Biochemical analysis of SARS-CoV-2 Nsp13 helicase implicated in COVID-19 and factors that regulate its catalytic functions.

Replication of the 30-kilobase genome of SARS-CoV-2, responsible for COVID-19, is a key step in the coronavirus life cycle that requires a set of virally encoded nonstructural proteins such as the highly conserved Nsp13 helicase. However, the features that contribute to catalytic properties of Nsp13 are not well established. Here, we biochemically characterized the purified recombinant SARS-CoV-2 Nsp13 helicase protein, focusing on its catalytic functions, nucleic acid substrate specificity, nucleotide/metal cofactor requirements, and displacement of proteins from RNA molecules proposed to be important for its proofreading role during coronavirus replication. We determined that Nsp13 preferentially interacts with single-stranded DNA compared with single-stranded RNA to unwind a partial duplex helicase substrate. We present evidence for functional cooperativity as a function of Nsp13 concentration, which suggests that oligomerization is important for optimal activity. In addition, under single-turnover conditions, Nsp13 unwound partial duplex RNA substrates of increasing double-stranded regions (16-30 base pairs) with similar efficiency, suggesting the enzyme unwinds processively in this range. We also show Nsp13-catalyzed RNA unwinding is abolished by a site-specific neutralizing linkage in the sugar-phosphate backbone, demonstrating continuity in the helicase-translocating strand is essential for unwinding the partial duplex substrate. Taken together, we demonstrate for the first time that coronavirus helicase Nsp13 disrupts a high-affinity RNA-protein interaction in a unidirectional and ATP-dependent manner. Furthermore, sensitivity of Nsp13 catalytic functions to Mg2+ concentration suggests a regulatory mechanism for ATP hydrolysis, duplex unwinding, and RNA protein remodeling, processes implicated in SARS-CoV-2 replication and proofreading.

Ambulatory blood pressure monitoring using telemedicine: proof-of-concept cohort and failure modes and effects analyses.

Background: The COVID-19 pandemic has accelerated adoption of remote consulting in healthcare. Despite opportunities posed by telemedicine, most hypertension services in Europe have suspended ambulatory blood pressure monitoring (ABPM). Methods: We examined the process and performance of remotely delivered ABPM using two methodologies: firstly, a Failure Modes and Effects Analysis (FMEA) and secondly, a quantitative analysis comparing ABPM data from a subgroup of 65 participants of the Screening for Hypertension in the INpatient Environment (SHINE) diagnostic accuracy study. The FMEA was performed over seven sessions from February to March 2021, with a multidisciplinary team comprising a patient representative, a research coordinator with technical expertise and four research clinicians. Results: The FMEA identified a single high-risk step in the remote ABPM process. This was cleaning of monitoring equipment in the context of the COVID-19 pandemic, unrelated to the remote setting. A total of 14 participants were scheduled for face-to-face ABPM appointments, before the UK March 2020 COVID-19 lockdown; 62 were scheduled for remote ABPM appointments since emergence of the COVID-19 pandemic between November 2020 and August 2021. A total of 65 (88%) participants completed ABPMs; all obtained sufficient successful measurements for interpretation. For the 10 participants who completed face-to-face ABPM, there were 402 attempted ABPM measurements and 361 (89%) were successful. For the 55 participants who completed remote ABPM, there were 2516 attempted measurements and 2114 (88%) were successful. There was no significant difference in the mean per-participant error rate between face-to-face (0.100, SD 0.009) and remote (0.143, SD 0.132) cohorts (95% CI for the difference -0.125 to 0.045 and two-tailed P-value 0.353). Conclusions: We have demonstrated that ABPM can be safely and appropriately provided in the community remotely and without face-to-face contact, using video technology for remote fitting appointments, alongside courier services for delivery of equipment to participants.

