LitCovid-sentences  

PMC:7170415 / 12574-20610 JSONTXT 10 Projects

Annnotations TAB TSV DIC JSON TextAE Lectin_function

Id Subject Object Predicate Lexical cue
T92 0-12 Sentence denotes How to Test:
T93 13-56 Sentence denotes Diagnostic Tests in Use or Under Evaluation
T94 57-340 Sentence denotes Although real-time reverse transcriptase polymerase chain reaction (RT-PCR)–based assays performed in the laboratory on respiratory specimens are the cornerstone of COVID-19 diagnostic testing, several novel or complementary diagnostic methods are being developed and evaluated (16).
T95 341-450 Sentence denotes Figure 2 depicts the adequacy of the principal assay types used or proposed for COVID-19 for 4 key use cases.
T96 451-609 Sentence denotes Among patients diagnosed with COVID-19, the occurrence of concomitant viral infections has been reported to range from below 6% (29) to greater than 60% (30).
T97 610-724 Sentence denotes As a result, it is not possible to rule out SARS–CoV-2 infection merely by detecting another respiratory pathogen.
T98 725-734 Sentence denotes Figure 2.
T99 736-818 Sentence denotes Heat map showing the adequacy of principal assay types (rows) for 4 key use cases.
T100 819-928 Sentence denotes * This assumes that assays in development or currently undergoing regulatory evaluation prove to be accurate.
T101 929-1124 Sentence denotes † The utility of antibody detection assays for diagnosing acute infections is probably very limited around the time of symptom onset, when viral shedding and transmission risk seem to be highest.
T102 1125-1264 Sentence denotes Thus, although such tests may have a role among persons presenting late in the course of their infection, the potential for misuse is high.
T103 1266-1300 Sentence denotes Laboratory-Based Molecular Testing
T104 1301-1535 Sentence denotes The current diagnostic strategy recommended by the CDC to identify patients with COVID-19 is to test samples taken from the respiratory tract to assess for the presence of 1 or several nucleic acid targets specific to SARS–CoV-2 (25).
T105 1536-1710 Sentence denotes A nasopharyngeal specimen is the preferred choice for swab-based SARS–CoV-2 testing, but oropharyngeal, mid-turbinate, or anterior nares samples also are acceptable (31, 32).
T106 1711-1836 Sentence denotes Samples should be obtained by using a flocked swab, if available, to enhance the collection and release of cellular material.
T107 1837-1891 Sentence denotes Swabs with an aluminum or plastic shaft are preferred.
T108 1892-2025 Sentence denotes Swabs that contain calcium alginate, wood, or cotton should be avoided, because they may contain substances that inhibit PCR testing.
T109 2026-2162 Sentence denotes Ideally, swabs should be transferred into universal transport medium immediately after sample collection to preserve viral nucleic acid.
T110 2163-2391 Sentence denotes Samples taken from sputum, endotracheal aspirates, and bronchoalveolar lavage also may be sent directly to the microbiology laboratory for processing, and may have greater sensitivity than upper respiratory tract specimens (33).
T111 2392-2457 Sentence denotes Inadequate sample collection may result in a false-negative test.
T112 2458-2568 Sentence denotes After specimen collection, samples undergo RNA extraction followed by qualitative RT-PCR for target detection.
T113 2569-2651 Sentence denotes In the United States, the CDC has developed the most widely used SARS–CoV-2 assay.
T114 2652-2824 Sentence denotes The kit contains PCR primer–probe sets for 2 regions of the viral nucleocapsid gene (N1 and N2), and for the human RNase P gene to ensure the RNA extraction was successful.
T115 2825-2990 Sentence denotes This assay differs from the World Health Organization primer–probe sets, which target the SARS–CoV-2 RNA-dependent RNA polymerase (RdRP) and envelope (E) genes (25).
T116 2991-3224 Sentence denotes Both assays have high analytic sensitivity and specificity for SARS–CoV-2, with minimal cross-reactivity with other circulating strains of coronaviruses, and both use a cycle threshold of less than 40 as the criterion for positivity.
T117 3225-3508 Sentence denotes The CDC kit may be used by state public health laboratories, other laboratories determined by the state to be qualified, and clinical laboratories that meet the regulatory requirements of the Clinical Laboratories Improvement Amendment (CLIA) to perform high-complexity testing (27).
T118 3509-3643 Sentence denotes Dozens of laboratories have applied for Emergency Use Authorization (EUA) from the FDA for their own laboratory-developed assays (34).
T119 3644-3798 Sentence denotes The FDA also has granted an EUA for several commercial assays (35), further expanding the ability of clinical laboratories to use these platforms (Table).
T120 3799-3805 Sentence denotes Table.
