PMC:7068163 / 661-15070
Annnotations
LitCovid-PubTator
| Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
|---|---|---|---|---|---|
| 9 | 53-70 | Species | denotes | novel coronavirus | Tax:2697049 |
| 15 | 574-591 | Species | denotes | novel coronavirus | Tax:2697049 |
| 16 | 717-764 | Species | denotes | severe acute respiratory syndrome coronavirus 2 | Tax:2697049 |
| 17 | 766-776 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 18 | 1054-1064 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 19 | 782-792 | Disease | denotes | infections | MESH:D007239 |
| 27 | 1351-1354 | Gene | denotes | ran | Gene:5901 |
| 28 | 1365-1375 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 29 | 1627-1637 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 30 | 1668-1675 | Species | denotes | persons | Tax:9606 |
| 31 | 1300-1316 | Chemical | denotes | oligonucleotides | MESH:D009841 |
| 32 | 1449-1473 | Disease | denotes | coronavirus disease 2019 | MESH:C000657245 |
| 33 | 1475-1483 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 45 | 1911-1914 | Gene | denotes | Rox | Gene:4335 |
| 46 | 2375-2376 | Gene | denotes | E | Gene:43740570 |
| 47 | 1792-1805 | Species | denotes | Coronaviruses | Tax:11118 |
| 48 | 2352-2369 | Species | denotes | Wuhan coronavirus | Tax:2697049 |
| 49 | 2424-2432 | Species | denotes | SARS-CoV | Tax:694009 |
| 50 | 2535-2538 | Species | denotes | CoV | Tax:11118 |
| 51 | 2596-2606 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 52 | 2695-2703 | Species | denotes | patients | Tax:9606 |
| 53 | 2716-2723 | Species | denotes | persons | Tax:9606 |
| 54 | 2761-2786 | Chemical | denotes | phosphate buffered saline | |
| 55 | 2788-2791 | Chemical | denotes | PBS | |
| 60 | 3146-3154 | Species | denotes | SARS-CoV | Tax:694009 |
| 61 | 3159-3169 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 62 | 3188-3198 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 63 | 3241-3246 | Species | denotes | human | Tax:9606 |
| 67 | 3387-3397 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 68 | 3553-3563 | Species | denotes | SARS CoV-2 | Tax:2697049 |
| 69 | 3588-3596 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 71 | 3675-3683 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 73 | 3743-3761 | Species | denotes | COVID: coronavirus | Tax:2697049 |
| 78 | 4406-4409 | Gene | denotes | Rox | Gene:4335 |
| 79 | 4347-4355 | Species | denotes | SARS-CoV | Tax:694009 |
| 80 | 4519-4526 | Species | denotes | patient | Tax:9606 |
| 81 | 4789-4797 | Species | denotes | SARS-CoV | Tax:694009 |
| 87 | 5303-5306 | Gene | denotes | Rox | Gene:4335 |
| 88 | 5361-5368 | Species | denotes | patient | Tax:9606 |
| 89 | 5514-5521 | Species | denotes | patient | Tax:9606 |
| 90 | 5551-5561 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 91 | 5625-5633 | Species | denotes | patients | Tax:9606 |
| 93 | 4959-4969 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 96 | 5805-5813 | Species | denotes | SARS-CoV | Tax:694009 |
| 97 | 5867-5874 | Species | denotes | patient | Tax:9606 |
| 100 | 6085-6086 | Gene | denotes | E | Gene:43740570 |
| 101 | 6005-6013 | Species | denotes | SARS-CoV | Tax:694009 |
| 106 | 6134-6135 | Gene | denotes | E | Gene:43740570 |
| 107 | 6205-6206 | Gene | denotes | E | Gene:43740570 |
| 108 | 6182-6199 | Species | denotes | Wuhan coronavirus | Tax:2697049 |
| 109 | 6224-6232 | Species | denotes | SARS-CoV | Tax:694009 |
| 111 | 6359-6360 | Gene | denotes | E | Gene:43740570 |
| 113 | 6435-6438 | Chemical | denotes | RFU | |
| 118 | 6503-6504 | Gene | denotes | E | Gene:43740570 |
| 119 | 6480-6497 | Species | denotes | Wuhan coronavirus | Tax:2697049 |
| 120 | 6531-6539 | Species | denotes | SARS-CoV | Tax:694009 |
| 121 | 6592-6599 | Species | denotes | patient | Tax:9606 |
| 123 | 6776-6777 | Gene | denotes | E | Gene:43740570 |
| 130 | 7137-7140 | Gene | denotes | Rox | Gene:4335 |
| 131 | 8086-8087 | Gene | denotes | E | Gene:43740570 |
| 132 | 7803-7804 | Gene | denotes | E | Gene:43740570 |
| 133 | 7947-7954 | Species | denotes | patient | Tax:9606 |
| 134 | 8063-8080 | Species | denotes | Wuhan coronavirus | Tax:2697049 |
| 135 | 8097-8105 | Species | denotes | SARS-CoV | Tax:694009 |
| 138 | 8628-8629 | Gene | denotes | E | Gene:43740570 |
| 139 | 8544-8554 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 145 | 8955-8956 | Gene | denotes | E | Gene:43740570 |
| 146 | 8933-8943 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 147 | 9123-9133 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 148 | 9197-9207 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 149 | 9332-9342 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 151 | 10223-10233 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 155 | 10370-10387 | Species | denotes | novel coronavirus | Tax:2697049 |
| 156 | 10685-10693 | Species | denotes | patients | Tax:9606 |
| 157 | 10946-10956 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 161 | 11139-11149 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 162 | 11340-11347 | Species | denotes | patient | Tax:9606 |
| 163 | 11331-11339 | Disease | denotes | COVID-19 | MESH:C000657245 |
| 168 | 12296-12297 | Gene | denotes | E | Gene:43740570 |
| 169 | 12032-12033 | Gene | denotes | E | Gene:43740570 |
| 170 | 11581-11589 | Species | denotes | SARS-CoV | Tax:694009 |
| 171 | 12043-12053 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 178 | 13067-13068 | Gene | denotes | E | Gene:43740570 |
| 179 | 13572-13573 | Gene | denotes | E | Gene:43740570 |
| 180 | 13419-13420 | Gene | denotes | E | Gene:43740570 |
| 181 | 12967-12968 | Gene | denotes | E | Gene:43740570 |
| 182 | 12832-12833 | Gene | denotes | E | Gene:43740570 |
| 183 | 12577-12593 | Chemical | denotes | oligonucleotides | MESH:D009841 |
| 189 | 13800-13801 | Gene | denotes | E | Gene:43740570 |
| 190 | 13652-13662 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
| 191 | 14062-14073 | Species | denotes | coronavirus | Tax:11118 |
| 192 | 14092-14095 | Species | denotes | CoV | Tax:11118 |
