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PMC:7068163 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
2 54-71 Species denotes novel coronavirus Tax:2697049
3 72-82 Species denotes SARS-CoV-2 Tax:2697049
6 262-309 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
7 311-321 Species denotes SARS-CoV-2 Tax:2697049
9 714-731 Species denotes novel coronavirus Tax:2697049
15 1235-1252 Species denotes novel coronavirus Tax:2697049
16 1378-1425 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
17 1427-1437 Species denotes SARS-CoV-2 Tax:2697049
18 1715-1725 Species denotes SARS-CoV-2 Tax:2697049
19 1443-1453 Disease denotes infections MESH:D007239
27 2012-2015 Gene denotes ran Gene:5901
28 2026-2036 Species denotes SARS-CoV-2 Tax:2697049
29 2288-2298 Species denotes SARS-CoV-2 Tax:2697049
30 2329-2336 Species denotes persons Tax:9606
31 1961-1977 Chemical denotes oligonucleotides MESH:D009841
32 2110-2134 Disease denotes coronavirus disease 2019 MESH:C000657245
33 2136-2144 Disease denotes COVID-19 MESH:C000657245
45 2572-2575 Gene denotes Rox Gene:4335
46 3036-3037 Gene denotes E Gene:43740570
47 2453-2466 Species denotes Coronaviruses Tax:11118
48 3013-3030 Species denotes Wuhan coronavirus Tax:2697049
49 3085-3093 Species denotes SARS-CoV Tax:694009
50 3196-3199 Species denotes CoV Tax:11118
51 3257-3267 Species denotes SARS-CoV-2 Tax:2697049
52 3356-3364 Species denotes patients Tax:9606
53 3377-3384 Species denotes persons Tax:9606
54 3422-3447 Chemical denotes phosphate buffered saline
55 3449-3452 Chemical denotes PBS
60 3807-3815 Species denotes SARS-CoV Tax:694009
61 3820-3830 Species denotes SARS-CoV-2 Tax:2697049
62 3849-3859 Species denotes SARS-CoV-2 Tax:2697049
63 3902-3907 Species denotes human Tax:9606
67 4048-4058 Species denotes SARS-CoV-2 Tax:2697049
68 4214-4224 Species denotes SARS CoV-2 Tax:2697049
69 4249-4257 Disease denotes COVID-19 MESH:C000657245
71 4336-4344 Disease denotes COVID-19 MESH:C000657245
73 4404-4422 Species denotes COVID: coronavirus Tax:2697049
78 5067-5070 Gene denotes Rox Gene:4335
79 5008-5016 Species denotes SARS-CoV Tax:694009
80 5180-5187 Species denotes patient Tax:9606
81 5450-5458 Species denotes SARS-CoV Tax:694009
87 5964-5967 Gene denotes Rox Gene:4335
88 6022-6029 Species denotes patient Tax:9606
89 6175-6182 Species denotes patient Tax:9606
90 6212-6222 Species denotes SARS-CoV-2 Tax:2697049
91 6286-6294 Species denotes patients Tax:9606
93 5620-5630 Species denotes SARS-CoV-2 Tax:2697049
96 6466-6474 Species denotes SARS-CoV Tax:694009
97 6528-6535 Species denotes patient Tax:9606
100 6746-6747 Gene denotes E Gene:43740570
101 6666-6674 Species denotes SARS-CoV Tax:694009
106 6795-6796 Gene denotes E Gene:43740570
107 6866-6867 Gene denotes E Gene:43740570
108 6843-6860 Species denotes Wuhan coronavirus Tax:2697049
109 6885-6893 Species denotes SARS-CoV Tax:694009
111 7020-7021 Gene denotes E Gene:43740570
113 7096-7099 Chemical denotes RFU
118 7164-7165 Gene denotes E Gene:43740570
119 7141-7158 Species denotes Wuhan coronavirus Tax:2697049
120 7192-7200 Species denotes SARS-CoV Tax:694009
121 7253-7260 Species denotes patient Tax:9606
123 7437-7438 Gene denotes E Gene:43740570
130 7798-7801 Gene denotes Rox Gene:4335
131 8747-8748 Gene denotes E Gene:43740570
132 8464-8465 Gene denotes E Gene:43740570
133 8608-8615 Species denotes patient Tax:9606
134 8724-8741 Species denotes Wuhan coronavirus Tax:2697049
135 8758-8766 Species denotes SARS-CoV Tax:694009
138 9289-9290 Gene denotes E Gene:43740570
139 9205-9215 Species denotes SARS-CoV-2 Tax:2697049
145 9616-9617 Gene denotes E Gene:43740570
146 9594-9604 Species denotes SARS-CoV-2 Tax:2697049
147 9784-9794 Species denotes SARS-CoV-2 Tax:2697049
148 9858-9868 Species denotes SARS-CoV-2 Tax:2697049
149 9993-10003 Species denotes SARS-CoV-2 Tax:2697049
151 10884-10894 Species denotes SARS-CoV-2 Tax:2697049
155 11031-11048 Species denotes novel coronavirus Tax:2697049
156 11346-11354 Species denotes patients Tax:9606
157 11607-11617 Species denotes SARS-CoV-2 Tax:2697049
161 11800-11810 Species denotes SARS-CoV-2 Tax:2697049
162 12001-12008 Species denotes patient Tax:9606
163 11992-12000 Disease denotes COVID-19 MESH:C000657245
168 12957-12958 Gene denotes E Gene:43740570
169 12693-12694 Gene denotes E Gene:43740570
170 12242-12250 Species denotes SARS-CoV Tax:694009
171 12704-12714 Species denotes SARS-CoV-2 Tax:2697049
178 13728-13729 Gene denotes E Gene:43740570
179 14233-14234 Gene denotes E Gene:43740570
180 14080-14081 Gene denotes E Gene:43740570
181 13628-13629 Gene denotes E Gene:43740570
182 13493-13494 Gene denotes E Gene:43740570
183 13238-13254 Chemical denotes oligonucleotides MESH:D009841
189 14461-14462 Gene denotes E Gene:43740570
190 14313-14323 Species denotes SARS-CoV-2 Tax:2697049
191 14723-14734 Species denotes coronavirus Tax:11118
192 14753-14756 Species denotes CoV Tax:11118
193 14770-14780 Species denotes SARS-CoV-2 Tax:2697049
195 15939-15941 Disease denotes VF MESH:D014693

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 2384-2388 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T2 2398-2402 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T3 3038-3042 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T4 3106-3109 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T5 3205-3209 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T6 3329-3335 Body_part denotes sputum http://purl.org/sig/ont/fma/fma312401
T7 3386-3392 Body_part denotes Sputum http://purl.org/sig/ont/fma/fma312401
