> top > docs > PMC:7160441 > annotations

PMC:7160441 JSONTXT

Annnotations TAB JSON ListView MergeView

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
3 16-25 Species denotes influenza Tax:11309
4 58-77 Disease denotes coronavirus disease MESH:D018352
5 79-87 Disease denotes COVID-19 MESH:C000657245
11 500-547 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
12 549-559 Species denotes SARS-CoV-2 Tax:2697049
13 157-176 Disease denotes coronavirus disease MESH:D018352
14 178-186 Disease denotes COVID-19 MESH:C000657245
15 438-446 Disease denotes COVID-19 MESH:C000657245
25 1125-1172 Species denotes severe acute respiratory syndrome coronavirus 2 Tax:2697049
26 1174-1184 Species denotes SARS-CoV-2 Tax:2697049
27 656-665 Species denotes influenza Tax:11309
28 773-782 Species denotes influenza Tax:11309
29 1324-1333 Species denotes influenza Tax:11309
30 691-719 Disease denotes acute respiratory infections MESH:D012120
31 1347-1366 Disease denotes coronavirus disease MESH:D018352
32 1368-1376 Disease denotes COVID-19 MESH:C000657245
33 1518-1526 Disease denotes COVID-19 MESH:C000657245
35 1554-1563 Species denotes influenza Tax:11309
51 1901-1907 Species denotes people Tax:9606
52 2077-2092 Species denotes Influenza virus Tax:11309
53 2111-2138 Species denotes respiratory syncytial virus Tax:12814
54 2140-2156 Species denotes human rhinovirus Tax:169066
55 2161-2182 Species denotes human metapneumovirus Tax:162145
56 2213-2223 Species denotes SARS-CoV-2 Tax:2697049
57 2386-2396 Species denotes SARS-CoV-2 Tax:2697049
58 2482-2490 Species denotes patients Tax:9606
59 2505-2513 Species denotes patients Tax:9606
60 2564-2574 Species denotes SARS-CoV-2 Tax:2697049
61 1706-1721 Disease denotes fever of sudden MESH:D005334
62 1743-1760 Disease denotes respiratory signs MESH:D012818
63 1762-1767 Disease denotes cough MESH:D003371
64 1787-1794 Disease denotes myalgia MESH:D063806
65 1857-1874 Disease denotes respiratory signs MESH:D012818
70 3267-3270 Gene denotes CrI
71 2650-2657 Species denotes patient Tax:9606
72 2840-2849 Species denotes influenza Tax:11309
73 3136-3145 Species denotes influenza Tax:11309
75 3567-3576 Species denotes influenza Tax:11309
79 3886-3895 Species denotes influenza Tax:11309
80 3741-3744 Disease denotes ARA
81 3839-3842 Disease denotes HDF
85 4212-4220 Disease denotes COVID-19 MESH:C000657245
86 4358-4366 Disease denotes COVID-19 MESH:C000657245
87 4749-4752 Disease denotes HDF
92 5646-5691 Gene denotes Nouvelle Aquitaine (NAQ) −3 (−110 to 32) −9
93 5105-5113 Disease denotes COVID-19 MESH:C000657245
94 5213-5216 Disease denotes ARA
95 5526-5529 Disease denotes HDF
98 4947-4966 Disease denotes coronavirus disease MESH:D018352
99 4968-4976 Disease denotes COVID-19 MESH:C000657245
101 6341-6349 Disease denotes COVID-19 MESH:C000657245
105 6739-6748 Species denotes influenza Tax:11309
106 6957-6966 Species denotes influenza Tax:11309
107 7021-7029 Disease denotes COVID-19 MESH:C000657245
112 7054-7058 Species denotes H1N1 Tax:114727
113 7041-7050 Species denotes Influenza Tax:11309
114 7069-7078 Species denotes influenza Tax:11309
115 7414-7423 Species denotes influenza Tax:11309
120 7596-7604 Species denotes patients Tax:9606
121 7927-7938 Species denotes coronavirus Tax:11118
122 7529-7537 Disease denotes COVID-19 MESH:C000657245
123 8144-8152 Disease denotes COVID-19 MESH:C000657245
131 8334-8344 Species denotes SARS-CoV-2 Tax:2697049
132 8367-8375 Species denotes patients Tax:9606
133 8227-8236 Species denotes influenza Tax:11309
134 8214-8222 Disease denotes COVID-19 MESH:C000657245
135 8302-8310 Disease denotes COVID-19 MESH:C000657245
136 8732-8735 Disease denotes HDF
137 8814-8822 Disease denotes COVID-19 MESH:C000657245
142 8863-8871 Disease denotes COVID-19 MESH:C000657245
143 9064-9072 Disease denotes COVID-19 MESH:C000657245
144 9378-9381 Disease denotes HDF
145 9420-9428 Disease denotes COVID-19 MESH:C000657245
147 9688-9698 Species denotes SARS-CoV-2 Tax:2697049
150 9996-9998 Gene denotes CS Gene:1431
151 10028-10030 Gene denotes CS Gene:1431