| 193 | 14109-14119 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
LitCovid-PD-FMA-UBERON
| Id | Subject | Object | Predicate | Lexical cue | fma_id |
|---|---|---|---|---|---|
| T1 | 1723-1727 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T2 | 1737-1741 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T3 | 2377-2381 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T4 | 2445-2448 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T5 | 2544-2548 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T6 | 2668-2674 | Body_part | denotes | sputum | http://purl.org/sig/ont/fma/fma312401 |
| T7 | 2725-2731 | Body_part | denotes | Sputum | http://purl.org/sig/ont/fma/fma312401 |
| T8 | 2794-2797 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T9 | 2982-2986 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T10 | 3034-3038 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T11 | 3270-3273 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T12 | 3564-3567 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T13 | 4358-4362 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T14 | 4810-4813 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T15 | 4853-4857 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T16 | 5205-5209 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T17 | 5251-5255 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T18 | 5816-5820 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T19 | 5961-5965 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T20 | 6026-6029 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T21 | 6087-6091 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T22 | 6136-6140 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T23 | 6207-6211 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T24 | 6245-6248 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T25 | 6361-6365 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T26 | 6505-6509 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T27 | 6552-6555 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T28 | 6778-6782 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T29 | 7326-7329 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T30 | 7805-7809 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T31 | 7874-7878 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T32 | 8088-8092 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T33 | 8126-8129 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T34 | 8630-8634 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T35 | 8957-8961 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T36 | 9576-9579 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T37 | 11592-11596 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T38 | 11640-11644 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T39 | 11737-11741 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T40 | 12034-12038 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T41 | 12065-12069 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T42 | 12298-12302 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T43 | 12719-12722 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T44 | 12770-12773 | Body_part | denotes | RNA | http://purl.org/sig/ont/fma/fma67095 |
| T45 | 12834-12838 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T46 | 12969-12973 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T47 | 13069-13073 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T48 | 13421-13425 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T49 | 13574-13578 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
| T50 | 13802-13806 | Body_part | denotes | gene | http://purl.org/sig/ont/fma/fma74402 |
LitCovid-PD-UBERON
| Id | Subject | Object | Predicate | Lexical cue | uberon_id |
|---|---|---|---|---|---|
| T1 | 2668-2674 | Body_part | denotes | sputum | http://purl.obolibrary.org/obo/UBERON_0007311 |
| T2 | 2725-2731 | Body_part | denotes | Sputum | http://purl.obolibrary.org/obo/UBERON_0007311 |
| T3 | 6698-6703 | Body_part | denotes | scale | http://purl.obolibrary.org/obo/UBERON_0002542 |
LitCovid_AGAC
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| p13283s8 | 8407-8416 | NegReg | denotes | decreased |
LitCovid-PD-MONDO
| Id | Subject | Object | Predicate | Lexical cue | mondo_id |
|---|---|---|---|---|---|
| T5 | 518-526 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T6 | 717-764 | Disease | denotes | severe acute respiratory syndrome coronavirus 2 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T7 | 717-750 | Disease | denotes | severe acute respiratory syndrome | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T8 | 766-774 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T9 | 782-795 | Disease | denotes | infections in | http://purl.obolibrary.org/obo/MONDO_0005550 |
| T10 | 1054-1062 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T11 | 1365-1373 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T12 | 1449-1473 | Disease | denotes | coronavirus disease 2019 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T13 | 1475-1483 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T14 | 1627-1635 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T15 | 2424-2432 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T16 | 2596-2604 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T17 | 3146-3154 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T18 | 3159-3167 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T19 | 3188-3196 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T20 | 3387-3395 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T21 | 3553-3557 | Disease | denotes | SARS | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T22 | 3588-3596 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T23 | 3675-3683 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T24 | 4347-4355 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T25 | 4789-4797 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T26 | 4959-4967 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T27 | 5132-5134 | Disease | denotes | R2 | http://purl.obolibrary.org/obo/MONDO_0019903 |
