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Background The distribution of the duration that clinical cases of COVID-19 occupy hospital beds (the ‘length of stay’) is a key factor in determining how incident caseloads translate into health system burden. Robust estimation of length of stay in real-time requires the use of survival methods that can account for right-censoring induced by yet unobserved events in patient progression (e.g. discharge, death). In this study, we estimate in real-time the length of stay distributions of hospitalised COVID-19 cases in New South Wales, Australia, comparing estimates between a period where Delta was the dominant variant and a subsequent period where Omicron was dominant. Methods Using data on the hospital stays of 19,574 individuals who tested positive to COVID-19 prior to admission, we performed a competing-risk survival analysis of COVID-19 clinical progression. Results During the mixed Omicron-Delta epidemic, we found that the mean length of stay for individuals who were discharged directly from ward without an ICU stay was, for age groups 0–39, 40–69 and 70 +, respectively, 2.16 (95% CI: 2.12–2.21), 3.93 (95% CI: 3.78–4.07) and 7.61 days (95% CI: 7.31–8.01), compared to 3.60 (95% CI: 3.48–3.81), 5.78 (95% CI: 5.59–5.99) and 12.31 days (95% CI: 11.75–12.95) across the preceding Delta epidemic (1 July 2021–15 December 2021). We also considered data on the stays of individuals within the Hunter New England Local Health District, where it was reported that Omicron was the only circulating variant, and found mean ward-to-discharge length of stays of 2.05 (95% CI: 1.80–2.30), 2.92 (95% CI: 2.50–3.67) and 6.02 days (95% CI: 4.91–7.01) for the same age groups. Conclusions Hospital length of stay was substantially reduced across all clinical pathways during a mixed Omicron-Delta epidemic compared to a prior Delta epidemic, contributing to a lessened health system burden despite a greatly increased infection burden. Our results demonstrate the utility of survival analysis in producing real-time estimates of hospital length of stay for assisting in situational assessment and planning of the COVID-19 response.

We report on an analysis of Australian COVID-19 case data to estimate the impact of TTIQ systems on SARS-CoV-2 transmission in 2020–21. We estimate that in a low prevalence period in the state of New South Wales (tens of cases per day), TTIQ contributed to a 54% reduction in transmission. In a higher prevalence period in the state of Victoria (hundreds of cases per day), TTIQ contributed to a 42% reduction in transmission. Our results also suggest that case-initiated contact tracing can support timely quarantine in times of system stress. Contact tracing systems for COVID-19 in Australia were highly effective and adaptable in supporting the national suppression strategy through 2020 and 2021.

BackgroundIn mid-2021, widespread availability of COVID-19 vaccines with demonstrated impacts on transmission promised relief from the strict public health and social measures (PHSMs) imposed in many countries to limit spread and burden. We were asked to define vaccine coverage thresholds for transition through the stages of Australia’s ‘National Plan’ to easing restrictions and reopening international borders.MethodsUsing available evidence of vaccine effectiveness against the then-circulating Delta variant, we used a mathematical model to determine vaccine coverage targets. The absence of any COVID-19 infections in many sub-national jurisdictions in Australia posed particular methodological challenges for modelling in this setting. We used a novel metric called Transmission Potential (TP) as a proxy measure of the population-level effective reproduction number. We estimated TP of the Delta variant under a range of PHSMs, test-trace-isolate-quarantine (TTIQ) efficiencies, vaccination coverage thresholds, and age-based vaccine allocation strategies.FindingsWe found that high coverage of vaccination across all age groups (≤ 70%) combined with ongoing TTIQ and minimal PHSMs was sufficient to avoid strict lockdowns. At lesser coverage (≥ 60%) rapid case escalation risked overwhelming of the health sector and would prompt a need to reimpose strict restrictions, with substantive economic impacts in order to achieve the goals of the National Plan. Maintaining low case numbers was the most beneficial strategy for health and the economy, and at higher coverage levels (≥ 80%) further easing of restrictions was deemed possible.InterpretationThese results reinforced recommendations from other modelling groups that some level of PHSMs should be continued to minimise the burden of the Delta variant following achievement of high population vaccine coverage. They directly informed easing of COVID-19 restrictions in Australia.FundingThis study was supported by the Australian Government Department of Health and Ageing, and the National Health and Medical Research Council’s Centre of Research Excellence scheme (GNT1170960).

As of January 2021, Australia had effectively controlled local transmission of COVID-19 despite a steady influx of imported cases and several local, but contained, outbreaks in 2020. Throughout 2020, state and territory public health responses were informed by weekly situational reports that included an ensemble forecast for each jurisdiction. We present here an analysis of one forecasting model included in this ensemble across the variety of scenarios experienced by each jurisdiction from May to October 2020. We examine how successfully the forecasts characterised future case incidence, subject to variations in data timeliness and completeness, showcase how we adapted these forecasts to support decisions of public health priority in rapidly-evolving situations, evaluate the impact of key model features on forecast skill, and demonstrate how to assess forecast skill in real-time before the ground truth is known. Conditioning the model on the most recent, but incomplete, data improved the forecast skill, emphasising the importance of developing strong quantitative models of surveillance system characteristics, such as ascertainment delay distributions. Forecast skill was highest when there were at least 10 reported cases per day, the circumstances in which authorities were most in need of forecasts to aid in planning and response.