Ambulatory blood pressure monitoring using telemedicine: proof-of-concept cohort and failure modes and effects analyses [version 3;peer review: 2 approved]

Background: The COVID-19 pandemic has accelerated adoption of remote consulting in healthcare. Despite opportunities posed by telemedicine, most hypertension services in Europe have suspended ambulatory blood pressure monitoring (ABPM). Methods: We examined the process and performance of remotely delivered ABPM using two methodologies: firstly, a Failure Modes and Effects Analysis (FMEA) and secondly, a quantitative analysis comparing ABPM data from a subgroup of 65 participants of the Screening for Hypertension in the INpatient Environment (SHINE) diagnostic accuracy study. The FMEA was performed over seven sessions from February to March 2021, with a multidisciplinary team comprising a patient representative, a research coordinator with technical expertise and four research clinicians. Results: The FMEA identified a single high-risk step in the remote ABPM process. This was cleaning of monitoring equipment in the context of the COVID-19 pandemic, unrelated to the remote setting. A total of 14 participants were scheduled for face-to-face ABPM appointments, before the UK March 2020 COVID-19 lockdown;62 were scheduled for remote ABPM appointments since emergence of the COVID-19 pandemic between November 2020 and August 2021. A total of 65 (88%) participants completed ABPMs;all obtained sufficient successful measurements for interpretation. For the 10 participants who completed face-to-face ABPM, there were 402 attempted ABPM measurements and 361 (89%) were successful. For the 55 participants who completed remote ABPM, there were 2516 attempted measurements and 2214 (88%) were successful. There was no significant difference in the mean per-participant error rate between face-to-face (0.100, SD 0.009) and remote (0.143, SD 0.132) cohorts (95% CI for the difference -0.125 to 0.045 and two-tailed P-value 0.353). Conclusions: We have demonstrated that ABPM can be safely and appropriately provided in the community remotely and without face-to-face contact, using video technology for remote fitting appointments, alongside courier services for delivery of equipment to participants.

Use of behavioural activation to manage pain: a scoping review protocol

IntroductionChronic pain is a distressing condition and often poorly treated and managed. Psychological therapies are considered first-line intervention for people with chronic pain. Common psychological therapies require extensive clinician training and specialist qualifications. One approach that does not need lengthy training nor specialist qualification, but has empirical support in other health domains, is behavioural activation (BA). BA seeks to increase engagement in behaviours that are valued by the person and progress through behaviours that can increase mood and develop skills that build satisfying routines. BA can help people to manage their condition through scheduling behaviours, promoting routine and mastery over their condition. The extent to which BA has been used to support people living with chronic pain is not clear.Methods and analysisThis scoping review aims to identify published studies describing the application of BA to support people living with chronic pain. To map the evidence regarding BA and chronic pain, including the study type and the associated evidence, a scoping review was adopted. The search will be conducted in bibliographic databases, clinical trial registries and grey literature. No date limits will be applied to the search strategy. Screening of titles and s, and full-text screening, will be independently undertaken by two investigators using Covidence software. Any disagreement between investigators will be resolved by a third investigator. Data from included publications will be extracted using a customised data extraction tool.Ethics and disseminationThe scoping review is an analysis of existing data and therefore ethics approval is not required. The findings of this scoping review will further our understanding of how BA has been used to support people living with chronic pain and inform future training and education programmes in this area.

Beyond the black stump: rapid reviews of health research issues affecting regional, rural and remote Australia.