T8 3455-3458 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T9 3643-3647 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T10 3695-3699 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T11 3931-3934 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T12 4225-4228 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T13 5019-5023 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T14 5471-5474 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T15 5514-5518 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T16 5866-5870 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T17 5912-5916 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T18 6477-6481 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T19 6622-6626 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T20 6687-6690 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T21 6748-6752 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T22 6797-6801 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T23 6868-6872 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T24 6906-6909 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T25 7022-7026 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T26 7166-7170 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T27 7213-7216 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T28 7439-7443 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T29 7987-7990 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T30 8466-8470 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T31 8535-8539 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T32 8749-8753 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T33 8787-8790 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T34 9291-9295 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T35 9618-9622 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T36 10237-10240 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T37 12253-12257 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T38 12301-12305 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T39 12398-12402 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T40 12695-12699 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T41 12726-12730 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T42 12959-12963 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T43 13380-13383 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T44 13431-13434 Body_part denotes RNA http://purl.org/sig/ont/fma/fma67095
T45 13495-13499 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T46 13630-13634 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T47 13730-13734 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T48 14082-14086 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T49 14235-14239 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402
T50 14463-14467 Body_part denotes gene http://purl.org/sig/ont/fma/fma74402

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 3329-3335 Body_part denotes sputum http://purl.obolibrary.org/obo/UBERON_0007311
T2 3386-3392 Body_part denotes Sputum http://purl.obolibrary.org/obo/UBERON_0007311
T3 7359-7364 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542

LitCovid_AGAC

Id Subject Object Predicate Lexical cue
p13283s8 9068-9077 NegReg denotes decreased

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 72-80 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T2 262-309 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T3 262-295 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T4 311-319 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T5 1179-1187 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T6 1378-1425 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T7 1378-1411 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T8 1427-1435 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T9 1443-1456 Disease denotes infections in http://purl.obolibrary.org/obo/MONDO_0005550
T10 1715-1723 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T11 2026-2034 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T12 2110-2134 Disease denotes coronavirus disease 2019 http://purl.obolibrary.org/obo/MONDO_0100096
T13 2136-2144 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T14 2288-2296 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T15 3085-3093 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T16 3257-3265 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T17 3807-3815 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T18 3820-3828 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T19 3849-3857 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T20 4048-4056 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T21 4214-4218 Disease denotes SARS http://purl.obolibrary.org/obo/MONDO_0005091
T22 4249-4257 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T23 4336-4344 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T24 5008-5016 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T25 5450-5458 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T26 5620-5628 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T27 5793-5795 Disease denotes R2 http://purl.obolibrary.org/obo/MONDO_0019903
T28 6212-6220 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T29 6466-6474 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T30 6666-6674 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T31 6885-6893 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T32 7192-7200 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T33 8758-8766 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T34 9205-9213 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T35 9594-9602 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T36 9784-9792 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T37 9858-9866 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T38 9993-10001 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T39 10695-10704 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T40 10884-10892 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T41 11607-11615 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T42 11800-11808 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T43 11992-12000 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T44 12242-12250 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T45 12704-12712 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T46 14313-14321 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T47 14770-14778 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T48 15355-15365 Disease denotes Infectious http://purl.obolibrary.org/obo/MONDO_0005550
T49 15885-15887 Disease denotes AD http://purl.obolibrary.org/obo/MONDO_0004975
T50 15939-15941 Disease denotes VF http://purl.obolibrary.org/obo/MONDO_0000190
T51 15972-15974 Disease denotes BL http://purl.obolibrary.org/obo/MONDO_0007243