The ability of health systems to cope with coronavirus disease (COVID-19) cases is of major concern. In preparation, we used clinical pathway models to estimate healthcare requirements for COVID-19 patients in the context of broader public health measures in Australia. An age- and risk-stratified transmission model of COVID-19 demonstrated that an unmitigated epidemic would dramatically exceed the capacity of the health system of Australia over a prolonged period. Case isolation and contact quarantine alone are insufficient to constrain healthcare needs within feasible levels of expansion of health sector capacity. Overlaid social restrictions must be applied over the course of the epidemic to ensure systems do not become overwhelmed and essential health sector functions, including care of COVID-19 patients, can be maintained. Attention to the full pathway of clinical care is needed, along with ongoing strengthening of capacity.

In controlling transmission of COVID-19, the effectiveness of border quarantine strategies is a key concern for jurisdictions in which the local prevalence of disease and immunity is low. In settings like this such as China, Australia, and New Zealand, rare outbreak events can lead to escalating epidemics and trigger the imposition of large scale lockdown policies. Here, we examine to what degree vaccination status of incoming arrivals and the quarantine workforce can allow relaxation of quarantine requirements. To do so, we develop and apply a detailed model of COVID-19 disease progression and transmission taking into account nuanced timing factors. Key among these are disease incubation periods and the progression of infection detectability during incubation. Using the disease characteristics associated with the ancestral lineage of SARS-CoV-2 to benchmark the level of acceptable risk, we examine the performance of the border quarantine system for vaccinated arrivals. We examine disease transmission and vaccine efficacy parameters over a wide range, covering plausible values for the Delta variant currently circulating globally. Our results indicate a threshold in outbreak potential as a function of vaccine efficacy, with the time until an outbreak increasing by up to two orders of magnitude as vaccine efficacy against transmission increases from 70% to 90%. For parameters corresponding to the Delta variant, vaccination is able to maintain the capacity of quarantine systems to reduce case importation and outbreak risk, by counteracting the pathogen's increased infectiousness. To prevent outbreaks, heightened vaccination in border quarantine systems must be combined with mass vaccination. The ultimate success of these programs will depend sensitively on the efficacy of vaccines against viral transmission.

AimTo estimate the length of stay distributions of hospitalised COVID-19 cases during a mixed Omicron-Delta epidemic in New South Wales, Australia (16 Dec 2021 – 7 Feb 2022), and compare these to estimates produced over a Delta-only epidemic in the same population (1 Jul 2021 – 15 Dec 2022).BackgroundThe distribution of the duration that clinical cases of COVID-19 occupy hospital beds (the ‘length of stay’) is a key factor in determining how incident caseloads translate into health system burden as measured through ward and ICU occupancy.ResultsUsing data on the hospital stays of 19,574 individuals, we performed a competing-risk survival analysis of COVID-19 clinical progression. During the mixed Omicron-Delta epidemic, we found that the mean length of stay for individuals who were discharged directly from ward without an ICU stay was, for age groups 0-39, 40-69 and 70+ respectively, 2.16 (95% CI: 2.12–2.21), 3.93 (95% CI: 3.78–4.07) and 7.61 days (95% CI: 7.31–8.01), compared to 3.60 (95% CI: 3.48–3.81), 5.78 (95% CI: 5.59–5.99) and 12.31 days (95% CI: 11.75–12.95) across the preceding Delta epidemic (15 Jul 2021 – 15 Dec 2021). We also considered data on the stays of individuals within the Hunter New England Local Health District, where it was reported that Omicron was the only circulating variant, and found mean ward-to-discharge length of stays of 2.05 (95% CI: 1.80–2.30), 2.92 (95% CI: 2.50–3.67) and 6.02 days (95% CI: 4.91–7.01) for the same age groups.ConclusionsHospital length of stay was substantially reduced across all clinical pathways during a mixed Omicron-Delta epidemic compared to a prior Delta epidemic. These changes in length of stay have contributed to lessened health system burden despite greatly increased infection burden and should be considered in future planning of response to the COVID-19 pandemic in Australia and internationally.

Scientific knowledge and advances are a cornerstone of modern society. They improve our understanding of the world we live in and help us navigate global challenges including emerging infectious diseases, climate change and the biodiversity crisis. For any scientist, whether they work primarily in fundamental knowledge generation or in the applied sciences, it is important to understand how science fits into a decision-making framework. Decision science is a field that aims to pinpoint evidence-based management strategies. It provides a framework for scientists to directly impact decisions or to understand how their work will fit into a decision process. Decision science is more than undertaking targeted and relevant scientific research or providing tools to assist policy makers; it is an approach to problem formulation, bringing together mathematical modelling, stakeholder values and logistical constraints to support decision making. In this paper we describe decision science, its use in different contexts, and highlight current gaps in methodology and application. The COVID-19 pandemic has thrust mathematical models into the public spotlight, but it is one of innumerable examples in which modelling informs decision making. Other examples include models of storm systems (eg. cyclones, hurricanes) and climate change. Although the decision timescale in these examples differs enormously (from hours to decades), the underlying decision science approach is common across all problems. Bridging communication gaps between different groups is one of the greatest challenges for scientists. However, by better understanding and engaging with the decision-making processes, scientists will have greater impact and make stronger contributions to important societal problems.

