Rates and predictors of data and code sharing in the medical and health sciences: Protocol for a systematic review and individual participant data meta-analysis

Numerous studies have demonstrated low but increasing rates of data and code sharing within medical and health research disciplines. However, it remains unclear how commonly data and code are shared across all fields of medical and health research, as well as whether sharing rates are positively associated with implementation of progressive policies by publishers and funders, or growing expectations from the medical and health research community at large. Therefore this systematic review aims to synthesise the findings of medical and health science studies that have empirically investigated the prevalence of data or code sharing, or both. Objectives include the investigation of: (i) the prevalence of public sharing of research data and code alongside published articles (including preprints), (ii) the prevalence of private sharing of research data and code in response to reasonable requests, and (iii) factors associated with the sharing of either research output (e.g., the year published, the publisher's policy on sharing, the presence of a data or code availability statement). It is hoped that the results will provide some insight into how often research data and code are shared publicly and privately, how this has changed over time, and how effective some measures such as the institution of data sharing policies and data availability statements have been in motivating researchers to share their underlying data and code.

Rapid antigen detection and molecular tests for group A streptococcal infections for acute sore throat: systematic reviews and economic evaluation

BACKGROUND

Sore throat is a common condition caused by an infection of the airway. Most cases are of a viral nature; however, a number of these infections may be caused by the group A Streptococcus bacterium. Most viral and bacterial sore throat infections resolve spontaneously within a few weeks. Point-of-care testing in primary care has been recognised as an emerging technology for aiding targeted antibiotic prescribing for sore throat in cases that do not spontaneously resolve.

OBJECTIVE

Systematically review the evidence for 21 point-of-care tests for detecting group A Streptococcus bacteria and develop a de novo economic model to compare the cost-effectiveness of point-of-care tests alongside clinical scoring tools with the cost-effectiveness of clinical scoring tools alone for patients managed in primary care and hospital settings.

DATA SOURCES

Multiple electronic databases were searched from inception to March 2019. The following databases were searched in November and December 2018 and searches were updated in March 2019: MEDLINE [via OvidSP (Health First, Rockledge, FL, USA)], MEDLINE In-Process & Other Non-Indexed Citations (via OvidSP), MEDLINE Epub Ahead of Print (via OvidSP), MEDLINE Daily Update (via OvidSP), EMBASE (via OvidSP), Cochrane Database of Systematic Reviews [via Wiley Online Library (John Wiley & Sons, Inc., Hoboken, NJ, USA)], Cochrane Central Register of Controlled Trials (CENTRAL) (via Wiley Online Library), Database of Abstracts of Reviews of Effects (DARE) (via Centre for Reviews and Dissemination), Health Technology Assessment database (via the Centre for Reviews and Dissemination), Science Citation Index and Conference Proceedings [via the Web of Science™ (Clarivate Analytics, Philadelphia, PA, USA)] and the PROSPERO International Prospective Register of Systematic Reviews (via the Centre for Reviews and Dissemination).

REVIEW METHODS

Eligible studies included those of people aged ≥ 5 years presenting with sore throat symptoms, studies comparing point-of-care testing with antibiotic-prescribing decisions, studies of test accuracy and studies of cost-effectiveness. Quality assessment of eligible studies was undertaken. Meta-analysis of sensitivity and specificity was carried out for tests with sufficient data. A decision tree model estimated costs and quality-adjusted life-years from an NHS and Personal Social Services perspective.

RESULTS

The searches identified 38 studies of clinical effectiveness and three studies of cost-effectiveness. Twenty-six full-text articles and abstracts reported on the test accuracy of point-of-care tests and/or clinical scores with biological culture as a reference standard. In the population of interest (patients with Centor/McIsaac scores of ≥ 3 points or FeverPAIN scores of ≥ 4 points), point estimates were 0.829 to 0.946 for sensitivity and 0.849 to 0.991 for specificity. There was considerable heterogeneity, even for studies using the same point-of-care test, suggesting that is unlikely that any single study will have accurately captured a test's true performance. There is some randomised controlled trial evidence to suggest that the use of rapid antigen detection tests may help to reduce antibiotic-prescribing rates. Sensitivity and specificity estimates for each test in each age group and care setting combination were obtained using meta-analyses where appropriate. Any apparent differences in test accuracy may not be attributable to the tests, and may have been caused by known differences in the studies, latent characteristics or chance. Fourteen of the 21 tests reviewed were included in the economic modelling, and these tests were not cost-effective within the current National Institute for Health and Care Excellence's cost-effectiveness thresholds. Uncertainties in the cost-effectiveness estimates included model parameter inputs and assumptions that increase the cost of testing, and the penalty for antibiotic overprescriptions.

LIMITATIONS

No information was identified for the elderly population or pharmacy setting. It was not possible to identify which test is the most accurate owing to the paucity of evidence.

CONCLUSIONS

The systematic review and the cost-effectiveness models identified uncertainties around the adoption of point-of-care tests in primary and secondary care settings. Although sensitivity and specificity estimates are promising, we have little information to establish the most accurate point-of-care test. Further research is needed to understand the test accuracy of point-of-care tests in the proposed NHS pathway and in comparable settings and patient groups.

STUDY REGISTRATION

The protocol of the review is registered as PROSPERO CRD42018118653.

FUNDING

This project was funded by the National Institute for Health Research (NIHR) Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 24, No. 31. See the NIHR Journals Library website for further project information.

