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Performance Characteristics of a Rapid Severe Acute Respiratory Syndrome Coronavirus 2 Antigen Detection Assay at a Public Plaza Testing Site in San Francisco.

ABSTRACT: 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).

SUBMITTER: Pilarowski G

PROVIDER: S-EPMC7799021 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

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Performance Characteristics of a Rapid Severe Acute Respiratory Syndrome Coronavirus 2 Antigen Detection Assay at a Public Plaza Testing Site in San Francisco.

Pilarowski Genay G Lebel Paul P Sunshine Sara S Liu Jamin J Crawford Emily E Marquez Carina C Rubio Luis L Chamie Gabriel G Martinez Jackie J Peng James J Black Douglas D Wu Wesley W Pak John J Laurie Matthew T MT Jones Diane D Miller Steve S Jacobo Jon J Rojas Susana S Rojas Susy S Nakamura Robert R Tulier-Laiwa Valerie V Petersen Maya M Havlir Diane V DV DeRisi Joseph J

The Journal of infectious diseases 20210401 7

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 poly ...[more]

PMID: 33394052

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Project description:BackgroundSequencing of the severe acute respiratory syndrome coronavirus 2 (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.MethodsSARS-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 22 November to 1 December, 2020, and 10-29 January 2021. Secondary household attack rates and mean sample viral load were estimated and compared across observed variants.ResultsA total of 12 124 tests were performed yielding 1099 positives. From these, 928 high-quality genomes were generated. Certain viral lineages bearing spike mutations, defined in part by L452R, S13I, and W152C, comprised 54.4% of the total sequences from January, compared to 15.7% in November. Household contacts exposed to the "California" or "West Coast" variants (B.1.427 and B.1.429) were at higher risk of infection compared to household contacts exposed to lineages lacking these variants (0.36 vs 0.29, risk ratio [RR] = 1.28; 95% confidence interval [CI]: 1.00-1.64). 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 64.3%).ConclusionsThe increase in prevalence, relative household attack rates, and reproductive number are consistent with a modest transmissibility increase of the West Coast variants. Summary: We observed a growing prevalence and modestly elevated attack rate for "West Coast" severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in a community testing setting in San Francisco during January 2021, suggesting its modestly higher transmissibility.

Project description:The Covid-19 pandemic challenged health care delivery systems worldwide. Many acute care hospitals in communities that experienced surges in cases and hospitalizations had to make decisions such as rationing scarce resources. Hospitals serving low-income communities, communities of color, and those in other historically marginalized or vulnerable groups reported the greatest operational impacts of surges. However, cross-institutional collaborations within jurisdictions offer unique opportunities to prevent or mitigate health disparities in resource utilization and access to care. In January 2020, in response to the emerging coronavirus epidemic, the San Francisco Department of Public Health (SFDPH) and local hospital and health systems partners convened to align and coordinate medical surge planning and response. Adopting a governance structure of mutual accountability and transparency, the San Francisco Health Systems Collaborative guided local medical and public health response in the areas of medical surge, vaccination administration, testing, and therapeutics. Four principles guided the collaborative response: (1) shared priorities, (2) clear governance and accountability, (3) data transparency, and (4) operational coordination. High-level priorities established included protecting vulnerable people, protecting health care workers, and maintaining health system capacity. The governance structure consisted of three layers: local hospital and health systems' CEOs coordinating with SFDPH executives; hospital chief medical and nursing officers coordinating high-level surge capacity assessments and mitigation plans; and local clinical operational managers working with public health response operational leaders to coordinate scarce resource utilization. Fluctuating with the tempo of the disease indicators and medical surge, governance and coordination were maintained through a tiered meeting and reporting system. Data visibility and transparency were key principles facilitating operational decision-making and executive-level coordination of resources, including identifying additional surge bed capacity for use systemwide, as well as ensuring efficient and equitable vaccine distribution through implementation of five mass-vaccination sites with prioritized access for vulnerable communities. Applying these four principles of shared priorities, accountability, transparency, and operational coordination and pragmatism helped the public health and individual hospital systems make contributions to the overall response that were aligned with their unique strengths and resources. Publication here represents the first official public use of the name San Francisco Health Systems Collaborative (which had served as the term used internally to refer to the group) and the first time codifying this structure. Through this coordination, San Francisco achieved one of the lowest Covid-19 death rates and had one of the highest vaccination and booster rates, compared with rates across California or the United States. Similar principles and implementation methods can be adopted by other health jurisdictions for future emergency outbreak response.

Dataset Information

Performance Characteristics of a Rapid Severe Acute Respiratory Syndrome Coronavirus 2 Antigen Detection Assay at a Public Plaza Testing Site in San Francisco.

Publications

Performance Characteristics of a Rapid Severe Acute Respiratory Syndrome Coronavirus 2 Antigen Detection Assay at a Public Plaza Testing Site in San Francisco.

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