Highlights • Japanese encephalitis virus (JEV) remains a leading cause of neurological infection in Asia. • A systematic review identified 20,212 published human cases of laboratory-confirmed JEV infections from 205 studies. • 15,167 (75%) of cases were confirmed with the lowest confidence diagnostic test, i.e., level 3 or 4, or level 4. • Only 109 (53%) of the studies reported contemporaneous testing for dengue-specific antibodies. • A fundamental pre-requisite for the control of JE is lacking — that of a simple and specific diagnostic procedure that can be adapted for point-of-care tests and readily used throughout JE endemic regions of the world., Objective Japanese encephalitis virus infection (JE) remains a leading cause of neurological disease in Asia, mainly involving individuals living in remote areas with limited access to treatment centers and diagnostic facilities. Laboratory confirmation is fundamental for the justification and implementation of vaccination programs. We reviewed the literature on historical developments and current diagnostic capability worldwide, to identify knowledge gaps and instill urgency to address them. Methods Searches were performed in Web of Science and PubMed using the term 'Japanese encephalitis' up to 13th October 2019. Studies reporting laboratory-confirmed symptomatic JE cases in humans were included, and data on details of diagnostic tests were extracted. A JE case was classified according to confirmatory levels (Fischer et al., 2008; Campbell et al., 2011; Pearce et al., 2018; Heffelfinger et al., 2017), where level 1 represented the highest level of confidence. Findings 20,212 published JE cases were identified from 205 studies. 15,167 (75%) of these positive cases were confirmed with the lowest-confidence diagnostic tests (level 3 or 4, or level 4). Only 109 (53%) of the studies reported contemporaneous testing for dengue-specific antibodies. Conclusion A fundamental pre-requisite for the control of JEV is lacking — that of a simple and specific diagnostic procedure that can be adapted for point-of-care tests and readily used throughout JE-endemic regions of the world.

Initiation of antiretroviral therapy (ART) in early compared with chronic human immunodeficiency virus (HIV) infection is associated with a smaller HIV reservoir. This longitudinal analysis of 60 individuals who began ART during primary HIV infection (PHI) investigates which pre- and posttherapy factors best predict HIV DNA levels (a correlate of reservoir size) after treatment initiation during PHI. The best predictor of HIV DNA at 1 year was pre-ART HIV DNA, which was in turn significantly associated with CD8 memory T-cell differentiation (effector memory, naive, and T-bet−Eomes− subsets), CD8 T-cell activation (CD38 expression) and T-cell immunoglobulin and mucin-domain containing-3 (Tim-3) expression on memory T cells. No associations were found for any immunological variables after 1 year of ART. Levels of HIV DNA are determined around the time of ART initiation in individuals treated during PHI. CD8 T-cell activation and memory expansion are linked to HIV DNA levels, suggesting the importance of the initial host-viral interplay in eventual reservoir size., Human immunodeficiency virus (HIV) DNA persists within the viral reservoir despite therapy. A longitudinal analysis of 60 individuals treated during early HIV infection showed that HIV DNA levels are “set” early in infection and predicted by an activated immune response.

Against a backdrop of widespread global transmission, a number of countries have successfully brought large outbreaks of COVID-19 under control and maintained near-elimination status. A key element of epidemic response is the tracking of disease transmissibility in near real-time. During major outbreaks, the reproduction rate can be estimated from a time-series of case, hospitalisation or death counts. In low or zero incidence settings, knowing the potential for the virus to spread is a response priority. Absence of case data means that this potential cannot be estimated directly.We present a semi-mechanistic modelling framework that draws on time-series of both behavioural data and case data (when disease activity is present) to estimate the transmissibility of SARS-CoV-2 from periods of high to low – or zero – case incidence, with a coherent transition in interpretation across the changing epidemiological situations. Of note, during periods of epidemic activity, our analysis recovers the effective reproduction number, while during periods of low – or zero – case incidence, it provides an estimate of transmission risk. This enables tracking and planning of progress towards the control of large outbreaks, maintenance of virus suppression, and monitoring the risk posed by re-introduction of the virus.We demonstrate the value of our methods by reporting on their use throughout 2020 in Australia, where they have become a central component of the national COVID-19 response.

During the COVID-19 pandemic, evidence has accumulated that movement restrictions enacted to combat virus spread produce disparate consequences along socioeconomic lines. We investigate the hypothesis that people engaged in financially secure employment are better able to adhere to mobility restrictions, due to occupational factors that link the capacity for flexible work arrangements to income security. We use high-resolution spatial data on household internet traffic as a surrogate for adaptation to home-based work, together with the geographical clustering of occupation types, to investigate the relationship between occupational factors and increased internet traffic during work hours under lockdown in two Australian cities. By testing our hypothesis based on the observed trends, and exploring demographic factors associated with divergences from our hypothesis, we are left with a picture of unequal impact dominated by two major influences: the types of occupations in which people are engaged, and the composition of households and families. During lockdown, increased internet traffic was correlated with income security and, when school activity was conducted remotely, to the proportion of families with children. Our findings suggest that response planning and provision of social and economic support for residents within lockdown areas should explicitly account for income security and household structure. Overall, the results we present contribute to the emerging picture of the impacts of COVID-19 on human behaviour, and will help policy makers to understand the balance between public health and social impact in making decisions about mitigation policies.

