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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]

In response to the rapidly evolving coronavirus disease 2019 (COVID-19) pandemic, the All of Us Research Program longitudinal cohort study developed the COVID-19 Participant Experience (COPE) survey to better understand the pandemic experiences and health impacts of COVID-19 on diverse populations within the United States. Six survey versions were deployed between May 2020 and March 2021, covering mental health, loneliness, activity, substance use, and discrimination, as well as COVID-19 symptoms, testing, treatment, and vaccination. A total of 104,910 All of Us Research Program participants, of whom over 73% were from communities traditionally underrepresented in biomedical research, completed 275,201 surveys; 9,693 completed all 6 surveys. Response rates varied widely among demographic groups and were lower among participants from certain racial and ethnic minority populations, participants with low income or educational attainment, and participants with a Spanish language preference. Survey modifications improved participant response rates between the first and last surveys (13.9% to 16.1%, P  < 0.001). This paper describes a data set with longitudinal COVID-19 survey data in a large, diverse population that will enable researchers to address important questions related to the pandemic, a data set that is of additional scientific value when combined with the program's other data sources. [ABSTRACT FROM AUTHOR]

The coronavirus disease 2019 (COVID-19) pandemic has been a globally dangerous crisis that causes an increasingly high death rate. Applying machine learning to the computed-tomography (CT)-based COVID-19 diagnosis is essential and attracts the attention of the research community. This paper introduces an approach for simultaneously identifying COVID-19 disease and segmenting its manifestations on lung images. The proposed method is an asymmetric U-Net-like model improved with skip connections. The experiment was conducted on a light-weighted feature extractor called CRNet with a feature enhancement technique called atrous spatial pyramid pooling. Classifying between COVID-19 and non-COVID-19 cases recorded the highest mean scores of 97.1, 94.4, and 97.0% for accuracy, dice similarity coefficient (DSC) and F1 score, respectively. Alternatively, the respective highest mean scores of the classification between COVID-19 and community-acquired pneumonia were 99.89, 99.79, and 99.97%. The lesion segmentation performance was with the highest mean of 99.6 and 84.7% for, respectively, accuracy and DSC. [ABSTRACT FROM AUTHOR]

Background We aimed to review the evidence from studies relating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) culture with the results of reverse-transcription polymerase chain reaction (RT-PCR) and other variables that may influence the interpretation of the test, such as time from symptom onset. Methods We searched LitCovid, medRxiv, Google Scholar, and the World Health Organization coronavirus disease 2019 (COVID-19) database for COVID-19 up to 10 September 2020. We included studies attempting to culture or observe SARS-CoV-2 in specimens with RT-PCR positivity. Studies were dual-extracted and the data summarized narratively by specimen type. Where necessary, we contacted corresponding authors of included papers for additional information. We assessed quality using a modified Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS 2) risk-of-bias tool. Results We included 29 studies reporting attempts at culturing, or observing tissue infection by, SARS-CoV-2 in sputum, nasopharyngeal or oropharyngeal, urine, stool, blood, and environmental specimens. The quality of the studies was moderate with lack of standardized reporting. The data suggest a relationship between the time from onset of symptom to the timing of the specimen test, cycle threshold (Ct), and symptom severity. Twelve studies reported that Ct values were significantly lower and log copies higher in specimens producing live virus culture. Two studies reported that the odds of live virus culture were reduced by approximately 33% for every 1-unit increase in Ct. Six of 8 studies reported detectable RNA for >14 days, but infectious potential declined after day 8 even among cases with ongoing high viral loads. Four studies reported viral culture from stool specimens. Conclusions Complete live viruses are necessary for transmission, not the fragments identified by PCR. Prospective routine testing of reference and culture specimens and their relationship to symptoms, signs, and patient co-factors should be used to define the reliability of PCR for assessing infectious potential. Those with high Ct are unlikely to have infectious potential. [ABSTRACT FROM AUTHOR]

: Biological, Clinical, and Technical Considerations These considerations are important when performing serology studies, with anti-S1/S2 serology tests preferably used to assess true seroprevalence; anti-RBD-specific serology immunoassays may be better suited to reflecting the presence of neutralizing antibodies. We read with interest the report by Geisler et al[1] and commend the authors for their efforts to address the important need to evaluate the clinical performance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostic assays in pediatric populations, especially with respect to serology, given the noted differences in immune responses between children and adults.[2] We do feel, however, that the title of this paper may be misleading. This behavior would make it challenging to define whether anti-RBD antibodies are false negatives or if anti-S1 antibodies are false positives. [Extracted from the article]

The author comments on a research paper on mass testing as a means to mitigate further transmission of COVID-19 infection in care homes in Great Britain, which references a study by S. Tang et al., published in an issue of "Age and Ageing." Topics discussed include the basis to declare an outbreak under the British policy, the requirement for a polymerase chain reaction testing during an outbreak, and the significant role of an intensive testing regimens in public health.

We read with interest the paper by Molero-Salinas I et al i . on coronavirus disease of 2019 (COVID-19) false negative travellers arriving to Spain in 2021.[1] This study challenges the effectiveness of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing prior to flight departure to control COVID-19 spread. The authors report 196 COVID-19 false negative passengers with an average PCR Ct value of 20.3, meaning a high viral load. [Extracted from the article]

The article presents the discussion on Labmedicine.com website featuring papers on COVID-19 relevant to today's laboratory professionals and pathologists including utility of antigen-based rapid diagnostic test for detection of SARS-CoV-2 virus in routine hospital setting.