LitCovid-sentences  

PMC:7574920 / 2878-9446 JSONTXT 10 Projects

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Id Subject Object Predicate Lexical cue
T21 0-12 Sentence denotes INTRODUCTION
T22 13-187 Sentence denotes The coronavirus disease 2019 (COVID-19) pandemic, caused by the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) coronavirus (1), is a major global health threat.
T23 188-399 Sentence denotes A still unknown proportion of people, especially the elderly and those with preexisting conditions, are at high risk of a severe course of COVID-19 (2), leading to a high burden on health care systems worldwide.
T24 400-642 Sentence denotes Further, because of limited testing capacity, only people with symptoms are usually tested for SARS-CoV-2 infection, although studies have confirmed that many individuals infected with SARS-CoV-2 are asymptomatic carriers of the virus (3, 4).
T25 643-767 Sentence denotes This suggests that infection control strategies focusing on symptomatic patients are not sufficient to prevent virus spread.
T26 768-915 Sentence denotes Therefore, large-scale diagnostic methods are needed to determine the spread of the virus in populations quickly, comprehensively, and sensitively.
T27 916-1014 Sentence denotes This would allow for the rapid isolation of infected persons during an existing wave of infection.
T28 1015-1252 Sentence denotes In addition, continuous and repeated testing of large groups within a population may be required as a long-term strategy to contain new outbreaks while keeping societies and economies functional until effective vaccines become available.
T29 1253-1385 Sentence denotes An active SARS-CoV-2 infection can be diagnosed by detecting either the viral genome or viral antigens in appropriate human samples.
T30 1386-1587 Sentence denotes Assays for detecting SARS-CoV-2 antigens are limited by the sensitivity, specificity, and production speed of diagnostic antibodies, whereas detecting viral RNA only requires specific oligonucleotides.
T31 1588-1673 Sentence denotes Therefore, an assay that detects SARS-CoV-2 RNA facilitates testing of large cohorts.
T32 1674-1952 Sentence denotes The SARS-CoV-2 diagnostic pipeline that has proven to be successful and that is currently used in many test centers consists of three steps: collecting nasopharyngeal or oropharyngeal swab specimens, isolation of total RNA, and specific detection of the viral genome by RT-qPCR.
T33 1953-2169 Sentence denotes The latter comprises a reverse transcriptase (RT) step, which translates the viral RNA into DNA, followed by a semiquantitative DNA polymerase chain reaction using oligonucleotides specific for the viral cDNA (qPCR).
T34 2170-2336 Sentence denotes As a result, a short piece of the viral genome is strongly amplified and then is detected by a sequence-specific oligonucleotide probe labeled with a fluorescent dye.
T35 2337-2588 Sentence denotes This procedure includes several steps that require sample handling; therefore, the detection process in a clinical diagnostic laboratory takes about 3 to 24 hours or more, depending on the number of samples and process optimization of the test center.
T36 2589-2782 Sentence denotes In addition, in the context of the COVID-19 pandemic, many of the reagents required are only slowly being replenished due to insufficient production capacity or lack of international transport.
T37 2783-2907 Sentence denotes Therefore, increasing daily test capacities for RT-qPCR–based diagnostics for SARS-CoV-2 RNA detection is currently limited.
T38 2908-3038 Sentence denotes To accelerate and optimize such diagnostics, new scalable methods for RNA isolation and the detection of viral genomes are needed.
T39 3039-3145 Sentence denotes An alternative to RT-qPCR is reverse transcription loop-mediated isothermal amplification (RT-LAMP) (5–7).
T40 3146-3359 Sentence denotes RT-LAMP reactions include a reverse transcriptase and a DNA polymerase with strong strand displacement activity and tolerance for elevated temperatures and up to six DNA oligonucleotides of a certain architecture.
T41 3360-3498 Sentence denotes Samples with potential template molecules are added to the reaction and incubated for 20 to 60 min at a constant temperature (e.g., 65°C).
T42 3499-3678 Sentence denotes The oligonucleotides act as primers for the reverse transcriptase, and additional oligonucleotides for the DNA polymerase are designed so the DNA products loop back at their ends.
T43 3679-3750 Sentence denotes These, in turn, serve as self-priming templates for the DNA polymerase.
T44 3751-3939 Sentence denotes In the presence of a few RNA template molecules, a chain reaction is set in motion, which then runs until the added reagents (in particular, the deoxynucleotide triphosphates) are used up.
T45 3940-4023 Sentence denotes To detect DNA production in RT-LAMP assays, various approaches have been described.
T46 4024-4138 Sentence denotes One possibility is to use a pH indicator (e.g., phenol red) and run the reaction in a weakly buffered environment.
T47 4139-4310 Sentence denotes As the chain reaction proceeds, the pH is lowered, which results in a visible color change from red to yellow making it an appealing assay for point-of-care diagnosis (8).
T48 4311-4432 Sentence denotes Previously, RT-LAMP assays have been proposed for diagnostic detection of other RNA viruses, such as influenza virus (9).
T49 4433-4555 Sentence denotes Also, several studies have demonstrated the use of isothermal DNA amplification to detect small amounts of SARS-CoV-2 RNA.
T50 4556-4755 Sentence denotes The majority of these studies used in vitro transcribed (IVT) short fragments of the viral genomic RNA (10–12) and showed a detection limit of somewhere between 10 and 100 RNA molecules per reaction.
T51 4756-5008 Sentence denotes For the detection of SARS-CoV-2 RNA, a few commercial rapid tests have been developed [reviewed in (13)] using isothermal DNA amplification reactions involving proprietary enzyme formulations that are not commercially available in a ready-to-go format.
T52 5009-5149 Sentence denotes Further, their exact sensitivity is still subject to discussion owing to a lack of studies using sufficiently large numbers of test samples.
T53 5150-5430 Sentence denotes The performance of an RT-LAMP assay does not require expensive special equipment such as a thermal cycler with real-time fluorescence measurement, because positive samples are determined by a color change from red to yellow within 30 min after the start of the incubation at 65°C.
T54 5431-5576 Sentence denotes For detection, simple mobile phone cameras, copy machines, office scanners, or plate scanners with spectrophotometric quantification can be used.
T55 5577-6029 Sentence denotes During the early phase of the COVID-19 pandemic (early March 2020) in Germany, we tested the sensitivity and specificity of a colorimetric RT-LAMP assay for detecting SARS-CoV-2 RNA in clinical RNA samples isolated from pharyngeal swab specimens collected from individuals being tested for COVID-19 (and provided by the Heidelberg University Hospital’s diagnostic laboratory after removal of an aliquot for SARS-CoV-2 RNA testing by RT-qPCR) (fig. S1).
T56 6030-6168 Sentence denotes We also developed a swab–to–RT-LAMP assay that used naso/oropharyngeal swab specimens directly without the need for an RNA isolation step.
T57 6169-6331 Sentence denotes We tested >700 clinical RNA samples with a wide range of viral loads, allowing us to determine accurately the sensitivity range of the colorimetric RT-LAMP assay.
T58 6332-6568 Sentence denotes We also developed a multiplexed LAMP-sequencing protocol using barcoded Tn5 transposase tagmentation that enabled rapid identification of positive results in thousands of RT-LAMP reactions within the same next-generation sequencing run.