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PMC:7449695 / 1021-24375 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T1 1867-1871 Body_part denotes face http://purl.org/sig/ont/fma/fma24728
T2 5489-5493 Body_part denotes face http://purl.org/sig/ont/fma/fma24728
T3 6335-6342 Body_part denotes Capital http://purl.org/sig/ont/fma/fma23727
T4 7519-7529 Body_part denotes grey lines http://purl.org/sig/ont/fma/fma74591
T5 8492-8502 Body_part denotes grey lines http://purl.org/sig/ont/fma/fma74591
T6 9465-9475 Body_part denotes grey lines http://purl.org/sig/ont/fma/fma74591
T7 10966-10975 Body_part denotes grey line http://purl.org/sig/ont/fma/fma74591

LitCovid-PD-UBERON

Id Subject Object Predicate Lexical cue uberon_id
T1 1867-1871 Body_part denotes face http://purl.obolibrary.org/obo/UBERON_0001456
T2 5489-5493 Body_part denotes face http://purl.obolibrary.org/obo/UBERON_0001456
T3 21143-21148 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542
T4 22301-22306 Body_part denotes scale http://purl.obolibrary.org/obo/UBERON_0002542

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T5 66-74 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T6 570-578 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T7 1112-1120 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T8 1603-1611 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T9 2337-2345 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T10 2442-2450 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T11 2710-2718 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T12 2795-2803 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T13 3822-3830 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T14 4102-4112 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T15 5872-5880 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T16 6857-6865 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T17 7351-7365 Disease denotes infectiousness http://purl.obolibrary.org/obo/MONDO_0005550
T18 7830-7838 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T19 8324-8338 Disease denotes infectiousness http://purl.obolibrary.org/obo/MONDO_0005550
T20 8803-8811 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T21 9297-9311 Disease denotes infectiousness http://purl.obolibrary.org/obo/MONDO_0005550
T22 9887-9895 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T23 10016-10024 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T24 10326-10334 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T25 10547-10555 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T26 11075-11083 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T27 11205-11213 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T28 11934-11942 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T29 12584-12592 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T30 15273-15282 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T31 15563-15573 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T32 16093-16101 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T33 16565-16575 Disease denotes Infectious http://purl.obolibrary.org/obo/MONDO_0005550
T34 17364-17373 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550
T35 17438-17448 Disease denotes infectious http://purl.obolibrary.org/obo/MONDO_0005550
T36 17608-17622 Disease denotes infectiousness http://purl.obolibrary.org/obo/MONDO_0005550
T37 18463-18473 Disease denotes Infectious http://purl.obolibrary.org/obo/MONDO_0005550
T38 20489-20497 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T39 21297-21305 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T40 21580-21588 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T41 21683-21691 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T42 22089-22097 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T43 22624-22632 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T44 22635-22645 Disease denotes infections http://purl.obolibrary.org/obo/MONDO_0005550
T45 22783-22792 Disease denotes infection http://purl.obolibrary.org/obo/MONDO_0005550

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T2 13-14 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T3 159-171 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T4 495-507 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T5 861-864 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T6 883-884 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T7 945-946 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T8 1794-1797 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T9 1867-1871 http://purl.obolibrary.org/obo/UBERON_0001456 denotes face
T10 2094-2095 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T11 2505-2507 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T12 2917-2919 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T13 3282-3289 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T14 3367-3368 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T15 3645-3646 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T16 3966-3968 http://purl.obolibrary.org/obo/CLO_0050507 denotes 22
T17 4705-4712 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T18 4789-4790 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T19 5489-5493 http://purl.obolibrary.org/obo/UBERON_0001456 denotes face
T20 6532-6533 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T21 6562-6563 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T22 7487-7489 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T23 7645-7647 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T24 7677-7679 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T25 8460-8462 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T26 8618-8620 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T27 8650-8652 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T28 9433-9435 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T29 9586-9588 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T30 9618-9620 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T31 9908-9909 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T32 11427-11432 http://purl.obolibrary.org/obo/NCBITaxon_10239 denotes virus
T33 11680-11687 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T34 11779-11780 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T35 11993-12005 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T36 12117-12118 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T37 12780-12787 http://purl.obolibrary.org/obo/UBERON_0000473 denotes testing
T38 13139-13151 http://purl.obolibrary.org/obo/OBI_0000245 denotes Organization
T39 13219-13220 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T40 13441-13443 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T41 14212-14213 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T42 14399-14400 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T43 14646-14648 http://purl.obolibrary.org/obo/CLO_0050509 denotes 27
T44 14659-14660 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T45 14944-14954 http://purl.obolibrary.org/obo/CLO_0001658 denotes activities
T46 15442-15443 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T47 15795-15796 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T48 15881-15882 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T49 16219-16220 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T50 16728-16731 http://purl.obolibrary.org/obo/CLO_0050236 denotes lag
T51 16942-16945 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T52 17145-17146 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T53 17277-17278 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T54 17534-17535 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T55 17652-17653 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T56 17975-17976 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T57 18112-18113 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T58 18271-18272 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T59 18837-18838 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T60 19062-19063 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T61 19152-19153 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T62 19310-19311 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T63 19537-19538 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T64 20054-20055 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T65 20133-20135 http://purl.obolibrary.org/obo/CLO_0053733 denotes 11
T66 20741-20743 http://purl.obolibrary.org/obo/CLO_0050510 denotes 18
T67 21251-21254 http://purl.obolibrary.org/obo/CLO_0051582 denotes has
T68 21649-21650 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T69 21919-21920 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T70 22378-22386 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T71 22493-22494 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T72 22872-22873 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T73 22903-22911 http://purl.obolibrary.org/obo/CLO_0001658 denotes activity
T74 23083-23084 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T75 23305-23306 http://purl.obolibrary.org/obo/CLO_0001020 denotes a

