Early detection of emerging infectious diseases - implications for vaccine development.

Vast quantities of open-source data from news reports, social media and other sources can be harnessed using artificial intelligence and machine learning, and utilised to generate valid early warning signals of emerging epidemics. Early warning signals from open-source data are not a replacement for traditional, validated disease surveillance, but provide a trigger for earlier investigation and diagnostics. This may yield earlier pathogen characterisation and genomic data, which can enable earlier vaccine development or deployment of vaccines. Early warning also provides a more feasible prospect of stamping out epidemics before they spread. There are several of such systems currently, but they are not used widely in public health practice, and only some are publicly available. Routine and widespread use of open-source intelligence, as well as training and capacity building in digital surveillance, will improve pandemic preparedness and early response capability.

Estimated Mask Use and Temporal Relationship to COVID-19 Epidemiology of Black Lives Matter Protests in 12 Cities.

BACKGROUND: There is an increased risk of SARS-CoV-2 transmission during mass gatherings and a risk of asymptomatic infection. We aimed to estimate the use of masks during Black Lives Matter (BLM) protests and whether these protests increased the risk of COVID-19. Two reviewers screened 496 protest images for mask use, with high inter-rater reliability. Protest intensity, use of tear gas, government control measures, and testing rates were estimated in 12 cities. A correlation analysis was conducted to assess the potential effect of mask use and other measures, adjusting for testing rates, on COVID-19 epidemiology 4 weeks (two incubation periods) post-protests. Mask use ranged from 69 to 96% across protests. There was no increase in the incidence of COVID-19 post-protest in 11 cities. After adjusting for testing rates, only Miami, which involved use of tear gas and had high protest intensity, showed a clear increase in COVID-19 after one incubation period post-protest. No significant correlation was found between incidence and protest factors. Our study showed that protests in most cities studied did not increase COVID-19 incidence in 2020, and a high level of mask use was seen. The absence of an epidemic surge within two incubation periods of a protest is indicative that the protests did not have a major influence on epidemic activity, except in Miami. With the globally circulating highly transmissible Alpha, Delta, and Omicron variants, layered interventions such as mandated mask use, physical distancing, testing, and vaccination should be applied for mass gatherings in the future.

Factors associated with repeated influenza vaccine uptake among aged care staff in an Australian sample from 2017 to 2019.

BACKGROUND/AIM: Influenza vaccination is strongly recommended every year for aged care staff to protect themselves and minimise risk of transmission to residents. This study aimed to determine the factors associated with repeated annual influenza vaccine uptake among Australian aged care staff from 2017 to 2019. METHODS: Demographic, medical and vaccination data collected from the staff, who participated in an observational study from nine aged care facilities under a single provider in Sydney Australia, were analysed retrospectively. Based on the pattern of repeated influenza vaccination from 2017 to 2019, three groups were identified: (1) unvaccinated all three years; (2) vaccinated occasionally(once or twice) over three years; and (3)vaccinated all threeyears. Multinomial logistic regression analysis was performed to better understand the factors associated with the pattern of repeated influenza vaccination. RESULTS: From a total of 138 staff, between 2017 and 2019, 28.9 % (n = 40) never had a vaccination, while 44.2 % (n = 61) had vaccination occasionally and 26.8 % (n = 37) had vaccination all three years. In the multinomial logistic regression model, those who were<40 years old (OR = 0.57, 95 % CI: 0.19-0.90, p < 0.05) and those who were current smokers (OR = 0.20; 95 % CI: 0.03-0.76, p < 0.05) were less likely to have repeated vaccination for all three years compared to the unvaccinated group. Those who were<40 years old (OR = 0.61; 95 % CI: 0.22-0.68, p < 0.05) and those who were born overseas (OR = 0.50; 95 % CI:0.27-0.69, p < 0.05) were more likely to be vaccinated occasionally compared to the unvaccinated group. CONCLUSION: The significant predictors of repeated vaccine uptake across the three-year study period among aged care staff were age, smoking status and country of birth (Other vs Australia). Targeted interventions towards the younger age group (<40 years old), smokers and those who were born overseas could improve repeated influenza vaccination uptake in the aged care workforce.

