PMC:7650537 / 13574-18439
Annnotations
LitCovid-PD-FMA-UBERON
Id | Subject | Object | Predicate | Lexical cue | fma_id |
---|---|---|---|---|---|
T98 | 49-52 | Body_part | denotes | IgG | http://purl.org/sig/ont/fma/fma62872 |
T99 | 62-70 | Body_part | denotes | Antibody | http://purl.org/sig/ont/fma/fma62871 |
T100 | 196-199 | Body_part | denotes | IgG | http://purl.org/sig/ont/fma/fma62872 |
T101 | 209-217 | Body_part | denotes | antibody | http://purl.org/sig/ont/fma/fma62871 |
T102 | 525-530 | Body_part | denotes | serum | http://purl.org/sig/ont/fma/fma63083 |
T103 | 652-655 | Body_part | denotes | IgG | http://purl.org/sig/ont/fma/fma62872 |
T104 | 1405-1408 | Body_part | denotes | IgG | http://purl.org/sig/ont/fma/fma62872 |
T105 | 1642-1650 | Body_part | denotes | antibody | http://purl.org/sig/ont/fma/fma62871 |
T106 | 1831-1834 | Body_part | denotes | IgG | http://purl.org/sig/ont/fma/fma62872 |
T107 | 1841-1849 | Body_part | denotes | antibody | http://purl.org/sig/ont/fma/fma62871 |
T108 | 2052-2055 | Body_part | denotes | IgG | http://purl.org/sig/ont/fma/fma62872 |
T109 | 2216-2219 | Body_part | denotes | IgG | http://purl.org/sig/ont/fma/fma62872 |
T110 | 2226-2234 | Body_part | denotes | antibody | http://purl.org/sig/ont/fma/fma62871 |
T111 | 2275-2278 | Body_part | denotes | IgG | http://purl.org/sig/ont/fma/fma62872 |
T112 | 2317-2319 | Body_part | denotes | v1 | http://purl.org/sig/ont/fma/fma13444|http://purl.org/sig/ont/fma/fma68614 |
T114 | 2472-2475 | Body_part | denotes | IgG | http://purl.org/sig/ont/fma/fma62872 |
T115 | 2687-2689 | Body_part | denotes | v1 | http://purl.org/sig/ont/fma/fma13444|http://purl.org/sig/ont/fma/fma68614 |
T117 | 2708-2710 | Body_part | denotes | v2 | http://purl.org/sig/ont/fma/fma13443|http://purl.org/sig/ont/fma/fma68615 |
T119 | 2822-2825 | Body_part | denotes | IgG | http://purl.org/sig/ont/fma/fma62872 |
T120 | 2842-2845 | Body_part | denotes | IgG | http://purl.org/sig/ont/fma/fma62872 |
T121 | 2874-2884 | Body_part | denotes | Antibodies | http://purl.org/sig/ont/fma/fma62871 |
T122 | 3178-3181 | Body_part | denotes | IgG | http://purl.org/sig/ont/fma/fma62872 |
T123 | 3482-3485 | Body_part | denotes | IgG | http://purl.org/sig/ont/fma/fma62872 |
T124 | 3620-3623 | Body_part | denotes | IgG | http://purl.org/sig/ont/fma/fma62872 |
T125 | 3818-3821 | Body_part | denotes | IgG | http://purl.org/sig/ont/fma/fma62872 |
T126 | 3956-3959 | Body_part | denotes | IgG | http://purl.org/sig/ont/fma/fma62872 |
T127 | 4184-4187 | Body_part | denotes | IgG | http://purl.org/sig/ont/fma/fma62872 |
T128 | 4335-4338 | Body_part | denotes | IgG | http://purl.org/sig/ont/fma/fma62872 |
LitCovid-PD-UBERON
Id | Subject | Object | Predicate | Lexical cue | uberon_id |
---|---|---|---|---|---|
T9 | 525-530 | Body_part | denotes | serum | http://purl.obolibrary.org/obo/UBERON_0001977 |
LitCovid-PD-MONDO
Id | Subject | Object | Predicate | Lexical cue | mondo_id |
---|---|---|---|---|---|
T65 | 38-46 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T66 | 139-147 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T67 | 150-159 | Disease | denotes | infection | http://purl.obolibrary.org/obo/MONDO_0005550 |
T68 | 185-193 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T69 | 333-341 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T70 | 641-649 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T71 | 945-953 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T72 | 1145-1153 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T73 | 1240-1248 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T74 | 1394-1402 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T75 | 1631-1639 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T76 | 1758-1766 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T77 | 1820-1828 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T78 | 1978-1986 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T79 | 2205-2213 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T80 | 2264-2272 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T81 | 2461-2469 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T82 | 2811-2819 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T83 | 2962-2970 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T84 | 3167-3175 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T85 | 4164-4172 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T86 | 4478-4486 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T87 | 4567-4575 | Disease | denotes | SARS-CoV | http://purl.obolibrary.org/obo/MONDO_0005091 |
