Performance characteristics of a rapid SARS-CoV-2 antigen detection assay at a public plaza testing site in San Francisco.
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ABSTRACT:
SUBMITTER: Pilarowski G
PROVIDER: S-EPMC7654907 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:We evaluated the performance of the Abbott BinaxNOW rapid antigen test for coronavirus disease 2019 (Binax-CoV2) to detect virus among persons, regardless of symptoms, at a public plaza site of ongoing community transmission. Titration with cultured severe acute respiratory syndrome coronavirus 2 yielded a human observable threshold between 1.6 × 104-4.3 × 104 viral RNA copies (cycle threshold [Ct], 30.3-28.8). Among 878 subjects tested, 3% (26 of 878) were positive by reverse-transcription polymerase chain reaction, of whom 15 of 26 had a Ct <30, indicating high viral load; of these, 40% (6 of 15) were asymptomatic. Using this Ct threshold (<30) for Binax-CoV2 evaluation, the sensitivity of Binax-CoV2 was 93.3% (95% confidence interval, 68.1%-99.8%) (14 of 15) and the specificity was 99.9% (99.4%-99.9%) (855 of 856).
| S-EPMC7799021 | biostudies-literature
Project description:COVID-19 oral treatments require initiation within 5 days of symptom onset. Although antigen tests are less sensitive than RT-PCR, rapid results could facilitate entry to treatment. We collected anterior nasal swabs for BinaxNOW and RT-PCR testing and clinical data at a walk-up, community site in San Francisco, California between January and June 2022. SARS-CoV-2 genomic sequences were generated from positive samples and classified according to subtype and variant. Monte Carlo simulations were conducted to estimate the expected proportion of SARS-CoV-2 infected persons who would have been diagnosed within 5 days of symptom onset using RT-PCR versus BinaxNOW testing. Among 25,309 persons tested with BinaxNOW, 2,799 had concomitant RT-PCR. 1137/2799 (40.6%) were SARS-CoV-2 RT-PCR positive. We identified waves of predominant omicron BA.1, BA.2, BA.2.12, BA.4, and BA.5 among 720 sequenced samples. Among 1,137 RT-PCR positive samples, 788/1137 (69%) were detected by BinaxNOW; 94% (669/711) of those with Ct value <30 were detected by BinaxNOW. BinaxNOW detection was consistent over lineages. In analyses to evaluate entry to treatment, BinaxNOW detected 81.7% (361/442, 95% CI: 77-85%) of persons with COVID-19 within 5 days of symptom onset. In comparison, RT-PCR (24-hour turnaround) detected 84.2% (372/442, 95% CI: 80-87%) and RT-PCR (48-hour turnaround) detected 67.0% (296/442, 95% CI: 62-71%) of persons with COVID-19 within 5 days of symptom onset. BinaxNOW detected high viral load from anterior nasal swabs consistently across omicron sublineages emerging between January and June of 2022. Simulations support BinaxNOW as an entry point for COVID-19 treatment in a community field setting.
| S-EPMC10038282 | biostudies-literature
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
Project description:Sequencing of the SARS-CoV-2 viral genome from patient samples is an important epidemiological tool for monitoring and responding to the pandemic, including the emergence of new mutations in specific communities. SARS-CoV-2 genomic sequences were generated from positive samples collected, along with epidemiological metadata, at a walk-up, rapid testing site in the Mission District of San Francisco, California during November 22-December 2, 2020 and January 10-29, 2021. Secondary household attack rates and mean sample viral load were estimated and compared across observed variants. A total of 12,124 tests were performed yielding 1,099 positives. From these, 811 high quality genomes were generated. Certain viral lineages bearing spike mutations, defined in part by L452R, S13I, and W152C, comprised 54.9% of the total sequences from January, compared to 15.7% in November. Household contacts exposed to "West Coast" variants were at higher risk of infection compared to household contacts exposed to lineages lacking these variants (0.357 vs 0.294, RR=1.29; 95% CI:1.01-1.64). The reproductive number was estimated to be modestly higher than other lineages spreading in California during the second half of 2020. Viral loads were similar among persons infected with West Coast versus non-West Coast strains, as was the proportion of individuals with symptoms (60.9% vs 64.1%). The increase in prevalence, relative household attack rates, and reproductive number are consistent with a modest transmissibility increase of the West Coast variants; however, additional laboratory and epidemiological studies are required to better understand differences between these variants. We observed a growing prevalence and elevated attack rate for "West Coast" SARS-CoV-2 variants in a community testing setting in San Francisco during January 2021, suggesting its modestly higher transmissibility.
| S-EPMC7941666 | biostudies-literature
Project description: Not available
| S-EPMC2901012 | biostudies-literature
Project description:ObjectivesIn 2017, the Centers for Disease Control and Prevention reported more than 47,600 deaths as a result of opioid overdose in the United States. In an effort to reduce these deaths, California passed legislation providing pharmacists with the ability to furnish naloxone without a prescription. Our study examined pharmacies in San Francisco that furnished naloxone and provided guidance for pharmacies seeking to develop similar programs. The study aims were to (1) identify the legal, structural, social-environmental, and financial components of a pharmacy model that allows for successful naloxone distribution, (2) evaluate the attitudes and beliefs of pharmacy staff members toward patients receiving or requesting naloxone, and (3) assess relationships between these attitudes and beliefs and naloxone furnishing at the pharmacy.MethodsThis cross-sectional study used a series of semistructured interviews of pharmacy staff in San Francisco conducted April-October 2019. Through a thematic, inductive analysis of collected data, emerging themes were mapped to the primary study aims.ResultsWe interviewed 14 pharmacists and pharmacy technicians at 4 community pharmacies. We identified 4 factors for success in implementing a naloxone furnishing protocol: administrative-led efforts, pharmacist-led efforts, increasing pharmacist engagement, and increasing patient engagement. The respondents also discussed the approaches they used to overcome previously identified barriers: cost, time, expectations of unwanted clientele, and patients' feelings of stigma.ConclusionPharmacists' approaches to implementing naloxone furnishing had common features across locations, suggesting many of these strategies could be replicated in other community pharmacies.