Mathematically aggregating experts' predictions of possible futures

Structured protocols offer a transparent and systematic way to elicit and combine/aggregate, probabilistic predictions from multiple experts. These judgements can be aggregated behaviourally or mathematically to derive a final group prediction. Mathematical rules (e.g., weighted linear combinations of judgments) provide an objective approach to aggregation. The quality of this aggregation can be defined in terms of accuracy, calibration and informativeness. These measures can be used to compare different aggregation approaches and help decide on which aggregation produces the "best" final prediction. When experts' performance can be scored on similar questions ahead of time, these scores can be translated into performance-based weights, and a performance-based weighted aggregation can then be used. When this is not possible though, several other aggregation methods, informed by measurable proxies for good performance, can be formulated and compared. Here, we develop a suite of aggregation methods, informed by previous experience and the available literature. We differentially weight our experts' estimates by measures of reasoning, engagement, openness to changing their mind, informativeness, prior knowledge, and extremity, asymmetry or granularity of estimates. Next, we investigate the relative performance of these aggregation methods using three datasets. The main goal of this research is to explore how measures of knowledge and behaviour of individuals can be leveraged to produce a better performing combined group judgment. Although the accuracy, calibration, and informativeness of the majority of methods are very similar, a couple of the aggregation methods consistently distinguish themselves as among the best or worst. Moreover, the majority of methods outperform the usual benchmarks provided by the simple average or the median of estimates.

Australian and Italian Psychologists’ View of Replication

Solutions to the crisis in confidence in the psychological literature have been proposed in many recent articles, including increased publication of replication studies, a solution that requires engagement by the psychology research community. We surveyed Australian and Italian academic research psychologists about the meaning and role of replication in psychology. When asked what they consider to be a replication study, nearly all participants (98% of Australians and 96% of Italians) selected options that correspond to a direct replication. Only 14% of Australians and 8% of Italians selected any options that included changing the experimental method. Majorities of psychologists from both countries agreed that replications are very important, that more replications should be done, that more resources should be allocated to them, and that they should be published more often. Majorities of psychologists from both countries reported that they or their students sometimes or often replicate studies, yet they also reported having no replication studies published in the prior 5 years. When asked to estimate the percentage of published studies in psychology that are replications, both Australians (with a median estimate of 13%) and Italians (with a median estimate of 20%) substantially overestimated the actual rate. When asked what constitute the main obstacles to replications, difficulty publishing replications was the most frequently cited obstacle, coupled with the high value given to innovative or novel research and the low value given to replication studies.

Eliminating hepatitis C in a rural Appalachian county: protocol for the Kentucky Viral Hepatitis Treatment Study (KeY Treat), a phase IV, single-arm, open-label trial of sofosbuvir/velpatasvir for the treatment of hepatitis C

OBJECTIVES

The overall goal of the Kentucky Viral Hepatitis Treatment Study (KeY Treat) is to eliminate hepatitis C transmission from a county in Appalachian Kentucky by removing the barriers to accessing hepatitis C virus (HCV) treatment.

METHODS/ANALYSIS

KeY Treat is a phase IV, open-label, single-arm clinical trial of sofosbuvir/velpatasvir (SOF/VEL) for the treatment of viraemic HCV infections. Those eligible for KeY Treat are at least 18 years of age, viraemic and are residents of the target county. Pregnant women are not eligible. Rapid HCV RNA screening is used to determine eligibility, and those with a quantifiable viral load (VL) consenting to participate initiate SOF/VEL on the same day. All pharmacologic treatment and related medical care is provided free of charge using a non-specialist provider model. Follow-up visits occur at 2, 6 and 12 weeks during treatment to assess medication adherence (measured via VL and self-report), side effects and engagement in risk behaviours. Post-treatment visits occur at 12 weeks (sustained virologic response (SVR12) visit), 6 months and 12 months post-treatment completion to assess re-infection. A control county has also been identified, and prevalence and incidence of chronic HCV infections will be compared with the target community longitudinally. The primary outcome to assess elimination is SVR12. However, several outcomes will be measured to assess the effectiveness of removing the barriers to HCV treatment, including treatment entry, completion and re-infection. Analyses will be conducted via a generalised linear model framework that can incorporate flexible covariate adjustment and multiple outcome types with a compatible link function. Mathematical modelling will be completed assessing the impact and cost-effectiveness of the intervention.

ETHICS AND DISSEMINATION

KeY Treat has been approved by the Institutional Review Board at the University of Kentucky. Results from KeY Treat will be presented at conferences and published in peer-reviewed journals.

TRIAL REGISTRATION NUMBER

NCT03949764.

Testing strategies for Lynch syndrome in people with endometrial cancer: systematic reviews and economic evaluation

BACKGROUND

Lynch syndrome is an inherited genetic condition that is associated with an increased risk of certain cancers. The National Institute for Health and Care Excellence has recommended that people with colorectal cancer are tested for Lynch syndrome. Routine testing for Lynch syndrome among people with endometrial cancer is not currently conducted.

OBJECTIVES

To systematically review the evidence on the test accuracy of immunohistochemistry- and microsatellite instability-based strategies to detect Lynch syndrome among people who have endometrial cancer, and the clinical effectiveness and the cost-effectiveness of testing for Lynch syndrome among people who have been diagnosed with endometrial cancer.

DATA SOURCES

Searches were conducted in the following databases, from inception to August 2019 - MEDLINE ALL, EMBASE (both via Ovid), Cochrane Database of Systematic Reviews, Cochrane Central Register of Controlled Trials (both via Wiley Online Library), Database of Abstracts of Reviews of Effects, Health Technology Assessment Database (both via the Centre for Reviews and Dissemination), Science Citation Index, Conference Proceedings Citation Index - Science (both via Web of Science), PROSPERO international prospective register of systematic reviews (via the Centre for Reviews and Dissemination), NHS Economic Evaluation Database, Cost-Effectiveness Analysis Registry, EconPapers (Research Papers in Economics) and School of Health and Related Research Health Utilities Database. The references of included studies and relevant systematic reviews were also checked and experts on the team were consulted.

REVIEW METHODS

Eligible studies included people with endometrial cancer who were tested for Lynch syndrome using immunohistochemistry- and/or microsatellite instability-based testing [with or without mutL homologue 1 (MLH1) promoter hypermethylation testing], with Lynch syndrome diagnosis being established though germline testing of normal (non-tumour) tissue for constitutional mutations in mismatch repair. The risk of bias in studies was assessed using the Quality Assessment of Diagnostic Accuracy Studies-2 tool, the Consolidated Health Economic Reporting Standards and the Philips' checklist. Two reviewers independently conducted each stage of the review. A meta-analysis of test accuracy was not possible because of the number and heterogeneity of studies. A narrative summary of test accuracy results was provided, reporting test accuracy estimates and presenting forest plots. The economic model constituted a decision tree followed by Markov models for the impact of colorectal and endometrial surveillance, and aspirin prophylaxis with a lifetime time horizon.