Effectiveness estimates for enhanced trivalent influenza vaccines in an aged care summer outbreak.

An influenza outbreak occurred during summer (February 2019) in an aged-care facility in Sydney, Australia. Residents had not received the annual 2019 influenza vaccine while 76.7% had received 2018 influenza vaccines about 9 months prior. Overall, 2018 influenza vaccine effectiveness during this outbreak was high (93.6%). The effectiveness of the high-dose trivalent vaccine (HD-TIV) and adjuvanted trivalent (a-TIV) vaccine were 89.8% (95% confidence interval: 18.8%-98.7%) and 72.5% (95% confidence interval: -106.7%-96.3%) respectively. The differences in effectiveness between HD-TIV, a-TIV and SD-QIV, during the summer outbreak were not significant.

Policy Analysis for Prevention and Control of Influenza in Aged Care.

OBJECTIVE: This study aimed to analyze national influenza infection control policy documents within aged care settings by identifying the consistencies, inconsistencies, and gaps with the current evidence and by evaluating methodological quality. Aged care providers can use these findings to identify their policy documents' strengths and weaknesses. DESIGN: A quality and content analysis of national level policy documents. SETTING AND PARTICIPANTS: Aged care settings rely on national agencies' policy recommendations to control and prevent outbreaks. There is limited research on the effectiveness of control measures to prevent and treat influenza within aged care settings. Because of the complexities around aged care governance, the primary responsibility in developing a comprehensive facility-level, infection-prevention policy, falls to the providers. METHODS: The analysis was conducted using the (1) International Appraisal of Guidelines, Research and Evaluation assessment tool, containing 23 items across 6 domains; and the (2) Influenza Related Control Measures in Aged Care settings checklist, developed by the authors, with 82 recommendations covering: medical interventions, nonmedical interventions, and physical layout. RESULTS: There were 19 documents from 9 different high-income countries, with a moderately high methodological quality in general. The quality assessment's average score was 40.2% (95% CI 31.9%-44.7%). "Stakeholder involvement" ranked third, and "Editorial independence" and "Rigor of development" had the lowest average scores across all domains. The content analysis' average score was 37.2% (95% CI 10.5%-21.5%). The highest scoring document (59.1%) included term definitions, cited evidence for recommendations, and clear measurable instructions. "Physical Layout" had the least coverage and averaged 21.9% (95% CI 4.2%-37.5%), which shows a substantial gap in built environment recommendations. CONCLUSIONS AND IMPLICATIONS: Existing policy documents vary in their comprehensiveness. The higher scoring documents provide an ideal model for providers. The checklist tools can be used to assess and enhance documents. Further research on document end-user evaluation would be useful, as there is room for improvement in methodological quality and coverage of recommendation coverage, especially related to physical layout.

Influenza cases in nine aged care facilities in Sydney, Australia over a three-year surveillance period, 2018-2020.

BACKGROUND: Influenza outbreaks in aged care facilities are a major public health concern. In response to the severe 2017 influenza season in Australia, enhanced influenza vaccines were introduced from 2018 onwards for those over 65 and more emphasis was placed on improving vaccination rates among aged care staff. During the COVID-19 pandemic, these efforts were then further escalated to reduce the additional burden that influenza could pose to facilities. METHODS: An observational epidemiological study was conducted from 2018 to 2020 in nine Sydney (Australia) aged care facilities of the same provider. De-identified vaccination data and physical layout data were collected from participating facility managers from 2018 to 2020. Active surveillance of influenza-like illness was carried out from 2018 to 2020 influenza seasons. Correlation and Poisson regression analyses were carried out to explore the relationship between physical layout variables to occurrence of influenza cases. RESULTS: Influenza cases were low in 2018 and 2019, and there were no confirmed influenza cases identified in 2020. Vaccination rates increased among staff by 50.5% and residents by 16.8% over the three-year period of surveillance from 2018 to 2020. For each unit increase in total number of beds, common areas, single rooms, all types of rooms (including double occupancy rooms), the influenza cases increased by 1.02 (95% confidence interval:1.018-1.025), 1.04 (95% confidence interval: 1.019-1.073), 1.03 (95% confidence interval: 1.016-1 0.038) and 1.02 (95% confidence interval:1.005-1.026) times which were found to be statistically significant. For each unit increase in the proportion of shared rooms, influenza cases increased by 1.004 (95% confidence interval:1.0001-1.207) which was found to be statistically significant. CONCLUSIONS: There is a relationship between influenza case counts and aspects of the physical layout such as facility size, and this should be considered in assessing risk of outbreaks in aged care facilities. Increased vaccination rates in staff and COVID-19 prevention and control measures may have eliminated influenza in the studied facilities in 2020.

