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PMC:7170415 / 12574-20610 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
188 457-465 Species denotes patients Tax:9606
189 177-188 Species denotes respiratory Tax:12814
190 703-714 Species denotes respiratory Tax:12814
191 222-230 Disease denotes COVID-19 MESH:C000657245
192 421-429 Disease denotes COVID-19 MESH:C000657245
193 481-489 Disease denotes COVID-19 MESH:C000657245
194 521-537 Disease denotes viral infections MESH:D001102
195 654-674 Disease denotes SARS–CoV-2 infection MESH:C000657245
199 1173-1180 Species denotes persons Tax:9606
200 987-1003 Disease denotes acute infections MESH:D007239
201 1220-1229 Disease denotes infection MESH:D007239
210 1368-1376 Species denotes patients Tax:9606
211 1519-1529 Species denotes SARS–CoV-2 Tax:2697049
212 1601-1611 Species denotes SARS–CoV-2 Tax:2697049
213 1425-1436 Species denotes respiratory Tax:12814
214 2358-2369 Species denotes respiratory Tax:12814
215 1851-1859 Chemical denotes aluminum MESH:D000535
216 1911-1927 Chemical denotes calcium alginate MESH:D000464
217 1382-1390 Disease denotes COVID-19 MESH:C000657245
225 2956-2960 Gene denotes RdRP Gene:43740578
226 2718-2730 Gene denotes nucleocapsid Gene:43740575
227 2634-2644 Species denotes SARS–CoV-2 Tax:2697049
228 2761-2766 Species denotes human Tax:9606
229 2915-2925 Species denotes SARS–CoV-2 Tax:2697049
230 3054-3064 Species denotes SARS–CoV-2 Tax:2697049
231 3130-3143 Species denotes coronaviruses Tax:11118
239 4503-4510 Species denotes patient Tax:9606
240 4701-4711 Species denotes SARS–CoV-2 Tax:2697049
241 4408-4419 Species denotes respiratory Tax:12814
242 4616-4627 Species denotes respiratory Tax:12814
243 4183-4193 Species denotes SARS–CoV-2 Tax:2697049
244 4090-4099 Disease denotes infection MESH:D007239
245 4377-4385 Disease denotes COVID-19 MESH:C000657245
248 4846-4874 Disease denotes respiratory viral infections
249 5030-5039 Disease denotes Abbott ID MESH:C537985
253 5192-5202 Species denotes SARS–CoV-2 Tax:2697049
254 5299-5309 Species denotes SARS–CoV-2 Tax:2697049
255 5426-5438 Disease denotes tuberculosis MESH:D014376
262 6439-6451 Gene denotes nucleocapsid Gene:43740575
263 5765-5792 Species denotes respiratory syncytial virus Tax:12814
264 6036-6063 Species denotes respiratory syncytial virus Tax:12814
265 6173-6183 Species denotes SARS–CoV-2 Tax:2697049
266 6306-6325 Species denotes novel coronaviruses Tax:2697049
267 6463-6473 Species denotes SARS–CoV-2 Tax:2697049
280 6643-6646 Gene denotes IgG
281 6651-6661 Species denotes SARS–CoV-2 Tax:2697049
282 7286-7296 Species denotes SARS–CoV-2 Tax:2697049
283 7297-7308 Species denotes coronavirus Tax:11118
284 7430-7435 Species denotes human Tax:9606
285 7436-7449 Species denotes coronaviruses Tax:11118
286 7518-7526 Species denotes patients Tax:9606
287 6912-6928 Disease denotes acute infections MESH:D007239
288 7072-7081 Disease denotes infection MESH:D007239
289 7168-7188 Disease denotes SARS–CoV-2 infection MESH:C000657245
290 7409-7418 Disease denotes infection MESH:D007239
291 7556-7585 Disease denotes late complications of disease MESH:D002493
294 7760-7770 Species denotes SARS–CoV-2 Tax:2697049
295 7734-7743 Disease denotes infection MESH:D007239