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T1 1297-1306 Chemical denotes explosive http://purl.obolibrary.org/obo/CHEBI_63490
T2 5711-5716 Chemical denotes radio http://purl.obolibrary.org/obo/CHEBI_33325
T3 6398-6401 Chemical denotes TAS http://purl.obolibrary.org/obo/CHEBI_73657
T4 15448-15457 Chemical denotes indicator http://purl.obolibrary.org/obo/CHEBI_47867
T5 16598-16603 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T6 18496-18501 Chemical denotes group http://purl.obolibrary.org/obo/CHEBI_24433
T7 20126-20128 Chemical denotes SD http://purl.obolibrary.org/obo/CHEBI_74807
T8 20637-20639 Chemical denotes Pr http://purl.obolibrary.org/obo/CHEBI_26308|http://purl.obolibrary.org/obo/CHEBI_49828|http://purl.obolibrary.org/obo/CHEBI_8645
T11 20675-20677 Chemical denotes Pr http://purl.obolibrary.org/obo/CHEBI_26308|http://purl.obolibrary.org/obo/CHEBI_49828|http://purl.obolibrary.org/obo/CHEBI_8645

LitCovid-PD-HP

Id Subject Object Predicate Lexical cue hp_id
T1 22768-22792 Phenotype denotes susceptible to infection http://purl.obolibrary.org/obo/HP_0002719|http://purl.obolibrary.org/obo/HP_0002719
T1 22768-22792 Phenotype denotes susceptible to infection http://purl.obolibrary.org/obo/HP_0002719|http://purl.obolibrary.org/obo/HP_0002719

LitCovid-PD-GO-BP

Id Subject Object Predicate Lexical cue
T2 5842-5854 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction
T3 6260-6272 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction
T4 6827-6839 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction
T5 7246-7258 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction
T6 7800-7812 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction
T7 8219-8231 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction
T8 8773-8785 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction
T9 9192-9204 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction
T10 15502-15514 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction
T11 18026-18038 http://purl.obolibrary.org/obo/GO_0000003 denotes reproduction

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
12 66-74 Disease denotes COVID-19 MESH:C000657245
13 350-356 Disease denotes deaths MESH:D003643
16 570-578 Disease denotes COVID-19 MESH:C000657245
17 610-614 Disease denotes died MESH:D003643
19 1112-1120 Disease denotes COVID-19 MESH:C000657245
21 2337-2345 Disease denotes COVID-19 MESH:C000657245
25 2719-2727 Species denotes patients Tax:9606
26 2442-2450 Disease denotes COVID-19 MESH:C000657245
27 2710-2718 Disease denotes COVID-19 MESH:C000657245
29 3822-3830 Disease denotes COVID-19 MESH:C000657245
31 4102-4112 Disease denotes infections MESH:D007239
33 5176-5184 Species denotes children Tax:9606
35 2795-2803 Disease denotes COVID-19 MESH:C000657245
37 6857-6865 Disease denotes COVID-19 MESH:C000657245
39 7830-7838 Disease denotes COVID-19 MESH:C000657245
41 8803-8811 Disease denotes COVID-19 MESH:C000657245
43 5872-5880 Disease denotes COVID-19 MESH:C000657245
45 10547-10555 Disease denotes COVID-19 MESH:C000657245
47 11075-11083 Disease denotes COVID-19 MESH:C000657245
53 9896-9904 Species denotes patients Tax:9606
54 10335-10343 Species denotes patients Tax:9606
55 9887-9895 Disease denotes COVID-19 MESH:C000657245
56 10016-10024 Disease denotes COVID-19 MESH:C000657245
57 10326-10334 Disease denotes COVID-19 MESH:C000657245
59 11205-11213 Disease denotes COVID-19 MESH:C000657245
61 11934-11942 Disease denotes COVID-19 MESH:C000657245
63 12584-12592 Disease denotes COVID-19 MESH:C000657245
65 13084-13090 Disease denotes deaths MESH:D003643
67 14997-15003 Species denotes people Tax:9606
71 15273-15282 Disease denotes infection MESH:D007239
72 15553-15573 Disease denotes secondary infections MESH:D060085
73 15587-15595 Disease denotes infected MESH:D007239
75 16093-16101 Disease denotes COVID-19 MESH:C000657245
77 17364-17373 Disease denotes infection MESH:D007239
79 20489-20497 Disease denotes COVID-19 MESH:C000657245
83 21580-21590 Species denotes SARS-CoV-2 Tax:2697049
84 21683-21693 Species denotes SARS-CoV-2 Tax:2697049
85 21297-21305 Disease denotes COVID-19 MESH:C000657245
87 22089-22097 Disease denotes COVID-19 MESH:C000657245
90 22624-22645 Disease denotes SARS-CoV-2 infections MESH:C000657245
91 22783-22792 Disease denotes infection MESH:D007239

