LitCovid-sentences  

PMC:7386785 / 24096-43932 JSONTXT 10 Projects

Annnotations TAB TSV DIC JSON TextAE Lectin_function

Id Subject Object Predicate Lexical cue
T267 0-7 Sentence denotes Methods
T268 9-57 Sentence denotes Criteria for considering studies for this review
T269 59-75 Sentence denotes Types of studies
T270 76-304 Sentence denotes We kept the eligibility criteria purposely broad to include all patient groups and all variations of a test at this initial stage of reviewing the evidence (that is, if the patient population was unclear, we included the study).
T271 305-433 Sentence denotes We included studies of all designs that produce estimates of test accuracy or provide data from which estimates can be computed.
T272 434-653 Sentence denotes We included both single‐gate (studies that recruit from a patient pathway before disease status has been ascertained) and multi‐gate (where people with and without the target condition are recruited separately) designs.
T273 654-756 Sentence denotes This means that we included studies that were cross‐sectional or diagnostic case‐control type studies.
T274 757-914 Sentence denotes When interpreting the results, we made sure that the limitations of different study designs were carefully considered, using quality assessment and analysis.
T275 916-928 Sentence denotes Participants
T276 929-1063 Sentence denotes Studies recruiting people presenting to primary care or outpatient hospital settings with suspicion of COVID‐19 disease were eligible.
T277 1064-1242 Sentence denotes For the initial version of this review, we included studies that recruited symptomatic people either known to have SARS‐CoV‐2 infection or known not to have SARS‐CoV‐2 infection.
T278 1243-1309 Sentence denotes Studies had to have a sample size of a minimum of 10 participants.
T279 1311-1322 Sentence denotes Index tests
T280 1323-1357 Sentence denotes All signs and symptoms, including:
T281 1358-1430 Sentence denotes signs such as oxygen saturation, measured by oximetry or blood pressure;
T282 1431-1472 Sentence denotes classic symptoms, such as fever or cough.
T283 1473-1655 Sentence denotes We included combinations of signs and symptoms, but not when they were combined with laboratory, imaging, or other types of index tests as these will be covered in the other reviews.
T284 1657-1674 Sentence denotes Target conditions
T285 1675-1730 Sentence denotes To be eligible studies had to identify at least one of:
T286 1731-1765 Sentence denotes mild or moderate COVID‐19 disease;
T287 1766-1785 Sentence denotes COVID‐19 pneumonia.
T288 1786-1956 Sentence denotes Asymptomatic infection with SARS‐CoV‐2 infection is out of scope for this review, considering it is by definition not possible to detect this based on signs and symptoms.
T289 1958-1977 Sentence denotes Reference standards
T290 1978-2047 Sentence denotes We anticipated that studies would use a range of reference standards.
T291 2048-2247 Sentence denotes Although RT‐PCR is considered the best available test, due to rapidly evolving knowledge about the target conditions, multiple reference standards on their own as well as in combination have emerged.
T292 2248-2290 Sentence denotes We expected to encounter cases defined by:
T293 2291-2304 Sentence denotes RT‐PCR alone;
T294 2305-2370 Sentence denotes RT‐PCR, clinical expertise, and imaging (for example, CT thorax);
T295 2371-2432 Sentence denotes repeated RT‐PCR several days apart or from different samples;
T296 2433-2527 Sentence denotes plaque reduction neutralisation test (PRNT) or enzyme‐linked immunosorbent assay(ELISA) tests;
T297 2528-2577 Sentence denotes information available at a subsequent time point;
T298 2578-2654 Sentence denotes World Health Organization (WHO) and other case definitions (see Appendix 1).
T299 2655-2736 Sentence denotes This list is not exhaustive, and we recorded all reference standards encountered.
T300 2737-2928 Sentence denotes With a group of methodological and clinical experts, we are producing a ranking of reference standards according to their ability to correctly classify participants using a consensus process.
T301 2929-3042 Sentence denotes We will use the ranking for informing the assessment of methodological quality in the next update of this review.
T302 3044-3088 Sentence denotes Search methods for identification of studies
T303 3089-3159 Sentence denotes The final search date for this version of the review is 27 April 2020.
T304 3161-3180 Sentence denotes Electronic searches
T305 3181-3327 Sentence denotes We conducted a single literature search to cover our suite of Cochrane COVID‐19 diagnostic test accuracy (DTA) reviews (Deeks 2020; McInnes 2020).