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 380-381 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T2 503-504 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T3 712-713 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T4 795-798 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T5 1078-1079 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T6 1102-1103 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T7 1233-1234 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 1785-1797 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T9 2047-2049 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T10 2310-2317 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T11 2384-2388 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T12 2398-2402 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T13 2492-2498 http://purl.obolibrary.org/obo/CLO_0001929 denotes Berlin
T14 2565-2570 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T15 2900-2906 http://purl.obolibrary.org/obo/CLO_0001929 denotes Berlin
T16 2965-2970 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T17 3038-3042 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T18 3205-3209 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T19 3223-3229 http://purl.obolibrary.org/obo/CLO_0001929 denotes Berlin
T20 3516-3517 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T21 3591-3597 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T22 3643-3647 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T23 3695-3699 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T24 3774-3776 http://purl.obolibrary.org/obo/CLO_0008285 denotes P1
T25 3792-3794 http://purl.obolibrary.org/obo/CLO_0008307 denotes P2
T26 3886-3888 http://purl.obolibrary.org/obo/CLO_0008307 denotes P2
T27 3902-3907 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T28 3981-3987 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T29 4233-4235 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T30 4353-4359 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T31 4555-4567 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T32 4598-4604 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T33 4668-4674 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T34 4739-4740 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 4765-4770 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tests
T36 4856-4860 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T37 4864-4866 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T38 4876-4877 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T39 4982-4988 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T40 5019-5023 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T41 5060-5065 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T42 5126-5133 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T43 5173-5179 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T44 5383-5390 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T45 5514-5518 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T46 5665-5666 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T47 5678-5682 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T48 5779-5780 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T49 5847-5854 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T50 5866-5870 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T51 5899-5906 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T52 5912-5916 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T53 5926-5927 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T54 5957-5962 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T55 6018-6021 http://purl.obolibrary.org/obo/CLO_0001445 denotes 617
T56 6168-6170 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T57 6171-6174 http://purl.obolibrary.org/obo/CLO_0001195 denotes 219
T58 6363-6366 http://purl.obolibrary.org/obo/CLO_0051456 denotes a E
T59 6385-6386 http://purl.obolibrary.org/obo/CLO_0001021 denotes b
T60 6451-6458 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T61 6477-6481 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T62 6521-6527 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T63 6622-6626 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T64 6635-6641 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T65 6748-6752 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T66 6797-6801 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T67 6803-6809 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T68 6868-6872 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T69 7022-7026 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T70 7049-7056 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T71 7166-7170 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T72 7336-7342 http://purl.obolibrary.org/obo/SO_0000418 denotes Signal
T73 7439-7443 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T74 7558-7561 http://purl.obolibrary.org/obo/CLO_0001313 denotes 3–6
T75 7578-7585 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T76 7675-7682 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T77 7791-7796 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T78 7902-7903 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T79 7935-7941 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T80 7991-7996 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes Virus
T81 8059-8060 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T82 8092-8098 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T83 8466-8470 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T84 8471-8478 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T85 8518-8525 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T86 8535-8539 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T87 8601-8607 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T88 8749-8753 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T89 9145-9146 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T90 9173-9177 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T91 9291-9295 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T92 9296-9303 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T93 9305-9306 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T94 9361-9367 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T95 9497-9504 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T96 9542-9543 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T97 9618-9622 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T98 9642-9644 http://purl.obolibrary.org/obo/CLO_0054055 denotes 71