| T28 | 5551-5559 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T29 | 5805-5813 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T30 | 6005-6013 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T31 | 6224-6232 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T32 | 6531-6539 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T33 | 8097-8105 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T34 | 8544-8552 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T35 | 8933-8941 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T36 | 9123-9131 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T37 | 9197-9205 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T38 | 9332-9340 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T39 | 10034-10043 | Disease | denotes | influenza | http://purl.obolibrary.org/obo/MONDO_0005812 |
| T40 | 10223-10231 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T41 | 10946-10954 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T42 | 11139-11147 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T43 | 11331-11339 | Disease | denotes | COVID-19 | http://purl.obolibrary.org/obo/MONDO_0100096 |
| T44 | 11581-11589 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T45 | 12043-12051 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T46 | 13652-13660 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
| T47 | 14109-14117 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
LitCovid-PD-CLO
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T3 | 51-52 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T4 | 134-137 | http://purl.obolibrary.org/obo/CLO_0051582 | denotes | has |
| T5 | 417-418 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T6 | 441-442 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T7 | 572-573 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T8 | 1124-1136 | http://purl.obolibrary.org/obo/OBI_0000245 | denotes | Organization |
| T9 | 1386-1388 | http://purl.obolibrary.org/obo/CLO_0050509 | denotes | 27 |
| T10 | 1649-1656 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T11 | 1723-1727 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T12 | 1737-1741 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T13 | 1831-1837 | http://purl.obolibrary.org/obo/CLO_0001929 | denotes | Berlin |
| T14 | 1904-1909 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | Virus |
| T15 | 2239-2245 | http://purl.obolibrary.org/obo/CLO_0001929 | denotes | Berlin |
| T16 | 2304-2309 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | Virus |
| T17 | 2377-2381 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T18 | 2544-2548 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T19 | 2562-2568 | http://purl.obolibrary.org/obo/CLO_0001929 | denotes | Berlin |
| T20 | 2855-2856 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T21 | 2930-2936 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
| T22 | 2982-2986 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T23 | 3034-3038 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T24 | 3113-3115 | http://purl.obolibrary.org/obo/CLO_0008285 | denotes | P1 |
| T25 | 3131-3133 | http://purl.obolibrary.org/obo/CLO_0008307 | denotes | P2 |
| T26 | 3225-3227 | http://purl.obolibrary.org/obo/CLO_0008307 | denotes | P2 |
| T27 | 3241-3246 | http://purl.obolibrary.org/obo/NCBITaxon_9606 | denotes | human |
| T28 | 3320-3326 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
| T29 | 3572-3574 | http://purl.obolibrary.org/obo/CLO_0053733 | denotes | 11 |
| T30 | 3692-3698 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
| T31 | 3894-3906 | http://purl.obolibrary.org/obo/OBI_0000245 | denotes | Organization |
| T32 | 3937-3943 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
| T33 | 4007-4013 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
| T34 | 4078-4079 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T35 | 4104-4109 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tests |
| T36 | 4195-4199 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
| T37 | 4203-4205 | http://purl.obolibrary.org/obo/CLO_0050509 | denotes | 27 |
| T38 | 4215-4216 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T39 | 4321-4327 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
| T40 | 4358-4362 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T41 | 4399-4404 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | Virus |
| T42 | 4465-4472 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signals |
| T43 | 4512-4518 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
| T44 | 4722-4729 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signals |
| T45 | 4853-4857 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T46 | 5004-5005 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T47 | 5017-5021 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
| T48 | 5118-5119 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T49 | 5186-5193 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signals |
| T50 | 5205-5209 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T51 | 5238-5245 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signals |
| T52 | 5251-5255 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T53 | 5265-5266 | http://purl.obolibrary.org/obo/CLO_0001021 | denotes | b |
| T54 | 5296-5301 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | Virus |
| T55 | 5357-5360 | http://purl.obolibrary.org/obo/CLO_0001445 | denotes | 617 |
| T56 | 5507-5509 | http://purl.obolibrary.org/obo/CLO_0053733 | denotes | 11 |
| T57 | 5510-5513 | http://purl.obolibrary.org/obo/CLO_0001195 | denotes | 219 |
| T58 | 5702-5705 | http://purl.obolibrary.org/obo/CLO_0051456 | denotes | a E |
| T59 | 5724-5725 | http://purl.obolibrary.org/obo/CLO_0001021 | denotes | b |
| T60 | 5790-5797 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signals |