T306 3328-3387 Sentence denotes We conducted electronic searches using two primary sources.
T307 3388-3551 Sentence denotes Both of these searches aimed to identify all published articles and preprints related to COVID‐19, and were not restricted to those evaluating biomarkers or tests.
T308 3552-3640 Sentence denotes Thus, there are no test terms, diagnosis terms, or methodological terms in the searches.
T309 3641-3753 Sentence denotes Searches were limited to 2019 and 2020, and for this version of the review have been conducted to 27 April 2020.
T310 3755-3796 Sentence denotes Cochrane COVID‐19 Study Register searches
T311 3797-3908 Sentence denotes We used the Cochrane COVID‐19 Study Register (covid-19.cochrane.org/), for searches conducted to 28 March 2020.
T312 3909-4091 Sentence denotes At that time, the register was populated by searches of PubMed, as well as trials registers at ClinicalTrials.gov and the WHO International Clinical Trials Registry Platform (ICTRP).
T313 4092-4219 Sentence denotes Search strategies were designed for maximum sensitivity, to retrieve all human studies on COVID‐19 and with no language limits.
T314 4220-4235 Sentence denotes See Appendix 2.
T315 4237-4298 Sentence denotes COVID‐19 Living Evidence Database from the University of Bern
T316 4299-4543 Sentence denotes From 28 March 2020, we used the COVID‐19 Living Evidence database from the Institute of Social and Preventive Medicine (ISPM) at the University of Bern (www.ispm.unibe.ch), as the primary source of records for the Cochrane COVID‐19 DTA reviews.
T317 4544-4636 Sentence denotes This search includes PubMed, Embase, and preprints indexed in bioRxiv and medRxiv databases.
T318 4637-4735 Sentence denotes The strategies as described on the ISPM website are described here (ispmbern.github.io/covid-19/).
T319 4736-4751 Sentence denotes See Appendix 3.
T320 4752-4894 Sentence denotes The decision to focus primarily on the 'Bern' feed was due to the exceptionally large numbers of COVID‐19 studies available only as preprints.
T321 4895-5130 Sentence denotes The Cochrane COVID‐19 Study Register has undergone a number of iterations since the end of March 2020 and we anticipate moving back to the Cochrane COVID‐19 Study Register as the primary source of records for subsequent review updates.
T322 5132-5157 Sentence denotes Searching other resources
T323 5158-5431 Sentence denotes We obtained Embase records through Martha Knuth for the Centers for Disease Control and Prevention (CDC), Stephen B Thacker CDC Library, COVID‐19 Research Articles Downloadable Database and de‐duplicated them against the Cochrane COVID‐19 Study Register up to 1 April 2020.
T324 5432-5447 Sentence denotes See Appendix 4.
T325 5448-5554 Sentence denotes We also checked our search results against two additional repositories of COVID‐19 publications including:
T326 5555-5653 Sentence denotes the Evidence for Policy and Practice Information and Co‐ordinating Centre (EPPI‐Centre) 'COVID‐19:
T327 5654-5729 Sentence denotes Living map of the evidence' (eppi.ioe.ac.uk/COVID19_MAP/covid_map_v4.html);
T328 5730-5879 Sentence denotes the Norwegian Institute of Public Health 'NIPH systematic and living map on COVID‐19 evidence' (www.nornesk.no/forskningskart/NIPH_diagnosisMap.html)
T329 5880-6078 Sentence denotes Both of these repositories allow their contents to be filtered according to studies potentially relating to diagnosis, and both have agreed to provide us with updates of new diagnosis studies added.
T330 6079-6185 Sentence denotes For this iteration of the review, we examined all diagnosis studies from both sources up to 16 April 2020.
T331 6186-6229 Sentence denotes We did not apply any language restrictions.
T332 6231-6259 Sentence denotes Data collection and analysis
T333 6261-6281 Sentence denotes Selection of studies
T334 6282-6337 Sentence denotes Pairs of review authors independently screened studies.
T335 6338-6540 Sentence denotes We resolved disagreements by discussion with a third, experienced review author for initial title and abstract screening, and through discussion between three review authors for eligibility assessments.
T336 6542-6572 Sentence denotes Data extraction and management
T337 6573-6637 Sentence denotes Pairs of review authors independently performed data extraction.
T338 6638-6707 Sentence denotes We resolved disagreements by discussion between three review authors.
T339 6708-6810 Sentence denotes We intended to contact study authors where we needed to clarify details or obtain missing information.