T99 9699-9701 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T100 9763-9764 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T101 9805-9806 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T102 10106-10107 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T103 10186-10193 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T104 10289-10290 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T105 10547-10551 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T106 11029-11030 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T107 11381-11387 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T108 11625-11627 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T109 11681-11682 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T110 11699-11706 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T111 11938-11939 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T112 12136-12143 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T113 12197-12198 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T114 12253-12257 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T115 12301-12305 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T116 12398-12402 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T117 12449-12450 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T118 12498-12501 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T119 12591-12592 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T120 12695-12699 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T121 12726-12730 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T122 12757-12764 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T123 12820-12827 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T124 12918-12926 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T125 12959-12963 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T126 13056-13057 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T127 13105-13106 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T128 13129-13136 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T129 13313-13314 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T130 13409-13410 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T131 13448-13449 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T132 13467-13468 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T133 13495-13499 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T134 13630-13634 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T135 13730-13734 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T136 13818-13819 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T137 13872-13879 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T138 13909-13916 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T139 14082-14086 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T140 14235-14239 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T141 14259-14260 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T142 14463-14467 http://purl.obolibrary.org/obo/OGG_0000000002 denotes gene
T143 14547-14553 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T144 14619-14626 http://purl.obolibrary.org/obo/SO_0000418 denotes signals
T145 14751-14752 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T146 14796-14797 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T147 15927-15929 http://purl.obolibrary.org/obo/CLO_0002040 denotes BT
T148 15935-15937 http://purl.obolibrary.org/obo/CLO_0007074 denotes KB
T149 15935-15937 http://purl.obolibrary.org/obo/CLO_0051988 denotes KB
T150 15963-15970 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 1112-1115 Chemical denotes CFX http://purl.obolibrary.org/obo/CHEBI_209807
T2 1961-1977 Chemical denotes oligonucleotides http://purl.obolibrary.org/obo/CHEBI_7754
T3 3422-3431 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 3774-3776 Chemical denotes P1 http://purl.obolibrary.org/obo/CHEBI_60949
T8 3792-3794 Chemical denotes P2 http://purl.obolibrary.org/obo/CHEBI_33472
T9 3869-3874 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T10 3886-3888 Chemical denotes P2 http://purl.obolibrary.org/obo/CHEBI_33472
T11 5987-5989 Chemical denotes ND http://purl.obolibrary.org/obo/CHEBI_73419
T12 5991-5993 Chemical denotes ND http://purl.obolibrary.org/obo/CHEBI_73419
T13 6343-6345 Chemical denotes ND http://purl.obolibrary.org/obo/CHEBI_73419
T14 7456-7461 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T15 8349-8354 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T16 13238-13254 Chemical denotes oligonucleotides http://purl.obolibrary.org/obo/CHEBI_7754
T17 13273-13281 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T18 13545-13553 Chemical denotes reagents http://purl.obolibrary.org/obo/CHEBI_33893
T19 14099-14104 Chemical denotes probe http://purl.obolibrary.org/obo/CHEBI_50406
T20 15669-15671 Chemical denotes RK http://purl.obolibrary.org/obo/CHEBI_73816
T21 15885-15887 Chemical denotes AD http://purl.obolibrary.org/obo/CHEBI_73803
T22 15927-15929 Chemical denotes BT http://purl.obolibrary.org/obo/CHEBI_45993
T23 15939-15941 Chemical denotes VF http://purl.obolibrary.org/obo/CHEBI_75016
T24 16016-16018 Chemical denotes NA http://purl.obolibrary.org/obo/CHEBI_33696

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 3200-3204 http://purl.obolibrary.org/obo/GO_0003968 denotes RdRP
T2 3908-3915 http://purl.obolibrary.org/obo/GO_0004526 denotes RNAse P
T3 6104-6121 http://purl.obolibrary.org/obo/GO_0003887 denotes TaqDNA Polymerase
T4 8179-8196 http://purl.obolibrary.org/obo/GO_0003887 denotes TaqDNA Polymerase

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-117 Sentence denotes Rapid establishment of laboratory diagnostics for the novel coronavirus SARS-CoV-2 in Bavaria, Germany, February 2020
T2 119-127 Sentence denotes Abstract
T3 128-333 Sentence denotes The need for timely establishment of diagnostic assays arose when Germany was confronted with the first travel-associated outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Europe.