T88 | 4626-4628 | Disease | denotes | R4 | http://purl.obolibrary.org/obo/MONDO_0015439 |
T89 | 4843-4845 | Disease | denotes | R2 | http://purl.obolibrary.org/obo/MONDO_0019903 |
LitCovid-PD-CLO
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T125 | 71-76 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | Tests |
T126 | 123-124 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T127 | 504-506 | http://purl.obolibrary.org/obo/CLO_0001302 | denotes | 34 |
T128 | 587-590 | http://purl.obolibrary.org/obo/CLO_0050884 | denotes | ten |
T129 | 602-603 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T130 | 621-627 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
T131 | 725-726 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T132 | 843-848 | http://purl.obolibrary.org/obo/NCBITaxon_10239 | denotes | virus |
T133 | 886-887 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T134 | 920-922 | http://purl.obolibrary.org/obo/CLO_0050050 | denotes | S1 |
T135 | 1168-1169 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
T136 | 1179-1182 | http://purl.obolibrary.org/obo/CLO_0050884 | denotes | ten |
T137 | 1296-1298 | http://purl.obolibrary.org/obo/CLO_0050050 | denotes | S1 |
T138 | 1341-1347 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tested |
T139 | 1882-1887 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tests |
T140 | 2077-2081 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
T141 | 2145-2148 | http://purl.obolibrary.org/obo/CLO_0050884 | denotes | ten |
T142 | 2235-2240 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | tests |
T143 | 2418-2422 | http://purl.obolibrary.org/obo/CLO_0001185 | denotes | 2018 |
T144 | 3665-3666 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T145 | 3798-3799 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | A |
T146 | 3917-3919 | http://purl.obolibrary.org/obo/CLO_0050507 | denotes | 22 |
T147 | 3946-3947 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T148 | 4133-4137 | http://purl.obolibrary.org/obo/UBERON_0000473 | denotes | test |
T149 | 4375-4377 | http://purl.obolibrary.org/obo/CLO_0050050 | denotes | S1 |
T150 | 4591-4592 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T151 | 4667-4668 | http://purl.obolibrary.org/obo/CLO_0001020 | denotes | a |
T152 | 4709-4711 | http://purl.obolibrary.org/obo/CLO_0008922 | denotes | S2 |
T153 | 4709-4711 | http://purl.obolibrary.org/obo/CLO_0050052 | denotes | S2 |
LitCovid-PD-CHEBI
Id | Subject | Object | Predicate | Lexical cue | chebi_id |
---|---|---|---|---|---|
T67 | 2512-2514 | Chemical | denotes | CO | http://purl.obolibrary.org/obo/CHEBI_17245 |
T68 | 2531-2533 | Chemical | denotes | CO | http://purl.obolibrary.org/obo/CHEBI_17245 |
T69 | 2556-2563 | Chemical | denotes | antigen | http://purl.obolibrary.org/obo/CHEBI_59132 |
T70 | 2982-2989 | Chemical | denotes | epitope | http://purl.obolibrary.org/obo/CHEBI_53000 |
T71 | 3040-3047 | Chemical | denotes | antigen | http://purl.obolibrary.org/obo/CHEBI_59132 |
T72 | 3573-3578 | Chemical | denotes | group | http://purl.obolibrary.org/obo/CHEBI_24433 |
T73 | 4066-4073 | Chemical | denotes | antigen | http://purl.obolibrary.org/obo/CHEBI_59132 |
T74 | 4445-4452 | Chemical | denotes | antigen | http://purl.obolibrary.org/obo/CHEBI_59132 |
T75 | 4461-4463 | Chemical | denotes | S3 | http://purl.obolibrary.org/obo/CHEBI_29388 |
T76 | 4709-4711 | Chemical | denotes | S2 | http://purl.obolibrary.org/obo/CHEBI_29387 |
T77 | 4861-4863 | Chemical | denotes | S4 | http://purl.obolibrary.org/obo/CHEBI_29401 |
LitCovid-sentences
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T101 | 0-2 | Sentence | denotes | 3. |
T102 | 3-10 | Sentence | denotes | Results |
T103 | 12-16 | Sentence | denotes | 3.1. |
T104 | 17-76 | Sentence | denotes | Performance of Eight SARS-CoV-2 IgG or Total Antibody Tests |
T105 | 77-225 | Sentence | denotes | Thirty-seven samples taken from patients with a PCR-confirmed SARS-CoV-2 infection were analyzed with eight SARS-CoV-2 IgG or total antibody assays. |
T106 | 226-369 | Sentence | denotes | Samples #1, #7, and #9 were taken nine days before to four days after PCR and were all found to be free of SARS-CoV-2 antibodies by the assays. |
T107 | 370-482 | Sentence | denotes | These samples were not considered for calculation of the sensitivity but demonstrated seroconversion (Figure 1). |