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 1777-1781 Body_part denotes nose http://purl.org/sig/ont/fma/fma46472
T2 9996-9998 Body_part denotes CS http://purl.org/sig/ont/fma/fma284995
T3 10028-10030 Body_part denotes CS http://purl.org/sig/ont/fma/fma284995

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 1777-1781 Body_part denotes nose http://purl.obolibrary.org/obo/UBERON_0000004

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T1 16-25 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T2 79-87 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T3 178-186 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T4 438-446 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T5 500-547 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T6 500-533 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T7 549-557 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T8 656-665 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T9 697-719 Disease denotes respiratory infections http://purl.obolibrary.org/obo/MONDO_0024355
T10 773-782 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T11 1125-1172 Disease denotes severe acute respiratory syndrome coronavirus 2 http://purl.obolibrary.org/obo/MONDO_0100096
T12 1125-1158 Disease denotes severe acute respiratory syndrome http://purl.obolibrary.org/obo/MONDO_0005091
T13 1174-1182 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T14 1324-1333 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T15 1368-1376 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T16 1518-1526 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T17 1554-1563 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T18 2077-2086 Disease denotes Influenza http://purl.obolibrary.org/obo/MONDO_0005812
T19 2213-2221 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T20 2386-2394 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T21 2564-2572 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T22 2840-2849 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T23 3136-3145 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T24 3567-3576 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T25 3768-3771 Disease denotes BRE http://purl.obolibrary.org/obo/MONDO_0007295
T26 3861-3864 Disease denotes IDF http://purl.obolibrary.org/obo/MONDO_0016039
T27 3886-3895 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T28 4212-4220 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T29 4358-4366 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T30 4694-4697 Disease denotes IDF http://purl.obolibrary.org/obo/MONDO_0016039
T31 4968-4976 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T32 5105-5113 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T33 5272-5275 Disease denotes BRE http://purl.obolibrary.org/obo/MONDO_0007295
T34 5593-5596 Disease denotes IDF http://purl.obolibrary.org/obo/MONDO_0016039
T35 6341-6349 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T36 6739-6748 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T37 6957-6966 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T38 7021-7029 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T39 7041-7059 Disease denotes Influenza A (H1N1) http://purl.obolibrary.org/obo/MONDO_0005460
T40 7069-7078 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T41 7414-7423 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T42 7529-7537 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T43 8144-8152 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T44 8214-8222 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T45 8227-8236 Disease denotes influenza http://purl.obolibrary.org/obo/MONDO_0005812
T46 8302-8310 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T47 8334-8342 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T48 8722-8725 Disease denotes IDF http://purl.obolibrary.org/obo/MONDO_0016039
T49 8814-8822 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T50 8863-8871 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T51 9064-9072 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T52 9327-9330 Disease denotes IDF http://purl.obolibrary.org/obo/MONDO_0016039
T53 9420-9428 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T54 9688-9696 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T55 10000-10002 Disease denotes TB http://purl.obolibrary.org/obo/MONDO_0018076
T56 10104-10106 Disease denotes BL http://purl.obolibrary.org/obo/MONDO_0007243
T57 10164-10166 Disease denotes BL http://purl.obolibrary.org/obo/MONDO_0007243
T58 10174-10177 Disease denotes DLB http://purl.obolibrary.org/obo/MONDO_0007488

