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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T15 1331-1337 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T16 1543-1546 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T17 1632-1635 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T18 1893-1896 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T19 1934-1940 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T20 2036-2039 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T21 2045-2048 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T22 2081-2084 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T23 2210-2216 Body_part denotes genome http://purl.org/sig/ont/fma/fma84116
T24 2872-2875 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T25 2978-2981 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T26 3019-3026 Body_part denotes genomes http://purl.org/sig/ont/fma/fma84116
T27 3202-3205 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T28 3312-3315 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T29 3606-3609 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T30 3641-3644 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T31 3659-3663 Body_part denotes back http://purl.org/sig/ont/fma/fma25056
T32 3735-3738 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T33 3776-3779 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T34 3950-3953 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T35 4391-4394 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T36 4495-4498 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T37 4551-4554 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T38 4655-4658 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T39 4728-4741 Body_part denotes RNA molecules http://purl.org/sig/ont/fma/fma84126
T40 4728-4731 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T41 4788-4791 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T42 4878-4881 Body_part denotes DNA http://purl.org/sig/ont/fma/fma74412
T43 5755-5758 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T44 5771-5774 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T45 5995-5998 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T46 6149-6152 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T47 6193-6196 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T2 785-790 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T19 17-41 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T20 43-51 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T21 77-85 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 89-136 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T23 89-122 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T24 327-335 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T25 495-503 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T26 506-515 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T27 585-593 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T28 662-671 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T29 1004-1013 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T30 1263-1271 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T31 1274-1283 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T32 1407-1415 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T33 1621-1629 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T34 1678-1686 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T35 2624-2632 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T36 2861-2869 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T37 4412-4421 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T38 4540-4548 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T39 4777-4785 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T40 5607-5615 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T41 5744-5752 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T42 5867-5875 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T43 5984-5992 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T33 158-159 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 188-189 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T35 308-309 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T36 352-353 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 428-435 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T38 484-490 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T39 629-634 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T40 636-640 http://purl.obolibrary.org/obo/CLO_0001302 denotes 3, 4
T41 691-699 http://purl.obolibrary.org/obo/CLO_0009985 denotes focusing
T42 754-759 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T43 852-857 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T44 1052-1059 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T45 1083-1084 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T46 1115-1116 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T47 1256-1262 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T48 1371-1376 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T49 1648-1655 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T50 1714-1717 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T51 1777-1781 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T52 1974-1975 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T53 2062-2063 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T54 2173-2174 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T55 2183-2184 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T56 2263-2264 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T57 2305-2312 http://purl.obolibrary.org/obo/CLO_0007225 denotes labeled
T58 2318-2319 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T59 2441-2442 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T60 2576-2580 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T61 2811-2815 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T62 3172-3173 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T63 3200-3201 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T64 3249-3257 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T65 3336-3337 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T66 3462-3463 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T67 3770-3771 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T68 3800-3801 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T69 4050-4051 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T70 4108-4109 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T71 4207-4208 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T72 4395-4402 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T73 4422-4427 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T74 4678-4679 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T75 4793-4794 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T76 4816-4821 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T77 4987-4988 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T78 5082-5083 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T79 5136-5140 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T80 5239-5240 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T81 5340-5341 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T82 5659-5665 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T83 5701-5702 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T84 5856-5862 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T85 5999-6006 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T86 6025-6027 http://purl.obolibrary.org/obo/CLO_0050050 denotes S1
T87 6048-6049 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T88 6172-6178 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T89 6210-6211 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T90 6350-6351 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 613-621 Chemical denotes carriers http://purl.obolibrary.org/obo/CHEBI_78059
T2 1347-1355 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T3 1418-1426 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T4 1570-1586 Chemical denotes oligonucleotides http://purl.obolibrary.org/obo/CHEBI_7754
T5 2045-2048 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T6 2081-2084 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T7 2117-2133 Chemical denotes oligonucleotides http://purl.obolibrary.org/obo/CHEBI_7754
T8 2283-2298 Chemical denotes oligonucleotide http://purl.obolibrary.org/obo/CHEBI_7754
T9 2299-2304 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T10 2320-2335 Chemical denotes fluorescent dye http://purl.obolibrary.org/obo/CHEBI_51121
T11 2332-2335 Chemical denotes dye http://purl.obolibrary.org/obo/CHEBI_37958
T12 2655-2663 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T13 3202-3205 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T14 3312-3315 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T15 3316-3332 Chemical denotes oligonucleotides http://purl.obolibrary.org/obo/CHEBI_7754
T16 3392-3401 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T17 3503-3519 Chemical denotes oligonucleotides http://purl.obolibrary.org/obo/CHEBI_7754
T18 3581-3597 Chemical denotes oligonucleotides http://purl.obolibrary.org/obo/CHEBI_7754
T19 3606-3609 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T20 3641-3644 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T21 3735-3738 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T22 3789-3798 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T23 3867-3875 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T24 3950-3953 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T25 4055-4064 Chemical denotes indicator http://purl.obolibrary.org/obo/CHEBI_47867
T26 4072-4082 Chemical denotes phenol red http://purl.obolibrary.org/obo/CHEBI_31991
T27 4072-4078 Chemical denotes phenol http://purl.obolibrary.org/obo/CHEBI_15882
T28 4495-4498 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991
T29 4732-4741 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T30 4878-4881 Chemical denotes DNA http://purl.obolibrary.org/obo/CHEBI_16991