T108 | 483-583 | Sentence | denotes | Out of the remaining 34 samples, only one serum (#20; Figure 1), which was obtained from patient no. |
T109 | 584-693 | Sentence | denotes | 12 ten days after a positive RT-PCR, tested negative for SARS-CoV-2 IgG/total antibodies in the eight assays. |
T110 | 694-742 | Sentence | denotes | However, this sample exhibited a PRNT 1:10–1:20. |
T111 | 743-808 | Sentence | denotes | All other samples were reactive in at least one assay (Figure 1). |
T112 | 809-924 | Sentence | denotes | Twenty (76.9%) patients developed virus-neutralizing antibodies, as shown by a PRNT >1:10 (Figure 1 and Figure S1). |
T113 | 925-1066 | Sentence | denotes | With respect to the SARS-CoV-2 PCR (reference 1) or the PRNT results (reference 2), assay sensitivities ranged from 80.8% to 96.3% (Table 1). |
T114 | 1067-1167 | Sentence | denotes | Specificity was calculated using 100 archived samples that should not contain SARS-CoV-2 antibodies. |
T115 | 1168-1224 | Sentence | denotes | A total of ten sera were reactive in one or more assays. |
T116 | 1225-1300 | Sentence | denotes | None contained SARS-CoV-2 neutralizing antibodies (Figure 2 and Figure S1). |
T117 | 1301-1446 | Sentence | denotes | The residual 90 stored samples were not tested in the PRNT, as they were found to be free of SARS-CoV-2 IgG/total antibodies in all eight assays. |
T118 | 1447-1552 | Sentence | denotes | Thus, assay specificities ranged from 96.0% to 100%, and accuracies varied from 93.7% to 99.2% (Table 1). |
T119 | 1553-1707 | Sentence | denotes | Twelve routine samples obtained from individuals who were interested in their SARS-CoV-2 antibody status were re-evaluated by all eight assays (Figure 3). |
T120 | 1708-1789 | Sentence | denotes | Six of them—including three family members of the SARS-CoV-2-infected patient no. |
T121 | 1790-1888 | Sentence | denotes | 14 (Figure 1)—were classified SARS-CoV-2 IgG/total antibody-positive by the majority of the tests. |
T122 | 1889-1947 | Sentence | denotes | Isolated reactivity was observed in three sera (Figure 3). |
T123 | 1948-2129 | Sentence | denotes | Twenty-four (92.3%) of the 26 SARS-CoV-2 infected patients were reactive in one or both versions of the IgG recomLine assay; the test results differed only in three sera (Figure 1). |
T124 | 2130-2364 | Sentence | denotes | One out of the ten archived sera that were reactive in at least one of the SARS-CoV-2 IgG/total antibody tests was also classified as SARS-CoV-2 IgG-positive by the prototype immunoblot (v1) but was negative in the improved version 2. |
T125 | 2365-2615 | Sentence | denotes | The underlying sample #7 was collected in the winter 2018/2019 and was found to be reactive for SARS-CoV-2 IgG/total antibodies by the Mikrogen (S/CO 1.33), Roche (S/CO 3.46), and Viramed (N antigen 125 ViraChip® Units) assays in parallel (Figure 2). |
T126 | 2616-2792 | Sentence | denotes | The twelve routine samples were analyzed by both versions of the blot (v1: nine samples and v2: all samples), and results of the immunoassays were largely confirmed (Figure 3). |
T127 | 2794-2798 | Sentence | denotes | 3.2. |
T128 | 2799-2884 | Sentence | denotes | Kinetics of SARS-CoV-2 IgG, Development of IgG Avidities, and Neutralizing Antibodies |
T129 | 2885-3111 | Sentence | denotes | In the validation part of our study, the Abbott assay, which is based on the SARS-CoV-2 N as the epitope, and the Virion-Serion assay, which uses S as the antigen, proved to be the most sensitive and specific assays (Table 1). |
T130 | 3112-3267 | Sentence | denotes | Therefore, both were selected to study the kinetics of SARS-CoV-2 IgG in eleven patients and five individuals (including four family members of patient no. |
T131 | 3268-3297 | Sentence | denotes | 14) from routine diagnostics. |
T132 | 3298-3401 | Sentence | denotes | The median of the last sample submission was 153 days after the PCR, the range between 80 and 165 days. |
T133 | 3402-3470 | Sentence | denotes | Results from the validation part of this study were also considered. |
T134 | 3471-3528 | Sentence | denotes | N-specific IgG antibodies were detectable in all persons. |
T135 | 3529-3687 | Sentence | denotes | Two groups of individuals were evident: one group of six patients showed relatively stable IgG levels over time, while the other showed a short-term decrease. |