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T8 741-744 Body_part denotes map http://purl.org/sig/ont/fma/fma67847
T9 946-954 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T10 1425-1442 Body_part denotes respiratory tract http://purl.org/sig/ont/fma/fma265130
T11 1644-1653 Body_part denotes turbinate http://purl.org/sig/ont/fma/fma57456
T12 2182-2188 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T13 2352-2375 Body_part denotes upper respiratory tract http://purl.org/sig/ont/fma/fma45661
T14 2501-2504 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T15 2731-2735 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T16 2775-2779 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T17 2794-2797 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T18 2926-2929 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T19 2940-2943 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T20 4207-4212 Body_part denotes Serum http://purl.org/sig/ont/fma/fma63083
T21 4217-4222 Body_part denotes urine http://purl.org/sig/ont/fma/fma12274
T22 4402-4425 Body_part denotes upper respiratory tract http://purl.org/sig/ont/fma/fma45661
T23 4610-4633 Body_part denotes upper respiratory tract http://purl.org/sig/ont/fma/fma45661
T24 5443-5446 Body_part denotes HIV http://purl.org/sig/ont/fma/fma278683
T25 6452-6459 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T26 6629-6632 Body_part denotes IgA http://purl.org/sig/ont/fma/fma62874
T27 6634-6637 Body_part denotes IgM http://purl.org/sig/ont/fma/fma62873
T28 6643-6646 Body_part denotes IgG http://purl.org/sig/ont/fma/fma62872
T29 6695-6700 Body_part denotes blood http://purl.org/sig/ont/fma/fma9670
T30 6704-6710 Body_part denotes saliva http://purl.org/sig/ont/fma/fma59862
T31 7050-7058 Body_part denotes Antibody http://purl.org/sig/ont/fma/fma62871
T32 7270-7278 Body_part denotes antibody http://purl.org/sig/ont/fma/fma62871
T33 7309-7317 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T4 1425-1442 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065
T5 2182-2188 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T6 2352-2375 Body_part denotes upper respiratory tract http://purl.obolibrary.org/obo/UBERON_0001557
T7 2358-2375 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065
T8 4207-4212 Body_part denotes Serum http://purl.obolibrary.org/obo/UBERON_0001977
T9 4217-4222 Body_part denotes urine http://purl.obolibrary.org/obo/UBERON_0001088
T10 4402-4425 Body_part denotes upper respiratory tract http://purl.obolibrary.org/obo/UBERON_0001557
T11 4408-4425 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065
T12 4610-4633 Body_part denotes upper respiratory tract http://purl.obolibrary.org/obo/UBERON_0001557
T13 4616-4633 Body_part denotes respiratory tract http://purl.obolibrary.org/obo/UBERON_0000065
T14 5537-5542 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T15 6695-6700 Body_part denotes blood http://purl.obolibrary.org/obo/UBERON_0000178
T16 6704-6710 Body_part denotes saliva http://purl.obolibrary.org/obo/UBERON_0001836