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T10 0-12 Sentence denotes Introduction
T11 13-180 Sentence denotes A small cluster of cases of the disease now known as COVID-19 was first reported on December 29, 2019, in the Chinese city of Wuhan (World Health Organization, 2020a).
T12 181-309 Sentence denotes By early May 2020, the disease had spread to all global regions, and overwhelmed some the world’s most developed health systems.
T13 310-516 Sentence denotes More than 2.8 million cases and 260,000 deaths had been confirmed globally, and the vast majority of countries with confirmed cases were reporting escalating transmission (World Health Organization, 2020b).
T14 517-592 Sentence denotes As of 1 May 2020, there were 6808 confirmed cases of COVID-19 in Australia.
T15 593-632 Sentence denotes Of these, 98 had died from the disease.
T16 633-831 Sentence denotes Encouragingly, the daily count of new confirmed cases had been declining since late March 2020, with 308 cases reported nationally since 14 April (Australian Government Department of Health, 2020a).
T17 832-1093 Sentence denotes This suggests that Australia has (to date) avoided a “worst-case” scenario — one where planning models estimated a peak daily demand for 35,000 ICU beds by around May 2020, far exceeding the health system’s capacity of around 2,200 ICU beds (Moss et al., 2020).
T18 1094-1217 Sentence denotes The first wave of COVID-19 epidemics, and the government and public responses to them, have varied vastly across the globe.
T19 1218-1395 Sentence denotes For example, many European countries and the United States are in the midst of explosive outbreaks with overwhelmed health systems (Remuzzi and Remuzzi, 2020; The Lancet, 2020).
T20 1396-1743 Sentence denotes Meanwhile, countries such as Singapore and South Korea had early success in containing the spread, partly attributed to their extensive surveillance efforts and case targeted interventions (Ng et al., 2020; COVID-19 National Emergency Response Center, Epidemiology and Case Management Team, Korea Centers for Disease Control and Prevention, 2020).
T21 1744-1952 Sentence denotes However, despite those early successes, Singapore has recently taken additional steps to further limit transmission in the face of increasing importations and community spread (Government of Singapore, 2020).
T22 1953-2164 Sentence denotes Other locations in the region, including Taiwan, Hong Kong and New Zealand, have had similar epidemic experiences, achieving control through a combination of border, case targeted and social distancing measures.
T23 2165-2406 Sentence denotes Analysing key epidemiological and response factors — such as the intensity and timing of public health interventions — that contribute to individual country experiences of COVID-19 will assist in the next stage of response planning globally.
T24 2407-2562 Sentence denotes Here we describe the course of the COVID-19 epidemic and public health response in Australia from 22 January up to mid-April 2020 (summarised in Figure 1).
T25 2563-2739 Sentence denotes We then quantify the impact of the public health response on disease transmission (Figure 2) and forecast the short-term health system demand from COVID-19 patients (Figure 3).
T26 2740-2749 Sentence denotes Figure 1.
T27 2751-2972 Sentence denotes Time series of new daily confirmed cases of COVID-19 in Australia by import status (purple = overseas acquired, blue = locally acquired, green = unknown origin) from 22 January 2020 (first case detected) to 13 April 2020.
T28 2973-3130 Sentence denotes Dates of selected key border and social distancing measures implemented by Australian authorities are indicated by annotations above the plotted case counts.
T29 3131-3441 Sentence denotes These measures were in addition to case targeted interventions (case isolation and contact quarantine) and further border measures, including enhanced testing and provision of advice, on arrivals from other selected countries, based on a risk-assessment tool developed in early February (Shearer et al., 2020).
T30 3442-3644 Sentence denotes Note that Australian citizens and residents (and their dependants) were exempt from travel restrictions, but upon returning to Australia were required to quarantine for 14 days from the date of arrival.
T31 3645-3746 Sentence denotes A full timeline of social distancing and border measures is provided in Figure 1—figure supplement 2.
T32 3747-3776 Sentence denotes Figure 1—figure supplement 1.
T33 3778-4021 Sentence denotes Time series of new daily confirmed cases of COVID-19 in each Australian state/territory by import status (purple = overseas acquired, blue = locally acquired, green = unknown origin) from 22 January 2020 (first case detected) to 13 April 2020.
T34 4022-4254 Sentence denotes Details on the epidemiological characteristics of locally and overseas acquired infections are available in the Australian Department of Health fortnightly epidemiological reports (Australian Government Department of Health, 2020e).
T35 4255-4284 Sentence denotes Figure 1—figure supplement 2.
T36 4286-4380 Sentence denotes Timeline of border and social distancing measures implemented in Australia up to 4 April 2020.
T37 4381-4506 Sentence denotes These measures were in addition to case targeted interventions, specifically case isolation and quarantine of their contacts.
T38 4507-4603 Sentence denotes Contact tracing was initiated from 29 January 2020 and was performed by public health officials.
T39 4604-4611 Sentence denotes Note 1:
T40 4612-4863 Sentence denotes Between 1 February and 15 March, further border measures were introduced, including enhanced testing and provision of advice on arrivals from other selected countries, based on a risk-assessment tool developed in early February (Shearer et al., 2020).
T41 4864-4871 Sentence denotes Note 2:
T42 4872-5063 Sentence denotes Australian citizens and residents (and their dependants) were exempt from travel restrictions but upon returning to Australia were required to quarantine for 14 days from the date of arrival.
T43 5064-5071 Sentence denotes Note 3:
T44 5072-5327 Sentence denotes School attendance is reported to have reduce substantially following government recommendations to keep children from school (National Centre for Immunisation Research and Surveillance, 2020), and in some cases, prior to these announcements (Carey, 2020).
T45 5328-5469 Sentence denotes It should also be noted that school holidays in some states/territories overlapped with the restriction periods (late March and early April).
T46 5470-5477 Sentence denotes Note 4:
T47 5478-5581 Sentence denotes The use of face masks by the general public was not recommended at any time during the analysis period.
T48 5582-5589 Sentence denotes Note 5:
T49 5590-5791 Sentence denotes Personal hygiene measures and the ‘1.5 m distancing rule’ were promoted to the general public through television, print, radio and social media campaigns commissioned by national and state governments.
T50 5792-5801 Sentence denotes Figure 2.
T51 5803-6065 Sentence denotes Time-varying estimate of the effective reproduction number (R𝑒𝑓𝑓) of COVID-19 by Australian state (light blue ribbon = 90% credible interval; dark blue ribbon = 50% credible interval) from 1 March to 5 April 2020, based on data up to and including 13 April 2020.
T52 6066-6182 Sentence denotes Confidence in the estimated values is indicated by shading with reduced shading corresponding to reduced confidence.
T53 6183-6301 Sentence denotes The horizontal dashed line indicates the target value of 1 for the effective reproduction number required for control.
T54 6302-6468 Sentence denotes Not presented are the Australian Capital Territory (ACT), Northern Territory (NT) and Tasmania (TAS), as these states/territories had insufficient local transmission.
T55 6469-6727 Sentence denotes The uncertainty in the R𝑒𝑓𝑓 estimates represent variability in a population-level average as a result of imperfect data, rather than individual-level heterogeneity in transmission (i.e., the variation in the number of secondary cases generated by each case).
T56 6728-6757 Sentence denotes Figure 2—figure supplement 1.
T57 6759-6787 Sentence denotes Sensitivity analysis 1 of 3.
T58 6788-7050 Sentence denotes Time-varying estimate of the effective reproduction number (R𝑒𝑓𝑓) of COVID-19 by Australian state (light blue ribbon = 90% credible interval; dark blue ribbon = 50% credible interval) from 1 March to 5 April 2020, based on data up to and including 13 April 2020.
T59 7051-7168 Sentence denotes Confidence in the estimated values is indicated by shading, with reduced shading corresponding to reduced confidence.
T60 7169-7287 Sentence denotes The horizontal dashed line indicates the target value of 1 for the effective reproduction number required for control.
T61 7288-7531 Sentence denotes Results are produced assuming stepwise changes in the relative infectiousness of locally acquired to imported cases according to quarantine requirements for returning travellers introduced on 15 and 27 March (indicated by vertical grey lines).
T62 7532-7700 Sentence denotes We assumed that 90%, 50%, and 1% of imported cases contributed to transmission prior to 15 March, between 15 and 27 March (inclusive), and after 27 March, respectively.
T63 7701-7730 Sentence denotes Figure 2—figure supplement 2.
T64 7732-7760 Sentence denotes Sensitivity analysis 2 of 3.
T65 7761-8023 Sentence denotes Time-varying estimate of the effective reproduction number (R𝑒𝑓𝑓) of COVID-19 by Australian state (light blue ribbon = 90% credible interval; dark blue ribbon = 50% credible interval) from 1 March to 5 April 2020, based on data up to and including 13 April 2020.
T66 8024-8141 Sentence denotes Confidence in the estimated values is indicated by shading, with reduced shading corresponding to reduced confidence.
T67 8142-8260 Sentence denotes The horizontal dashed line indicates the target value of 1 for the effective reproduction number required for control.
T68 8261-8504 Sentence denotes Results are produced assuming stepwise changes in the relative infectiousness of locally acquired to imported cases according to quarantine requirements for returning travellers introduced on 15 and 27 March (indicated by vertical grey lines).
T69 8505-8673 Sentence denotes We assumed that 80%, 50%, and 1% of imported cases contributed to transmission prior to 15 March, between 15 and 27 March (inclusive), and after 27 March, respectively.
T70 8674-8703 Sentence denotes Figure 2—figure supplement 3.
T71 8705-8733 Sentence denotes Sensitivity analysis 3 of 3.
T72 8734-8996 Sentence denotes Time-varying estimate of the effective reproduction number (R𝑒𝑓𝑓) of COVID-19 by Australian state (light blue ribbon = 90% credible interval; dark blue ribbon = 50% credible interval) from 1 March to 5 April 2020, based on data up to and including 13 April 2020.
T73 8997-9114 Sentence denotes Confidence in the estimated values is indicated by shading, with reduced shading corresponding to reduced confidence.
T74 9115-9233 Sentence denotes The horizontal dashed line indicates the target value of 1 for the effective reproduction number required for control.