T4 334-520 Sentence denotes We describe our laboratory experiences during a large contact tracing investigation, comparing previously published real-time RT-PCR assays in different PCR systems and a commercial kit.
T5 521-659 Sentence denotes We found that assay performance using the same primers and probes with different PCR systems varied and the commercial kit performed well.
T6 661-762 Sentence denotes At the end of December 2019, an outbreak caused by a novel coronavirus was announced in Wuhan, China.
T7 763-939 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 940-1126 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 1128-1189 Sentence denotes Timely implementation of molecular diagnostics for SARS-CoV-2
T10 1190-1589 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 1590-1756 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 1757-1928 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 1929-2067 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 2068-2175 Sentence denotes On the same day, the first German case of coronavirus disease 2019 (COVID-19) was diagnosed in Bavaria [1].
T15 2176-2337 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 2338-2503 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 2504-2701 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 2702-2824 Sentence denotes The kit was chosen for its frequent and successful use in our laboratory with other assays and its immediate availability.
T19 2825-2917 Sentence denotes Primers and probes were used as described [5] and provided by TIB Molbiol (Berlin, Germany).
T20 2918-3144 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 3145-3283 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 3284-3385 Sentence denotes Respiratory samples (nasopharyngeal swabs or sputum) were obtained from patients and contact persons.
T23 3386-3454 Sentence denotes Sputum samples were diluted in 2 mL phosphate buffered saline (PBS).
T24 3455-3574 Sentence denotes RNA was extracted using the QIAamp Bio Robot kit (QIAGEN) on a Hamilton Microlab Star (Hamilton, Bonaduz, Switzerland).
T25 3575-3893 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 3894-3950 Sentence denotes We used human RNAse P as control for RNA extraction [7].
T27 3951-4018 Sentence denotes The cumulative numbers of all tested samples are shown in Figure 1.
T28 4019-4167 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 4168-4229 Sentence denotes Among them, seven showed positive results for SARS CoV-2 RNA.
T30 4230-4293 Sentence denotes By 11 February, 14 COVID-19 cases had been detected in Bavaria.
T31 4294-4403 Sentence denotes Figure 1 Cumulative numbers of suspected COVID-19 samples tested during week 5 and 6 2020, Bavaria (n = 675)
T32 4404-4493 Sentence denotes COVID: coronavirus disease; PHEIC: public health emergency of international concern; LGL:
T33 4494-4541 Sentence denotes Bavarian Health and Food Safety Authority; WHO:
T34 4542-4568 Sentence denotes World Health Organization.
T35 4569-4708 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 4709-4777 Sentence denotes All data are cumulative, with a final total of positive tests of 13.
T37 4779-4816 Sentence denotes Comparison of one-step RT-PCR systems
T38 4817-4989 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 4990-5325 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 5326-5406 Sentence denotes The RdRp assays were basically free from such unspecific signals in late cycles.
T41 5407-5545 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 5546-5735 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 5736-5945 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 5946-6050 Sentence denotes QuantiTect Virus +Rox Vial kit (QIAGEN) ND ND 451/743(75/126 NC, 376/617 patient samples) 60.7 1:50
T45 6051-6202 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 6203-6312 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 6313-6362 Sentence denotes NC: negative control samples; ND: not determined.
T48 6363-6384 Sentence denotes a E = 10−1/slope − 1.
T49 6385-6605 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 6606-6737 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 6738-6779 Sentence denotes For the E gene, the assay was not linear.