CHAPTER 1: RETAIL INITIATIVES TO IMPROVE THE HEALTHINESS OF FOOD ENVIRONMENTS IN RURAL, REGIONAL AND REMOTE COMMUNITIES: Objective: To synthesise the evidence for effectiveness of initiatives aimed at improving food retail environments and consumer dietary behaviour in rural, regional and remote populations in Australia and comparable countries, and to discuss the implications for future food environment initiatives for rural, regional and remote areas of Australia. STUDY DESIGN: Rapid review of articles published between January 2000 and May 2020. DATA SOURCES: We searched MEDLINE (EBSCOhost), Health and Society Database (Informit) and Rural and Remote Health Database (Informit), and included studies undertaken in rural food environment settings in Australia and other countries. DATA SYNTHESIS: Twenty-one articles met the inclusion criteria, including five conducted in Australia. Four of the Australian studies were conducted in very remote populations and in grocery stores, and one was conducted in regional Australia. All of the overseas studies were conducted in rural North America. All of them revealed a positive influence on food environment or consumer behaviour, and all were conducted in disadvantaged, rural communities. Positive outcomes were consistently revealed by studies of initiatives that focused on promotion and awareness of healthy foods and included co-design to generate community ownership and branding. CONCLUSION: Initiatives aimed at improving rural food retail environments were effective and, when implemented in different rural settings, may encourage improvements in population diets. The paucity of studies over the past 20 years in Australia shows a need for more research into effective food retail environment initiatives, modelled on examples from overseas, with studies needed across all levels of remoteness in Australia. Several retail initiatives that were undertaken in rural North America could be replicated in rural Australia and could underpin future research. CHAPTER 2: WHICH INTERVENTIONS BEST SUPPORT THE HEALTH AND WELLBEING NEEDS OF RURAL POPULATIONS EXPERIENCING NATURAL DISASTERS?: Objective: To explore and evaluate health and social care interventions delivered to rural and remote communities experiencing natural disasters in Australia and other high income countries. STUDY DESIGN: We used systematic rapid review methods. First we identified a test set of citations and generated a frequency table of Medical Subject Headings (MeSH) to index articles. Then we used combinations of MeSH terms and keywords to search the MEDLINE (Ovid) database, and screened the titles and abstracts of the retrieved references. DATA SOURCES: We identified 1438 articles via database searches, and a further 62 articles via hand searching of key journals and reference lists. We also found four relevant grey literature resources. After removing duplicates and undertaking two stages of screening, we included 28 studies in a synthesis of qualitative evidence. DATA SYNTHESIS: Four of us read and assessed the full text articles. We then conducted a thematic analysis using the three phases of the natural disaster response cycle. CONCLUSION: There is a lack of robust evaluation of programs and interventions supporting the health and wellbeing of people in rural communities affected by natural disasters. To address the cumulative and long term impacts, evidence suggests that continuous support of people's health and wellbeing is needed. By using a lens of rural adversity, the complexity of the lived experience of natural disasters by rural residents can be better understood and can inform development of new models of community-based and integrated care services. CHAPTER 3: THE IMPACT OF BUSHFIRE ON THE WELLBEING OF CHILDREN LIVING IN RURAL AND REMOTE AUSTRALIA: Objective: To investigate the impact of bushfire events on the wellbeing of children living in rural and remote Australia. STUDY DESIGN: Literature review completed using rapid realist review methods, and taking into consideration the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) statement for systematic reviews. DATA SOURCES: We sourced data from six databases: EBSCOhost (Education), EBSCOhost (Health), EBSCOhost (Psychology), Informit, MEDLINE and PsycINFO. We developed search terms to identify articles that could address the research question based on the inclusion criteria of peer reviewed full text journal articles published in English between 1983 and 2020. We initially identified 60 studies and, following closer review, extracted data from eight studies that met the inclusion criteria. DATA SYNTHESIS: Children exposed to bushfires may be at increased risk of poorer wellbeing outcomes. Findings suggest that the impact of bushfire exposure may not be apparent in the short term but may become more pronounced later in life. Children particularly at risk are those from more vulnerable backgrounds who may have compounding factors that limit their ability to overcome bushfire trauma. CONCLUSION: We identified the short, medium and long term impacts of bushfire exposure on the wellbeing of children in Australia. We did not identify any evidence-based interventions for supporting outcomes for this population. Given the likely increase in bushfire events in Australia, research into effective interventions should be a priority. CHAPTER 4: THE ROLE OF NATIONAL POLICIES TO ADDRESS RURAL ALLIED HEALTH, NURSING AND DENTISTRY WORKFORCE MALDISTRIBUTION: Objective: Maldistribution of the health workforce between rural, remote and metropolitan communities contributes to longstanding health inequalities. Many developed countries have implemented policies to encourage health care professionals to work in rural and remote communities. This scoping review is