T75 9234-9477 Sentence denotes Results are produced assuming stepwise changes in the relative infectiousness of locally acquired to imported cases according to quarantine requirements for returning travellers introduced on 15 and 27 March (indicated by vertical grey lines).
T76 9478-9641 Sentence denotes We assumed 50%, 20%, and 1% of imported cases contributed to transmission prior to 15 March, between 15 and 27 March (inclusive), and after 27 March, respectively.
T77 9642-9651 Sentence denotes Figure 3.
T78 9653-9843 Sentence denotes Forecasted daily hospital ward (left) and intensive care unit (right) occupancy (dark ribbons = 50% confidence intervals; light ribbons = 95% confidence intervals) from 17 March to 28 April.
T79 9844-9920 Sentence denotes Occupancy = the number of beds occupied by COVID-19 patients on a given day.
T80 9921-10046 Sentence denotes Black dots indicate the reported ward and ICU occupancy available from the Australian national COVID-19 database at the time.
T81 10047-10136 Sentence denotes These data were retrospectively updated where complete data were available (red crosses).
T82 10137-10395 Sentence denotes Australian health system ward and ICU bed capacities are estimated to be over 25,000 and 1,100, respectively, under the assumption that 50% of total capacity could possibly be dedicated to COVID-19 patients (Australian Institute of Health and Welfare, 2019).
T83 10396-10471 Sentence denotes The forecasted daily case counts are shown in Figure 3—figure supplement 1.
T84 10472-10501 Sentence denotes Figure 3—figure supplement 1.
T85 10503-10745 Sentence denotes Time series of new daily confirmed cases of COVID-19 in Australia from 1 March to 13 April 2020 (grey bars) overlaid by daily case counts estimated from the forecasting model up to April 13 and projected forward from 14 to 28 April inclusive.
T86 10746-10787 Sentence denotes Inner shading = 50% confidence intervals.
T87 10788-10829 Sentence denotes Outer shading = 95% confidence intervals.
T88 10830-11025 Sentence denotes Note that forecasting model estimates prior to 13 April — the last recorded data point at the time of analysis (indicated by the dashed grey line) — use data up to and including the previous day.
T89 11026-11113 Sentence denotes Black dots show the number of new daily cases of COVID-19 reported from 14 to 28 April.
T90 11115-11150 Sentence denotes Timeline of the Australian epidemic
T91 11151-11214 Sentence denotes Australia took an early and precautionary approach to COVID-19.
T92 11215-11433 Sentence denotes On 1 February, when China was the only country reporting uncontained transmission, Australian authorities restricted all travel from mainland China to Australia, in order to reduce the risk of importation of the virus.
T93 11434-11545 Sentence denotes Only Australian citizens and residents (and their dependants) were permitted to travel from China to Australia.
T94 11546-11635 Sentence denotes These individuals were advised to self-quarantine for 14 days from their date of arrival.
T95 11636-11853 Sentence denotes Further border measures, including enhanced testing and provision of additional advice, were placed on arrivals from other countries, based on a risk-assessment tool developed in early February (Shearer et al., 2020).
T96 11854-12014 Sentence denotes The day before Australia imposed these restrictions (January 31), 9720 cases of COVID-19 had been reported in mainland China (World Health Organization, 2020c).
T97 12015-12208 Sentence denotes Australia had so far detected and managed nine imported cases, all with recent travel history from or a direct epidemiological link to Wuhan (Australian Government Department of Health, 2020b).
T98 12209-12387 Sentence denotes Before the restrictions, Australia was expecting to receive approximately 200,000 air passengers from mainland China during February 2020 (Australian Bureau of Statistics, 2019).
T99 12388-12463 Sentence denotes Travel numbers fell dramatically following the imposed travel restrictions.
T100 12464-12608 Sentence denotes These restrictions were not intended (and highly unlikely [Errett et al., 2020]) to prevent the ultimate importation of COVID-19 into Australia.
T101 12609-12734 Sentence denotes Their purpose was to delay the establishment of an epidemic, buying valuable time for health authorities to plan and prepare.
T102 12735-12984 Sentence denotes During the month of February, with extensive testing and case targeted interventions (case isolation and contact quarantine) initiated from 29 January (Australian Government Department of Health, 2020d), Australia detected and managed only 12 cases.
T103 12985-13160 Sentence denotes Meanwhile, globally, the geographic extent of transmission and daily counts of confirmed cases and deaths continued to increase drastically (World Health Organization, 2020d).
T104 13161-13497 Sentence denotes In early March, Australia extended travel restrictions to a number of countries with large uncontained outbreaks, namely Iran (as of 1 March) (Commonwealth Government of Australia, 2020a), South Korea (as of 5 March) (Commonwealth Government of Australia, 2020b) and Italy (as of 11 March) (Commonwealth Government of Australia, 2020c).
T105 13498-13601 Sentence denotes Despite these measures, the daily case counts rose sharply in Australia during the first half of March.
T106 13602-13856 Sentence denotes While the vast majority of these cases were connected to travellers returning to Australia from overseas, localised community transmission had been reported in areas of Sydney (NSW) and Melbourne (VIC) (Australian Government Department of Health, 2020c).