This chapter presents evidence to inform evolving Coronavirus disease (COVID-19) response planning by analysing how Australians were thinking, feeling and behaving in response to the so-called “first wave” of the COVID-19 epidemic and the associated public health measures. Australia has a federated political system featuring overlapping responsibilities between a federal government, eight state and territory governments and local governments. The political geography of Australia, as an island continent, has informed the shape of the responses. The questionnaire was administered online to members of the YouGov Australia panel of individuals who have agreed to take part in surveys of public opinion. Respondents were asked to report their level of worry about the COVID-19 situation in Australia. High numbers of respondents in both Surveys provided free text responses criticising the behaviour of other people, suggesting some sort of moral, character or behavioural flaw.

During the COVID-19 pandemic, evidence has accumulated that movement restrictions enacted to combat virus spread produce disparate consequences along socioeconomic lines. We investigate the hypothesis that people engaged in financially secure employment are better able to adhere to mobility restrictions, due to occupational factors that link the capacity for flexible work arrangements to income security. We use high-resolution spatial data on household internet traffic as a surrogate for adaptation to home-based work, together with the geographical clustering of occupation types, to investigate the relationship between occupational factors and increased internet traffic during work hours under lockdown in two Australian cities. By testing our hypothesis based on the observed trends, and exploring demographic factors associated with divergences from our hypothesis, we are left with a picture of unequal impact dominated by two major influences: the types of occupations in which people are engaged, and the composition of households and families. During lockdown, increased internet traffic was correlated with income security and, when school activity was conducted remotely, to the proportion of families with children. Our findings suggest that response planning and provision of social and economic support for residents within lockdown areas should explicitly account for income security and household structure. Overall, the results we present contribute to the emerging picture of the impacts of COVID-19 on human behaviour, and will help policy makers to understand the balance between public health and social impact in making decisions about mitigation policies.

As of 18 April 2020, there had been 6,533 confirmed cases of COVID-19 in Australia [1]. Of these, 67 had died from the disease. The daily count of new confirmed cases was declining. This suggests that the collective actions of the Australian public and government authorities in response to COVID-19 were sufficiently early and assiduous to avert a public health crisis — for now. Analysing factors, such as the intensity and timing public health interventions, that contribute to individual country experiences of COVID-19 will assist in the next stage of response planning globally. Using data from the Australian national COVID-19 database, we describe how the epidemic and public health response unfolded in Australia up to 13 April 2020. We estimate that the effective reproduction number was likely below 1 (the threshold value for control) in each Australian state since mid-March and forecast that hospital ward and intensive care unit occupancy will remain below capacity thresholds over the next two weeks.

Modern data and computational resources, coupled with algorithmic and theoretical advances to exploit these, allow disease dynamic models to be parameterised with increasing detail and accuracy. While this enhances models' usefulness in prediction and policy, major challenges remain. In particular, lack of identifiability of a model's parameters may limit the usefulness of the model. While lack of parameter identifiability may be resolved through incorporation into an inference procedure of prior knowledge, formulating such knowledge is often difficult. Furthermore, there are practical challenges associated with acquiring data of sufficient quantity and quality. Here, we discuss recent progress on these issues.

During the early stages of an emerging disease outbreak, governments are required to make critical decisions on how to respond, despite limited data being available to inform these decisions. Analytical risk assessment is a valuable approach to guide decision-making on travel restrictions and border measures during the early phase of an outbreak. Here we describe a rapid risk assessment framework that was developed in February 2020 to support time-critical decisions on the risk of SARS-CoV-2 importation into Australia. We briefly describe the context in which our framework was developed, the framework itself, and provide an example of the type of decision support provided to the Australian government. We then report a critical evaluation of the modelling choices made in February 2020, assessing the impact of our assumptions on estimated rates of importation, and provide a summary of "lessons learned". The framework presented and evaluated here provides a flexible approach to rapid assessment of importation risk, of relevance to current and future pandemic scenarios.

BackgroundThe ability of global health systems to cope with increasing numbers of COVID-19 cases is of major concern. In readiness for this challenge, Australia has drawn on clinical pathway models developed over many years in preparation for influenza pandemics. These models have been used to estimate health care requirements for COVID-19 patients, in the context of broader public health measures.MethodsAn age and risk stratified transmission model of COVID-19 infection was used to simulate an unmitigated epidemic with parameter ranges reflecting uncertainty in current estimates of transmissibility and severity. Overlaid public health measures included case isolation and quarantine of contacts, and broadly applied social distancing. Clinical presentations and patient flows through the Australian health care system were simulated, including expansion of available intensive care capacity and alternative clinical assessment pathways.FindingsAn unmitigated COVID-19 epidemic would dramatically exceed the capacity of the Australian health system, over a prolonged period. Case isolation and contact quarantine alone will be insufficient to constrain case presentations within a feasible level of expansion of health sector capacity. Overlaid social restrictions will need to be applied at some level over the course of the epidemic to ensure that systems do not become overwhelmed, and that essential health sector functions, including care of COVID-19 patients, can be maintained. Attention to the full pathway of clinical care is needed to ensure access to critical care.InterpretationReducing COVID-19 morbidity and mortality will rely on a combination of measures to strengthen and extend public health and clinical capacity, along with reduction of overall infection transmission in the community. Ongoing attention to maintaining and strengthening the capacity of health care systems and workers to manage cases is needed.FundingAustralian Government Department of Health Office of Health Protection, Australian Government National Health and Medical Research Council