RESULTS

The clinical effectiveness search identified 3308 studies; 38 studies of test accuracy were included. (No studies of clinical effectiveness of endometrial cancer surveillance met the inclusion criteria.) Four test accuracy studies compared microsatellite instability with immunohistochemistry. No clear difference in accuracy between immunohistochemistry and microsatellite instability was observed. There was some evidence that specificity of immunohistochemistry could be improved with the addition of methylation testing. There was high concordance between immunohistochemistry and microsatellite instability. The economic model indicated that all testing strategies, compared with no testing, were cost-effective at a willingness-to-pay threshold of £20,000 per quality-adjusted life-year. Immunohistochemistry with MLH1 promoter hypermethylation testing was the most cost-effective strategy, with an incremental cost-effectiveness ratio of £9420 per quality-adjusted life-year. The second most cost-effective strategy was immunohistochemistry testing alone, but incremental analysis produced an incremental cost-effectiveness ratio exceeding £130,000. Results were robust across all scenario analyses. Incremental cost-effectiveness ratios ranged from £5690 to £20,740; only removing the benefits of colorectal cancer surveillance produced an incremental cost-effectiveness ratio in excess of the £20,000 willingness-to-pay threshold. A sensitivity analysis identified the main cost drivers of the incremental cost-effectiveness ratio as percentage of relatives accepting counselling and prevalence of Lynch syndrome in the population. A probabilistic sensitivity analysis showed, at a willingness-to-pay threshold of £20,000 per quality-adjusted life-year, a 0.93 probability that immunohistochemistry with MLH1 promoter hypermethylation testing is cost-effective, compared with no testing.

LIMITATIONS

The systematic review excluded grey literature, studies written in non-English languages and studies for which the reference standard could not be established. Studies were included when Lynch syndrome was diagnosed by genetic confirmation of constitutional variants in the four mismatch repair genes (i.e. MLH1, mutS homologue 2, mutS homologue 6 and postmeiotic segregation increased 2). Variants of uncertain significance were reported as per the studies. There were limitations in the economic model around uncertainty in the model parameters and a lack of modelling of the potential harms of gynaecological surveillance and specific pathway modelling of genetic testing for somatic mismatch repair mutations.

CONCLUSION

The economic model suggests that testing women with endometrial cancer for Lynch syndrome is cost-effective, but that results should be treated with caution because of uncertain model inputs.

FUTURE WORK

Randomised controlled trials could provide evidence on the effect of earlier intervention on outcomes and the balance of benefits and harms of gynaecological cancer surveillance. Follow-up of negative cases through disease registers could be used to determine false negative cases.

STUDY REGISTRATION

This study is registered as PROSPERO CRD42019147185.

FUNDING

This project was funded by the National Institute for Health Research (NIHR) Evidence Synthesis programme and will be published in full in Health Technology Assessment; Vol. 25, No. 42. See the NIHR Journals Library website for further project information.

Homelessness, unstable housing, and risk of HIV and hepatitis C virus acquisition among people who inject drugs: a systematic review and meta-analysis

BACKGROUND

People who inject drugs (PWID) are at increased risk for HIV and hepatitis C virus (HCV) infection and also have high levels of homelessness and unstable housing. We assessed whether homelessness or unstable housing is associated with an increased risk of HIV or HCV acquisition among PWID compared with PWID who are not homeless or are stably housed.

METHODS

In this systematic review and meta-analysis, we updated an existing database of HIV and HCV incidence studies published between Jan 1, 2000, and June 13, 2017. Using the same strategy as for this existing database, we searched MEDLINE, Embase, and PsycINFO for studies, including conference abstracts, published between June 13, 2017, and Sept 14, 2020, that estimated HIV or HCV incidence, or both, among community-recruited PWID. We only included studies reporting original results without restrictions to study design or language. We contacted authors of studies that reported HIV or HCV incidence, or both, but did not report on an association with homelessness or unstable housing, to request crude data and, where possible, adjusted effect estimates. We extracted effect estimates and pooled data using random-effects meta-analyses to quantify the associations between recent (current or within the past year) homelessness or unstable housing compared with not recent homelessness or unstable housing, and risk of HIV or HCV acquisition. We assessed risk of bias using the Newcastle-Ottawa Scale and between-study heterogeneity using the I2 statistic and p value for heterogeneity.

FINDINGS

We identified 14 351 references in our database search, of which 392 were subjected to full-text review alongside 277 studies from our existing database. Of these studies, 55 studies met inclusion criteria. We contacted the authors of 227 studies that reported HIV or HCV incidence in PWID but did not report association with the exposure of interest and obtained 48 unpublished estimates from 21 studies. After removal of duplicate data, we included 37 studies with 70 estimates (26 for HIV; 44 for HCV). Studies originated from 16 countries including in North America, Europe, Australia, east Africa, and Asia. Pooling unadjusted estimates, recent homelessness or unstable housing was associated with an increased risk of acquiring HIV (crude relative risk [cRR] 1·55 [95% CI 1·23-1·95; p=0·0002]; I2= 62·7%; n=17) and HCV (1·65 [1·44-1·90; p<0·0001]; I2= 44·8%; n=28]) among PWID compared with those who were not homeless or were stably housed. Associations for both HIV and HCV persisted when pooling adjusted estimates (adjusted relative risk for HIV: 1·39 [95% CI 1·06-1·84; p=0·019]; I2= 65·5%; n=9; and for HCV: 1·64 [1·43-1·89; p<0·0001]; I2= 9·6%; n=14). For risk of HIV acquisition, the association for unstable housing (cRR 1·82 [1·13-2·95; p=0·014]; n=5) was higher than for homelessness (1·44 [1·13-1·83; p=0·0036]; n=12), whereas no difference was seen between these outcomes for risk of HCV acquisition (1·72 [1·48-1·99; p<0·0001] for unstable housing, 1·66 [1·37-2·00; p<0·0001] for homelessness).