T52 6780-6961 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 6962-7095 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 7096-7129 Sentence denotes RFU: relative fluorescence units.
T55 7130-7137 Sentence denotes Curves:
T56 7138-7140 Sentence denotes 1:
T57 7141-7335 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 7336-7386 Sentence denotes Signal is given in log scale with threshold = 200.
T59 7387-7482 Sentence denotes PCR was performed with SuperScript III system and E gene primers and probe as published in [5].
T60 7483-7550 Sentence denotes Curves of positive controls (1 and 2) show expected sigmoid curves.
T61 7551-7616 Sentence denotes Curves 3–6 show unspecific signals with increase above threshold.
T62 7617-7693 Sentence denotes Curves below threshold were not considered as significant signals (7 and 8).
T63 7694-8238 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 8239-8401 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 8402-8479 Sentence denotes They all showed comparable results in reduction of unspecific E gene signals.
T66 8480-8841 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 8842-8854 Sentence denotes 29.1; range:
T68 8855-8901 Sentence denotes 26.8–32.4; n = 85) and Superscript (median Ct:
T69 8902-8914 Sentence denotes 28.1; range:
T70 8915-8941 Sentence denotes 26.4–31.0; n = 30) setups.
T71 8942-9109 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 9110-9195 Sentence denotes Moreover, we additionally included a newly launched commercial test kit in our study:
T73 9196-9304 Sentence denotes RealStar SARS-CoV-2 RT-PCR kit 1.0 (Altona, Hamburg, Germany), which did not show unspecific E gene signals.
T74 9305-9413 Sentence denotes A summary of the assay features of the three PCR setups tested and compared in detail is shown in the Table.
T75 9414-9611 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 9612-9844 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 9845-9970 Sentence denotes The specific SARS-CoV-2 assays gave in 67 (92%) identical results (60 negative and seven positive) and six divergent results.
T78 9971-10036 Sentence denotes Overall, the RealStar SARS-CoV-2 kit seemed to be more sensitive.
T79 10038-10046 Sentence denotes Workflow
T80 10047-10213 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 10214-10378 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 10379-10536 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 10537-10579 Sentence denotes Our daily test capacity was ca 80 samples.
T84 10580-10753 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 10754-10835 Sentence denotes Overall, we managed to report the results for 97% of samples within the same day.
T86 10836-10949 Sentence denotes Figure 3 Flowchart and routine timeline of the SARS-CoV-2 diagnostic workflow at the LGL, Bavaria, February 2020
T87 10950-10954 Sentence denotes LGL:
T88 10955-10997 Sentence denotes Bavarian Health and Food Safety Authority.
T89 10999-11009 Sentence denotes Discussion
T90 11010-11141 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 11142-11262 Sentence denotes The main task of public health authorities is to react quickly to emerging pathogens of global threat to prevent spread.
T92 11263-11400 Sentence denotes These responses include containment strategies, which means that close contacts of patients have to be identified and tested immediately.
T93 11401-11629 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 11630-11726 Sentence denotes National and local public health laboratories play a crucial role in testing emerging pathogens.
T95 11727-12085 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 12086-12215 Sentence denotes Evaluation and verification of the new assays and testing real samples had to take place simultaneously within a very short time.
T97 12216-12382 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 12383-12482 Sentence denotes However, our E gene assay showed high background levels hampering a clear evaluation of the assays.
T99 12483-12611 Sentence denotes Each mastermix has its own proprietary composition, which may explain the differences in the performance of a certain PCR assay.
T100 12612-12776 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 12777-13087 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 13088-13356 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 13357-13423 Sentence denotes Sample preparation and RNA extraction took place in a second room.
T104 13424-13478 Sentence denotes Sample RNA was added in a third room under a PCR hood.
T105 13479-13540 Sentence denotes The synthetic E gene control was added last to the mastermix.
T106 13541-13597 Sentence denotes All reagents were aliquoted and aliquots used once only.
T107 13598-13880 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 13881-14047 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 14048-14296 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 14298-14308 Sentence denotes Conclusion
T111 14309-14502 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 14503-14810 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 14811-14976 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 14977-15070 Sentence denotes Assay optimisation will further speed up and improve the management of this ongoing outbreak.
T115 15072-15088 Sentence denotes Acknowledgements
T116 15089-15179 Sentence denotes We want to thank for excellent technical assistance in diagnostic and validation lab work:
T117 15180-15426 Sentence denotes Juliane Breitenberger, Jasmin Fräßdorf, Christine Hartberger, Sabine Lohrer, Linda Ploß, and all others who contributed to sample and lab logistics, especially the Task Force Infectious Diseases at the LGL and the local public health authorities.
T118 15427-15437 Sentence denotes Dedication
T119 15438-15606 Sentence denotes We dedicate this publication to Andreas Zapf, President of the Bavarian LGL and long-term supporter of Public Health Microbiology, on the occasion of his 60th birthday.
T120 15608-15629 Sentence denotes Conflict of interest:
T121 15630-15644 Sentence denotes None declared.
T122 15645-15672 Sentence denotes Authors’ contributions: RK:
T123 15673-15771 Sentence denotes Planned and conducted experiments, conceptualised the laboratory work, wrote the manuscript draft.
T124 15772-15775 Sentence denotes UE:
T125 15776-15884 Sentence denotes Planned and conducted experiments, conceptualised the laboratory work, data analysis, co-writing manuscript.
T126 15885-15926 Sentence denotes AD: data analysis, co-writing manuscript.
T127 15927-15971 Sentence denotes BT, AB, KB, VF: participated in lab testing.
T128 15972-16015 Sentence denotes BL: coordinated the public health response.
T129 16016-16075 Sentence denotes NA: conceptualised the laboratory work, manuscript writing.
T130 16076-16196 Sentence denotes AS: overall conceptualised the laboratory work, manuscript writing, coordinated the public health microbiology response.

2_test

Id Subject Object Predicate Lexical cue
32156330-32003551-29325810 1584-1585 32003551 denotes 1
32156330-32003551-29325811 2172-2173 32003551 denotes 1
32156330-31992387-29325812 2500-2501 31992387 denotes 5
32156330-31992387-29325813 2868-2869 31992387 denotes 5
32156330-30059721-29325814 3141-3142 30059721 denotes 6
32156330-31992387-29325815 3734-3735 31992387 denotes 5
32156330-31992387-29325816 3890-3891 31992387 denotes 5
32156330-16274752-29325817 3947-3948 16274752 denotes 7
32156330-31992387-29325818 5658-5659 31992387 denotes 5
32156330-30059721-29325819 6692-6693 30059721 denotes 6
32156330-30059721-29325820 6916-6917 30059721 denotes 6
32156330-31992387-29325821 7479-7480 31992387 denotes 5
32156330-31992387-29325822 8398-8399 31992387 denotes 5
32156330-31992387-29325823 9044-9045 31992387 denotes 5
32156330-32004165-29325824 11135-11136 32004165 denotes 9
32156330-32015508-29325825 11137-11139 32015508 denotes 10
32156330-32046815-29325826 11625-11627 32046815 denotes 11
32156330-16274752-29325827 14350-14351 16274752 denotes 7

MyTest

Id Subject Object Predicate Lexical cue
32156330-32003551-29325810 1584-1585 32003551 denotes 1
32156330-32003551-29325811 2172-2173 32003551 denotes 1
32156330-31992387-29325812 2500-2501 31992387 denotes 5
32156330-31992387-29325813 2868-2869 31992387 denotes 5
32156330-30059721-29325814 3141-3142 30059721 denotes 6
32156330-31992387-29325815 3734-3735 31992387 denotes 5
32156330-31992387-29325816 3890-3891 31992387 denotes 5
32156330-16274752-29325817 3947-3948 16274752 denotes 7
32156330-31992387-29325818 5658-5659 31992387 denotes 5
32156330-30059721-29325819 6692-6693 30059721 denotes 6
32156330-30059721-29325820 6916-6917 30059721 denotes 6
32156330-31992387-29325821 7479-7480 31992387 denotes 5
32156330-31992387-29325822 8398-8399 31992387 denotes 5
32156330-31992387-29325823 9044-9045 31992387 denotes 5
32156330-32004165-29325824 11135-11136 32004165 denotes 9
32156330-32015508-29325825 11137-11139 32015508 denotes 10
32156330-32046815-29325826 11625-11627 32046815 denotes 11
32156330-16274752-29325827 14350-14351 16274752 denotes 7