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T1 188-191 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T2 221-222 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T3 396-397 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T4 959-960 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T5 1105-1111 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T6 1777-1781 http://www.ebi.ac.uk/efo/EFO_0000828 denotes nose
T7 1798-1799 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 2087-2092 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T9 2133-2138 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T10 2140-2145 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T11 2161-2166 http://purl.obolibrary.org/obo/NCBITaxon_9606 denotes human
T12 2284-2291 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T13 2366-2372 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T14 2667-2668 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 2809-2810 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T16 3044-3046 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T17 3081-3082 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T18 3127-3128 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 3427-3429 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T20 3618-3620 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T21 3795-3798 http://purl.obolibrary.org/obo/CLO_0037067 denotes Val
T22 5239-5241 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T23 5326-5329 http://purl.obolibrary.org/obo/CLO_0037067 denotes Val
T24 5404-5406 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T25 5542-5544 http://purl.obolibrary.org/obo/CLO_0001527 denotes 94
T26 5565-5567 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T27 5569-5572 http://purl.obolibrary.org/obo/CLO_0001003 denotes 163
T28 5632-5634 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T29 5814-5816 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T30 5876-5878 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36
T31 5891-5893 http://purl.obolibrary.org/obo/CLO_0001527 denotes 94
T32 5910-5912 http://purl.obolibrary.org/obo/CLO_0001407 denotes 52
T33 5978-5979 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T34 6145-6146 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 6222-6225 http://purl.obolibrary.org/obo/CLO_0001195 denotes 219
T36 6377-6378 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 7051-7052 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T38 7079-7080 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T39 7081-7088 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses
T40 7165-7166 http://purl.obolibrary.org/obo/CLO_0001021 denotes B
T41 7167-7172 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T42 7197-7198 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T43 7227-7228 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T44 7444-7447 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T45 7689-7690 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T46 7837-7838 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T47 7959-7960 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T48 8055-8056 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T49 8951-8952 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T50 9098-9099 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T51 9129-9135 http://purl.obolibrary.org/obo/UBERON_0000473 denotes tested
T52 9254-9255 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T53 9649-9650 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T54 9992-9994 http://purl.obolibrary.org/obo/PR_000005794 denotes CP
T55 10127-10134 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes viruses

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 721-724 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T2 1594-1597 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T3 1828-1831 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T4 2026-2029 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T5 2501-2504 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T6 3741-3744 Chemical denotes ARA http://purl.obolibrary.org/obo/CHEBI_15843
T7 3795-3798 Chemical denotes Val http://purl.obolibrary.org/obo/CHEBI_16414|http://purl.obolibrary.org/obo/CHEBI_30015
T9 3866-3869 Chemical denotes Ile http://purl.obolibrary.org/obo/CHEBI_17191|http://purl.obolibrary.org/obo/CHEBI_30009
T11 3985-3988 Chemical denotes PDL http://purl.obolibrary.org/obo/CHEBI_53413|http://purl.obolibrary.org/obo/CHEBI_61489
T13 4679-4682 Chemical denotes Ile http://purl.obolibrary.org/obo/CHEBI_17191|http://purl.obolibrary.org/obo/CHEBI_30009
T15 5213-5216 Chemical denotes ARA http://purl.obolibrary.org/obo/CHEBI_15843
T16 5326-5329 Chemical denotes Val http://purl.obolibrary.org/obo/CHEBI_16414|http://purl.obolibrary.org/obo/CHEBI_30015
T18 5578-5581 Chemical denotes Ile http://purl.obolibrary.org/obo/CHEBI_17191|http://purl.obolibrary.org/obo/CHEBI_30009
T20 5792-5795 Chemical denotes PDL http://purl.obolibrary.org/obo/CHEBI_53413|http://purl.obolibrary.org/obo/CHEBI_61489
T22 6039-6042 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T23 6233-6236 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T24 6394-6397 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T25 6452-6455 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T26 7839-7841 Chemical denotes GP http://purl.obolibrary.org/obo/CHEBI_70744
T27 9443-9446 Chemical denotes ARI http://purl.obolibrary.org/obo/CHEBI_35640
T28 9988-9990 Chemical denotes VC http://purl.obolibrary.org/obo/CHEBI_28509
T29 9992-9994 Chemical denotes CP http://purl.obolibrary.org/obo/CHEBI_3380|http://purl.obolibrary.org/obo/CHEBI_73461
T31 9996-9998 Chemical denotes CS http://purl.obolibrary.org/obo/CHEBI_73462
T32 10028-10030 Chemical denotes CS http://purl.obolibrary.org/obo/CHEBI_73462
T33 10032-10034 Chemical denotes TL http://purl.obolibrary.org/obo/CHEBI_74860
T34 10054-10056 Chemical denotes CG http://purl.obolibrary.org/obo/CHEBI_4047
T35 10062-10064 Chemical denotes TH http://purl.obolibrary.org/obo/CHEBI_73663
T36 10100-10102 Chemical denotes VE http://purl.obolibrary.org/obo/CHEBI_75011