Factors Associated With SARS-CoV-2 Attack Rates in Aged Care-A Meta-analysis.

BACKGROUND: The coronavirus disease 2019 (COVID-19) pandemic has resulted in significant morbidity and mortality in aged-care facilities worldwide. The attention of infection control in aged care needs to shift towards the built environment, especially in relation to using the existing space to allow social distancing and isolation. Physical infrastructure of aged care facilities has been shown to present challenges to the implementation of isolation procedures. To explore the relationship of the physical layout of aged care facilities with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) attack rates among residents, a meta-analysis was conducted. METHODS: Using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis Protocol (PRISMA-P), studies were identified from 5 databases using a registered search strategy with PROSPERO. Meta-analysis for pooled attack rates of SARS-CoV-2 in residents and staff was conducted, with subgroup analysis for physical layout variables such as total number of beds, single rooms, number of floors, number of buildings in the facility, and staff per 100 beds. RESULTS: We included 41 articles across 11 countries, reporting on 90 657 residents and 6521 staff in 757 facilities. The overall pooled attack rate was 42.0% among residents (95% CI, 38.0%-47.0%) and 21.7% in staff (95% CI, 15.0%-28.4%). Attack rates in residents were significantly higher in single-site facilities with standalone buildings than facilities with smaller, detached buildings. Staff-to-bed ratio significantly explains some of the heterogeneity of the attack rate between studies. CONCLUSIONS: The design of aged care facilities should be smaller in size, with adequate space for social distancing.

Pacific Eclipse - A tabletop exercise on smallpox pandemic response.

BACKGROUND: In December 2019, we ran Pacific Eclipse, a pandemic tabletop exercise using smallpox originating in Fiji as a case study. Pacific Eclipse brought together international stakeholders from health, defence, law enforcement, emergency management and a range of other organisations. AIM: To review potential gaps in preparedness and identify modifiable factors which could prevent a pandemic or mitigate the impact of a pandemic. METHODS: Pacific Eclipse was held on December 9-10 in Washington DC, Phoenix and Honolulu simultaneously. The scenario began in Fiji and becomes a pandemic. Mathematical modelling of smallpox transmission was used to simulate the epidemic under different conditions and to test the effect of interventions. Live polling, using Poll Everywhere software that participants downloaded onto their smart phones, was used to gather participant decisions as the scenario unfolded. Stakeholders from state and federal government and non-government organisations from The United States, The United Kingdom, Australia, New Zealand, Canada, as well as industry and non-government organisations attended. RESULTS: The scenario progressed in three phases and participants were able to make decisions during each phase using live polling. The polling showed very diverse and sometimes conflicting decision making. Factors influential to pandemic severity were identified and categorised as modifiable or unmodifiable. A series of recommendations were made on the modifiable determinants of pandemic severity and how these can be incorporated into pandemic planning. These included preventing an attack through intelligence, law enforcement and legislation, improved speed of diagnosis, speed and completeness of case finding and case isolation, speed and security of vaccination response (including stockpiling), speed and completeness of contact tracing, protecting critical infrastructure and business continuity, non-pharmaceutical interventions (social distancing, PPE, border control) and protecting first responders. DISCUSSION: Pacific Eclipse illustrated the impact of a pandemic of smallpox under different response scenarios, which were validated to some extent by the COVID-19 pandemic. The framework developed from the scenario draws out modifiable determinants of pandemic severity which can inform pandemic planning for the ongoing COVID-19 pandemic and for future pandemics.