| T61 | 5816-5820 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T62 | 5860-5866 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
| T63 | 5961-5965 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T64 | 5974-5980 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
| T65 | 6087-6091 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T66 | 6136-6140 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T67 | 6142-6148 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
| T68 | 6207-6211 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T69 | 6361-6365 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T70 | 6388-6395 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signals |
| T71 | 6505-6509 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T72 | 6675-6681 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | Signal |
| T73 | 6778-6782 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T74 | 6897-6900 | http://purl.obolibrary.org/obo/CLO_0001313 | denotes | 3–6 |
| T75 | 6917-6924 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signals |
| T76 | 7014-7021 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signals |
| T77 | 7130-7135 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | Virus |
| T78 | 7241-7242 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T79 | 7274-7280 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
| T80 | 7330-7335 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | Virus |
| T81 | 7398-7399 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T82 | 7431-7437 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
| T83 | 7805-7809 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T84 | 7810-7817 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signals |
| T85 | 7857-7864 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signals |
| T86 | 7874-7878 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T87 | 7940-7946 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
| T88 | 8088-8092 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T89 | 8484-8485 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T90 | 8512-8516 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
| T91 | 8630-8634 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T92 | 8635-8642 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signals |
| T93 | 8644-8645 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
| T94 | 8700-8706 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
| T95 | 8836-8843 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signals |
| T96 | 8881-8882 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T97 | 8957-8961 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T98 | 8981-8983 | http://purl.obolibrary.org/obo/CLO_0054055 | denotes | 71 |
| T99 | 9038-9040 | http://purl.obolibrary.org/obo/CLO_0053733 | denotes | 11 |
| T100 | 9102-9103 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T101 | 9144-9145 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T102 | 9445-9446 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T103 | 9525-9532 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T104 | 9628-9629 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T105 | 9886-9890 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
| T106 | 10368-10369 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T107 | 10720-10726 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
| T108 | 10964-10966 | http://purl.obolibrary.org/obo/CLO_0053733 | denotes | 11 |
| T109 | 11020-11021 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T110 | 11038-11045 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T111 | 11277-11278 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T112 | 11475-11482 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | testing |
| T113 | 11536-11537 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T114 | 11592-11596 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T115 | 11640-11644 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T116 | 11737-11741 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T117 | 11788-11789 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T118 | 11837-11840 | http://purl.obolibrary.org/obo/CLO_0051582 | denotes | has |
| T119 | 11930-11931 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T120 | 12034-12038 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T121 | 12065-12069 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T122 | 12096-12103 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signals |
| T123 | 12159-12166 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signals |
| T124 | 12257-12265 | http://purl.obolibrary.org/obo/CLO_0001658 | denotes | activity |
| T125 | 12298-12302 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T126 | 12395-12396 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T127 | 12444-12445 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T128 | 12468-12475 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signals |
| T129 | 12652-12653 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T130 | 12748-12749 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T131 | 12787-12788 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T132 | 12806-12807 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T133 | 12834-12838 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T134 | 12969-12973 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T135 | 13069-13073 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T136 | 13157-13158 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T137 | 13211-13218 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signals |
| T138 | 13248-13255 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signals |
| T139 | 13421-13425 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T140 | 13574-13578 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T141 | 13598-13599 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
| T142 | 13802-13806 | http://purl.obolibrary.org/obo/OGG_0000000002 | denotes | gene |