INTERPRETATION

Homelessness and unstable housing are associated with increased risk of HIV and HCV acquisition among PWID. Our findings support the development of interventions that simultaneously address homelessness and unstable housing and HIV and HCV transmission in this population.

FUNDING

National Institute for Health Research, National Institute on Drug Abuse, National Institute of Allergy and Infectious Diseases, and Commonwealth Scholarship Commission.

The Status and Value of Replications in Animal Behavior Science

Replications are widely considered an essential tool to evaluate scientific claims. However, many fields have recently reported that replication rates are low and - when they are conducted - many findings do not successfully replicate. These circumstances have led to widespread debates about the value of replications for research quality, credibility of research findings, and factors contributing to current problems with replicability. This special issue brings together researchers from various areas within the field of animal behavior to offer their perspective on the status and value of replications in animal behavior science.

Hepatitis C Care Cascades for 3 Populations at High Risk: Low-income Trans Women, Young People Who Inject Drugs, and Men Who Have Sex With Men and Inject Drugs

BACKGROUND

To achieve elimination of hepatitis C virus (HCV) infection, limited resources can be best allocated through estimation of "care cascades" among groups disproportionately affected. In San Francisco and elsewhere, these groups include young (age ≤ 30 years) people who inject drugs (YPWID), men who have sex with men who inject drugs (MSM-IDU), and low-income trans women.

METHODS

We developed cross-sectional HCV care cascades for YPWID, MSM-IDU, and trans women using diverse data sources. Population sizes were estimated using an inverse variance-weighted average of estimates from the peer-reviewed literature between 2013 and 2019. Proportions of past/current HCV infection, diagnosed infection, treatment initiation, and evidence of cure (sustained virologic response at 12 weeks posttreatment) were estimated from the literature using data from 7 programs and studies in San Francisco between 2015 and 2020.

RESULTS

The estimated number of YPWID in San Francisco was 3748; 58.4% had past/current HCV infection, of whom 66.4% were diagnosed with current infection, 9.1% had initiated treatment, and 50% had confirmed cure. The corresponding figures for the 8135 estimated MSM-IDU were: 29.4% with past/current HCV infection, 70.3% diagnosed with current infection, 28.4% initiated treatment, and 38.9% with confirmed cure. For the estimated 951 low-income trans women, 24.8% had past/current HCV infection, 68.9% were diagnosed with current infection, 56.5% initiated treatment, and 75.5% had confirmed cure.

CONCLUSIONS

In all 3 populations, diagnosis rates were relatively high; however, attention is needed to urgently increase treatment initiation in all groups, with a particular unmet need among YPWID.

Estimating the contribution of key populations towards HIV transmission in South Africa

INTRODUCTION

In generalized epidemic settings, there is insufficient understanding of how the unmet HIV prevention and treatment needs of key populations (KPs), such as female sex workers (FSWs) and men who have sex with men (MSM), contribute to HIV transmission. In such settings, it is typically assumed that HIV transmission is driven by the general population. We estimated the contribution of commercial sex, sex between men, and other heterosexual partnerships to HIV transmission in South Africa (SA).

METHODS

We developed the "Key-Pop Model"; a dynamic transmission model of HIV among FSWs, their clients, MSM, and the broader population in SA. The model was parameterized and calibrated using demographic, behavioural and epidemiological data from national household surveys and KP surveys. We estimated the contribution of commercial sex, sex between men and sex among heterosexual partnerships of different sub-groups to HIV transmission over 2010 to 2019. We also estimated the efficiency (HIV infections averted per person-year of intervention) and prevented fraction (% IA) over 10-years from scaling-up ART (to 81% coverage) in different sub-populations from 2020.

RESULTS

Sex between FSWs and their paying clients, and between clients with their non-paying partners contributed 6.9% (95% credibility interval 4.5% to 9.3%) and 41.9% (35.1% to 53.2%) of new HIV infections in SA over 2010 to 2019 respectively. Sex between low-risk groups contributed 59.7% (47.6% to 68.5%), sex between men contributed 5.3% (2.3% to 14.1%) and sex between MSM and their female partners contributed 3.7% (1.6% to 9.8%). Going forward, the largest population-level impact on HIV transmission can be achieved from scaling up ART to clients of FSWs (% IA = 18.2% (14.0% to 24.4%) or low-risk individuals (% IA = 20.6% (14.7 to 27.5) over 2020 to 2030), with ART scale-up among KPs being most efficient.

CONCLUSIONS

Clients of FSWs play a fundamental role in HIV transmission in SA. Addressing the HIV prevention and treatment needs of KPs in generalized HIV epidemics is central to a comprehensive HIV response.

Newborn Screening for Long-Chain 3-Hydroxyacyl-CoA Dehydrogenase and Mitochondrial Trifunctional Protein Deficiencies Using Acylcarnitines Measurement in Dried Blood Spots-A Systematic Review of Test Accuracy