National influenza pandemic plans have evolved substantially over recent decades, as has the scientific research that underpins the advice contained within them. While the knowledge generated by many research activities has been directly incorporated into the current generation of pandemic plans, scientists and policymakers are yet to capitalise fully on the potential for near real-time analytics to formally contribute to epidemic decision-making. Theoretical studies demonstrate that it is now possible to make robust estimates of pandemic impact in the earliest stages of a pandemic using first few hundred household cohort (FFX) studies and algorithms designed specifically for analysing FFX data. Pandemic plans already recognise the importance of both situational awareness i.e., knowing pandemic impact and its key drivers, and the need for pandemic special studies and related analytic methods for estimating these drivers. An important next step is considering how information from these situational assessment activities can be integrated into the decision-making processes articulated in pandemic planning documents. Here we introduce a decision support tool that directly uses outputs from FFX algorithms to present recommendations on response options, including a quantification of uncertainty, to decision makers. We illustrate this approach using response information from within the Australian influenza pandemic plan.

Freya Shearer and co-authors discuss the use of decision analysis in planning for infectious disease pandemics.

Summary Background Substantial outbreaks of yellow fever in Angola and Brazil in the past 2 years, combined with global shortages in vaccine stockpiles, highlight a pressing need to assess present control strategies. The aims of this study were to estimate global yellow fever vaccination coverage from 1970 through to 2016 at high spatial resolution and to calculate the number of individuals still requiring vaccination to reach population coverage thresholds for outbreak prevention. Methods For this adjusted retrospective analysis, we compiled data from a range of sources (eg, WHO reports and health-service-provider registeries) reporting on yellow fever vaccination activities between May 1, 1939, and Oct 29, 2016. To account for uncertainty in how vaccine campaigns were targeted, we calculated three population coverage values to encompass alternative scenarios. We combined these data with demographic information and tracked vaccination coverage through time to estimate the proportion of the population who had ever received a yellow fever vaccine for each second level administrative division across countries at risk of yellow fever virus transmission from 1970 to 2016. Findings Overall, substantial increases in vaccine coverage have occurred since 1970, but notable gaps still exist in contemporary coverage within yellow fever risk zones. We estimate that between 393·7 million and 472·9 million people still require vaccination in areas at risk of yellow fever virus transmission to achieve the 80% population coverage threshold recommended by WHO; this represents between 43% and 52% of the population within yellow fever risk zones, compared with between 66% and 76% of the population who would have required vaccination in 1970. Interpretation Our results highlight important gaps in yellow fever vaccination coverage, can contribute to improved quantification of outbreak risk, and help to guide planning of future vaccination efforts and emergency stockpiling. Funding The Rhodes Trust, Bill & Melinda Gates Foundation, the Wellcome Trust, the National Library of Medicine of the National Institutes of Health, the European Union's Horizon 2020 research and innovation programme.

Dengue is a mosquito-borne viral infection that has spread throughout the tropical world over the past 60 years and now affects over half the world’s population. The geographical range of dengue is expected to further expand due to ongoing global phenomena including climate change and urbanization. We applied statistical mapping techniques to the most extensive database of case locations to date to predict global environmental suitability for the virus as of 2015. We then made use of climate, population and socioeconomic projections for the years 2020, 2050 and 2080 to project future changes in virus suitability and human population at risk. This study is the first to consider the spread of Aedes mosquito vectors to project dengue suitability. Our projections provide a key missing piece of evidence for the changing global threat of vector-borne disease and will help decision-makers worldwide to better prepare for and respond to future changes in dengue risk., SCOPUS: ar.j, info:eu-repo/semantics/published

Summary Background Routine childhood vaccination is among the most cost-effective, successful public health interventions available. Amid substantial investments to expand vaccine delivery throughout Africa and strengthen administrative reporting systems, most countries still require robust measures of local routine vaccine coverage and changes in geographical inequalities over time. Methods This analysis drew from 183 surveys done between 2000 and 2016, including data from 881 268 children in 49 African countries. We used a Bayesian geostatistical model calibrated to results from the Global Burden of Diseases, Injuries, and Risk Factors Study 2017, to produce annual estimates with high-spatial resolution (5 × 5 km) of diphtheria-pertussis-tetanus (DPT) vaccine coverage and dropout for children aged 12–23 months in 52 African countries from 2000 to 2016. Findings Estimated third-dose (DPT3) coverage increased in 72·3% (95% uncertainty interval [UI] 64·6–80·3) of second-level administrative units in Africa from 2000 to 2016, but substantial geographical inequalities in DPT coverage remained across and within African countries. In 2016, DPT3 coverage at the second administrative (ie, district) level varied by more than 25% in 29 of 52 countries, with only two (Morocco and Rwanda) of 52 countries meeting the Global Vaccine Action Plan target of 80% DPT3 coverage or higher in all second-level administrative units with high confidence (posterior probability ≥95%). Large areas of low DPT3 coverage (≤50%) were identified in the Sahel, Somalia, eastern Ethiopia, and in Angola. Low first-dose (DPT1) coverage (≤50%) and high relative dropout (≥30%) together drove low DPT3 coverage across the Sahel, Somalia, eastern Ethiopia, Guinea, and Angola. Interpretation Despite substantial progress in Africa, marked national and subnational inequalities in DPT coverage persist throughout the continent. These results can help identify areas of low coverage and vaccine delivery system vulnerabilities and can ultimately support more precise targeting of resources to improve vaccine coverage and health outcomes for African children. Funding Bill & Melinda Gates Foundation.

Initiation of antiretroviral therapy (ART) in early compared with chronic HIV infection is associated with a smaller HIV reservoir. This longitudinal analysis of 63 individuals who commenced ART during primary HIV infection (PHI) investigates which pre-and post-therapy factors associate most closely with reservoir size (HIV DNA) following treatment initiation during PHI. The best predictor of reservoir size at one-year was pre-ART HIV DNA which was in turn significantly associated with CD8 memory differentiation (effector memory, naïve and T-betnegEomesnegsubsets), CD8 T cell activation (CD38 expression) and PD-1 and Tim-3 expression on memory CD4 T cells. No associations were found for any immunological variables following one-year of ART. HIV reservoir size is determined around the time of ART initiation in individuals treated during PHI. CD8 T cell activation and memory expansion are linked to HIV reservoir size, suggesting the importance of the initial host-viral interplay in eventual reservoir size.

Despite palliative care being standard for patients with chronic and/or life-limiting conditions, a perceived lack of clarity regarding the definition and scope of palliative care persists. We aimed to identify health care professionals' (HCPs) perspectives, education, and support needs related to palliative care provision in a large private Australian tertiary hospital.A validated survey was administered and four focus groups were conducted with multidisciplinary HCPs.The survey response rate was 50% (n = 302). Although critical care HCPs scored symptom management and patient/family interaction items more highly compared with other HCPs, mean scores (4.0) for both groups indicated participants lacked confidence to perform this aspect of care independently. Critical care HCPs were more comfortable caring for dying patients (p 0.001) and talking to families about death (p 0.001). Ward HCPs were more supportive of early referral to palliative care (p 0.001). Cancer diagnoses were overestimated as common causes of death. Education needs focused on ethical issues, end-of-life communication skills, dealing with delirium, and use of the Liverpool Care Pathway. Key themes identified from the four focus groups were (1) delays or nonreferral to palliative care created considerable stress and feelings of inadequacy despite a perceived understanding of the broader definition of palliative care and (2) HCPs commonly focused on end-of-life care.Ambiguity regarding the meaning and delivery of palliative care persists in the acute care setting across disciplines. Results confirmed that innovative approaches to education and upskilling HCPs in palliative care and referral pathways is warranted.

The yellow fever virus (YFV) epidemic in Brazil is the largest in decades. The recent discovery of YFV in Brazilian Aedes species mosquitos highlights a need to monitor the risk of reestablishment of urban YFV transmission in the Americas. We use a suite of epidemiological, spatial, and genomic approaches to characterize YFV transmission. We show that the age and sex distribution of human cases is characteristic of sylvatic transmission. Analysis of YFV cases combined with genomes generated locally reveals an early phase of sylvatic YFV transmission and spatial expansion toward previously YFV-free areas, followed by a rise in viral spillover to humans in late 2016. Our results establish a framework for monitoring YFV transmission in real time that will contribute to a global strategy to eliminate future YFV epidemics., info:eu-repo/semantics/published

Snakebite envenoming is a frequently overlooked cause of mortality and morbidity. Data for snake ecology and existing snakebite interventions are scarce, limiting accurate burden estimation initiatives. Low global awareness stunts new interventions, adequate health resources, and available health care. Therefore, we aimed to synthesise currently available data to identify the most vulnerable populations at risk of snakebite, and where additional data to manage this global problem are needed.We assembled a list of snake species using WHO guidelines. Where relevant, we obtained expert opinion range (EOR) maps from WHO or the Clinical Toxinology Resources. We also obtained occurrence data for each snake species from a variety of websites, such as VertNet and iNaturalist, using the spocc R package (version 0.7.0). We removed duplicate occurrence data and categorised snakes into three groups: group A (no available EOR map or species occurrence records), group B (EOR map but5 species occurrence records), and group C (EOR map and ≥5 species occurrence records). For group C species, we did a multivariate environmental similarity analysis using the 2008 WHO EOR maps and newly available evidence. Using these data and the EOR maps, we produced contemporary range maps for medically important venomous snake species at a 5 × 5 km resolution. We subsequently triangulated these data with three health system metrics (antivenom availability, accessibility to urban centres, and the Healthcare Access and Quality [HAQ] Index) to identify the populations most vulnerable to snakebite morbidity and mortality.We provide a map showing the ranges of 278 snake species globally. Although about 6·85 billion people worldwide live within range of areas inhabited by snakes, about 146·70 million live within remote areas lacking quality health-care provisioning. Comparing opposite ends of the HAQ Index, 272·91 million individuals (65·25%) of the population within the lowest decile are at risk of exposure to any snake for which no effective therapy exists compared with 519·46 million individuals (27·79%) within the highest HAQ Index decile, showing a disproportionate coverage in reported antivenom availability. Antivenoms were available for 119 (43%) of 278 snake species evaluated by WHO, while globally 750·19 million (10·95%) of those living within snake ranges live more than 1 h from population centres. In total, we identify about 92·66 million people living within these vulnerable geographies, including many sub-Saharan countries, Indonesia, and other parts of southeast Asia.Identifying exact populations vulnerable to the most severe outcomes of snakebite envenoming at a subnational level is important for prioritising new data collection and collation, reinforcing envenoming treatment, existing health-care systems, and deploying currently available and future interventions. These maps can guide future research efforts on snakebite envenoming from both ecological and public health perspectives and better target future estimates of the burden of this neglected tropical disease.BillMelinda Gates Foundation.

International audience; The Zika crisis drew attention to the long-overlooked problem of arboviruses transmitted by Aedes mosquitoes in Africa. Yellow fever, dengue, chikungunya and Zika are poorly controlled in Africa and often go unrecognized. However, to combat these diseases, both in Africa and worldwide, it is crucial that this situation changes. Here, we review available data on the distribution of each disease in Africa, their Aedes vectors, transmission potential, and challenges and opportunities for Aedes control. Data on disease and vector ranges are sparse, and consequently maps of risk are uncertain. Issues such as genetic and ecological diversity, and opportunities for integration with malaria control, are primarily African; others such as ever-increasing urbanization, insecticide resistance and lack of evidence for most control-interventions reflect problems throughout the tropics. We identify key knowledge gaps and future research areas, and in particular, highlight the need to improve knowledge of the distributions of disease and major vectors, insecticide resistance, and to develop specific plans and capacity for arboviral disease surveillance, prevention and outbreak responses.

Objective The primary aim was to investigate staff experiences and attitudes towards palliative care provision in a public metropolitan ED. Methods Using a previously validated survey tool, data were collected from ED clinical staff using Likert-type, open-ended and dichotomous items asking about perceptions of palliative care and education needs. Comparisons were made between nursing and medical staff. Results Medical staff and nurses' perceptions of palliative care were similar, differing on only 10 of 37 (Likert) items. All staff reported confidence with symptom management, whereas medical staff felt more confident with decision-oriented communication and nurses were more supportive of nasogastric feeding. Staff were moderately accurate in determining the five most common causes of death. Four out of five conditions selected as appropriate for palliative care were cancer diagnoses. End-of-life communication and ethical issues were the two most frequently requested areas for further education. Conclusions Our study suggests that overall ED staff were confident regarding symptom management in palliative care. Cancer diagnoses were overrepresented in both the top five causes of death and conditions most appropriate for a palliative approach, suggesting that staff might underestimate the role of a palliative approach in non-cancer diagnoses. Areas suggested for further education include communication and ethical issues surrounding end-of-life care.

Objective Understanding the reasons patients decide to attend a particular acute care service, and their expectations of that service, is important in providing optimal patient care. The present study aimed to determine factors influencing patient decisions to attend a private Australian ED, an issue that has not been previously addressed in the literature. Methods Semi-structured face-to-face interviews with ED patients, purposively sampled to broadly reflect the departmental caseload and casemix. The two primary questions asked were: ‘Why did you choose to come to this emergency department?’ and ‘What are your general expectations of this emergency department visit?’. Interviews were audio recorded, transcribed verbatim, and then analysed using manifest and then latent content analysis techniques. Results All patients approached (n = 30) agreed to interview. Four key themes were identified: prior experience of the hospital, convenient location of the hospital, anticipated high-quality care and anticipated short wait times. Conclusions Patients chose to use the private ED because of prior experience, proximity, and an expectation they would be seen promptly and be provided with competent care.

Zika virus was discovered in Uganda in 1947 and is transmitted by Aedes mosquitoes, which also act as vectors for dengue and chikungunya viruses throughout much of the tropical world. In 2007, an outbreak in the Federated States of Micronesia sparked public health concern. In 2013, the virus began to spread across other parts of Oceania and in 2015, a large outbreak in Latin America began in Brazil. Possible associations with microcephaly and Guillain-Barré syndrome observed in this outbreak have raised concerns about continued global spread of Zika virus, prompting its declaration as a Public Health Emergency of International Concern by the World Health Organization. We conducted species distribution modelling to map environmental suitability for Zika. We show a large portion of tropical and sub-tropical regions globally have suitable environmental conditions with over 2.17 billion people inhabiting these areas. DOI: http://dx.doi.org/10.7554/eLife.15272.001, eLife digest Zika virus is transmitted between humans by mosquitoes. The majority of infections cause mild flu-like symptoms, but neurological complications in adults and infants have been found in recent outbreaks. Although it was discovered in Uganda in 1947, Zika only caused sporadic infections in humans until 2007, when it caused a large outbreak in the Federated States of Micronesia. The virus later spread across Oceania, was first reported in Brazil in 2015 and has since rapidly spread across Latin America. This has led many people to question how far it will continue to spread. There was therefore a need to define the areas where the virus could be transmitted, including the human populations that might be risk in these areas. Messina et al. have now mapped the areas that provide conditions that are highly suitable for the spread of the Zika virus. These areas occur in many tropical and sub-tropical regions around the globe. The largest areas of risk in the Americas lie in Brazil, Colombia and Venezuela. Although Zika has yet to be reported in the USA, a large portion of the southeast region from Texas through to Florida is highly suitable for transmission. Much of sub-Saharan Africa (where several sporadic cases have been reported since the 1950s) also presents an environment that is highly suitable for the Zika virus. While no cases have yet been reported in India, a large portion of the subcontinent is also suitable for Zika transmission. Over 2 billion people live in Zika-suitable areas globally, and in the Americas alone, over 5.4 million births occurred in 2015 within such areas. It is important, however, to recognize that not all individuals living in suitable areas will necessarily be exposed to Zika. We still lack a great deal of basic epidemiological information about Zika. More needs to be known about the species of mosquito that spreads the disease and how the Zika virus interacts with related viruses such as dengue. As such information becomes available and clinical cases become routinely diagnosed, the global evidence base will be strengthened, which will improve the accuracy of future maps. DOI: http://dx.doi.org/10.7554/eLife.15272.002