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T1 4456-4462 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T2 4577-4583 http://purl.obolibrary.org/obo/GO_0040007 denotes growth
T3 6528-6538 http://purl.obolibrary.org/obo/GO_0009056 denotes break down
T4 6996-7005 http://purl.obolibrary.org/obo/GO_0007610 denotes behaviour
T5 7583-7592 http://purl.obolibrary.org/obo/GO_0007610 denotes behaviour
T6 8588-8594 http://purl.obolibrary.org/obo/GO_0040007 denotes growth

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T1 0-117 Sentence denotes Excess cases of influenza-like illnesses synchronous with coronavirus disease (COVID-19) epidemic, France, March 2020
T2 119-127 Sentence denotes Abstract
T3 128-303 Sentence denotes Several French regions where coronavirus disease (COVID-19) has been reported currently show a renewed increase in ILI cases in the general practice-based Sentinelles network.
T4 304-460 Sentence denotes We computed the number of excess cases by region from 24 February to 8 March 2020 and found a correlation with the number of reported COVID-19 cases so far.
T5 461-621 Sentence denotes The data suggest larger circulation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the French population than apparent from confirmed cases.
T6 623-760 Sentence denotes The Sentinelles network monitors influenza-like illnesses (ILI) and acute respiratory infections (ARI) in general practice in France [1].
T7 761-904 Sentence denotes The 2019/20 influenza epidemic reached its peak in mid-February in France [2] and it was expected that ILI incidence would decrease thereafter.
T8 905-1007 Sentence denotes However, in the first week of March 2020, we observed a renewed increase in ILI cases in some regions.
T9 1008-1186 Sentence denotes Several nasopharyngeal swabs collected in that period by Sentinelles general practitioners (GPs) tested positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
T10 1187-1343 Sentence denotes Here, we quantified the number of consultations for ILI in France in early March 2020 in excess of what was expected to be caused by the influenza epidemic.
T11 1344-1527 Sentence denotes As coronavirus disease (COVID-19) cases were first identified in France at the end of January 2020 [3] we examined the relationship between ILI reports and reported cases of COVID-19.
T12 1529-1576 Sentence denotes Sentinelles reporting of influenza-like illness
T13 1577-1674 Sentence denotes Cases of ILI and ARI are reported in real time by participating GPs (ca 600 GPs) all over France.
T14 1675-1818 Sentence denotes The case definition for ILI is fever of sudden onset (> 39 °C) with respiratory signs (cough, running nose) and myalgia in a person of any age.
T15 1819-1940 Sentence denotes Cases of ARI include any disease with respiratory signs and are only monitored in people older than 65 years, unlike ILI.
T16 1941-2076 Sentence denotes In addition, Sentinelles GPs take nasopharyngeal swabs in one ILI case and up to two ARI cases per week for viral characterisation [4].
T17 2077-2262 Sentence denotes Influenza virus (see Supplement), respiratory syncytial virus, human rhinovirus and human metapneumovirus are routinely looked for, and SARS-CoV-2 was added at the end of February 2020.
T18 2263-2397 Sentence denotes In the first week of testing, week 9 (the week starting 24 February 2020), none of 119 submitted swabs tested positive for SARS-CoV-2.
T19 2398-2575 Sentence denotes In week 10 of 2020 (the week starting 2 March 2020), 93 swabs were collected in ILI patients and 23 in ARI patients, and two swabs in each category were positive for SARS-CoV-2.
T20 2576-2728 Sentence denotes For ILI, one of the two positive ILI cases had been collected because the patient reported a direct link with an existing cluster in the east of France.
T21 2729-2895 Sentence denotes We computed the expected number of ILI consultations using the superposition of a seasonal [5] and an epidemic influenza component [6], as detailed in the Supplement.
T22 2896-2985 Sentence denotes Excess cases were computed as the difference between observed cases and expected numbers.
T23 2986-3184 Sentence denotes This modelling approach allowed computing excess cases in 11 of 13 regions but did not provide a good fit in the remaining two regions where a marked influenza peak was not present (see Supplement).
T24 3185-3354 Sentence denotes The overall ILI incidence showed renewed increase with 33 (95% credible interval (CrI): −8 to 64) consultations per 100,000 in excess during week 9 and with 84 (95% CrI:
T25 3355-3414 Sentence denotes 447 to 108) consultations per 100,000 in excess in week 10.