an international synthesis of those policies, examining their effectiveness at recruiting and retaining nursing, dental and allied health professionals in rural communities. STUDY DESIGN: Using scoping review methods, we included primary research - published between 1 September 2009 and 30 June 2020 - that reported an evaluation of existing policy initiatives to address workforce maldistribution in high income countries with a land mass greater than 100 000 km2 . DATA SOURCES: We searched MEDLINE, Ovid Embase, Ovid Emcare, Informit, Scopus, and Web of Science. We screened 5169 articles for inclusion by title and abstract, of which we included 297 for full text screening. We then extracted data on 51 studies that had been conducted in Australia, the United States, Canada, United Kingdom and Norway. DATA SYNTHESIS: We grouped the studies based on World Health Organization recommendations on recruitment and retention of health care workers: education strategies (n = 27), regulatory change (n = 11), financial incentives (n = 6), personal and professional support (n = 4), and approaches with multiple components (n = 3). CONCLUSION: Considerable work has occurred to address workforce maldistribution at a local level, underpinned by good practice guidelines, but rarely at scale or with explicit links to coherent overarching policy. To achieve policy aspirations, multiple synergistic evidence-based initiatives are needed, and implementation must be accompanied by well designed longitudinal evaluations that assess the effectiveness of policy objectives. CHAPTER 5: AVAILABILITY AND CHARACTERISTICS OF PUBLICLY AVAILABLE HEALTH WORKFORCE DATA SOURCES IN AUSTRALIA: Objective: Many data sources are used in Australia to inform health workforce planning, but their characteristics in terms of relevance, accessibility and accuracy are uncertain. We aimed to identify and appraise publicly available data sources used to describe the Australian health workforce. STUDY DESIGN: We conducted a scoping review in which we searched bibliographic databases, websites and grey literature. Two reviewers independently undertook title and abstract screening and full text screening using Covidence software. We then assessed the relevance, accessibility and accuracy of data sources using a customised appraisal tool. DATA SOURCES: We searched for potential workforce data sources in nine databases (MEDLINE, Embase, Ovid Emcare, Scopus, Web of Science, Informit, the JBI Evidence-based Practice Database, PsycINFO and the Cochrane Library) and the grey literature, and examined several pre-defined websites. DATA SYNTHESIS: During the screening process we identified 6955 abstracts and examined 48 websites, from which we identified 12 publicly available data sources - eight primary and four secondary data sources. The primary data sources were generally of modest quality, with low scores in terms of reference period, accessibility and missing data. No single primary data source scored well across all domains of the appraisal tool. CONCLUSION: We identified several limitations of data sources used to describe the Australian health workforce. Establishment of a high quality, longitudinal, linked database that can inform all aspects of health workforce development is urgently needed, particularly for rural health workforce and services planning. CHAPTER 6: RAPID REALIST REVIEW OF OPIOID TAPERING IN THE CONTEXT OF LONG TERM OPIOID USE FOR NON-CANCER PAIN IN RURAL AREAS: Objective: To describe interventions, barriers and enablers associated with opioid tapering for patients with chronic non-cancer pain in rural primary care settings. STUDY DESIGN: Rapid realist review registered on the international register of systematic reviews (PROSPERO) and conducted in accordance with RAMESES standards. DATA SOURCES: English language, peer-reviewed articles reporting qualitative, quantitative and mixed method studies, published between January 2016 and July 2020, and accessed via MEDLINE, Embase, CINAHL Complete, PsycINFO, Informit or the Cochrane Library during June and July 2020. Grey literature relating to prescribing,deprescribing or tapering of opioids in chronic non-cancer pain, published between January 2016 and July 2020, was identified by searching national and international government, health service and peek organisation websites using Google Scholar. DATA SYNTHESIS: Our analysis of reported approaches to tapering conducted across rural and non-rural contexts showed that tapering opioids is complex and challenging, and identified several barriers and enablers. Successful outcomes in rural areas appear likely through therapeutic relationships, coordination and support, by using modalities and models of care that are appropriate in rural settings and by paying attention to harm minimisation. CONCLUSION: Rural primary care providers do not have access to resources available in metropolitan centres for dealing with patients who have chronic non-cancer pain and are taking opioid medications. They often operate alone or in small group practices, without peer support and access to multidisciplinary and specialist teams. Opioid tapering approaches described in the literature include regulation, multimodal and multidisciplinary approaches, primary care provider support, guidelines, and patient-centred strategies. There is little research to inform tapering in rural contexts. Our review provides a synthesis of the current evidence in the form of a conceptual model. This preliminary model could inform the development of a model of care for use in implementation research, which could test a variety of mechanisms for supporting decision making, reducing primary care providers' concerns about potential harms arising from opioid tapering, and improving patient outcomes.