As the outbreak of Ebola virus disease (EVD) in West Africa is now contained, attention is turning from control to future outbreak prediction and prevention. Building on a previously published zoonotic niche map (Pigott et al., 2014), this study incorporates new human and animal occurrence data and expands upon the way in which potential bat EVD reservoir species are incorporated. This update demonstrates the potential for incorporating and updating data used to generate the predicted suitability map. A new data portal for sharing such maps is discussed. This output represents the most up-to-date estimate of the extent of EVD zoonotic risk in Africa. These maps can assist in strengthening surveillance and response capacity to contain viral haemorrhagic fevers.

Introduction To identify and measure paramedics’ perspectives and educational needs regarding palliative care provision, as well as their understanding of the common causes of death. Methods All St John Ambulance Western Australia paramedics were invited to complete a mixed methods qualitative and quantitative survey using a tool previously validated in studies involving other emergency care providers. Quantitative results are reported using descriptive statistics, while Likert-type scales were converted to ordinal variables and expressed as means +/- SD. Qualitative data was analysed using content analysis techniques and reported as themes. Results Completed surveys were returned by 29 paramedics. They considered palliative care to be strongly focussed on end-of-life care, symptom control and holistic care. The dominant educational needs identified were ethical issues, end-of-life communication and the use of structured patient care pathways. Cancer diagnoses were overrepresented as conditions considered most suitable for palliative care, compared with their frequency as a cause of death. Conditions often experienced in ambulance practice, such as heart failure, trauma and cardiac arrhythmias were overestimated in their frequency as causes of death. Conclusions Paramedics have a sound grasp of some important aspects of palliative care including symptom control and the holistic nature of the palliative approach. They did however tend to equate palliative care with that occurring in the terminal phase and saw it as being particularly applied to cancer diagnoses. Paramedic palliative care educational efforts should focus on ethical issues and end-of-life communication, as well as increasing understanding of the common causes of death and those where a palliative approach might be beneficial.

Dengue and chikungunya are increasing global public health concerns due to their rapid geographical spread and increasing disease burden. Knowledge of the contemporary distribution of their shared vectors, Aedes aegypti and Aedes albopictus remains incomplete and is complicated by an ongoing range expansion fuelled by increased global trade and travel. Mapping the global distribution of these vectors and the geographical determinants of their ranges is essential for public health planning. Here we compile the largest contemporary database for both species and pair it with relevant environmental variables predicting their global distribution. We show Aedes distributions to be the widest ever recorded; now extensive in all continents, including North America and Europe. These maps will help define the spatial limits of current autochthonous transmission of dengue and chikungunya viruses. It is only with this kind of rigorous entomological baseline that we can hope to project future health impacts of these viruses. DOI: http://dx.doi.org/10.7554/eLife.08347.001, eLife digest Mosquitoes spread many disease-causing viruses and parasites between people and other animals, including viral infections such as dengue and chikungunya. Both infections cause high fevers often accompanied with excruciating joint pain or other flu-like symptoms. Dengue and chikungunya have become growing public health problems over the last fifty years. Today about half of the world's population is at risk of dengue infection, while chikungunya outbreaks, which were previously limited to Africa and Asia, have recently been reported in the Caribbean, South America and Europe. The dengue and chikungunya viruses are transmitted between people by two species of mosquitoes called Aedes aegypti and Ae. albopictus. Therefore it is important to work out where these mosquito species are found around the globe to identify the areas at risk. It is also important to predict where these species could become established if they were introduced, in order to identify areas that could become at risk in the future. Kraemer et al. now provide updated predictions about the distribution of these two mosquito species around the globe. These predictions are based upon the most up-to-date data on the known locations of the species combined with information on environmental conditions across the globe. The updated maps show that these Aedes mosquitoes are now found across all continents, including North America and Europe. Aedes albopictus mosquitoes in particular are rapidly expanding their territory around the globe. Kraemer et al. used their new maps to show that, unlike in the United States, many of the areas in Europe and China that could support this mosquito species do not yet appear to have been colonized. These findings provide a map of the distribution of both species as it stands at the moment. Further work is now needed to better understand which factors are contributing to the rapid expansion of these mosquitoes' range and what might be done to control this spread. DOI: http://dx.doi.org/10.7554/eLife.08347.002