AITHM James Cook University

COVID-19 research is moving as fast as the pandemic itself. We are now rewriting the rulebook for much of the way we do things in our daily lives. For scientists, we have always relied on the peer-review process to keep work as accurate and high-quality as possible. However, in the current environment the process is too slow.

My group is writing important analyses of COVID-19, with an Australian perspective, which may be very valuable right now, but have limited value in one month, after peer review is completed. We have also read about the frustration with the government “black-boxing” its models. We at AITHM have therefore decided to make all our preprints publically available on this site (see below).

Emma McBryde
MB BS, MBios, FRACP, PhD
Professor of Infectious Diseases Modelling and Epidemiology
Australian Institute of Tropical Health and Medicine
James Cook University, Townsville, Australia

Reports:

13th May - Stepping out of lockdown should start with schools re-opening while maintaining social distancing measures

13th May - Supporting online materials: Developing next generation matrices from existing data

7th May - Employee presenteeism  and occupational acquisition of COVID-19

14th April - Estimating the case detection rate and temporal variation in transmission of COVID-19 in Aus

11th April - Researchers warn Nigerians to practice "physical" distancing this Easter period

6th April - Plain English explainer about the explainer

30th March - Flattening the curve is not enough, we need to squash it:an explainer using a simple model

30th March - Modelling the impact of COVID-19 upon intensive care services in New South Wales

27th March - Economic consequences of the COVID-19 outbreak: the need for epidemic preparedness

24th March - Delaying the epidemic in Australia: Evaluating the effectiveness of international travel bans

15th March - Change in outbreak epicenter and its impact on the importation risks: a modelling study

11th March - The value of early transmission dynamic studies in emerging infectious diseases

Webinars:
21st April 2020 - COVID-19: Exit Strategies with Dr Diana Rojas Alvarez & Prof Emma McBryde

Stepping out of lockdown should start with school re-openings while maintaining distancing measures. Insights from mixing matrices and mathematical models

13th May 2020

Authors: Emma S McBryde1, James M Trauer2, Adeshina Adekunle1, Romain Ragonnet2, Michael T Meehan1

1 Australian Tropical Health and Medicine, James Cook University
2 Monash University

Abstract:

Australia is one of a few countries which has managed to control its first COVID-19 epidemic. Australia is seeing less than 20 new cases per day in May 2020. This is a positive outcome but makes estimation of current effective reproduction numbers difficult. 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 and school attendances. 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.

See full report here

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Supporting online materials

Developing next generation matrices from existing data

13th May 2020

The estimates of transmission rates in each sector (i.e., home, school, work and other locations) and the overall reproduction number are derived from baseline estimates of the daily, age-specific contact rates between individuals of different age groups. These contact rates are provided by the analysis in Prem et al.(1) where data from population-based contact diaries in eight European countries were projected to generate contact intensities for 144 other countries using Bayesian modelling techniques. The inferred values π‘π‘Žπ‘Ž′ give the number of (pre-COVID-19) typical daily contacts an individual of age π‘Ž′ makes with an individual of age π‘Ž. In the dataset, age bands are separated into 5 year age groups and contacts are further divided into four locations: work, home, school and other.


To estimate the transmission capacity associated with these contacts we convert the contact intensity matrices to next-generation matrices, 𝐾, whose elements, π‘˜π‘Žπ‘Ž′, give the number of new infections of age π‘Ž generated by individuals of age π‘Ž′. As a first step, we compute an unscaled next-generation matrix 𝐾̅ by weighting the elements of the contact matrix π‘π‘Žπ‘Ž′ by the age-dependent relative susceptibility (πœŽπ‘Ž) and infectivity (π›½π‘Ž) of individuals in the population and the distribution of susceptible (π‘ π‘Ž) and total (π‘›π‘Ž) individuals in each age group. In particular, the elements, π‘˜Μ…
π‘Žπ‘Ž′, of the unscaled next-generation matrix (NGM), 𝐾̅, are given by

π‘˜Μ…π‘Žπ‘Ž′=πœŽπ‘Žπ‘ π‘Žπ‘π‘Žπ‘Ž′π›½π‘Ž′π‘›π‘Ž′.

Here πœŽπ‘Ž is the relative susceptibility to infection for an individual in age group π‘Ž and π›½π‘Ž is their corresponding transmissibility once infected. Since the population is entirely susceptible upon first introduction of the infection such that π‘ π‘Ž=π‘›π‘Ž.

For symmetry, we assume that the age-dependent susceptibility and transmissibility profiles are equal equivalent, i.e., πœŽπ‘Ž=π›½π‘Ž, and are given by the following parametric equation:

πœŽπ‘Ž=1−𝜎rel2tanh(𝑏(π‘Ž−𝑐))+1+𝜎rel2

where 𝜎rel is approximately equal to the relative susceptibility between individuals in the youngest (<5) and those in the oldest (>80) age groups. In the following analysis we assume baseline values of 𝜎min = 0.1, 𝑏 = 0.3 and 𝑐 = 27.

We choose values to match the proportion of each age group infected in China (the country used to calibrate the model) and then applied the calibrated values to Australian mixing matrices.

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Employee presenteeism and occupational acquisition of COVID-19

MJA published online: 7th May 2020

Author: Damon Eisen

Abstract:

Presenteeism, where SARS-CoV-2 infected workers attend work while symptomatic, contributes to occupational acquisition of COVID-19. This is documented to have occurred in the North West Regional Hospital Outbreak among Tasmanian Health Care workers. It is also likely to be present among a newly recognised Melbourne abattoir outbreak. Infection prevention practices must account for presenteeism.

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Estimating the case detection rate and temporal variation in transmission of COVID-19 in Australia
Technical Report

14th April 2020

Authors: David J. Price1,2, Freya M. Shearer2, Michael Meehan3, Emma McBryde3, Nick Golding4, Jodie McVernon1, James M. McCaw1,2,5

1 Victorian Infectious Diseases Laboratory Epidemiology Unit at The Peter Doherty Institute for Infection and Immunity; The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia
2 Modelling and Simulation Unit, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
3 Australian Institute of Tropical Health & Medicine, James Cook University, Townsville, Australia
4 Telethon Kids Institute, Curtin University, Perth, Australia
5 School of Mathematics and Statistics, The University of Melbourne, Melbourne, Australia

Key messages:
  • We adapted and applied the method developed by colleagues at the London School of Hygiene and Tropical Medicine that uses the Case Fatality Rate in a region (adjusted for cases with known outcomes) to provide estimates of the symptomatic case detection rate in Australia. We note that LSHTM added Australia to their analysis on 1 April. The present authors have since updated the analysis, including the ability to estimate a time-dependent detection rate, at national level and for each state/territory.
  • As of 9th April 2020, our estimate of the symptomatic case detection rate for Australia is 93%
    (95% CI 77–100%). The corresponding estimates for each state/territory are all greater than
    80% (Figures 1 and 2).
  • Analyses were performed to identify temporal changes in the effective reproduction number
    (Reff) during the early course of the COVID-19 pandemic in each Australian state/territory.
  • These analyses produced broadly consistent results showing that the effective reproduction
    number is likely less than 1 in NSW, VIC, QLD, SA, and WA as of 5 April 2020 (Figures 3–5). It
    should be noted that these estimates are averaged across the whole of each jurisdiction, and
    may reflect Reff >> 1 in a number of localised settings and Reff << 1 elsewhere.
  • Reff is estimated to be above 1 in TAS, which should be interpreted with caution given the
    small cumulative number of cases and the large relative increase in cases recently reported
    (32 cases reported between 10 and 12 April).

See full report here

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Researchers warn about potential increase in COVID-19 cases and remind Nigerians to practice "physical" distancing this Easter period

11th April 2020

Authors: Oyelola Adegboye1, Adeshina Adekunle1, Ezra Gayawan2

1 Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Australia
2 Federal University of Technology, Akure, Nigeria


Researchers from James Cook University (JCU) in Australia and Federal University of Technology in Akure, Nigeria (FUTA) Drs Oyelola Adegboye, