Medicine (RMH) - Research Publications
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ItemNo Preview AvailableModelling the Economic Impacts of Epidemics in Developing Countries Under Alternative Intervention Strategies(Springer, 2020)Modern levels of global travel have intensified the risk of new infectious diseases becoming pandemics. Particularly at risk are developing countries whose health systems may be less well equipped to detect quickly and respond effectively to the importation of new infectious diseases. This chapter examines what might have been the economic consequences if the 2014 West African Ebola epidemic had been imported to a small Asia-Pacific country. Hypothetical outbreaks in two countries were modelled. The post-importation estimations were carried out with two linked models: a stochastic disease transmission (SEIR) model and a quarterly version of the multi-country GTAP model, GTAP-Q. The SEIR model provided daily estimates of the number of persons in various disease states. For each intervention strategy the stochastic disease model was run 500 times to obtain the probability distribution of disease outcomes. Typical daily country outcomes for both controlled and uncontrolled outbreaks under five alternative intervention strategies were converted to quarterly disease-state results, which in turn were used in the estimation of GTAP-Q shocks to country-specific health costs and labour productivity during the outbreak, and permanent reductions in each country’s population and labour force due to mortality. Estimated behavioural consequences (severe reductions in international tourism and crowd avoidance) formed further shocks. The GTAP-Q simulations revealed very large economic costs for each country if they experienced an uncontrolled Ebola outbreak, and considerable economic costs for controlled outbreaks in Fiji due to the importance of the tourism sector to its economy. A major finding was that purely reactive strategies had virtually no effect on preventing uncontrolled outbreaks, but pre-emptive strategies substantially reduced the proportion of uncontrolled outbreaks, and in turn the economic and social costs.
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ItemIs Nigeria really on top of COVID-19? Message from effective reproduction number( 2020)Following the importation of Covid-19 into Nigeria on the 27 February 2020 and then the outbreak, the question is: how do we anticipate the progression of the ongoing epidemics following all the intervention measures put in place? This kind of question is appropriate for public health responses and it will depend on the early estimates of the key epidemiological parameters of the virus in a defined population. In this study, we combined a likelihood-based method using a Bayesian framework and compartmental model of the epidemic of Covid-19 in Nigeria to estimate the effective reproduction number (R(t)) and basic reproduction number (R_0). This also enables us to estimate the daily transmission rate (β) that determines the effect of social distancing. We further estimate the reported fraction of symptomatic cases. The models are applied to the NCDC data on Covid-19 symptomatic and death cases from 27 February 2020 and 7 May 2020. In this period, the effective reproduction number is estimated with a minimum value of 0.18 and a maximum value of 1.78. Most importantly, the R(t) is strictly greater than one from April 13 till 7 May 2020. The R_0 is estimated to be 2.42 with credible interval: (2.37, 2.47). Comparing this with the R(t) shows that control measures are working but not effective enough to keep R(t) below one. Also, the estimated fractional reported symptomatic cases are between 10 to 50%. Our analysis has shown evidence that the existing control measures are not enough to end the epidemic and more stringent measures are needed.
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ItemFlattening the curve is not enough, we need to squash it: An explainer using a simple model( 2020)
Background
Around the world there are examples of both effective control (e.g., South Korea, Japan) and less successful control (e.g., Italy, Spain, United States) of COVID-19 with dramatic differences in the consequent epidemic curves. Models agree that flattening the curve without controlling the epidemic completely is insufficient and will lead to an overwhelmed health service. A recent model, calibrated for the UK and US, demonstrated this starkly.Methods
We used a simple compartmental deterministic model of COVID-19 transmission in Australia, to illustrate the dynamics resulting from shifting or flattening the curve versus completely squashing it.Results
We find that when the reproduction number is close to one, a small decrease in transmission leads to a large reduction in burden (i.e., cases, deaths and hospitalisations), but achieving this early in the epidemic through social distancing interventions also implies that the community will not reach herd immunity.Conclusions
Australia needs not just to shift and flatten the curve, but to squash it by getting the reproduction number below one. This will require Australia to achieve transmission rates at least two thirds lower than those seen in the most severely affected countries.The known
COVID-19 has been diagnosed in over 4,000 Australians. Up until mid-March, most were from international travel, but now we are seeing a rise in locally acquired cases.The new
This study uses a simple transmission dynamic model to demonstrate the difference between moderate changes to the reproduction number and forcing the reproduction number below one.The implications
Lowering local transmission is becoming important in reducing the transmission of COVID-19. To maintain control of the epidemic, the focus should be on those in the community who do not regard themselves as at risk. -
ItemNo Preview AvailableModelling insights into the COVID-19 pandemic(ELSEVIER SCI LTD, 2020-09-01)Coronavirus disease 2019 (COVID-19) is a newly emerged infectious disease caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that was declared a pandemic by the World Health Organization on 11th March, 2020. Response to this ongoing pandemic requires extensive collaboration across the scientific community in an attempt to contain its impact and limit further transmission. Mathematical modelling has been at the forefront of these response efforts by: (1) providing initial estimates of the SARS-CoV-2 reproduction rate, R0 (of approximately 2-3); (2) updating these estimates following the implementation of various interventions (with significantly reduced, often sub-critical, transmission rates); (3) assessing the potential for global spread before significant case numbers had been reported internationally; and (4) quantifying the expected disease severity and burden of COVID-19, indicating that the likely true infection rate is often orders of magnitude greater than estimates based on confirmed case counts alone. In this review, we highlight the critical role played by mathematical modelling to understand COVID-19 thus far, the challenges posed by data availability and uncertainty, and the continuing utility of modelling-based approaches to guide decision making and inform the public health response. †Unless otherwise stated, all bracketed error margins correspond to the 95% credible interval (CrI) for reported estimates.
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ItemNo Preview AvailableRole of modelling in COVID-19 policy development(ELSEVIER SCI LTD, 2020-09-01)Models have played an important role in policy development to address the COVID-19 outbreak from its emergence in China to the current global pandemic. Early projections of international spread influenced travel restrictions and border closures. Model projections based on the virus's infectiousness demonstrated its pandemic potential, which guided the global response to and prepared countries for increases in hospitalisations and deaths. Tracking the impact of distancing and movement policies and behaviour changes has been critical in evaluating these decisions. Models have provided insights into the epidemiological differences between higher and lower income countries, as well as vulnerable population groups within countries to help design fit-for-purpose policies. Economic evaluation and policies have combined epidemic models and traditional economic models to address the economic consequences of COVID-19, which have informed policy calls for easing restrictions. Social contact and mobility models have allowed evaluation of the pathways to safely relax mobility restrictions and distancing measures. Finally, models can consider future end-game scenarios, including how suppression can be achieved and the impact of different vaccination strategies.
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ItemNo Preview AvailableOn the probability of strain invasion in endemic settings: Accounting for individual heterogeneity and control in multi-strain dynamics(ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD, 2020-02-21)Pathogen evolution is an imminent threat to global health that has warranted, and duly received, considerable attention within the medical, microbiological and modelling communities. Outbreaks of new pathogens are often ignited by the emergence and transmission of mutant variants descended from wild-type strains circulating in the community. In this work we investigate the stochastic dynamics of the emergence of a novel disease strain, introduced into a population in which it must compete with an existing endemic strain. In analogy with past work on single-strain epidemic outbreaks, we apply a branching process approximation to calculate the probability that the new strain becomes established. As expected, a critical determinant of the survival prospects of any invading strain is the magnitude of its reproduction number relative to that of the background endemic strain. Whilst in most circumstances this ratio must exceed unity in order for invasion to be viable, we show that differential control scenarios can lead to less-fit novel strains invading populations hosting a fitter endemic one. This analysis and the accompanying findings will inform our understanding of the mechanisms that have led to past instances of successful strain invasion, and provide valuable lessons for thwarting future drug-resistant strain incursions.
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ItemNo Preview AvailableModelling the impact of COVID-19 on intensive care services in New South Wales(WILEY, 2020-05-08)
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ItemStepping out of lockdown should start with school re-openings while maintaining distancing measures. Insights from mixing matrices and mathematical models.(Cold Spring Harbor Laboratory, 2020)Australia is one of a few countries which has managed to control COVID-19 epidemic before a major epidemic took place. Currently with just under 7000 cases and 100 deaths, Australia is seeing less than 20 new cases per day. This is a positive outcome, but makes estimation of current effective reproduction numbers difficult to estimate. Australia, like much of the world is poised to step out of lockdown and looking at which measures to relax first. We use age-based contact matrices, calibrated to Chinese data on reproduction numbers and difference in infectiousness and susceptibility of children to generate next generation matrices (NGMs) for Australia. These matrices have a spectral radius of 2.49, which is hence our estimated basic reproduction number for Australia. The effective reproduction number (Reff) for Australia during the April/May lockdown period is estimated by other means to be around 0.8. We simulate the impact of lockdown on the NGM by first applying observations through Google Mobility Report for Australia at 3 locations: home (increased contacts by 18%), work (reduced contacts by 34%) and other (reduced contacts by 40%), and we reduce schools to 3% reflecting attendance rates during lockdown. Applying macro-distancing to the NGM leads to a spectral radius of 1.76. We estimate that the further reduction of the reproduction number to current levels of Reff = 0.8 is achieved by a micro-distancing factor of 0.26. That is, in a given location, people are 26% as likely as usual to have an effective contact with another person. We apply both macro and micro-distancing to the NGMs to examine the impact of different exit strategies. We find that reopening schools is estimated to reduce Reff from 0.8 to 0.78. This is because increase in school contact is offset by decrease in home contact. The NGMs all estimate that adults aged 30-50 are responsible for the majority of transmission. We also find that micro-distancing is critically important to maintain Reff <1. There is considerable uncertainty in these estimates and a sensitivity and uncertainty analysis is presented.
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ItemThe value of early transmission dynamic studies in emerging infectious diseases(ELSEVIER SCI LTD, 2020-05-01)
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ItemEvaluation of the malaria reporting system supported by the District Health Information System 2 in Solomon Islands(BMC, 2020-10-17)BACKGROUND: District Health Information Systems 2 (DHIS2) is used for supporting health information management in 67 countries, including Solomon Islands. However, there have been few published evaluations of the performance of DHIS2-enhanced disease reporting systems, in particular for monitoring infectious diseases such as malaria. The aim of this study was to evaluate DHIS2 supported malaria reporting in Solomon Islands and to develop recommendations for improving the system. METHODS: The evaluation was conducted in three administrative areas of Solomon Islands: Honoria City Council, and Malaita and Guadalcanal Provinces. Records of nine malaria indicators including report submission date, total malaria cases, Plasmodium falciparum case record, Plasmodium vivax case record, clinical malaria, malaria diagnosed with microscopy, malaria diagnosed with (rapid diagnostic test) (RDT), record of drug stocks and records of RDT stocks from 1st January to 31st December 2016 were extracted from the DHIS2 database. The indicators permitted assessment in four core areas: availability, completeness, timeliness and reliability. To explore perceptions and point of view of the stakeholders on the performance of the malaria case reporting system, focus group discussions were conducted with health centre nurses, whilst in-depth interviews were conducted with stakeholder representatives from government (province and national) staff and World Health Organization officials who were users of DHIS2. RESULTS: Data were extracted from nine health centres in Honoria City Council and 64 health centres in Malaita Province. The completeness and timeliness from the two provinces of all nine indicators were 28.2% and 5.1%, respectively. The most reliable indicator in DHIS2 was 'clinical malaria' (i.e. numbers of clinically diagnosed malaria cases) with 62.4% reliability. Challenges to completeness were a lack of supervision, limited feedback, high workload, and a lack of training and refresher courses. Health centres located in geographically remote areas, a lack of regular transport, high workload and too many variables in the reporting forms led to delays in timely reporting. Reliability of reports was impacted by a lack of technical professionals such as statisticians and unavailability of tally sheets and reporting forms. CONCLUSION: The availability, completeness, timeliness and reliability of nine malaria indicators collected in DHIS2 were variable within the study area, but generally low. Continued onsite support, supervision, feedback and additional enhancements, such as electronic reporting will be required to further improve the malaria reporting system.