| T143 | 13886-13892 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
| T144 | 13958-13965 | http://purl.obolibrary.org/obo/SO_0000418 | denotes | signals |
| T145 | 14090-14091 | http://purl.obolibrary.org/obo/CLO_0001021 | denotes | B |
| T146 | 14135-14136 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
LitCovid-PD-CHEBI
| Id | Subject | Object | Predicate | Lexical cue | chebi_id |
|---|---|---|---|---|---|
| T1 | 451-454 | Chemical | denotes | CFX | http://purl.obolibrary.org/obo/CHEBI_209807 |
| T2 | 1300-1316 | Chemical | denotes | oligonucleotides | http://purl.obolibrary.org/obo/CHEBI_7754 |
| T3 | 2761-2770 | Chemical | denotes | phosphate | http://purl.obolibrary.org/obo/CHEBI_18367|http://purl.obolibrary.org/obo/CHEBI_26020|http://purl.obolibrary.org/obo/CHEBI_35780|http://purl.obolibrary.org/obo/CHEBI_43474 |
| T7 | 3113-3115 | Chemical | denotes | P1 | http://purl.obolibrary.org/obo/CHEBI_60949 |
| T8 | 3131-3133 | Chemical | denotes | P2 | http://purl.obolibrary.org/obo/CHEBI_33472 |
| T9 | 3208-3213 | Chemical | denotes | probe | http://purl.obolibrary.org/obo/CHEBI_50406 |
| T10 | 3225-3227 | Chemical | denotes | P2 | http://purl.obolibrary.org/obo/CHEBI_33472 |
| T11 | 5326-5328 | Chemical | denotes | ND | http://purl.obolibrary.org/obo/CHEBI_73419 |
| T12 | 5330-5332 | Chemical | denotes | ND | http://purl.obolibrary.org/obo/CHEBI_73419 |
| T13 | 5682-5684 | Chemical | denotes | ND | http://purl.obolibrary.org/obo/CHEBI_73419 |
| T14 | 6795-6800 | Chemical | denotes | probe | http://purl.obolibrary.org/obo/CHEBI_50406 |
| T15 | 7688-7693 | Chemical | denotes | probe | http://purl.obolibrary.org/obo/CHEBI_50406 |
| T16 | 12577-12593 | Chemical | denotes | oligonucleotides | http://purl.obolibrary.org/obo/CHEBI_7754 |
| T17 | 12612-12620 | Chemical | denotes | reagents | http://purl.obolibrary.org/obo/CHEBI_33893 |
| T18 | 12884-12892 | Chemical | denotes | reagents | http://purl.obolibrary.org/obo/CHEBI_33893 |
| T19 | 13438-13443 | Chemical | denotes | probe | http://purl.obolibrary.org/obo/CHEBI_50406 |
LitCovid-PD-GO-BP
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T1 | 2539-2543 | http://purl.obolibrary.org/obo/GO_0003968 | denotes | RdRP |
| T2 | 3247-3254 | http://purl.obolibrary.org/obo/GO_0004526 | denotes | RNAse P |
| T3 | 5443-5460 | http://purl.obolibrary.org/obo/GO_0003887 | denotes | TaqDNA Polymerase |
| T4 | 7518-7535 | http://purl.obolibrary.org/obo/GO_0003887 | denotes | TaqDNA Polymerase |
LitCovid-sentences
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| T6 | 0-101 | Sentence | denotes | At the end of December 2019, an outbreak caused by a novel coronavirus was announced in Wuhan, China. |
| T7 | 102-278 | Sentence | denotes | Since then, the number of cases has increased, especially in China but also in other countries, and public health authorities are in need to rapidly implement diagnostic tools. |
| T8 | 279-465 | Sentence | denotes | In this paper, we describe our laboratory experiences with the novel real-time RT-PCR assays comparing different one-step PCR systems and a commercial kit, using a Bio-Rad CFX 96 cycler. |
| T9 | 467-528 | Sentence | denotes | Timely implementation of molecular diagnostics for SARS-CoV-2 |
| T10 | 529-928 | Sentence | denotes | In connection with the ongoing outbreak of a novel coronavirus in the province Hubei and surrounding areas in China, it was expected that Europe would also be confronted with the emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as infections in travellers in several Asian countries outside of China were confirmed shortly after the announcement of the outbreak in Wuhan [1-4]. |
| T11 | 929-1095 | Sentence | denotes | Therefore, it was necessary to rapidly implement adequately quick and sensitive diagnostic assays for outbreak management of SARS-CoV-2 in public health laboratories. |
| T12 | 1096-1267 | Sentence | denotes | As soon as the World Health Organization (WHO) published the first protocols for real-time RT-PCR assays, the Bavarian Food and Health Authority started to implement them. |
| T13 | 1268-1406 | Sentence | denotes | We ordered control material and oligonucleotides (see details below) in week 4 and ran our first SARS-CoV-2 assays on 27 January (week 5). |
| T14 | 1407-1514 | Sentence | denotes | On the same day, the first German case of coronavirus disease 2019 (COVID-19) was diagnosed in Bavaria [1]. |
| T15 | 1515-1676 | Sentence | denotes | In the following days, health authorities implemented comprehensive measures to prevent further transmission of SARS-CoV-2, including testing of contact persons. |
| T16 | 1677-1842 | Sentence | denotes | We initially used the protocol based on the E gene and RdRp gene developed by the German Consiliary Laboratory for Coronaviruses hosted at the Charité in Berlin [5]. |
| T17 | 1843-2040 | Sentence | denotes | Real-time RT-PCR was initially performed with the QuantiTect Virus +Rox Vial kit (QIAGEN, Hilden, Germany) on the Bio-Rad CFX96 Touch Real-Time PCR Detection System (Bio-Rad, Feldkirchen, Germany). |
| T18 | 2041-2163 | Sentence | denotes | The kit was chosen for its frequent and successful use in our laboratory with other assays and its immediate availability. |
| T19 | 2164-2256 | Sentence | denotes | Primers and probes were used as described [5] and provided by TIB Molbiol (Berlin, Germany). |
| T20 | 2257-2483 | Sentence | denotes | Control material was ordered from the European Virus Archive (EVAg) and consisted of synthetic Wuhan coronavirus 2019 E gene control (reference number 026N-03866) and SARS-CoV Frankfurt 1 RNA (reference number 004N-02005) [6]. |
| T21 | 2484-2622 | Sentence | denotes | In addition, the control of LightMix Modular Wuhan CoV RdRP-gene (TibMolbiol, Berlin, Germany) was used for the SARS-CoV-2 specific assay. |
| T22 | 2623-2724 | Sentence | denotes | Respiratory samples (nasopharyngeal swabs or sputum) were obtained from patients and contact persons. |
| T23 | 2725-2793 | Sentence | denotes | Sputum samples were diluted in 2 mL phosphate buffered saline (PBS). |
