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Massive-scale SARS-CoV-2 testing using the SwabSeq diagnostic platform came with quality assurance challenges due to the novelty and scale of sequencing-based testing. The SwabSeq platform relies on accurate mapping between specimen identifiers and molecular barcodes to match a result back to a patient specimen. To identify and mitigate mapping errors, we instituted quality control using placement of negative controls within a rack of patient samples. We designed 2-dimensional paper templates to fit over a 96-position rack of specimens with holes to show the control tube placements. We designed and 3-dimensionally printed plastic templates that fit onto 4 racks of patient specimens and provide accurate indications of the correct control tube placements. The final plastic templates dramatically reduced plate mapping errors from 22.55% in January 2021 to less than 1% after implementation and training in January 2021. We show how 3D printing can be a cost-effective quality assurance tool to mitigate human error in the clinical laboratory. [ABSTRACT FROM AUTHOR]

Coronavirus disease 2019 (COVID-19) vaccines are highly efficacious at preventing symptomatic infection, severe disease, and death. Most of the evidence that COVID-19 vaccines also reduce transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is based on retrospective, observational studies. Specifically, an increasing number of studies are evaluating vaccine effectiveness against the secondary attack rate of SARS-CoV-2 using data available in existing health-care databases or contact-tracing databases. Since these types of databases were designed for clinical diagnosis or management of COVID-19, they are limited in their ability to provide accurate information on infection, infection timing, and transmission events. We highlight challenges with using existing databases to identify transmission units and confirm potential SARS-CoV-2 transmission events. We discuss the impact of common diagnostic testing strategies, including event-prompted and infrequent testing, and illustrate their potential biases in estimating vaccine effectiveness against the secondary attack rate of SARS-CoV-2. We articulate the need for prospective observational studies of vaccine effectiveness against the SARS-CoV-2 secondary attack rate, and we provide design and reporting considerations for studies using retrospective databases. [ABSTRACT FROM AUTHOR]

Background Twice weekly lateral flow tests (LFTs) for secondary school children was UK Government policy from 8 March 2021. We evaluate use of LFTs (both supervised at test centres, and home test kits) in school-aged children in Cheshire and Merseyside. Methods We report (i) number of LFT positives (ii) proportion of LFT positive with confirmatory reverse transcription polymerase chain reaction (PCR) test within 2 days, and (iii) agreement between LFT-positive and confirmatory PCR, and dependence of (i–iii) on COVID-19 prevalence. Findings 1 248 468 LFTs were taken by 211 255 12–18 years old, and 163 914 by 52 116 5–11 years old between 6 November 2020 and 31 July 2021. Five thousand three hundred and fourteen (2.5%) 12–18 years old and 1996 (3.8%) 5–11 years old returned LFT positives, with 3829 (72.1%) and 1535 (76.9%) confirmatory PCRs, and 3357 (87.7%) and 1383 (90.1%) confirmatory PCR-positives, respectively. Monthly proportions of LFT positive with PCR negative varied between 4.7% and 35.3% in 12–18 years old (corresponding proportion of all tests positive: 9.7% and 0.3%). Deprivation and non-White ethnicity were associated with reduced uptake of confirmatory PCR. Interpretation Substantial inequalities in confirmatory testing need more attention to avoid further disadvantage through education loss. When prevalence is low additional measures, including confirmatory testing, are needed. Local Directors of Public Health taking more control over schools testing may be needed. Funding DHSC, MRC, NIHR, EPSRC. [ABSTRACT FROM AUTHOR]

Pooled testing has been successfully used to expand SARS-CoV-2 testing, especially in settings requiring high volumes of screening of lower-risk individuals, but efficiency of pooling declines as prevalence rises. We propose a differentiated pooling strategy that independently optimizes pool sizes for distinct groups with different probabilities of infection to further improve the efficiency of pooled testing. We compared the efficiency (results obtained per test kit used) of the differentiated strategy with a traditional pooling strategy in which all samples are processed using uniform pool sizes under a range of scenarios. For most scenarios, differentiated pooling is more efficient than traditional pooling. In scenarios examined here, an improvement in efficiency of up to 3.94 results per test kit could be obtained through differentiated versus traditional pooling, with more likely scenarios resulting in 0.12 to 0.61 additional results per kit. Under circumstances similar to those observed in a university setting, implementation of our strategy could result in an improvement in efficiency between 0.03 to 3.21 results per test kit. Our results can help identify settings, such as universities and workplaces, where differentiated pooling can conserve critical testing resources. [ABSTRACT FROM AUTHOR]

Background Performance characteristics of SARS-CoV-2 antigen tests among children are limited despite the need for point-of-care testing in school and childcare settings. We describe children seeking SARS-CoV-2 testing at a community site and compare antigen test performance to real-time reverse transcription-polymerase chain reaction (RT-PCR) and viral culture. Methods Two anterior nasal specimens were self-collected for BinaxNOW antigen and RT-PCR testing, along with demographics, symptoms, and exposure information from individuals ≥5 years at a community testing site. Viral culture was attempted on residual antigen or RT-PCR-positive specimens. Demographic and clinical characteristics, and the performance of SARS-CoV-2 antigen tests, were compared among children (<18 years) and adults. Results About 1 in 10 included specimens were from children (225/2110); 16.4% (37/225) were RT-PCR-positive. Cycle threshold values were similar among RT-PCR-positive specimens from children and adults (22.5 vs 21.3, P =.46) and among specimens from symptomatic and asymptomatic children (22.5 vs 23.2, P =.39). Sensitivity of antigen test compared to RT-PCR was 73.0% (27/37) among specimens from children and 80.8% (240/297) among specimens from adults; among specimens from children, specificity was 100% (188/188), positive and negative predictive values were 100% (27/27) and 94.9% (188/198), respectively. Virus was isolated from 51.4% (19/37) of RT-PCR-positive pediatric specimens; all 19 had positive antigen test results. Conclusions With lower sensitivity relative to RT-PCR, antigen tests may not diagnose all positive COVID-19 cases; however, antigen testing identified children with live SARS-CoV-2 virus. [ABSTRACT FROM AUTHOR]

Introduction Care homes have been severely affected by the SARS-CoV-2 pandemic. Rapid antigen testing could identify most SARS-CoV-2 infected staff and visitors before they enter homes. We explored implementation of staff and visitor testing protocols using lateral flow devices (LFDs). Methods An evaluation of a SARS-CoV-2 LFD-based testing protocol in 11 care homes in Liverpool, UK, including staff and visitor testing, plus a qualitative exploratory study in nine of these homes. The proportion of pilot homes with outbreaks, and outbreak size, were compared to non-pilot homes in Liverpool. Adherence to testing protocols was evaluated. Fifteen staff were interviewed, and transcript data were thematically coded using an iterative analysis to identify and categorize factors influencing testing implementation. Results In total, 1,638 LFD rapid tests were performed on 407 staff. Protocol adherence was poor with 8.6% of staff achieving >75% protocol adherence, and 25.3% achieving |$\ge$| 50%. Six care homes had outbreaks during the study. Compared to non-pilot care homes, there was no evidence of significant difference in the proportion of homes with outbreaks, or the size of outbreaks. Qualitative data showed difficulty implementing testing strategies due to excessive work burden. Factors influencing adherence related to test integration and procedural factors, socio-economic factors, cognitive overload and the emotional value of testing. Conclusion Implementation of staff and visitor care home LFD testing protocols was poorly adhered to and consequently did not reduce the number or scale of COVID-19 outbreaks. More focus is needed on the contextual and behavioural factors that influence protocol adherence. [ABSTRACT FROM AUTHOR]