T107 13857-14144 Sentence denotes Crude plots of the cumulative number of cases by country showed Australia on an early trajectory similar to the outbreaks experienced in China, Europe and the United States, where health systems had become or were becoming overwhelmed (Australian Government Department of Health, 2020f).
T108 14145-14358 Sentence denotes From 16 March, the Australian Government progressively implemented a range of social distancing measures in order to reduce and prevent further community transmission (Commonwealth Government of Australia, 2020d).
T109 14359-14505 Sentence denotes The day before, authorities had imposed a self-quarantine requirement on all international arrivals (Commonwealth Government of Australia, 2020e).
T110 14506-14779 Sentence denotes On 19 March, Australia closed its borders to all non-citizens and non-residents (Commonwealth Government of Australia, 2020f), and on March 27, moved to a policy of mandatory quarantine for any returning citizens and residents (Commonwealth Government of Australia, 2020g).
T111 14780-15050 Sentence denotes By 29 March, social distancing measures had been escalated to the extent that all Australians were strongly advised to leave their homes only for limited essential activities and public gatherings were limited to two people (Commonwealth Government of Australia, 2020h).
T112 15051-15187 Sentence denotes By late March, daily counts of new cases appeared to be declining, suggesting that these measures had successfully reduced transmission.
T113 15189-15227 Sentence denotes Quantifying the impact of the response
T114 15228-15441 Sentence denotes Quantifying changes in the rate of spread of infection over the course of an epidemic is critical for monitoring the collective impact of public health interventions and forecasting the short-term clinical burden.
T115 15442-15713 Sentence denotes A key indicator of transmission in context is the effective reproduction number (R𝑒𝑓𝑓) — the average number of secondary infections caused by an infected individual in the presence of public health interventions and for which no assumption of 100% susceptibility is made.
T116 15714-15841 Sentence denotes If control efforts are able to bring R𝑒𝑓𝑓 below 1, then on average there will be a decline in the number of new cases reported.
T117 15842-16045 Sentence denotes The decline will become apparent after a delay of approximately one incubation period plus time to case detection and reporting following implementation of the control measure (i.e., at least two weeks).
T118 16046-16210 Sentence denotes Using case counts from the Australian national COVID-19 database, we estimated R𝑒𝑓𝑓 over time for each Australian state from 24 February to 5 April 2020 (Figure 2).
T119 16211-16611 Sentence denotes We used a statistical method that estimates time-varying R𝑒𝑓𝑓 by using an optimally selected moving average window (according to the continuous ranked probability score) to smooth the curve and reduce the impact of localised clusters and outbreaks that may cause large fluctuations (London School of Hygiene & Tropical Medicine Mathematical Modelling of Infectious Diseases nCoV working group, 2020).
T120 16612-16705 Sentence denotes Importantly, the method accounts for time delays between illness onset and case notification.
T121 16706-16918 Sentence denotes Incorporation of this lag is critical for accurate interpretation of the most recent data in the analysis, to be sure that an observed drop in the number of reported cases reflects an actual drop in case numbers.
T122 16919-17018 Sentence denotes Results show that R𝑒𝑓𝑓 has likely been below one in each Australian state since early-to-mid March.
T123 17019-17191 Sentence denotes These estimates are geographically averaged results over large areas and it is possible that R𝑒𝑓𝑓 was much higher than one in a number of localised settings (see Figure 2).
T124 17192-17374 Sentence denotes The estimated time-varying R𝑒𝑓𝑓 value is based on cases that have been identified as a result of local transmission, whereas imported cases only contribute to the force of infection.
T125 17375-17449 Sentence denotes Imported and locally acquired cases were assumed to be equally infectious.
T126 17450-17513 Sentence denotes The method for estimating R𝑒𝑓𝑓 is sensitive to this assumption.
T127 17514-17805 Sentence denotes Hence, we performed a sensitivity analysis to assess the impact of stepwise reductions in the infectiousness of imported cases on R𝑒𝑓𝑓 as a result of quarantine measures implemented over time (see Figure 2—figure supplement 1, Figure 2—figure supplement 2, and Figure 2—figure supplement 3).
T128 17806-17910 Sentence denotes The sensitivity analyses suggest that R𝑒𝑓𝑓 may well have dropped below one later than shown in Figure 2.
T129 17911-18270 Sentence denotes In Victoria and New South Wales, the two Australian states with a substantial number of local cases, the effective reproduction number likely dropped from marginally above one to well below one within a two week period (considering both our main result and those from the sensitivity analyses) coinciding with the implementation of social distancing measures.
T130 18271-18608 Sentence denotes A comparable trend was observed in New Zealand and many Western European countries, including France, Spain and Germany (London School of Hygiene & Tropical Medicine Mathematical Modelling of Infectious Diseases nCoV working group, 2020), where similar national, stage-wise social distancing policies were enacted (Flaxman et al., 2020).
T131 18609-18897 Sentence denotes However, most of these European countries experienced widespread community transmission prior to the implementation of social distancing measures, with R𝑒𝑓𝑓 estimates reaching between 1.5 and 2 in early March and declining over a longer period (three to four weeks) relative to Australia.