| T24 | 2794-2913 | Sentence | denotes | RNA was extracted using the QIAamp Bio Robot kit (QIAGEN) on a Hamilton Microlab Star (Hamilton, Bonaduz, Switzerland). |
| T25 | 2914-3232 | Sentence | denotes | Each sample was tested by three PCRs: the screening assay for the E gene and two confirmatory assays targeting the RdRp gene, all performed as recommended in [5], with either both probes (RdRP_SARSr-P1 and RdRP_SARSr-P2), detecting SARS-CoV and SARS-CoV-2, or only with the SARS-CoV-2-specific probe RdRP_SARSr-P2 [5]. |
| T26 | 3233-3289 | Sentence | denotes | We used human RNAse P as control for RNA extraction [7]. |
| T27 | 3290-3357 | Sentence | denotes | The cumulative numbers of all tested samples are shown in Figure 1. |
| T28 | 3358-3506 | Sentence | denotes | Two weeks after starting the SARS-CoV-2 diagnostics, we had analysed 669 respiratory samples at the Bavarian Health and Food Safety Authority (LGL). |
| T29 | 3507-3568 | Sentence | denotes | Among them, seven showed positive results for SARS CoV-2 RNA. |
| T30 | 3569-3632 | Sentence | denotes | By 11 February, 14 COVID-19 cases had been detected in Bavaria. |
| T31 | 3633-3742 | Sentence | denotes | Figure 1 Cumulative numbers of suspected COVID-19 samples tested during week 5 and 6 2020, Bavaria (n = 675) |
| T32 | 3743-3832 | Sentence | denotes | COVID: coronavirus disease; PHEIC: public health emergency of international concern; LGL: |
| T33 | 3833-3880 | Sentence | denotes | Bavarian Health and Food Safety Authority; WHO: |
| T34 | 3881-3907 | Sentence | denotes | World Health Organization. |
| T35 | 3908-4047 | Sentence | denotes | The figure shows all samples tested at LGL, negative and positive, as well as six positive samples tested in other laboratories in Bavaria. |
| T36 | 4048-4116 | Sentence | denotes | All data are cumulative, with a final total of positive tests of 13. |
| T37 | 4118-4155 | Sentence | denotes | Comparison of one-step RT-PCR systems |
| T38 | 4156-4328 | Sentence | denotes | During the 2 weeks after the first PCR test on 27 January, a rapidly increasing number of case contacts in Bavaria was identified and their respiratory samples were tested. |
| T39 | 4329-4664 | Sentence | denotes | We found that the SARS-CoV E gene screening assay with the QuantiTect Virus +Rox Vial kit showed moderate to high amounts of unspecific signals in late cycles in 61% (451/743) of the tested patient samples and also of negative extraction and non-template controls (Table, Figure 2), which complicated the evaluation of the qPCR result. |
| T40 | 4665-4745 | Sentence | denotes | The RdRp assays were basically free from such unspecific signals in late cycles. |
| T41 | 4746-4884 | Sentence | denotes | Cycle threshold (Ct) values of the control SARS-CoV Frankfurt 1 RNA were reached three cycles earlier in E gene assay than in RdRp assays. |
| T42 | 4885-5074 | Sentence | denotes | Table Comparison of two different one-step real-time RT-PCR systems with SARS-CoV-2 assays from Corman et al. [5] and a commercial test kit with kit-specific assays, Bavaria, February 2020 |
| T43 | 5075-5284 | Sentence | denotes | Real-time RT-PCR system PCR efficiency (%)a, linearity (R2) Limit of detection (copies/reaction) Unspecific signals count in E gene assay in totalb Unspecific signals in E gene assay (%)b Run time (hours) |
| T44 | 5285-5389 | Sentence | denotes | QuantiTect Virus +Rox Vial kit (QIAGEN) ND ND 451/743(75/126 NC, 376/617 patient samples) 60.7 1:50 |
| T45 | 5390-5541 | Sentence | denotes | SuperScript III One-step RT-PCR System with Platinum TaqDNA Polymerase (Invitrogen) 95 / 0,99c 50c 13/257(2/38 NC,11/219 patient samples) 5.1 1:28 |
| T46 | 5542-5651 | Sentence | denotes | RealStar SARS-CoV-2 RT-PCR kit 1.0 (Altona) 125 / 0,97d 10d 0/111(0/38 NC, 0/73 patients samples) 0 2:15 |
| T47 | 5652-5701 | Sentence | denotes | NC: negative control samples; ND: not determined. |
| T48 | 5702-5723 | Sentence | denotes | a E = 10−1/slope − 1. |
| T49 | 5724-5944 | Sentence | denotes | b Indicated counts and percentage values of unspecific background signals in the SARS-CoV E gene assay are based on the total number of tested patient samples as well as the negative extraction and non-template controls. |
| T50 | 5945-6076 | Sentence | denotes | c Only for RdRp gene assays, tested with four replicates of SARS-CoV Frankfurt 1 RNA [6]; 10-fold serial dilutions were determined. |
| T51 | 6077-6118 | Sentence | denotes | For the E gene, the assay was not linear. |
| T52 | 6119-6300 | Sentence | denotes | d Only for the E gene, tested with two replicates of synthetic Wuhan coronavirus 2019 E gene control and SARS-CoV Frankfurt 1 RNA each [6]; 10-fold serial dilutions were determined. |
| T53 | 6301-6434 | Sentence | denotes | Figure 2 Example image of real-time RT-PCR curves of the E gene assay with unspecific signals at late cycles, Bavaria, February 2020 |
| T54 | 6435-6468 | Sentence | denotes | RFU: relative fluorescence units. |
| T55 | 6469-6476 | Sentence | denotes | Curves: |
| T56 | 6477-6479 | Sentence | denotes | 1: |
| T57 | 6480-6674 | Sentence | denotes | Wuhan coronavirus 2019 E gene positive control; 2: SARS-CoV Frankfurt 1 RNA positive control; 3,4,6,8: negative patient samples; 5: extraction negative control; 7: non-template negative control. |
| T58 | 6675-6725 | Sentence | denotes | Signal is given in log scale with threshold = 200. |
| T59 | 6726-6821 | Sentence | denotes | PCR was performed with SuperScript III system and E gene primers and probe as published in [5]. |
| T60 | 6822-6889 | Sentence | denotes | Curves of positive controls (1 and 2) show expected sigmoid curves. |
| T61 | 6890-6955 | Sentence | denotes | Curves 3–6 show unspecific signals with increase above threshold. |
| T62 | 6956-7032 | Sentence | denotes | Curves below threshold were not considered as significant signals (7 and 8). |