Voxelisation Algorithms and Data Structures: A Review.

Voxel-based data structures, algorithms, frameworks, and interfaces have been used in computer graphics and many other applications for decades. There is a general necessity to seek adequate digital representations, such as voxels, that would secure unified data structures, multi-resolution options, robust validation procedures and flexible algorithms for different 3D tasks. In this review, we evaluate the most common properties and algorithms for voxelisation of 2D and 3D objects. Thus, many voxelisation algorithms and their characteristics are presented targeting points, lines, triangles, surfaces and solids as geometric primitives. For lines, we identify three groups of algorithms, where the first two achieve different voxelisation connectivity, while the third one presents voxelisation of curves. We can say that surface voxelisation is a more desired voxelisation type compared to solid voxelisation, as it can be achieved faster and requires less memory if voxels are stored in a sparse way. At the same time, we evaluate in the paper the available voxel data structures. We split all data structures into static and dynamic grids considering the frequency to update a data structure. Static grids are dominated by SVO-based data structures focusing on memory footprint reduction and attributes preservation, where SVDAG and SSVDAG are the most advanced methods. The state-of-the-art dynamic voxel data structure is NanoVDB which is superior to the rest in terms of speed as well as support for out-of-core processing and data management, which is the key to handling large dynamically changing scenes. Overall, we can say that this is the first review evaluating the available voxelisation algorithms for different geometric primitives as well as voxel data structures.

Substitution, delegation or addition? Implications of workforce skill mix on efficiency and interruptions in computed tomography.

Objectives This study evaluated multiple computed tomography (CT) workforce models to identify any implications on efficiency (length of stay, scan frequency and workforce cost) and scanning radiographer interruptions through substituting or supplementing with a trained CT assistant. Methods The study was conducted in a CT unit of a tertiary Queensland hospital and prospectively compared four workforce models, including usual practice: Model 1 used an administrative assistant (AA) and one radiographer; Model 2 substituted a medical imaging assistant (MIA) for the AA; Model 3 was usual practice, consisting of two radiographers; and Model 4 included two radiographers, with a supplemented MIA. Observational data were collected over 7 days per model and were cross-checked against electronic records. Data for interruption type and frequency, as well as scan type and duration, were collected. Annual workforce costs were calculated as measures of efficiency. Results Similar scan frequency and parameters (complexity) occurred across all models, averaging 164 scans (interquartile range 160-172 scans) each. The median times from patient arrival to examination completion in Models 1-4 were 47, 35, 46 and 33min respectively. There were between 34 and 104 interruptions per day across all models, with the 'assistant role' fielding the largest proportion. Model 4 demonstrated the highest workforce cost, and Model 2 the lowest. Conclusion This study demonstrated that assistant models offer similar patient throughput to usual practice at a reduced cost. Model 2 was the most efficient of all two-staff models (Models 1-3), offering the cheapest workforce, slightly higher throughput and faster examination times. Not surprisingly, the additional staff model (Model 4) offered greater overall examination times and throughput, with fewer interruptions, although workforce cost and possible role ambiguity were both limitations of this model. These findings may assist decision makers in selecting the optimal workforce design for their own individual contexts. What is known about the topic? Innovative solutions are required to address ongoing health workforce sustainability concerns. Workforce substitution models using trained assistants have demonstrated numerous benefits internationally, with translation to the Australian allied health setting showing promise. What does this paper add? Building on existing research, this study provides clinical workforce alternatives that maintain patient throughput while offering cost efficiencies. This study also quantified the many daily interruptions that occur within the CT setting, highlighting a potential clinical risk. To the best of our knowledge, this study is the first to empirically test the use of allied health assistants within CT. What are the implications for practitioners? Role substitution in CT may offer solutions to skills shortages, increasing expenditure and service demand. Incorporating appropriate assistant workforce models can maintain throughput while demonstrating implications for efficiency and interruptions, potentially affecting staff stress and burnout. In addition, the assistant's scope and accepted level of interruptions should be considerations when choosing the most appropriate model.