T340 6812-6848 Sentence denotes Assessment of methodological quality
T341 6849-7128 Sentence denotes Pairs of review authors independently assessed risk of bias and applicability concerns using the QUADAS‐2 (Quality Assessment tool for Diagnostic Accuracy Studies) checklist, which was common to the suite of reviews but tailored to each particular review (Whiting 2011; Table 2).
T342 7129-7279 Sentence denotes For this review, we excluded the questions on the nature of the samples as these were not relevant, and we added a question on who assessed the signs.
T343 7280-7349 Sentence denotes We resolved disagreements by discussion between three review authors.
T344 7350-7371 Sentence denotes 1 QUADAS‐2 checklist
T345 7372-7406 Sentence denotes Index test(s) Signs and symptoms
T346 7407-7671 Sentence denotes Patients (setting, intended use of index test, presentation, prior testing) Primary care, hospital outpatient settings including emergency departmentsInpatients presenting with suspected COVID‐19No prior testingSigns and symptoms often used for triage or referral
T347 7672-7791 Sentence denotes Reference standard and target condition The focus will be on the diagnosis of COVID‐19 disease and COVID‐19 pneumonia.
T348 7792-7844 Sentence denotes For this review, the focus will not be on prognosis.
T349 7845-7866 Sentence denotes Participant selection
T350 7867-7923 Sentence denotes Was a consecutive or random sample of patients enrolled?
T351 7925-8389 Sentence denotes This will be similar for all index tests, target conditions, and populations.YES: if a study explicitly stated that all participants within a certain time frame were included; that this was done consecutively; or that a random selection was done.NO: if it was clear that a different selection procedure was employed; for example, selection based on clinician's preference, or based on institutions.UNCLEAR: if the selection procedure was not clear or not reported.
T352 8390-8424 Sentence denotes Was a case‐control design avoided?
T353 8426-8843 Sentence denotes This will be similar for all index tests, target conditions, and populations.YES: if a study explicitly stated that all participants came from the same group of (suspected) patients.NO: if it was clear that a different selection procedure was employed for the participants depending on their COVID‐19 (pneumonia) status or SARS‐CoV‐2 infection status.UNCLEAR: if the selection procedure was not clear or not reported.
T354 8844-8889 Sentence denotes Did the study avoid inappropriate exclusions?
T355 8891-9062 Sentence denotes Studies may have excluded participants, or selected participants in such a way that they avoided including those who were difficult to diagnose or likely to be borderline.
T356 9063-9328 Sentence denotes Although the inclusion and exclusion criteria will be different for the different index tests, inappropriate exclusions and inclusions will be similar for all index tests: for example, only elderly patients excluded, or children (as sampling may be more difficult).
T357 9329-9840 Sentence denotes This needs to be addressed on a case‐by‐case basis.YES: if a high proportion of eligible patients was included without clear selection.NO: if a high proportion of eligible patients was excluded without providing a reason; if, in a retrospective study, participants without index test or reference standard results were excluded; if exclusion was based on severity assessment post‐factum or comorbidities (cardiovascular disease, diabetes, immunosuppression).UNCLEAR: if the exclusion criteria were not reported.
T358 9841-9886 Sentence denotes Did the study avoid inappropriate inclusions?
T359 9888-10135 Sentence denotes YES: if samples included were likely to be representative of the spectrum of disease.NO: if the study oversampled patients with particular characteristics likely to affect estimates of accuracy.UNCLEAR: if the exclusion criteria were not reported.
T360 10136-10189 Sentence denotes Could the selection of patients have introduced bias?
T361 10191-10402 Sentence denotes HIGH: if one or more signalling questions were answered with NO, as any deviation from the selection process may lead to bias.LOW: if all signalling questions were answered with YES.UNCLEAR: all other instances.
T362 10403-10480 Sentence denotes Is there concern that the included patients do not match the review question?
T363 10482-10860 Sentence denotes HIGH: if accuracy of signs and symptoms were assessed in a case‐control design, or in an already highly selected group of participants, or the study was able to only estimate sensitivity or specificity.LOW: any situation where signs and symptoms were the first assessment/test to be done on the included participants.UNCLEAR: if a description about the participants was lacking.
T364 10861-10872 Sentence denotes Index tests
T365 10873-10972 Sentence denotes Were the index test results interpreted without knowledge of the results of the reference standard?