T136 | 3688-3797 | Sentence | denotes | Accordingly, the indices of six individuals fell below the limit of positivity during the observation period. |
T137 | 3798-3885 | Sentence | denotes | A stable S-specific IgG response was demonstrated in almost all individuals (Figure 4). |
T138 | 3886-3916 | Sentence | denotes | Only two subjects (patient no. |
T139 | 3917-3935 | Sentence | denotes | 22 and routine no. |
T140 | 3936-3990 | Sentence | denotes | 5) showed a drop in IgG below the limit of positivity. |
T141 | 3991-4013 | Sentence | denotes | The routine sample no. |
T142 | 4014-4118 | Sentence | denotes | 5 still possessed isolated reactivity against the N antigen in the improved line assay (data not shown). |
T143 | 4119-4266 | Sentence | denotes | In the latter test, three patients developed SARS-CoV-2-specific IgG of high avidity after 65–130 days, which was confirmed in consecutive samples. |
T144 | 4267-4311 | Sentence | denotes | The pattern of reactivity differed slightly: |
T145 | 4312-4465 | Sentence | denotes | Two patients developed IgG of high avidity against the RBD and S1 epitopes, while the third showed isolated reactivity against the N antigen (Figure S3). |
T146 | 4466-4621 | Sentence | denotes | Presence of SARS-CoV-2-neutralizing antibodies over several months was demonstrated in eight (72.7%) SARS-CoV-2 patients and a family member of patient no. |
T147 | 4622-4630 | Sentence | denotes | 14 (R4). |
T148 | 4631-4713 | Sentence | denotes | However, only one of them developed a stable titer >1:40 (Figure 5 and Figure S2). |
T149 | 4714-4865 | Sentence | denotes | Retests of sera that were already included in the validation part of this study showed an excellent reproducibility of the PRNT (R2 = 0.96, Figure S4). |
LitCovid-PubTator
Id | Subject | Object | Predicate | Lexical cue | tao:has_database_id |
---|---|---|---|---|---|
245 | 38-48 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
254 | 109-117 | Species | denotes | patients | Tax:9606 |
255 | 572-579 | Species | denotes | patient | Tax:9606 |
256 | 824-832 | Species | denotes | patients | Tax:9606 |
257 | 945-955 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
258 | 185-195 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
259 | 333-343 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
260 | 641-651 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
261 | 139-159 | Disease | denotes | SARS-CoV-2 infection | MESH:C000657245 |
265 | 1145-1155 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
266 | 1240-1250 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
267 | 1394-1404 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
272 | 1778-1785 | Species | denotes | patient | Tax:9606 |
273 | 1631-1641 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
274 | 1820-1830 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
275 | 1758-1777 | Disease | denotes | SARS-CoV-2-infected | MESH:C000657245 |
284 | 2554-2555 | Gene | denotes | N | Gene:43740575 |
285 | 2529-2530 | Gene | denotes | S | Gene:43740568 |
286 | 2510-2511 | Gene | denotes | S | Gene:43740568 |
287 | 1998-2006 | Species | denotes | patients | Tax:9606 |
288 | 2205-2215 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
289 | 2264-2274 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
290 | 2461-2471 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
291 | 1978-1997 | Disease | denotes | SARS-CoV-2 infected | MESH:C000657245 |
293 | 2811-2821 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
306 | 2973-2974 | Gene | denotes | N | Gene:43740575 |
307 | 3031-3032 | Gene | denotes | S | Gene:43740568 |
308 | 2962-2972 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
309 | 3192-3200 | Species | denotes | patients | Tax:9606 |
310 | 3256-3263 | Species | denotes | patient | Tax:9606 |
311 | 3520-3527 | Species | denotes | persons | Tax:9606 |
312 | 3586-3594 | Species | denotes | patients | Tax:9606 |
313 | 3905-3912 | Species | denotes | patient | Tax:9606 |
314 | 4145-4153 | Species | denotes | patients | Tax:9606 |
315 | 3167-3177 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
316 | 4164-4174 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
317 | 4316-4324 | Species | denotes | patients | Tax:9606 |
322 | 4567-4577 | Species | denotes | SARS-CoV-2 | Tax:2697049 |
323 | 4578-4586 | Species | denotes | patients | Tax:9606 |
324 | 4610-4617 | Species | denotes | patient | Tax:9606 |
325 | 4478-4488 | Species | denotes | SARS-CoV-2 | Tax:2697049 |