T26 3415-3530 Sentence denotes Four of the 11 regions displayed positive excess (CrI excluding 0) in week 9 and seven regions in week 10 (Figure).
T27 3531-3740 Sentence denotes Figure Number of consultations for influenza-like illness (per 100,000) in France and 11 French regions, with expected number of consultations fitted on the first eight weeks, week 1–10, 2020 (n = 11 regions)
T28 3741-3745 Sentence denotes ARA:
T29 3746-3772 Sentence denotes Auvergne-Rhone-Alpes; BRE:
T30 3773-3787 Sentence denotes Brittany; CVL:
T31 3788-3813 Sentence denotes Centre-Val de Loire; COR:
T32 3814-3827 Sentence denotes Corsica; GRE:
T33 3828-3843 Sentence denotes Grand-Est; HDF:
T34 3844-3865 Sentence denotes Hauts de France; IDF:
T35 3866-3914 Sentence denotes Ile de France; ILI: influenza-like illness; NAQ:
T36 3915-3939 Sentence denotes Nouvelle Aquitaine; OCC:
T37 3940-3956 Sentence denotes Occitanie; PACA:
T38 3957-3989 Sentence denotes Provence-Alpes-Cote d’Azur; PDL:
T39 3990-4007 Sentence denotes Pays de la Loire.
T40 4008-4110 Sentence denotes Blue: excess consultations, computed by difference between observations (squares) and expected counts.
T41 4111-4201 Sentence denotes Green: expected number of consultations fitted on the first eight weeks of 2020 (circles).
T42 4202-4290 Sentence denotes Confirmed COVID-19 case counts were obtained from the Santé Publique France website [7].
T43 4291-4434 Sentence denotes The number of excess cases correlated with the cumulated number of COVID-19 cases reported in the same regions (r = 0.59; p < 0.05) in week 10.
T44 4435-4615 Sentence denotes Assuming exponential growth (typical of early epidemics) from week 8 to 10, 2020, we found that the excess number of cases had an exponential growth rate per week of 0.69 (95% CrI:
T45 4616-4661 Sentence denotes 0.55–0.86) in Grand-Est (GRE), 0.67 (95% CrI:
T46 4662-4714 Sentence denotes 0.55 to 0.83) in Ile de France (IDF), 0.68 (95% CrI:
T47 4715-4769 Sentence denotes 0.56 to 0.83) in Hauts de France (HDF), 0.61 (95% CrI:
T48 4770-4861 Sentence denotes 0.48 to 0.75) in Occitanie (OCC) and 0.56 (95% CrI: −1.6 to 0.8) in France overall (Table).
T49 4862-5052 Sentence denotes Table Excess consultations per 100,000 by region and cumulative number of confirmed coronavirus disease (COVID-19) cases in the corresponding weeks, France, week 9–10, 2020 (n = 11 regions)
T50 5053-5157 Sentence denotes Region Consultations in excess/100,000) Confirmed COVID-19 cases (cumulative) Population(in millions)
T51 5158-5190 Sentence denotes Week 9 Week 10 Week 9 Week 10
T52 5191-5261 Sentence denotes Auvergne-Rhone-Alpes (ARA) 82 (17 to147) 115 (36 to 174) 28 146 8
T53 5262-5318 Sentence denotes Brittany (BRE) 9 (−32 to 44) 40 (−7 to 73) 5 59 3.3
T54 5319-5388 Sentence denotes Centre-Val de Loire (CVL) 72 (43 to 96) 117 (97 to 130) 0 17 2.6
T55 5389-5443 Sentence denotes Corsica (COR) 35 (32 to 37) 21 (20 to 23) 0 5 0.3
T56 5444-5508 Sentence denotes Grand-Est (GRE) −55 (−109 to −13) 107 (56 to 138) 5 259 5.5
T57 5509-5577 Sentence denotes Hauts de France (HDF) 51 (−3 to 94) 172 (111 to 208) 34 163 6.0
T58 5578-5645 Sentence denotes Ile de France (IDF) 40 (32 to 46) 107 (103 ti 110) 18 191 12.3
T59 5646-5715 Sentence denotes Nouvelle Aquitaine (NAQ) −3 (−110 to 32) −9 (−44 to 26) 4 28 6.0
T60 5716-5773 Sentence denotes Occitanie (OCC) 54 (30 to75) 99 (79 to 112) 4 37 5.9
T61 5774-5840 Sentence denotes Pays de la Loire (PDL) −25 (−70 to 5) 18 (−16 to 38) 4 25 3.5
T62 5841-5917 Sentence denotes Provence-Alpes-Cote d’Azur (PACA) 36 (−4 to 80) 94 (47 to 140) 8 52 5.0
T63 5918-5977 Sentence denotes France 33 (−8 to 64) 84 (44 to 108) 110 982 64.9a
T64 5978-6034 Sentence denotes a Total population of all 13 regions of mainland France.
T65 6035-6189 Sentence denotes For ARI, the two positive swabs had been collected in the regions Bourgogne-Franche Comté (BFC) and GRE, from a total of seven swabs in these two regions.
T66 6190-6221 Sentence denotes We estimated that 760 (95% CrI:
T67 6222-6406 Sentence denotes 219–1,706) ARI consultations in those older than 65 years in these two regions (BFC and GRE) could have been caused by COVID-19 during week 10 (2 in 7 for a total of 2,600 ARI visits).
T68 6407-6597 Sentence denotes We did not pursue modelling excess cases for ARI as the time series (shown in the Supplement) were too noisy to properly break down the data into an expected seasonal part plus excess cases.
T69 6599-6609 Sentence denotes Discussion
T70 6610-6848 Sentence denotes This is the first time that an increase in ILI cases was observed simultaneously in several regions after the peak of the annual influenza epidemic in the last 30 seasons of routine surveillance in France with the Sentinelles network [9].