Background: Long-chain 3-hydroxyacyl-CoA dehydrogenase (LCHAD) and mitochondrial trifunctional protein (MTP) deficiencies are rare autosomal recessive fatty acid β-oxidation disorders. Their clinical presentations are variable, and premature death is common. They are included in newborn blood spot screening programs in many countries around the world. The current process of screening, through the measurement of acylcarnitines (a metabolic by-product) in dried blood spots with tandem mass spectrometry, is subject to uncertainty regarding test accuracy. Methods: We conducted a systematic review of literature published up to 19th June 2018. We included studies that investigated newborn screening for LCHAD or MTP deficiencies by tandem mass spectrometry of acylcarnitines in dried blood spots. The reference standards were urine organic acids, blood acylcarnitine profiles, enzyme analysis in cultured fibroblasts or lymphocytes, mutation analysis, or at least 10-year follow-up. The outcomes of interest were sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). Assessment of titles, abstracts, and full-text papers and quality appraisal were carried out independently by two reviewers. One reviewer extracted study data. This was checked by a second reviewer. Results: Ten studies provided data on test accuracy. LCHAD or MTP deficiencies were identified in 23 babies. No cases of LCHAD/MTP deficiencies were identified in four studies. PPV ranged from 0% (zero true positives and 28 false positives from 276,565 babies screened) to 100% (13 true positives and zero false positives from 2,037,824 babies screened). Sensitivity, specificity, and NPV could not be calculated as there was no systematic follow-up of babies who screened negative. Conclusions: Test accuracy estimates of screening for LCHAD and MTP deficiencies with tandem mass spectrometry measurement of acylcarnitines in dried blood were variable in terms of PPVs. Screening methods (including markers and thresholds) varied between studies, and sensitivity, specificity, and NPVs are unknown.

Journal policies and editors' opinions on peer review

Peer review practices differ substantially between journals and disciplines. This study presents the results of a survey of 322 editors of journals in ecology, economics, medicine, physics and psychology. We found that 49% of the journals surveyed checked all manuscripts for plagiarism, that 61% allowed authors to recommend both for and against specific reviewers, and that less than 6% used a form of open peer review. Most journals did not have an official policy on altering reports from reviewers, but 91% of editors identified at least one situation in which it was appropriate for an editor to alter a report. Editors were also asked for their views on five issues related to publication ethics. A majority expressed support for co-reviewing, reviewers requesting access to data, reviewers recommending citations to their work, editors publishing in their own journals, and replication studies. Our results provide a window into what is largely an opaque aspect of the scientific process. We hope the findings will inform the debate about the role and transparency of peer review in scholarly publishing.

Towards HCV elimination among people who inject drugs in Hai Phong, Vietnam: study protocol for an effectiveness-implementation trial evaluating an integrated model of HCV care (DRIVE-C: DRug use & Infections in ViEtnam-hepatitis C)

INTRODUCTION

In Vietnam, people who inject drugs (PWID), who are the major population infected by hepatitis C virus (HCV), remain largely undiagnosed and unlinked to HCV prevention and care despite recommended universal hepatitis C treatment. The data on the outcomes of HCV treatment among PWID also remain limited in resource-limited settings. The DRug use & Infections in ViEtnam-hepatitis C (DRIVE-C) study examines the effectiveness of a model of hepatitis C screening and integrated care targeting PWID that largely uses community-based organisations (CBO) in Hai Phong, Vietnam. In a wider perspective, this model may have the potential to eliminate HCV among PWID in this city.

METHODS AND ANALYSIS

The model of care comprises large community-based mass screening, simplified treatment with direct-acting antivirals (DAAs) and major involvement of CBO for PWID reaching out, linkage to care, treatment adherence and prevention of reinfection. The effectiveness of DAA care strategy among PWID, the potential obstacles to widespread implementation and its impact at population level will be assessed. A cost-effectiveness analysis is planned to further inform policy-makers. The enrolment target is 1050 PWID, recruited from the DRIVE study in Hai Phong. After initiation of pan-genotypic treatment consisting of sofosbuvir and daclatasvir administrated for 12 weeks, with ribavirin added in cases of cirrhosis, participants are followed-up for 48 weeks. The primary outcome is the proportion of patients with sustained virological response at week 48, that will be compared with a theoretical expected rate of 70%.

ETHICS AND DISSEMINATION

The study was approved by Haiphong University of Medicine and Pharmacy's Ethics Review Board and the Vietnamese Ministry of Health. The sponsor and the investigators are committed to conducting this study in accordance with ethics principles contained in the World Medical Association's Declaration of Helsinki (Ethical Principles for Medical Research Involving Human Subjects). Informed consent is obtained before study enrolment. The data are anonymised and stored in a secure database. The study is ongoing. Results will be presented at international conferences and submitted to international peer-review journals.

TRIAL REGISTRATION NUMBER

NCT03537196.

The role of replication studies in ecology

Recent large-scale projects in other disciplines have shown that results often fail to replicate when studies are repeated. The conditions contributing to this problem are also present in ecology, but there have not been any equivalent replication projects. Here, we survey ecologists' understanding of and opinions about replication studies. The majority of ecologists in our sample considered replication studies to be important (97%), not prevalent enough (91%), worth funding even given limited resources (61%), and suitable for publication in all journals (62%). However, there is a disconnect between this enthusiasm and the prevalence of direct replication studies in the literature which is much lower (0.023%: Kelly 2019) than our participants' median estimate of 10%. This may be explained by the obstacles our participants identified including the difficulty of conducting replication studies and of funding and publishing them. We conclude by offering suggestions for how replications could be better integrated into ecological research.

Modeling the role of incarceration in HCV transmission and prevention amongst people who inject drugs in rural Kentucky

BACKGROUND

People who inject drugs (PWID) experience high incarceration rates, with current/recent incarceration being associated with increased hepatitis C virus (HCV) transmission. We assess the contribution of incarceration to HCV transmission amongst PWID in Perry County (PC), Kentucky, USA, and the impact of scaling-up community and in-prison opioid substitution therapy (OST), including the potential for reducing incarceration.

METHODS

A dynamic model of incarceration and HCV transmission amongst PWID was calibrated in a Bayesian framework to epidemiological and incarceration data from PC, incorporating an empirically estimated 2.8-fold (95%CI: 1.36-5.77) elevated HCV acquisition risk amongst currently incarcerated or recently released (<6 months) PWID compared to other PWID. We projected the percentage of new HCV infections that would be prevented among PWID over 2020-2030 if incarceration no longer elevated HCV transmission risk, if needle and syringe programmes (NSP) and OST are scaled-up, and/or if drug use was decriminalized (incarceration/reincarceration rates are halved) with 50% of PWID that would have been imprisoned being diverted onto OST. We assume OST reduces reincarceration by 10-42%.