Availability and quality of publicly available health workforce data sources in Australia: a scoping review protocol.

INTRODUCTION: The health workforce is an integral component of the healthcare system. Comprehensive, high-quality data on the health workforce are essential to identifying gaps in health service provision, as well as informing future health workforce and health services planning, and health policy. While many data sources are used in Australia for these purposes, the quality of the data sources with respect to relevance, accessibility and accuracy is not clear. METHODS AND ANALYSIS: This scoping review aims to identify and appraise publicly available data sources describing the Australian health workforce. The review will include any data source (eg, registry, administrative database and survey) or document reporting a data source (eg, journal article, report) on the Australian health workforce, which is publicly available and describes the characteristics of the workforce. The search will be conducted in 10 bibliographic databases and the grey literature using an iterative process. Screening of titles and abstracts will be undertaken by two investigators, independently, using Covidence software. Any disagreement between investigators will be resolved by a third investigator. Documents/data sources identified as potentially eligible will be retrieved in full text and reviewed following the same process. Data will be extracted using a customised data extraction tool. A customised appraisal tool will be used to assess the relevance, accessibility and accuracy of included data sources. ETHICS AND DISSEMINATION: The scoping review is a secondary analysis of existing, publicly available data sources and does not require ethics approval. The findings of this scoping review will further our understanding of the quality and availability of data sources used for health workforce and health services planning in Australia. The results will be submitted for publication in peer-reviewed journals and presented at conferences targeted at health workforce and public health topics.

"I have the strength to get through this using my past experiences with HIV": findings from a mixed-method survey of health outcomes, service accessibility, and psychosocial wellbeing among people living with HIV during the Covid-19 pandemic.

We examined the impact of Covid-19 restrictions on the wellbeing and access to care among people living with HIV (PLWH) in the UK. A cross-sectional anonymous online survey was circulated to PLWH attending care at three HIV services in Sussex. The questionnaire covered key themes: socio-demographic characteristics; changes in physical and mental health; accessibility of essential health services and information; and socio-economic concerns. Free-text qualitative responses were examined through framework analysis. Quantitative data from 653 respondents were available, with a subset of 385 free-text qualitative responses. In terms of mental health, 501 (77.6%) respondents reported feeling more anxious; 464 (71.8%) reported feeling more depressed than usual; and 128 (19.8%) reported having suicidal thoughts since the start of the pandemic. Respondents worried about running out of HIV medicine (n = 264, 40.7%); accessing HIV services (n = 246, 38.0%) as well as other health services (n = 408, 63.0%). Widespread resilience was also noted: 537 (83.3%) of respondents felt that living with HIV had equipped them with the strength to adapt to the Covid-19 pandemic. Findings highlight important gaps between the multifaceted needs of PLWH. Multisectoral collaborations and investments are needed to adequately support PLWH and to build resilience to future shocks within HIV services.

The Coronavirus Network Explorer: mining a large-scale knowledge graph for effects of SARS-CoV-2 on host cell function.

BACKGROUND: Leveraging previously identified viral interactions with human host proteins, we apply a machine learning-based approach to connect SARS-CoV-2 viral proteins to relevant host biological functions, diseases, and pathways in a large-scale knowledge graph derived from the biomedical literature. Our goal is to explore how SARS-CoV-2 could interfere with various host cell functions, and to identify drug targets amongst the host genes that could potentially be modulated against COVID-19 by repurposing existing drugs. The machine learning model employed here involves gene embeddings that leverage causal gene expression signatures curated from literature. In contrast to other network-based approaches for drug repurposing, our approach explicitly takes the direction of effects into account, distinguishing between activation and inhibition. RESULTS: We have constructed 70 networks connecting SARS-CoV-2 viral proteins to various biological functions, diseases, and pathways reflecting viral biology, clinical observations, and co-morbidities in the context of COVID-19. Results are presented in the form of interactive network visualizations through a web interface, the Coronavirus Network Explorer (CNE), that allows exploration of underlying experimental evidence. We find that existing drugs targeting genes in those networks are strongly enriched in the set of drugs that are already in clinical trials against COVID-19. CONCLUSIONS: The approach presented here can identify biologically plausible hypotheses for COVID-19 pathogenesis, explicitly connected to the immunological, virological and pathological observations seen in SARS-CoV-2 infected patients. The discovery of repurposable drugs is driven by prior knowledge of relevant functional endpoints that reflect known viral biology or clinical observations, therefore suggesting potential mechanisms of action. We believe that the CNE offers relevant insights that go beyond more conventional network approaches, and can be a valuable tool for drug repurposing. The CNE is available at https://digitalinsights.qiagen.com/coronavirus-network-explorer .