| T63 | 7033-7577 | Sentence | denotes | Three additional one-step real-time PCR systems were compared with the initially used QuantiTect Virus +Rox Vial kit (QIAGEN) (Table): (i) OneStep RT-PCR kit (QIAGEN; data not shown in the Table because only a limited number of samples were tested in only one run), (ii) LightCycler Multiplex RNA Virus Master (Roche, Mannheim, Germany; data not shown because only a limited number of samples were tested in only one run) and (iii) SuperScript III One-Step RT-PCR system with Platinum TaqDNA Polymerase (Invitrogen, Darmstadt, Germany) (Table). |
| T64 | 7578-7740 | Sentence | denotes | Each assay protocol and thermoprofile was adjusted to the recommendations of the manufacturer, but primer and probe concentrations were the same as published [5]. |
| T65 | 7741-7818 | Sentence | denotes | They all showed comparable results in reduction of unspecific E gene signals. |
| T66 | 7819-8180 | Sentence | denotes | Using SuperScript III, the unspecific signals in the E gene screening assay were significantly reduced to 5% (13/257) in tested patient samples and negative extraction and non-template controls (Table), whereas Ct values for positive controls (Wuhan coronavirus 2019 E gene and SARS-CoV Frankfurt 1 genomic RNA [3]) were in the same range in QuantiTect (median: |
| T67 | 8181-8193 | Sentence | denotes | 29.1; range: |
| T68 | 8194-8240 | Sentence | denotes | 26.8–32.4; n = 85) and Superscript (median Ct: |
| T69 | 8241-8253 | Sentence | denotes | 28.1; range: |
| T70 | 8254-8280 | Sentence | denotes | 26.4–31.0; n = 30) setups. |
| T71 | 8281-8448 | Sentence | denotes | In the following, we decided to switch to the SuperScript III system as recommended by Corman et al. [5], also because of its decreased thermoprofile run-time (Table). |
| T72 | 8449-8534 | Sentence | denotes | Moreover, we additionally included a newly launched commercial test kit in our study: |
| T73 | 8535-8643 | Sentence | denotes | RealStar SARS-CoV-2 RT-PCR kit 1.0 (Altona, Hamburg, Germany), which did not show unspecific E gene signals. |
| T74 | 8644-8752 | Sentence | denotes | A summary of the assay features of the three PCR setups tested and compared in detail is shown in the Table. |
| T75 | 8753-8950 | Sentence | denotes | For evaluation of assay performance regarding efficiency, linearity and unspecific signals, we used the SuperScript protocol in a direct comparison of 73 samples with the RealStar SARS-CoV-2 assay. |
| T76 | 8951-9183 | Sentence | denotes | The E gene assays showed 97% (71/73) identical results in both assays (60 negative and 11 positive results as well as two divergent results, both with a positive Real Star SARS-CoV-2 assay and a negative SuperScript protocol assay). |
| T77 | 9184-9309 | Sentence | denotes | The specific SARS-CoV-2 assays gave in 67 (92%) identical results (60 negative and seven positive) and six divergent results. |
| T78 | 9310-9375 | Sentence | denotes | Overall, the RealStar SARS-CoV-2 kit seemed to be more sensitive. |
| T79 | 9377-9385 | Sentence | denotes | Workflow |
| T80 | 9386-9552 | Sentence | denotes | With increasing sample numbers, it is crucial to implement a new assay into routine laboratory workflows that already exist for diagnostic testing of other pathogens. |
| T81 | 9553-9717 | Sentence | denotes | Sample preparation and RNA extraction were carried out at BSL2 level under a safety class 2 cabinet wearing FFP3 filter masks following the WHO recommendations [8]. |
| T82 | 9718-9875 | Sentence | denotes | Samples arriving at our laboratory before 10:00 h were analysed on the same day and results were reported 6–7 h later to local health authorities (Figure 3). |
| T83 | 9876-9918 | Sentence | denotes | Our daily test capacity was ca 80 samples. |
| T84 | 9919-10092 | Sentence | denotes | It should be taken into account that well trained and experienced personnel is needed and seasonal pathogens, e.g. influenza and noroviruses, had to be analysed in parallel. |
| T85 | 10093-10174 | Sentence | denotes | Overall, we managed to report the results for 97% of samples within the same day. |
| T86 | 10175-10288 | Sentence | denotes | Figure 3 Flowchart and routine timeline of the SARS-CoV-2 diagnostic workflow at the LGL, Bavaria, February 2020 |
| T87 | 10289-10293 | Sentence | denotes | LGL: |
| T88 | 10294-10336 | Sentence | denotes | Bavarian Health and Food Safety Authority. |
| T89 | 10338-10348 | Sentence | denotes | Discussion |
| T90 | 10349-10480 | Sentence | denotes | On 7 January 2020, a novel coronavirus was identified and shortly after, the first sequence of the new strain was published [9,10]. |
| T91 | 10481-10601 | Sentence | denotes | The main task of public health authorities is to react quickly to emerging pathogens of global threat to prevent spread. |
| T92 | 10602-10739 | Sentence | denotes | These responses include containment strategies, which means that close contacts of patients have to be identified and tested immediately. |
| T93 | 10740-10968 | Sentence | denotes | Reusken et al. identified the availability of positive control material and primer/probes as well as the lack of skilled personnel and time as the most prominent challenges in the implementation of the new SARS-CoV-2 assay [11]. |
| T94 | 10969-11065 | Sentence | denotes | National and local public health laboratories play a crucial role in testing emerging pathogens. |
| T95 | 11066-11424 | Sentence | denotes | The Public Health Microbiology Laboratory in Bavaria was confronted with SARS-CoV-2-related events very early: once the assays and control materials arrived and the PCR assays were performed for the first time, a large contact investigation around the first German COVID-19 patient (data not shown) was immediately started, with so far more than 700 samples. |
| T96 | 11425-11554 | Sentence | denotes | Evaluation and verification of the new assays and testing real samples had to take place simultaneously within a very short time. |
| T97 | 11555-11721 | Sentence | denotes | We realised soon that the SARS-CoV E gene assay was more sensitive than the two RdRp gene assays combined with the one-step RT-PCR system available in our laboratory. |