The potential impact of a recent measles epidemic on COVID-19 in Samoa.

BACKGROUND: The pandemic of COVID-19 has occurred close on the heels of a global resurgence of measles. In 2019, an unprecedented epidemic of measles affected Samoa, requiring a state of emergency to be declared. Measles causes an immune amnesia which can persist for over 2 years after acute infection and increases the risk of a range of other infections. METHODS: We modelled the potential impact of measles-induced immune amnesia on a COVID-19 epidemic in Samoa using data on measles incidence in 2018-2019, population data and a hypothetical COVID-19 epidemic. RESULTS: The young population structure and contact matrix in Samoa results in the most transmission occurring in young people < 20 years old. The highest rate of death is the 60+ years old, but a smaller peak in death may occur in younger people, with more than 15% of total deaths in the age group under 20 years old. Measles induced immune amnesia could increase the total number of cases by 8% and deaths by more than 2%. CONCLUSIONS: Samoa, which had large measles epidemics in 2019-2020 should focus on rapidly achieving high rates of measles vaccination and enhanced surveillance for COVID-19, as the impact may be more severe due to measles-induced immune paresis. This applies to other severely measles-affected countries in the Pacific, Europe and elsewhere.

The effectiveness of full and partial travel bans against COVID-19 spread in Australia for travellers from China during and after the epidemic peak in China.

BACKGROUND: Australia implemented a travel ban on China on 1 February 2020, while COVID-19 was largely localized to China. We modelled three scenarios to test the impact of travel bans on epidemic control. Scenario one was no ban; scenario two and three were the current ban followed by a full or partial lifting (allow over 100 000 university students to enter Australia, but not tourists) from the 8th of March 2020. METHODS: We used disease incidence data from China and air travel passenger movements between China and Australia during and after the epidemic peak in China, derived from incoming passenger arrival cards. We used the estimated incidence of disease in China, using data on expected proportion of under-ascertainment of cases and an age-specific deterministic model to model the epidemic in each scenario. RESULTS: The modelled epidemic with the full ban fitted the observed incidence of cases well, predicting 57 cases on March 6th in Australia, compared to 66 observed on this date; however, we did not account for imported cases from other countries. The modelled impact without a travel ban results in more than 2000 cases and about 400 deaths, if the epidemic remained localized to China and no importations from other countries occurred. The full travel ban reduced cases by about 86%, while the impact of a partial lifting of the ban is minimal and may be a policy option. CONCLUSIONS: Travel restrictions were highly effective for containing the COVID-19 epidemic in Australia during the epidemic peak in China and averted a much larger epidemic at a time when COVID-19 was largely localized to China. This research demonstrates the effectiveness of travel bans applied to countries with high disease incidence. This research can inform decisions on placing or lifting travel bans as a control measure for the COVID-19 epidemic.

The Sun Herald Sydney City-2-Surf Fun Run - Historical Injury Patterns and Factors Influencing Injury Type and Frequency.

INTRODUCTION: The Sydney City-2-Surf (Australia) fun run is the world's largest annual run entered by around 80,000 people. First aid planning at mass-participation running events such as the City-2-Surf is an area in the medical literature that has received little attention. Consequently, first aid planning for these events is based on experience rather than evidence. The models for predicting casualties that currently exist in the literature are either dated or not statistically significant. AIM: The aim of this study was to characterize patterns of injuries linked to geographic location across the course of the City-2-Surf, and to explore relationships of injury types with location and meteorological conditions. METHODS: Records for formally treated casualties and meteorological conditions were obtained for the race years 2010-2016 and statistically analyzed to find associations between meteorological conditions, geographic conditions, casualty types, and location. RESULTS: The most common casualties encountered were heat exhaustion or hyperthermia (39.2%), musculoskeletal (25.4%), and physical exhaustion (10.2%). Associations were found between gradient and the location. Type of casualty incidence with the individual distribution trends of casualty types were quite clear. Clusters of musculoskeletal casualties emerged in the parts of the course with the steepest negative gradients, while a cluster of cardiovascular events was found to occur at the top of the "heartbreak hill," the longest climb of the race. Regression analysis highlighted the linear relationship between the number of heat and physical exhaustion casualties and the apparent temperature (AT) at 12:00pm (R2 = 0.59; P = .044). This linear equation was used to formulate a model to predict these casualties. CONCLUSION: The findings of this study demonstrate the relationship between meteorological conditions, geographic conditions, and casualties. This will assist planners of other similar events to determine optimum allocation of resources to anticipated injury and illness burden.

