparison groups.

| 2743388 | ecrin-mdr-crc

Tools for interpretation of wastewater SARS-CoV-2 temporal and spatial trends demonstrated with data collected in the San Francisco Bay Area.

Project description:Wastewater surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA can be integrated with COVID-19 case data to inform timely pandemic response. However, more research is needed to apply and develop systematic methods to interpret the true SARS-CoV-2 signal from noise introduced in wastewater samples (e.g., from sewer conditions, sampling and extraction methods, etc.). In this study, raw wastewater was collected weekly from five sewersheds and one residential facility. The concentrations of SARS-CoV-2 in wastewater samples were compared to geocoded COVID-19 clinical testing data. SARS-CoV-2 was reliably detected (95% positivity) in frozen wastewater samples when reported daily new COVID-19 cases were 2.4 or more per 100,000 people. To adjust for variation in sample fecal content, four normalization biomarkers were evaluated: crAssphage, pepper mild mottle virus, Bacteroides ribosomal RNA (rRNA), and human 18S rRNA. Of these, crAssphage displayed the least spatial and temporal variability. Both unnormalized SARS-CoV-2 RNA signal and signal normalized to crAssphage had positive and significant correlation with clinical testing data (Kendall's Tau-b (τ)=0.43 and 0.38, respectively), but no normalization biomarker strengthened the correlation with clinical testing data. Locational dependencies and the date associated with testing data impacted the lead time of wastewater for clinical trends, and no lead time was observed when the sample collection date (versus the result date) was used for both wastewater and clinical testing data. This study supports that trends in wastewater surveillance data reflect trends in COVID-19 disease occurrence and presents tools that could be applied to make wastewater signal more interpretable and comparable across studies.

| S-EPMC8325558 | biostudies-literature

Repeat chlamydia screening by mail, San Francisco.

Project description:OBJECTIVES:To assess the feasibility and acceptability of home screening for repeat chlamydial infection using urine test kits sent through the mail. METHODS:A letter offering home rescreening was mailed to 399 adults who previously tested positive for chlamydia. Kits were then mailed to anyone who did not actively decline. The home testing kits contained instructions on how to collect a urine specimen and return the specimen by mail. Specimens were tested with strand displacement amplification. A short survey asked individuals their level of concern about confidentiality, safety, and privacy of mail screening. RESULTS:Among the 313 potential test kit recipients, 22.4% responded. Response rates were highest among homosexual and bisexual men (38.6%), people 35 years or older (34.3%), and white people (34.6%). The overall positivity rate was 3.2% (2/63). In women 18-25 years old, the positivity was 13.3% (2/15). CONCLUSIONS:Home testing with mailed urine collection kits is feasible and an acceptable method to screen for recurrent chlamydial infection. Young women would probably benefit most because of their higher rates of reinfection and risk for sequelae.

| S-EPMC1744608 | biostudies-literature

CancerCOVID - Allocating resources for cancer care in times of the Sars-CoV-2 outbreak. Evidence and ethical implications

Project description:Interventions: Group 1: A qualitative interview study as well as a cross-sectional questionnaire survey is conducted with patients, oncologists and nurses working in the field of oncology (subproject 1). This is complemented by retrospective analysis of quantitative data derived from the registry of colon cancer centres (subproject 2) and data from the statutory health insurance (subproject 3). Primary outcome(s): Aim: Assessment of ethical and psychosocial challenges in cancer care via semi-structured interviews with stakeholders (oncologists, nurses, patients) between January and July 2021. Assessment of psychosocial burden of oncologists, nurses and patients between February and July 2021 via questionnaires. patients: Mini-SCL, EORTC QLQ-C30, NCCN Distress Thermometer, FACT-19 oncologists: PHQ-9, PHQ-15, GAD-7, Maslach Burnout Inventory, Moral Distress Thermometer, FACT-19, sociodemographic questionnaire nurses: PHQ-9, PHQ-15, GAD-7, Maslach Burnout Inventory, Moral Distress Thermometer, FACT-19, BERNCA, sociodemographic questionnaire Study Design: Allocation: ; Masking: ; Control: ; Assignment: ; Study design purpose: other

| 2439669 | ecrin-mdr-crc

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data