T366 10974-11356 Sentence denotes This will be similar for all index tests, target conditions, and populations.YES: if blinding was explicitly stated or index test was recorded before the results from the reference standard were available.NO: if it was explicitly stated that the index test results were interpreted with knowledge of the results of the reference standard.UNCLEAR: if blinding was unclearly reported.
T367 11357-11402 Sentence denotes If a threshold was used, was it prespecified?
T368 11404-11930 Sentence denotes This will be similar for all index tests, target conditions, and populations.YES: if the test was dichotomous by nature, or if the threshold was stated in the methods section, or if authors stated that the threshold as recommended by the manufacturer was used.NO: if a receiver operating characteristic curve was drawn or multiple threshold reported in the results section; and the final result was based on one of these thresholds; if fever was not defined beforehand.UNCLEAR: if threshold selection was not clearly reported.
T369 11931-12006 Sentence denotes Could the conduct or interpretation of the index test have introduced bias?
T370 12008-12245 Sentence denotes HIGH: if one or more signalling questions were answered with NO, as even in a laboratory situation knowledge of the reference standard may lead to bias.LOW: if all signalling questions were answered with YES.UNCLEAR: all other instances.
T371 12246-12347 Sentence denotes Is there concern that the index test, its conduct, or interpretation differ from the review question?
T372 12349-12502 Sentence denotes This will probably be answered 'LOW' in all cases except when assessments were made in a different setting, or using personnel not available in practice.
T373 12503-12521 Sentence denotes Reference standard
T374 12522-12598 Sentence denotes Is the reference standard likely to correctly classify the target condition?
T375 12600-12880 Sentence denotes We will define acceptable reference standards using a consensus process once the list of reference standards that have been used has been obtained from the eligible studies.For severe pneumonia, we will consider how well processes adhered to the WHO case definition in Appendix 1.
T376 12881-12980 Sentence denotes Were the reference standard results interpreted without knowledge of the results of the index test?
T377 12982-13432 Sentence denotes YES: if it was explicitly stated that the reference standard results were interpreted without knowledge of the results of the index test, or if the result of the index test was obtained after the reference standard.NO: if it was explicitly stated that the reference standard results were interpreted with knowledge of the results of the index test or if the index test was used to make the final diagnosis.UNCLEAR: if blinding was unclearly reported.
T378 13433-13521 Sentence denotes Did the definition of the reference standard incorporate results from the index test(s)?
T379 13523-13790 Sentence denotes YES: if results from the index test were a component of the reference standard definition.NO: if the reference standard did not incorporate the index standard test.UNCLEAR: if it was unclear whether the results of the index test formed part of the reference standard.
T380 13791-13874 Sentence denotes Could the conduct or interpretation of the reference standard have introduced bias?
T381 13876-14025 Sentence denotes HIGH: if one or more signalling questions were answered with NO.LOW: if all signalling questions were answered with YES.UNCLEAR: all other instances.
T382 14026-14141 Sentence denotes Is there concern that the target condition as defined by the reference standard does not match the review question?
T383 14143-14552 Sentence denotes HIGH: if the target condition was COVID‐19 pneumonia, but only RT‐PCR was used; if alternative diagnosis was highly likely and not excluded (will happen in paediatric cases, where exclusion of other respiratory pathogens is also necessary); if tests used to follow up viral load in known test‐positives.LOW: if above situations were not present.UNCLEAR: if intention for testing was not reported in the study.
T384 14553-14568 Sentence denotes Flow and timing
T385 14569-14648 Sentence denotes Was there an appropriate interval between index test(s) and reference standard?
T386 14650-15237 Sentence denotes YES: this will be similar for all index tests, populations for the current infection target conditions: as the situation of a patient, including clinical presentation and disease progress, evolves rapidly and new/ongoing exposure can result in case status change, an appropriate time interval will be within 24 hours.NO: if there was more than 24 hours between the index test and the reference standard or if participants were otherwise reported to be assessed with the index versus reference standard test at moments of different severity.UNCLEAR: if the time interval was not reported.
T387 15238-15284 Sentence denotes Did all patients receive a reference standard?
T388 15286-15519 Sentence denotes YES: if all participants received a reference standard (clearly no partial verification).NO: if only (part of) the index test‐positives or index test‐negatives received the complete reference standard.UNCLEAR: if it was not reported.
T389 15520-15573 Sentence denotes Did all patients receive the same reference standard?
T390 15575-15814 Sentence denotes YES: if all participants received the same reference standard (clearly no differential verification).NO: if (part of) the index test‐positives or index test‐negatives received a different reference standard.UNCLEAR: if it was not reported.