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T53 222-230 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T54 421-429 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T55 481-489 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T56 521-537 Disease denotes viral infections http://purl.obolibrary.org/obo/MONDO_0005108
T57 654-658 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T58 665-674 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T59 993-1003 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T60 1220-1229 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T61 1382-1390 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T62 1519-1523 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T63 1601-1605 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T64 2634-2638 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T65 2915-2919 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T66 3054-3058 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T67 3824-3828 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T68 4090-4099 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T69 4183-4187 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T70 4377-4385 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T71 4701-4705 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T72 4858-4874 Disease denotes viral infections http://purl.obolibrary.org/obo/MONDO_0005108
T73 5192-5196 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T74 5299-5303 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T75 5426-5438 Disease denotes tuberculosis http://purl.obolibrary.org/obo/MONDO_0018076
T76 5796-5805 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T77 6022-6031 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T78 6173-6177 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T79 6463-6467 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T80 6651-6655 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T81 6918-6928 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T82 7072-7081 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T83 7168-7172 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T84 7179-7188 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T85 7286-7290 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T86 7409-7418 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T87 7734-7743 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T88 7760-7764 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T125 7-11 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Test
T126 24-29 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Tests
T127 242-249 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T128 538-541 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T129 613-614 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T130 1145-1150 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T131 1160-1161 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T132 1293-1300 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Testing
T133 1352-1355 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T134 1397-1401 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T135 1528-1534 http://purl.obolibrary.org/obo/CLO_0001196 denotes 2 (25)
T136 1536-1537 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T137 1612-1619 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T138 1747-1748 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T139 2017-2024 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T140 2435-2436 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T141 2452-2456 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T142 2595-2598 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T143 2599-2602 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T144 2731-2735 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T145 2761-2766 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T146 2775-2779 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T147 2866-2878 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T148 2979-2984 http://purl.obolibrary.org/obo/OGG_0000000002 denotes genes
T149 3158-3159 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T150 3229-3232 http://purl.obolibrary.org/obo/CL_0000990 denotes CDC
T151 3495-3502 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T152 3504-3506 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T153 3639-3641 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T154 3657-3660 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T155 3707-3709 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T156 4202-4204 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T157 4446-4447 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T158 4501-4502 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T159 4511-4514 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T160 4519-4520 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T161 4530-4534 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T162 4836-4841 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T163 5206-5217 http://purl.obolibrary.org/obo/OBI_0000968 denotes instruments
T164 5273-5280 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T165 5310-5314 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T166 5325-5328 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T167 5447-5454 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T168 5546-5553 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T169 5677-5684 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T170 5703-5704 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T171 5741-5746 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Tests
T172 5747-5752 http://purl.obolibrary.org/obo/UBERON_0000473 denotes Tests
T173 5787-5792 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T174 5806-5811 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T175 6058-6063 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T176 6120-6122 http://purl.obolibrary.org/obo/CLO_0053794 denotes 41
T177 6189-6194 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T178 6290-6295 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T179 6400-6402 http://purl.obolibrary.org/obo/CLO_0053799 denotes 45
T180 6525-6526 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T181 6558-6562 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T182 6589-6594 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T183 6695-6700 http://purl.obolibrary.org/obo/UBERON_0000178 denotes blood
T184 6695-6700 http://www.ebi.ac.uk/efo/EFO_0000296 denotes blood
T185 6792-6797 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T186 7243-7248 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T187 7326-7327 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T188 7430-7435 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T189 7664-7666 http://purl.obolibrary.org/obo/CLO_0001382 denotes 48

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T6 1486-1498 Chemical denotes nucleic acid http://purl.obolibrary.org/obo/CHEBI_33696
T7 1494-1498 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T8 1851-1859 Chemical denotes aluminum http://purl.obolibrary.org/obo/CHEBI_28984
T9 1911-1918 Chemical denotes calcium http://purl.obolibrary.org/obo/CHEBI_22984|http://purl.obolibrary.org/obo/CHEBI_29320
T11 1919-1927 Chemical denotes alginate http://purl.obolibrary.org/obo/CHEBI_58187
T12 2149-2161 Chemical denotes nucleic acid http://purl.obolibrary.org/obo/CHEBI_33696
T13 2157-2161 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T14 2680-2685 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T15 2744-2746 Chemical denotes N2 http://purl.obolibrary.org/obo/CHEBI_17997
T16 2886-2891 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T17 4270-4282 Chemical denotes nucleic acid http://purl.obolibrary.org/obo/CHEBI_33696
T18 4278-4282 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T19 5037-5039 Chemical denotes ID http://purl.obolibrary.org/obo/CHEBI_141439
T20 5812-5820 Chemical denotes antigens http://purl.obolibrary.org/obo/CHEBI_59132
T21 6452-6459 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T22 6540-6547 Chemical denotes antigen http://purl.obolibrary.org/obo/CHEBI_59132
T23 7309-7317 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T10 84-97 http://purl.obolibrary.org/obo/GO_0003968 denotes transcriptase
T11 84-97 http://purl.obolibrary.org/obo/GO_0003899 denotes transcriptase
T12 521-537 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infections
T13 1068-1082 http://purl.obolibrary.org/obo/GO_0019076 denotes viral shedding
T14 2078-2087 http://purl.obolibrary.org/obo/GO_0006810 denotes transport
T15 2767-2774 http://purl.obolibrary.org/obo/GO_0004526 denotes RNase P
T16 2956-2960 http://purl.obolibrary.org/obo/GO_0003968 denotes RdRP
T17 4858-4874 http://purl.obolibrary.org/obo/GO_0016032 denotes viral infections
T18 6988-7002 http://purl.obolibrary.org/obo/GO_0019076 denotes viral shedding
T19 7632-7646 http://purl.obolibrary.org/obo/GO_0019076 denotes viral shedding

LitCovid-sentences

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.