RESULTS

Over 2020-2030, removing the effect of incarceration on HCV transmission could prevent 42.7% (95% credibility interval: 15.0-67.4%) of new HCV infections amongst PWID. Conversely, scaling-up community OST and NSP to 50% coverage could prevent 28.5% (20.0-37.4%) of new infections, with this increasing to 32.7% (24.5-41.2%) if PWID are retained on OST upon incarceration, 36.4% (27.7-44.9%) if PWID initiate OST in prison, and 45.3% (35.9-54.1%) if PWID are retained on OST upon release. decriminalization (with diversion to OST) could further increase this impact, preventing 56.8% (45.3-64.5%) of new infections. The impact of these OST interventions decreases by 2.1-28.6% if OST does not reduce incarceration.

CONCLUSION

Incarceration is likely to be an important contributor to HCV transmission amongst PWID in PC. Prison-based OST could be an important intervention for reducing this risk.

Effects and cost of different strategies to eliminate hepatitis C virus transmission in Pakistan: a modelling analysis

BACKGROUND

The WHO elimination strategy for hepatitis C virus advocates scaling up screening and treatment to reduce global hepatitis C incidence by 80% by 2030, but little is known about how this reduction could be achieved and the costs of doing so. We aimed to evaluate the effects and cost of different strategies to scale up screening and treatment of hepatitis C in Pakistan and determine what is required to meet WHO elimination targets for incidence.

METHODS

We adapted a previous model of hepatitis C virus transmission, treatment, and disease progression for Pakistan, calibrating using available data to incorporate a detailed cascade of care for hepatitis C with cost data on diagnostics and hepatitis C treatment. We modelled the effect on various outcomes and costs of alternative scenarios for scaling up screening and hepatitis C treatment in 2018-30. We calibrated the model to country-level demographic data for 1960-2015 (including population growth) and to hepatitis C seroprevalence data from a national survey in 2007-08, surveys among people who inject drugs (PWID), and hepatitis C seroprevalence trends among blood donors. The cascade of care in our model begins with diagnosis of hepatitis C infection through antibody screening and RNA confirmation. Diagnosed individuals are then referred to care and started on treatment, which can result in a sustained virological response (effective cure). We report the median and 95% uncertainty interval (UI) from 1151 modelled runs.

FINDINGS

One-time screening of 90% of the 2018 population by 2030, with 80% referral to treatment, was projected to lead to 13·8 million (95% UI 13·4-14·1) individuals being screened and 350 000 (315 000-385 000) treatments started annually, decreasing hepatitis C incidence by 26·5% (22·5-30·7) over 2018-30. Prioritised screening of high prevalence groups (PWID and adults aged ≥30 years) and rescreening (annually for PWID, otherwise every 10 years) are likely to increase the number screened and treated by 46·8% and decrease incidence by 50·8% (95% UI 46·1-55·0). Decreasing hepatitis C incidence by 80% is estimated to require a doubling of the primary screening rate, increasing referral to 90%, rescreening the general population every 5 years, and re-engaging those lost to follow-up every 5 years. This approach could cost US$8·1 billion, reducing to $3·9 billion with lowest costs for diagnostic tests and drugs, including health-care savings, and implementing a simplified treatment algorithm.

INTERPRETATION

Pakistan will need to invest about 9·0% of its yearly health expenditure to enable sufficient scale up in screening and treatment to achieve the WHO hepatitis C elimination target of an 80% reduction in incidence by 2030.

FUNDING

UNITAID.

Interim effect evaluation of the hepatitis C elimination programme in Georgia: a modelling study

BACKGROUND

Georgia has a high prevalence of hepatitis C, with 5·4% of adults chronically infected. On April 28, 2015, Georgia launched a national programme to eliminate hepatitis C by 2020 (90% reduction in prevalence) through scaled-up treatment and prevention interventions. We evaluated the interim effect of the programme and feasibility of achieving the elimination goal.

METHODS

We developed a transmission model to capture the hepatitis C epidemic in Georgia, calibrated to data from biobehavioural surveys of people who inject drugs (PWID; 1998-2015) and a national survey (2015). We projected the effect of the administration of direct-acting antiviral treatments until Feb 28, 2019, and the effect of continuing current treatment rates until the end of 2020. Effect was estimated in terms of the relative decrease in hepatitis C incidence, prevalence, and mortality relative to 2015 and of the deaths and infections averted compared with a counterfactual of no treatment over the study period. We also estimated treatment rates needed to reach Georgia's elimination target.

FINDINGS

From May 1, 2015, to Feb 28, 2019, 54 313 patients were treated, with approximately 1000 patients treated per month since mid 2017. Compared with 2015, our model projects that these treatments have reduced the prevalence of adult chronic hepatitis C by a median 37% (95% credible interval 30-44), the incidence of chronic hepatitis C by 37% (29-44), and chronic hepatitis C mortality by 14% (3-30) and have prevented 3516 (1842-6250) new infections and averted 252 (134-389) deaths related to chronic hepatitis C. Continuing treatment of 1000 patients per month is predicted to reduce prevalence by 51% (42-61) and incidence by 51% (40-62), by the end of 2020. To reach a 90% reduction by 2020, treatment rates must increase to 4144 (2963-5322) patients initiating treatment per month.

INTERPRETATION

Georgia's hepatitis C elimination programme has achieved substantial treatment scale-up, which has reduced the burden of chronic hepatitis C. However, the country is unlikely to meet its 2020 elimination target unless treatment scales up considerably.

FUNDING

CDC Foundation, National Institute for Health Research, National Institutes of Health.