T71 6849-7040 Sentence denotes Several processes may have contributed to this observation, including, among others, characteristics of the influenza season, change in population behaviour or increase in COVID-19 incidence.
T72 7041-7146 Sentence denotes Influenza A (H1N1)pdm09 and influenza B viruses co-circulated in 2019/20 in France [10] (see Supplement).
T73 7147-7262 Sentence denotes Seasons with type B virus circulation can lead to a slow decay in incidence but a renewed increase is atypical [1].
T74 7263-7371 Sentence denotes The 2-week-long normal school holidays started between mid-February and early March depending on the region.
T75 7372-7524 Sentence denotes While holidays may change the dynamics of influenza [9], this generally has an effect in the ascending phase of the epidemic rather than after the peak.
T76 7525-7707 Sentence denotes The COVID-19 pandemic may have changed the health-seeking behaviour of patients and, to some extent, the reporting of the contributing GPs although they conform to a case definition.
T77 7708-7817 Sentence denotes In the crowdsourced surveillance system grippenet.fr [10], there was no evidence of increasing consultations:
T78 7818-7897 Sentence denotes 30% consulted with a GP in for ILI during week 10, compared with 38% in week 9.
T79 7898-8069 Sentence denotes As information regarding the coronavirus risk is widespread, a uniform increase in all regions could have been expected in this scenario rather than only in a few regions.
T80 8070-8190 Sentence denotes We however acknowledge that increased consultation rates in regions where COVID-19 is the most reported may be possible.
T81 8191-8317 Sentence denotes The similarity between COVID-19 and influenza symptoms makes it possible that the excess ILI cases were due to COVID-19 cases.
T82 8318-8402 Sentence denotes The presence of SARS-CoV-2-positive swabs in the patients supports this possibility.
T83 8403-8519 Sentence denotes The correlation between the number of confirmed cases and the computed excess is also consistent with this scenario.
T84 8520-8635 Sentence denotes In this case, the excess in cases is compatible with an exponential growth at an estimated rate of ca 0.7 per week.
T85 8636-8737 Sentence denotes Interestingly, this estimate was very similar in the four most affected regions (GRE, IDF, OCC, HDF).
T86 8738-8832 Sentence denotes It may prove useful to help calibrate models for studying the impact of the COVID-19 pandemic.
T87 8833-8987 Sentence denotes Estimating the true number of COVID-19 cases can only be tentative at this early stage of the epidemic with data from a non-dedicated surveillance system.
T88 8988-9079 Sentence denotes It is likely that the case definition of ILI does not allow identifying all COVID-19 cases.
T89 9080-9173 Sentence denotes In addition, only a few cases were virologically tested, adding uncertainty in the estimates.
T90 9174-9382 Sentence denotes Yet, the rate of excess ILI consultations applied to the French regions yielded a number of cases far in excess of confirmed cases, with 12,840 cases in IDF and around 10,000 cases in the regions GRE and HDF.
T91 9383-9636 Sentence denotes Likewise, the extrapolated number of COVID-19 presenting as ARI was 760 in those older than 65 years in the two eastern regions (GRE and BFC): this was already twice the number of reported cases in these regions at the time (n = 379), all ages combined.
T92 9637-9811 Sentence denotes As we enter a period of generalised circulation of SARS-CoV-2, surveillance based on clinical description and swabbing by GPs will prove essential in assessing the situation.
T93 9813-9829 Sentence denotes Acknowledgements
T94 9830-9888 Sentence denotes We thank all GPs participating to the Sentinelles network.
T95 9889-9897 Sentence denotes Funding:
T96 9898-9920 Sentence denotes Santé Publique France.
T97 9922-9943 Sentence denotes Conflict of interest:
T98 9944-9958 Sentence denotes None declared.
T99 9959-10022 Sentence denotes Authors’ contributions: PYB, VC, CP, CS, TB designed the study.
T100 10023-10053 Sentence denotes PYB, CS, TL analysed the data.
T101 10054-10095 Sentence denotes CG, CT, TH contributed data on incidence.
T102 10096-10135 Sentence denotes SB, VE, BL, SVDW characterised viruses.
T103 10136-10163 Sentence denotes PYB drafted the manuscript.
T104 10164-10208 Sentence denotes BL, SVDW, DLB contributed to the manuscript.
T105 10209-10247 Sentence denotes All authors approved the last version.
T106 10249-10267 Sentence denotes Supplementary Data
T107 10268-10278 Sentence denotes Supplement
T108 10279-10315 Sentence denotes Click here for additional data file.

