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PMC:7650537 / 13574-18439 JSONTXT

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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