T121 3806-4206 Sentence denotes The 28 Commercial SARS–CoV-2 in Vitro Diagnostic Assays Given an EUA From the FDA as of 4 April 2020 The lack of an established reference standard, use of differing sample collection and preparation methods, and an incomplete understanding of viral dynamics across the time course of infection hamper rigorous assessment of the diagnostic accuracy of the many newly introduced SARS–CoV-2 assays (36).
T122 4207-4320 Sentence denotes Serum and urine are usually negative for the presence of viral nucleic acid, regardless of illness severity (33).
T123 4321-4482 Sentence denotes Of importance, the ability of RT-PCR assays to rule out COVID-19 on the basis of upper respiratory tract samples obtained at a single time point remains unclear.
T124 4483-4731 Sentence denotes Conversely, after a patient has had a positive test result, several authorities have recommended obtaining at least 2 negative upper respiratory tract samples, collected at intervals of 24 hours or longer, to document SARS–CoV-2 clearance (37, 38).
T125 4733-4768 Sentence denotes Point-of-Care Molecular Diagnostics
T126 4769-5160 Sentence denotes Low-complexity, rapid (results within 1 hour) molecular diagnostic tests for respiratory viral infections that are CLIA waived (FDA approved for use outside the laboratory by nonlaboratory personnel) include cartridge-based assays on platforms that include the Abbott ID NOW (Abbott Laboratories), BioFire FilmArray (bioMérieux), cobas Liat (Roche Diagnostics), and GeneXpert (Cepheid) (39).
T127 5161-5281 Sentence denotes Rapid point-of-care assays for SARS–CoV-2 on instruments such as these will be critical to expand point-of-care testing.
T128 5282-5503 Sentence denotes The Xpert Xpress SARS–CoV-2 test (Cepheid) has received an FDA EUA and is performed on the GeneXpert platform, which is already widely used for tuberculosis and HIV testing, especially in low- and middle-income countries.
T129 5504-5721 Sentence denotes This capacity might be useful to scale up testing across the world as well as in settings where rapid results at the point of care would enable clinical decisions, although testing throughput may be a limiting factor.
T130 5723-5746 Sentence denotes Antigen Detection Tests
T131 5747-6003 Sentence denotes Tests that detect respiratory syncytial virus or influenza virus antigens by immunoassay directly from clinical specimens have been commercially available for decades, are of low complexity, and may provide results within minutes at the point of care (40).
T132 6004-6270 Sentence denotes Current tools for influenza and respiratory syncytial virus suffer from suboptimal sensitivity to rule out disease (41, 42); the same challenge would probably exist for SARS–CoV-2, and tests would need to be implemented with clear guidance on correct interpretation.
T133 6271-6404 Sentence denotes Prototypes of such tests for other novel coronaviruses have not received regulatory approval (43, 44) but are under development (45).
T134 6405-6568 Sentence denotes Monoclonal antibodies against the nucleocapsid protein of SARS–CoV-2 have been generated, which might form the basis of a future rapid antigen detection test (20).
T135 6570-6578 Sentence denotes Serology
T136 6579-6873 Sentence denotes Serologic tests that identify antibodies (such as IgA, IgM, and IgG) to SARS–CoV-2 from clinical specimens (such as blood or saliva), such as enzyme-linked immunosorbent assays, may be less complex than molecular tests and have the potential to be used for diagnosis in certain situations (46).
T137 6874-7049 Sentence denotes However, their utility for diagnosing acute infections is probably limited around the time of symptom onset, when viral shedding and transmission risk seem to be highest (32).
T138 7050-7132 Sentence denotes Antibody responses to infection take days to weeks to be reliably detectable (46).
T139 7133-7249 Sentence denotes Negative results would not exclude SARS–CoV-2 infection, particularly among those with recent exposure to the virus.
T140 7250-7455 Sentence denotes Cross-reactivity of antibody to non–SARS–CoV-2 coronavirus proteins is also a potential problem, whereby positive results may be the result of past or present infection with other human coronaviruses (47).
T141 7456-7668 Sentence denotes Serologic assays might be more relevant in scenarios in which patients present to medical care with late complications of disease, when RT-PCR may be falsely negative, because viral shedding drops over time (48).
T142 7669-7914 Sentence denotes The development of serologic assays that accurately assess prior infection and immunity to SARS–CoV-2 will be essential for epidemiologic studies, ongoing surveillance, vaccine studies, and potentially for risk assessment of health care workers.
T143 7915-8036 Sentence denotes Immunoassays are already on the market in some countries, but their diagnostic accuracy and optimal use remain undefined.