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
55 77-87 Species denotes SARS-CoV-2 Tax:2697049
56 89-136 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
57 138-149 Species denotes coronavirus Tax:11118
58 218-224 Species denotes people Tax:9606
59 451-457 Species denotes people Tax:9606
60 585-595 Species denotes SARS-CoV-2 Tax:2697049
61 715-723 Species denotes patients Tax:9606
62 17-41 Disease denotes coronavirus disease 2019 MESH:C000657245
63 43-51 Disease denotes COVID-19 MESH:C000657245
64 327-335 Disease denotes COVID-19 MESH:C000657245
65 495-515 Disease denotes SARS-CoV-2 infection MESH:C000657245
66 571-579 Disease denotes infected MESH:D007239
67 662-671 Disease denotes infection MESH:D007239
71 969-976 Species denotes persons Tax:9606
72 960-968 Disease denotes infected MESH:D007239
73 1004-1013 Disease denotes infection MESH:D007239
79 1371-1376 Species denotes human Tax:9606
80 1621-1631 Species denotes SARS-CoV-2 Tax:2697049
81 1407-1417 Species denotes SARS-CoV-2 Tax:2697049
82 1570-1586 Chemical denotes oligonucleotides MESH:D009841
83 1263-1283 Disease denotes SARS-CoV-2 infection MESH:C000657245
87 1678-1688 Species denotes SARS-CoV-2 Tax:2697049
88 2117-2133 Chemical denotes oligonucleotides MESH:D009841
89 2283-2298 Chemical denotes oligonucleotide MESH:D009841
92 2861-2871 Species denotes SARS-CoV-2 Tax:2697049
93 2624-2632 Disease denotes COVID-19 MESH:C000657245
98 3316-3332 Chemical denotes oligonucleotides MESH:D009841
99 3503-3519 Chemical denotes oligonucleotides MESH:D009841
100 3581-3597 Chemical denotes oligonucleotides MESH:D009841
101 3896-3925 Chemical denotes deoxynucleotide triphosphates
108 4175-4177 Gene denotes pH Gene:5053
109 4052-4054 Gene denotes pH Gene:5053
110 4412-4427 Species denotes influenza virus Tax:11309
111 4540-4550 Species denotes SARS-CoV-2 Tax:2697049
112 4777-4787 Species denotes SARS-CoV-2 Tax:2697049
113 4072-4082 Chemical denotes phenol red MESH:D010637
118 5744-5754 Species denotes SARS-CoV-2 Tax:2697049
119 5984-5994 Species denotes SARS-CoV-2 Tax:2697049
120 5607-5615 Disease denotes COVID-19 MESH:C000657245
121 5867-5875 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T25 1944-1946 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T26 1984-1997 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T27 1984-1997 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase
T28 1999-2001 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T29 2772-2781 http://purl.obolibrary.org/obo/GO_0006810 denotes transport
T30 2831-2833 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T31 3057-3059 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T32 3068-3089 http://purl.obolibrary.org/obo/GO_0001171 denotes reverse transcription
T33 3076-3089 http://purl.obolibrary.org/obo/GO_0006351 denotes transcription
T34 3130-3132 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T35 3146-3148 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T36 3182-3195 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T37 3182-3195 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase
T38 3229-3248 http://purl.obolibrary.org/obo/GO_0000732 denotes strand displacement
T39 3551-3564 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T40 3551-3564 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase
T41 3968-3970 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T42 4323-4325 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T43 4495-4512 http://purl.obolibrary.org/obo/GO_0006277 denotes DNA amplification
T44 4878-4895 http://purl.obolibrary.org/obo/GO_0006277 denotes DNA amplification
T45 5172-5174 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T46 5716-5718 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T47 6010-6012 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T48 6058-6060 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T49 6317-6319 http://purl.obolibrary.org/obo/GO_0001171 denotes RT
T50 6503-6505 http://purl.obolibrary.org/obo/GO_0001171 denotes RT

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T1 6404-6407 GlycoEpitope denotes Tn5 http://www.glycoepitope.jp/epitopes/AN0083

LitCovid-sentences

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.