| T98 | 11722-11821 | Sentence | denotes | However, our E gene assay showed high background levels hampering a clear evaluation of the assays. |
| T99 | 11822-11950 | Sentence | denotes | Each mastermix has its own proprietary composition, which may explain the differences in the performance of a certain PCR assay. |
| T100 | 11951-12115 | Sentence | denotes | Using commercial kits with optimised target regions and primer sequences (in the E gene and SARS-CoV-2-specific S gene) ruled out the unspecific signals completely. |
| T101 | 12116-12426 | Sentence | denotes | Hence, reasons for the observed unspecific signals may be dimerisation of primers and probes and/or unspecific primer binding and polymerase activity in the targeted region of the E gene, probably also depending on thermal profile and cycler-specific differences, or most likely a combination of these factors. |
| T102 | 12427-12695 | Sentence | denotes | Contamination as a reason for unspecific signals was ruled out, as stringent prevention measures were taken, e.g. strict separation of working areas: oligonucleotides and PCR mastermix reagents were handled in one room under a PCR hood with specified laboratory coats. |
| T103 | 12696-12762 | Sentence | denotes | Sample preparation and RNA extraction took place in a second room. |
| T104 | 12763-12817 | Sentence | denotes | Sample RNA was added in a third room under a PCR hood. |
| T105 | 12818-12879 | Sentence | denotes | The synthetic E gene control was added last to the mastermix. |
| T106 | 12880-12936 | Sentence | denotes | All reagents were aliquoted and aliquots used once only. |
| T107 | 12937-13219 | Sentence | denotes | Contaminations from synthetic E gene present in primer batches upon delivery can be ruled out as well, although only one batch of E gene primers and probes was used with the QuantiTect and Superscript III setup, as only a certain proportion of samples showed the unspecific signals. |
| T108 | 13220-13386 | Sentence | denotes | Furthermore, the unspecific signals were significantly reduced in the Superscript III setup, which showed that its sensitivity was comparable to the QuantiTect setup. |
| T109 | 13387-13635 | Sentence | denotes | In addition, the initially used E gene primers and probe were separately used as templates with the RealStar kit and no amplification was observed, whereas the corresponding artificial E gene template delivered a clear S-shaped curve with this kit. |
| T110 | 13637-13647 | Sentence | denotes | Conclusion |
| T111 | 13648-13841 | Sentence | denotes | The SARS-CoV-2 assay from Corman et al. [7] could be used rapidly with the published SuperScript III system, but further optimisation especially of the E gene assay may enhance the sensitivity. |
| T112 | 13842-14149 | Sentence | denotes | The RealStar kit outperformed the two other tested one-step PCR systems in sensitivity and by absence of unspecific signals with the used primer set and the RealStar workflow enhanced laboratory efficiency combining two coronavirus assays (lineage B CoV and specific SARS-CoV-2) with an IC in a triplex PCR. |
| T113 | 14150-14315 | Sentence | denotes | Overall, fast assay development and publication of protocols by expert laboratories allowed public health laboratories to establish diagnostics quickly and act fast. |
| T114 | 14316-14409 | Sentence | denotes | Assay optimisation will further speed up and improve the management of this ongoing outbreak. |
2_test
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32156330-32003551-29325810 | 923-924 | 32003551 | denotes | 1 |
| 32156330-32003551-29325811 | 1511-1512 | 32003551 | denotes | 1 |
| 32156330-31992387-29325812 | 1839-1840 | 31992387 | denotes | 5 |
| 32156330-31992387-29325813 | 2207-2208 | 31992387 | denotes | 5 |
| 32156330-30059721-29325814 | 2480-2481 | 30059721 | denotes | 6 |
| 32156330-31992387-29325815 | 3073-3074 | 31992387 | denotes | 5 |
| 32156330-31992387-29325816 | 3229-3230 | 31992387 | denotes | 5 |
| 32156330-16274752-29325817 | 3286-3287 | 16274752 | denotes | 7 |
| 32156330-31992387-29325818 | 4997-4998 | 31992387 | denotes | 5 |
| 32156330-30059721-29325819 | 6031-6032 | 30059721 | denotes | 6 |
| 32156330-30059721-29325820 | 6255-6256 | 30059721 | denotes | 6 |
| 32156330-31992387-29325821 | 6818-6819 | 31992387 | denotes | 5 |
| 32156330-31992387-29325822 | 7737-7738 | 31992387 | denotes | 5 |
| 32156330-31992387-29325823 | 8383-8384 | 31992387 | denotes | 5 |
| 32156330-32004165-29325824 | 10474-10475 | 32004165 | denotes | 9 |
| 32156330-32015508-29325825 | 10476-10478 | 32015508 | denotes | 10 |
| 32156330-32046815-29325826 | 10964-10966 | 32046815 | denotes | 11 |
| 32156330-16274752-29325827 | 13689-13690 | 16274752 | denotes | 7 |
MyTest
| Id | Subject | Object | Predicate | Lexical cue |
|---|---|---|---|---|
| 32156330-32003551-29325810 | 923-924 | 32003551 | denotes | 1 |
| 32156330-32003551-29325811 | 1511-1512 | 32003551 | denotes | 1 |
| 32156330-31992387-29325812 | 1839-1840 | 31992387 | denotes | 5 |
| 32156330-31992387-29325813 | 2207-2208 | 31992387 | denotes | 5 |
| 32156330-30059721-29325814 | 2480-2481 | 30059721 | denotes | 6 |
| 32156330-31992387-29325815 | 3073-3074 | 31992387 | denotes | 5 |
| 32156330-31992387-29325816 | 3229-3230 | 31992387 | denotes | 5 |
| 32156330-16274752-29325817 | 3286-3287 | 16274752 | denotes | 7 |
| 32156330-31992387-29325818 | 4997-4998 | 31992387 | denotes | 5 |
| 32156330-30059721-29325819 | 6031-6032 | 30059721 | denotes | 6 |
| 32156330-30059721-29325820 | 6255-6256 | 30059721 | denotes | 6 |
| 32156330-31992387-29325821 | 6818-6819 | 31992387 | denotes | 5 |
| 32156330-31992387-29325822 | 7737-7738 | 31992387 | denotes | 5 |
| 32156330-31992387-29325823 | 8383-8384 | 31992387 | denotes | 5 |
| 32156330-32004165-29325824 | 10474-10475 | 32004165 | denotes | 9 |
| 32156330-32015508-29325825 | 10476-10478 | 32015508 | denotes | 10 |
| 32156330-32046815-29325826 | 10964-10966 | 32046815 | denotes | 11 |
| 32156330-16274752-29325827 | 13689-13690 | 16274752 | denotes | 7 |