Translation of Real-Time Infectious Disease Modeling into Routine Public Health Practice.

Infectious disease dynamic modeling can support outbreak emergency responses. We conducted a workshop to canvas the needs of stakeholders in Australia for practical, real-time modeling tools for infectious disease emergencies. The workshop was attended by 29 participants who represented government, defense, general practice, and academia stakeholders. We found that modeling is underused in Australia and its potential is poorly understood by practitioners involved in epidemic responses. The development of better modeling tools is desired. Ideal modeling tools for operational use would be easy to use, clearly indicate underlying parameterization and assumptions, and assist with policy and decision making.

Does Zika Virus Cause Microcephaly - Applying the Bradford Hill Viewpoints.

INTRODUCTION: Zika virus has been documented since 1952, but been associated with mild, self-limiting disease. Zika virus is classified as an arbovirus from a family of Flaviviridae and primarily spread by Aedes Aegypti mosquitos. However, in a large outbreak in Brazil in 2015, Zika virus has been associated with microcephaly. METHODS: In this review we applied the Bradford-Hill viewpoints  to investigate the association between Zika virus and microcephaly. We examined historical studies, available data and also compared historical rates of microcephaly prior to the Zika virus outbreak. The available evidence was reviewed against the Bradford Hill viewpoints. RESULTS: All  the nine criteria were met to varying degrees: strength of association, consistency of the association, specificity, temporality, plausibility, coherence, experimental evidence, biological gradient and analogy. Conclusion: Using the Bradford Hill Viewpoints as an evaluation framework for causation is highly suggestive that the association between Zika virus and microcephaly is causal. Further studies using animal models on the viewpoints which were not as strongly fulfilled would be helpful.

Haemorrhage-evoked decompensation and recompensation mediated by distinct projections from rostral and caudal midline medulla in the rat.

The haemodynamic response to blood loss consists of three phases: (i) an initial compensatory phase during which resting arterial pressure is maintained; (ii) a decompensatory phase characterized by a sudden, life-threatening hypotension and bradycardia; and (iii) if blood loss ceases, a recompensatory phase during which arterial pressure returns to normal. Previous research indicates that topographically distinct, rostral and caudal parts of the caudal midline medulla (CMM) contain neurons that differentially regulate the timing and magnitude of each of the three phases. Specifically, decompensation depends critically on the integrity of the rostral CMM; whereas compensation and recompensation depend upon the integrity of the caudal CMM. This study aimed to determine, using retrograde and anterograde tracing techniques, if the rostral and caudal CMM gave rise to different sets of projections to the major cardiovascular region of the ventrolateral medulla (VLM) and spinal cord. It was found that rostral and caudal CMM each have projections of varying density to the region containing bulbospinal (presympathetic) motor neurons in the rostral VLM and preganglionic sympathetic motor neurons in the intermediolateral cell column of the spinal cord. Via these projections vasomotor tone and hence arterial pressure can be regulated. More strikingly: (i) consistent with a role in mediating bradycardia during decompensation, the rostral CMM projects uniquely to VLM regions containing vagal cardiac motor neurons; and (ii) consistent with its role in mediating recompensation, the caudal CMM projects uniquely onto tyrosine hydroxylase-containing, caudal VLM (A1) neurons whose activity mediates vasopressin release, on which recompensation depends.