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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]

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]

The article explores rapid identification of infected individuals in the early stages of an outbreak in order to isolate and prevent further transmission is of utmost importance. Public health responses utilized to accomplish this goal include identification and isolation of infected individuals based on symptom presentation then monitoring of contacts for symptoms before proceeding with further isolation.

The epidemiology of coronavirus disease 2019 in children has been challenging to establish, owing to the high prevalence of asymptomatic infection in this population. Lower secondary attack rates in children compared with adults have been observed in household contact studies, but there is evidence that this may reflect lower testing in children and reduced exposure, rather than a genuine difference in biological susceptibility. In addition, children may shed infectious virus for a shorter period than adults and their antibody response may be less broad, with implications for both polymerase chain reaction and serological testing. Improvements in study design, data collection, and data interpretation are required to better understand the epidemiology of coronavirus disease 2019 in children. [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]

The article offers information on reverse-transcription polymerase chain reaction (RT-PCR) as test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It mentions use of diagnostics tests could cause patient harm from unneeded interventions and is a major driver of increased healthcare costs.

A case study of 78-year-old man with a history of Type 2 diabetes mellitus, diabetic nephropathy on hemodialysis, chronic obstructive pulmonary disease (COPD), mixed central and obstructive sleep apnea, ischemic heart disease, is presented. Topics include Genomes were assembled with reference based assembly and a bioinformatics pipeline; and region of the genome and 50% cut-off for defining single nucleotide polymorphisms (SNPs).