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 697-719 Phenotype denotes respiratory infections http://purl.obolibrary.org/obo/HP_0011947
T2 1706-1711 Phenotype denotes fever http://purl.obolibrary.org/obo/HP_0001945
T3 1762-1767 Phenotype denotes cough http://purl.obolibrary.org/obo/HP_0012735
T4 1787-1794 Phenotype denotes myalgia http://purl.obolibrary.org/obo/HP_0003326

2_test

Id Subject Object Predicate Lexical cue
32290901-30703528-29335250 2073-2074 30703528 denotes 4
32290901-1983924-29335251 2821-2822 1983924 denotes 5
32290901-21909366-29335252 2861-2862 21909366 denotes 6
32290901-18401408-29335253 6845-6846 18401408 denotes 9
32290901-28830105-29335254 7125-7127 28830105 denotes 10
32290901-30428158-29335255 7259-7260 30428158 denotes 1
32290901-18401408-29335256 7425-7426 18401408 denotes 9
32290901-28830105-29335257 7762-7764 28830105 denotes 10

MyTest

Id Subject Object Predicate Lexical cue
32290901-30703528-29335250 2073-2074 30703528 denotes 4
32290901-1983924-29335251 2821-2822 1983924 denotes 5
32290901-21909366-29335252 2861-2862 21909366 denotes 6
32290901-18401408-29335253 6845-6846 18401408 denotes 9
32290901-28830105-29335254 7125-7127 28830105 denotes 10
32290901-30428158-29335255 7259-7260 30428158 denotes 1
32290901-18401408-29335256 7425-7426 18401408 denotes 9
32290901-28830105-29335257 7762-7764 28830105 denotes 10