Modelling the potential prevention benefits of a treat-all hepatitis C treatment strategy at global, regional and country levels: A modelling study

The World Health Organization (WHO) recently produced guidelines advising a treat-all policy for HCV to encourage widespread treatment scale-up for achieving HCV elimination. We modelled the prevention impact achieved (HCV infections averted [IA]) from initiating this policy compared with treating different subgroups at country, regional and global levels. We assessed what country-level factors affect impact. A dynamic, deterministic HCV transmission model was calibrated to data from global systematic reviews and UN data sets to simulate country-level HCV epidemics with ongoing levels of treatment. For each country, the model projected the prevention impact (in HCV IA per treatment undertaken) of initiating four treatment strategies; either selected randomly (treat-all) or targeted among people who inject drugs (PWID), people aged ≥35, or those with cirrhosis. The IA was assessed over 20 years. Linear regression was used to identify associations between IA per treatment and demographic factors. Eighty-eight countries (85% of the global population) were modelled. Globally, the model estimated 0.35 (95% credibility interval [95%CrI]: 0.16-0.61) IA over 20 years for every randomly allocated treatment, 0.30 (95%CrI: 0.12-0.53) from treating those aged ≥35 and 0.28 (95%CrI: 0.12-0.49) for those with cirrhosis. Globally, treating PWID achieved 1.27 (95%CrI: 0.68-2.04) IA per treatment. The IA per randomly allocated treatment was positively associated with a country's population growth rate and negatively associated with higher HCV prevalence among PWID. In conclusion, appreciable prevention benefits could be achieved from WHO's treat-all strategy, although greater benefits per treatment can be achieved through targeting PWID. Higher impact will be achieved in countries with high population growth.

Cost-effectiveness of scaling-up HCV prevention and treatment in the United States for people who inject drugs

AIMS

To examine the cost-effectiveness of hepatitis C virus (HCV) treatment of people who inject drugs (PWID), combined with medication-assisted treatment (MAT) and syringe-service programs (SSP), to tackle the increasing HCV epidemic in the United States.

DESIGN

HCV transmission and disease progression models with cost-effectiveness analysis using a health-care perspective.

SETTING

Rural Perry County, KY (PC) and urban San Francisco, CA (SF), USA. Compared with PC, SF has a greater proportion of PWID with access to MAT or SSP. HCV treatment of PWID is negligible in both settings.

PARTICIPANTS

PWID data were collected between 1998 and 2015 from Social Networks Among Appalachian People, U Find Out, Urban Health Study and National HIV Behavioral Surveillance System studies.

INTERVENTIONS AND COMPARATOR

Three intervention scenarios modeled: baseline-existing SSP and MAT coverage with HCV screening and treatment with direct-acting antiviral for ex-injectors only as per standard of care; intervention 1-scale-up of SSP and MAT without changes to treatment; and intervention 2-scale-up as intervention 1 combined with HCV screening and treatment for current PWID.

MEASUREMENTS

Incremental cost-effectiveness ratios (ICERs) and uncertainty using cost-effectiveness acceptability curves. Benefits were measured in quality-adjusted life-years (QALYs).

FINDINGS

For both settings, intervention 2 is preferred to intervention 1 and the appropriate comparator for intervention 2 is the baseline scenario. Relative to baseline, for PC intervention 2 averts 1852 more HCV infections, increases QALYS by 3095, costs $21.6 million more and has an ICER of $6975/QALY. For SF, intervention 2 averts 36 473 more HCV infections, increases QALYs by 7893, costs $872 million more and has an ICER of $11 044/QALY. The cost-effectiveness of intervention 2 was robust to several sensitivity analysis.

CONCLUSIONS

Hepatitis C screening and treatment for people who inject drugs, combined with medication-assisted treatment and syringe-service programs, is a cost-effective strategy for reducing hepatitis C burden in the United States.

Evaluation of earlier versus later dietary management in long-chain 3-hydroxyacyl-CoA dehydrogenase or mitochondrial trifunctional protein deficiency: a systematic review

Background

Mitochondrial trifunctional protein (MTP) and long-chain 3-hydroxyacyl-CoA dehydrogenase (LCHAD) deficiencies are rare fatty acid β-oxidation disorders. Without dietary management the conditions are life-threatening. We conducted a systematic review to investigate whether pre-symptomatic dietary management following newborn screening provides better outcomes than treatment following symptomatic detection.

Methods

We searched Web of Science, Medline, Pre-Medline, Embase and the Cochrane Library up to 23rd April 2018. Two reviewers independently screened titles, abstracts and full texts for eligibility and quality appraised the studies. Data extraction was performed by one reviewer and checked by another.

Results

We included 13 articles out of 7483 unique records. The 13 articles reported on 11 patient groups, including 174 people with LCHAD deficiency, 18 people with MTP deficiency and 12 people with undifferentiated LCHAD/MTP deficiency. Study quality was moderate to weak in all studies. Included studies suggested fewer heart and liver problems in screen-detected patients, but inconsistent results for mortality. Follow up analyses compared long-term outcomes of (1) pre-symptomatically versus symptomatically treated patients, (2) screened versus unscreened patients, and (3) asymptomatic screen-detected, symptomatic screen-detected, and clinically diagnosed patients in each study. For follow up analyses 1 and 2, we found few statistically significant differences in the long-term outcomes. For follow up analysis 3 we found a significant difference for only one comparison, in the incidence of cardiomyopathy between the three groups.

Conclusions

There is some evidence that dietary management following screen-detection might be associated with a lower incidence of some LCHAD and MTP deficiency-related complications. However, the evidence base is limited by small study sizes, quality issues and risk of confounding. An internationally collaborative research effort is needed to fully examine the risks and the benefits to pre-emptive dietary management with particular attention paid to disease severity and treatment group.

Evaluating the population impact of hepatitis C direct acting antiviral treatment as prevention for people who inject drugs (EPIToPe) - a natural experiment (protocol)

INTRODUCTION

Hepatitis C virus (HCV) is the second largest contributor to liver disease in the UK, with injecting drug use as the main risk factor among the estimated 200 000 people currently infected. Despite effective prevention interventions, chronic HCV prevalence remains around 40% among people who inject drugs (PWID). New direct-acting antiviral (DAA) HCV therapies combine high cure rates (>90%) and short treatment duration (8 to 12 weeks). Theoretical mathematical modelling evidence suggests HCV treatment scale-up can prevent transmission and substantially reduce HCV prevalence/incidence among PWID. Our primary aim is to generate empirical evidence on the effectiveness of HCV 'Treatment as Prevention' (TasP) in PWID.