T391 15815-15858 Sentence denotes Were all patients included in the analysis?
T392 15860-16286 Sentence denotes YES: if all included participants were included in the analyses.NO: if after the inclusion/exclusion process, participants were removed from the analyses for different reasons: no reference standard done, no index test done, intermediate results of both index test or reference standard, indeterminate results of both index test or reference standard, samples unusable.UNCLEAR: if this was not clear from the reported numbers.
T393 16287-16331 Sentence denotes Could the patient flow have introduced bias?
T394 16333-16482 Sentence denotes HIGH: if one or more signalling questions were answered with NO.LOW: if all signalling questions were answered with YES.UNCLEAR: all other instances.
T395 16483-16631 Sentence denotes ICU: intensive care unit; RT‐PCR: reverse transcription polymerase chain reaction; SARS‐CoV‐2: severe acute respiratory syndrome coronavirus 2; WHO:
T396 16632-16657 Sentence denotes World Health Organization
T397 16659-16698 Sentence denotes Statistical analysis and data synthesis
T398 16699-16825 Sentence denotes We present results of estimated sensitivity and specificity using paired forest plots and summarised in tables as appropriate.
T399 16826-17167 Sentence denotes We present the results without meta‐analysis, due to the small numbers of studies currently available, considerable heterogeneity across studies and the high risk of bias that we identified, as we felt doing so would otherwise produce a seemingly more accurate estimate than the underlying evidence is able to provide at this moment in time.
T400 17168-17378 Sentence denotes We present results of estimated sensitivity and specificity using paired forest plots in Review Manager 2014, and dumbbell plots to display the change in disease probability after a positive or negative result.
T401 17379-17622 Sentence denotes We disaggregated data by study design and organised by target condition, reporting results from cross‐sectional studies separately from studies that used a diagnostic case‐control or other design that we assessed as prone to high risk of bias.
T402 17623-17844 Sentence denotes When pooling does become possible in a future update of this review, we will estimate mean sensitivity and specificity using hierarchical models where tests either report binary results or at commonly reported thresholds.
T403 17845-17963 Sentence denotes Where data are sparse, we will use methods described by Takwoingi 2017 for obtaining estimates from simplified models.
T404 17964-18084 Sentence denotes We anticipate that over time sufficient data will accumulate to provide clear estimates of test accuracy for some tests.
T405 18085-18284 Sentence denotes We will undertake meta‐analysis in STATA version 16.0 (STATA), or SAS (SAS 2015), as detailed in the Cochrane Handbook for Systematic Reviews of Diagnostic Test Accuracy (Chapter 10; Macaskill 2013).
T406 18286-18317 Sentence denotes Investigations of heterogeneity
T407 18318-18439 Sentence denotes We have listed sources of heterogeneity that we investigated if adequate data were available in the Secondary objectives.
T408 18440-18580 Sentence denotes In this version of the review, we used stratification to investigate heterogeneity as we considered it was inappropriate to combine studies.
T409 18581-18693 Sentence denotes In future updates, if meta‐analysis becomes possible, we will investigate heterogeneity through meta‐regression.
T410 18694-18750 Sentence denotes We will stratify by reference standard and study design.
T411 18751-18883 Sentence denotes In this version of the review we have stratified by study design only, as stratification by reference standard was not yet possible.
T412 18885-18905 Sentence denotes Sensitivity analyses
T413 18906-18975 Sentence denotes We aimed to undertake sensitivity analyses considering the impact of:
T414 18976-18996 Sentence denotes unpublished studies;
T415 18997-19041 Sentence denotes studies with inadequate reference standards.
T416 19042-19103 Sentence denotes However, neither were possible in this version of the review.
T417 19105-19133 Sentence denotes Assessment of reporting bias
T418 19134-19306 Sentence denotes We aimed to publish lists of studies that we know exist but for which we have not managed to locate reports, and request information to include in updates of these reviews.
T419 19307-19405 Sentence denotes However, at the time of writing this version of the review, we are unaware of unpublished studies.
T420 19407-19426 Sentence denotes Summary of findings
T421 19427-19606 Sentence denotes We have listed our key findings in a 'Summary of findings' table to determine the strength of evidence for each test and findings, and to highlight important gaps in the evidence.
T422 19608-19616 Sentence denotes Updating
T423 19617-19836 Sentence denotes We will undertake the searches of published literature and preprints bi‐weekly, and, dependent on the number of new and important studies found, we will consider updating each review with each search if resources allow.