| S-EPMC7655520 | biostudies-literature
Project description:BackgroundHere we present a checklist of the bee species found on the C. Hart Merriam elevation gradient along the San Francisco Peaks in northern Arizona. Elevational gradients can serve as natural proxies for climate change, replacing time with space as they span multiple vegetation zones over a short geographic distance. Describing the distribution of bee species along this elevation gradient will help predict how bee communities might respond to changing climate. To address this, we initiated an inventory associated with ecological studies on pollinators that documented bees on the San Francisco Peaks. Sample sites spanned six life zones (vegetation zones) on the San Francisco Peaks from 2009 to 2019. We also include occurrence data from other studies, gathered by querying the Symbiota Collection of Arthropods Network (SCAN) portal covering the San Francisco Peaks region (hereafter referred to as "the Peaks").New informationOur checklist reports 359 bee species and morphospecies spanning five families and 46 genera that have been collected in the Peaks region. Prior to our concerted sampling effort there were records for 155 bee species, yet there has not been a complete list of bee species inhabiting the Peaks published to date. Over a 10-year period, we documented an additional 204 bee species inhabiting the Peaks. Our study documents range expansions to northern Arizona for 15 species. The majority of these are range expansions from either southern Arizona, southern Utah, or the Rocky Mountain region of Colorado. Nine species are new records for Arizona, four of which are the southernmost record for that species. An additional 15 species are likely undescribed.
| S-EPMC7145878 | biostudies-literature
Project description:This study utilizes satellite data to investigate water quality conditions in the San Francisco Estuary and its upstream delta, the Sacramento-San Joaquin River Delta. To do this, this study derives turbidity from the European Space Agency satellite Sentinel-2 acquired from September 2015 to June 2019 and conducts a rigorous validation with in situ measurements of turbidity from optical sensors at continuous monitoring stations. This validation includes 965 matchup comparisons between satellite and in situ sensor data across 22 stations, yielding R 2 = 0.63 and 0.75 for Nephelometric Turbidity Unit and Formazin Nephelometric Unit (FNU) stations, respectively. This study then applies remote sensing to evaluate patterns in turbidity during the Suisun Marsh Salinity Control Gates Action ("Gates action"), a pilot study designed to increase habitat access and quality for the endangered Delta Smelt. The basic strategy was to direct more freshwater into Suisun Marsh, creating more low salinity habitat that would then have higher (and more suitable) turbidity than upstream river channels. For all seven acquisitions considered from June 29 to September 27, 2018, turbidity conditions in Bays and Sloughs subregions were consistently higher (and more suitable) (26-47 FNU) than what was observed in the upstream River region (13-25 FNU). This overall pattern was observed when comparing images acquired during similar tidal stages and heights.
| S-EPMC9290138 | biostudies-literature
Project description:BackgroundLatinos have had higher case counts, hospitalization rates and deaths during the COVID-19 pandemic nationally and in the state of California. Meanwhile, Latino vaccination rates remain lower than those of non-Hispanic Whites. COVID-19 vaccine nonintent, defined as intent to not vaccinate against COVID-19, among Latino individuals continues to be an issue in the state of California.MethodsFamilies from three Latino longitudinal mother-child cohorts previously recruited in the San Francisco Bay Area were surveyed telephonically from February to June 2021 to assess attitudes towards vaccination against COVID-19 and prior vaccination, in general, for themselves and their children. Risk for vaccine nonintent was assessed using the Mann-Whitney rank sum non-parametric test for continuous predictors and chi-squared tests for categorical ones.ResultsThree hundred and nineteen families were surveyed from the Telomere at Birth (TAB), Hispanic Eating and Nutrition (HEN) and Latino Eating and Diabetes Cohort (LEAD). Approximately 36% from TAB and 28% from HEN/LEAD indicated COVID-19 vaccine nonintent for themselves and/or their children. Risk factors for vaccine nonintent included lower maternal age (p = 0.01), concern about vaccine side effects (p < 0.01) and prior history of a household members being infected with SARS-CoV-2 (p < 0.01) and indexes of household crowding including number of people sharing a bathroom (p = 0.048). Vaccine intent was also associated with receiving vaccine input from friends (p = 0.03), family (p < 0.01) and/or coworkers (p = 0.02) compared with those who were not planning on getting vaccinated against COVID-19.ConclusionsLatino families living in crowded living situations who may not have received any COVID-19 advice from family, coworkers or friends are at particular risk for nonintent for vaccinatation against COVID-19. Community-based grassroots or promotor/a based interventions centered on trusted individuals with close community ties and counseling concerning vaccination against COVID-19 could help boost vaccination rates in this population group.
| S-EPMC9171483 | biostudies-literature
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