METHODS AND ANALYSIS

We plan to establish a natural experiment with Tayside, Scotland, as a single intervention site where HCV care pathways are being expanded (including specialist drug treatment clinics, needle and syringe programmes (NSPs), pharmacies and prison) and HCV treatment for PWID is being rapidly scaled-up. Other sites in Scotland and England will act as potential controls. Over 2 years from 2017/2018, at least 500 PWID will be treated in Tayside, which simulation studies project will reduce chronic HCV prevalence among PWID by 62% (from 26% to 10%) and HCV incidence will fall by approximately 2/3 (from 4.2 per 100 person-years (p100py) to 1.4 p100py). Treatment response and re-infection rates will be monitored. We will conduct focus groups and interviews with service providers and patients that accept and decline treatment to identify barriers and facilitators in implementing TasP. We will conduct longitudinal interviews with up to 40 PWID to assess whether successful HCV treatment alters their perspectives on and engagement with drug treatment and recovery. Trained peer researchers will be involved in data collection and dissemination. The primary outcome - chronic HCV prevalence in PWID - is measured using information from the Needle Exchange Surveillance Initiative survey in Scotland and the Unlinked Anonymous Monitoring Programme in England, conducted at least four times before and three times during and after the intervention. We will adapt Bayesian synthetic control methods (specifically the Causal Impact Method) to generate the cumulative impact of the intervention on chronic HCV prevalence and incidence. We will use a dynamic HCV transmission and economic model to evaluate the cost-effectiveness of the HCV TasP intervention, and to estimate the contribution of the scale-up in HCV treatment to observe changes in HCV prevalence. Through the qualitative data we will systematically explore key mechanisms of TasP real world implementation from provider and patient perspectives to develop a manual for scaling up HCV treatment in other settings. We will compare qualitative accounts of drug treatment and recovery with a 'virtual cohort' of PWID linking information on HCV treatment with Scottish Drug treatment databases to test whether DAA treatment improves drug treatment outcomes.

ETHICS AND DISSEMINATION

Extending HCV community care pathways is covered by ethics (ERADICATE C, ISRCTN27564683, Super DOT C Trial clinicaltrials.gov: NCT02706223). Ethical approval for extra data collection from patients including health utilities and qualitative interviews has been granted (REC ref: 18/ES/0128) and ISCRCTN registration has been completed (ISRCTN72038467). Our findings will have direct National Health Service and patient relevance; informing prioritisation given to early HCV treatment for PWID. We will present findings to practitioners and policymakers, and support design of an evaluation of HCV TasP in England.

Scaling Up Hepatitis C Prevention and Treatment Interventions for Achieving Elimination in the United States: A Rural and Urban Comparison

In the United States, hepatitis C virus (HCV) transmission is rising among people who inject drugs (PWID). Many regions have insufficient prevention intervention coverage. Using modeling, we investigated the impact of scaling up prevention and treatment interventions on HCV transmission among PWID in Perry County, Kentucky, and San Francisco, California, where HCV seroprevalence among PWID is >50%. A greater proportion of PWID access medication-assisted treatment (MAT) or syringe service programs (SSP) in urban San Francisco (established community) than in rural Perry County (young, expanding community). We modeled the proportion of HCV-infected PWID needing HCV treatment annually to reduce HCV incidence by 90% by 2030, with and without MAT scale-up (50% coverage, both settings) and SSP scale-up (Perry County only) from 2017. With current MAT and SSP coverage during 2017-2030, HCV incidence would increase in Perry County (from 21.3 to 22.6 per 100 person-years) and decrease in San Francisco (from 12.9 to 11.9 per 100 person-years). With concurrent MAT and SSP scale-up, 5% per year of HCV-infected PWID would need HCV treatment in Perry County to achieve incidence targets-13% per year without MAT and SSP scale-up. In San Francisco, a similar proportion would need HCV treatment (10% per year) irrespective of MAT scale-up. Reaching the same impact by 2025 would require increases in treatment rates of 45%-82%. Achievable provision of HCV treatment, alongside MAT and SSP scale-up (Perry County) and MAT scale-up (San Francisco), could reduce HCV incidence.

The contribution of injection drug use to hepatitis C virus transmission globally, regionally, and at country level: a modelling study

BACKGROUND

WHO aims to eliminate the hepatitis C virus (HCV) as a public health threat by 2030. Injection drug use is an important risk factor for HCV transmission, but its contribution to country-level and global epidemics is unknown. We estimated the contribution of injection drug use to risk for HCV epidemics globally, regionally, and at country level.

METHODS

We developed a dynamic deterministic HCV transmission model to simulate country-level HCV epidemics among people who inject drugs and the general population. Each country's model was calibrated using country-specific data from UN datasets and systematic reviews on the prevalence of HCV and injection drug use. The population attributable fraction of HCV transmission associated with injection drug use was estimated-defined here as the percentage of HCV infections prevented if additional HCV transmission due to injection drug use was removed between 2018 and 2030.

FINDINGS

The model included 88 countries (85% of the global population). The model predicted 0·23% (95% credibility interval [CrI] 0·16-0·31) of the global population were injection drug users in 2017, and 8% (5-12) of prevalent HCV infections were among people who currently inject drugs. Globally, if the increased risk for HCV transmission among people who inject drugs was removed, an estimated 43% (95% CrI 25-67) of incident HCV infections would be prevented from 2018 to 2030, varying regionally. This population attributable fraction was higher in high-income countries (79%, 95% CrI 57-97) than in countries of low and middle income (38%, 24-64) and was associated with the percentage of a country's prevalent HCV infections that are among people who inject drugs.

INTERPRETATION

Unsafe injecting practices among people who inject drugs contribute substantially to incident HCV infections globally. Any intervention that can reduce HCV transmission among people who inject drugs will have a pronounced effect on country-level incidence of HCV.

FUNDING

None.