T132 18899-18930 Sentence denotes Forecasting the clinical burden
T133 18931-19035 Sentence denotes Next we used our estimates of time-varying R𝑒𝑓𝑓 to forecast the short-term clinical burden in Australia.
T134 19036-19151 Sentence denotes Estimates were input into a mathematical model of disease dynamics that was extended to account for imported cases.
T135 19152-19413 Sentence denotes A sequential Monte Carlo method was used to infer the model parameters and appropriately capture the uncertainty (Moss et al., 2019a), conditional on each of a number of sampled R𝑒𝑓𝑓 trajectories up to 5 April, from which point they were assumed to be constant.
T136 19414-19580 Sentence denotes The model was subsequently projected forward from April 14 to April 28, to forecast the number of reported cases, assuming a symptomatic detection probability of 80%.
T137 19581-19704 Sentence denotes The number of new daily hospitalisations and ICU admissions were estimated from recently observed and forecast case counts.
T138 19705-19967 Sentence denotes Specifically, the age distribution of projected cases, and age-specific probabilities of hospitalisation and ICU admission, were extracted from Australian age-specific data on confirmed cases, assuming that this distribution would remain unchanged (see Table 1).
T139 19968-20181 Sentence denotes In order to calculate the number of occupied ward/ICU beds per day, length-of-stay in a ward bed and ICU bed were assumed to be Gamma distributed with means (SD) of 11 (3.42) days and 14 (5.22) days, respectively.
T140 20182-20395 Sentence denotes Our results indicated that with the public health interventions in place as of 13 April, Australia’s hospital ward and ICU occupancy would remain well below capacity thresholds over the period from 14 to 28 April.
T141 20396-20404 Sentence denotes Table 1.
T142 20406-20610 Sentence denotes Age-specific proportions of confirmed cases extracted from the Australian national COVID-19 database and age-specific estimates of the probability of hospitalisation and ICU admission for confirmed cases.
T143 20611-20709 Sentence denotes Age Proportion of cases Pr(hospitalisation | confirmed case) Pr(ICU admission | confirmed case)
T144 20710-20737 Sentence denotes 0-9 0.0102 0.1475 0.0000
T145 20738-20767 Sentence denotes 10-18 0.0186 0.1081 0.0090
T146 20768-20797 Sentence denotes 19-29 0.2258 0.0504 0.0007
T147 20798-20827 Sentence denotes 30-39 0.1587 0.0865 0.0074
T148 20828-20857 Sentence denotes 40-49 0.1291 0.0947 0.0208
T149 20858-20887 Sentence denotes 50-59 0.1550 0.1112 0.0173
T150 20888-20917 Sentence denotes 60-69 0.1686 0.1529 0.0318
T151 20918-20947 Sentence denotes 70-79 0.1050 0.2440 0.0558
T152 20948-20975 Sentence denotes 80+ 0.0290 0.3815 0.0462
T153 20977-20988 Sentence denotes Conclusions
T154 20989-21306 Sentence denotes Our analysis suggests that Australia’s combined strategy of early, targeted management of the risk of importation, case targeted interventions, and broad-scale social distancing measures applied prior to the onset of (detected) widespread community transmission has substantially mitigated the first wave of COVID-19.
T155 21307-21481 Sentence denotes More detailed analyses are required to assess the relative impact of specific response measures, and this information will be crucial for the next phase of response planning.
T156 21482-21614 Sentence denotes Other factors, such as temperature, humidity and population density may influence transmission of SARS-CoV-2 (Kissler et al., 2020).
T157 21615-21738 Sentence denotes Whether these factors have played a role in the relative control of SARS-CoV-2 in some countries, remains an open question.
T158 21739-21982 Sentence denotes Noting that epidemics are established in both the northern and southern hemispheres, it may be possible to gain insight into such factors over the next six months, via for example a comparative analysis of transmission in Australia and Europe.
T159 21983-22151 Sentence denotes We further anticipated that the Australian health care system was well positioned to manage the projected COVID-19 case loads over the forecast period (up to 28 April).
T160 22152-22331 Sentence denotes Ongoing situational assessment and monitoring of forecast hospital and ICU demand will be essential for managing possible future relaxation of broad-scale community interventions.
T161 22332-22564 Sentence denotes Vigilance for localised increases in epidemic activity and in particular for outbreaks in vulnerable populations such as residential aged care facilities, where a high proportion of cases are likely to be severe, must be maintained.
T162 22565-22689 Sentence denotes One largely unknown factor at present is the proportion of SARS-CoV-2 infections that are asymptomatic, mild or undiagnosed.
T163 22690-22793 Sentence denotes Even if this number is high, the Australian population would still be largely susceptible to infection.
T164 22794-22912 Sentence denotes Accordingly, complete relaxation of the measures currently in place would see a rapid resurgence in epidemic activity.
T165 22913-22953 Sentence denotes This problem is not unique to Australia.
T166 22954-23145 Sentence denotes Many countries with intensive social distancing measures in place are starting to grapple with their options and time frames for a gradual return to relative normalcy (Gottlieb et al., 2020).
T167 23146-23354 Sentence denotes There are difficult decisions ahead for governments, and for now Australia is one of the few countries fortunate enough to be able to plan the next steps from a position of relative calm as opposed to crisis.

2_test

Id Subject Object Predicate Lexical cue
32788039-32191691-27152622 1597-1601 32191691 denotes 2020
32788039-32257773-27152623 1737-1741 32257773 denotes 2020
32788039-32512579-27152624 18602-18606 32512579 denotes 2020
32788039-32291278-27152625 21608-21612 32291278 denotes 2020

LitCovid-PMC-OGER-BB

Id Subject Object Predicate Lexical cue
T7 66-74 SP_7 denotes COVID-19
T8 294-308 UBERON:0000467 denotes health systems
T9 350-356 GO:0016265 denotes deaths
T10 570-578 SP_7 denotes COVID-19
T11 610-614 GO:0016265 denotes died
T12 1023-1036 UBERON:0000467 denotes health system
T13 1112-1120 SP_7 denotes COVID-19
T14 1211-1216 UBERON:0010230 denotes globe
T15 1334-1348 UBERON:0000467 denotes health systems
T16 1603-1611 SP_7 denotes COVID-19
T17 2078-2085 GO:0065007 denotes control
T18 2337-2345 SP_7 denotes COVID-19
T19 2442-2450 SP_7 denotes COVID-19
T20 2710-2718 SP_7 denotes COVID-19
T21 2795-2803 SP_7 denotes COVID-19
T22 3822-3830 SP_7 denotes COVID-19
T23 10547-10555 SP_7 denotes COVID-19

MyTest

Id Subject Object Predicate Lexical cue
32788039-32191691-27152622 1597-1601 32191691 denotes 2020
32788039-32257773-27152623 1737-1741 32257773 denotes 2020
32788039-32512579-27152624 18602-18606 32512579 denotes 2020
32788039-32291278-27152625 21608-21612 32291278 denotes 2020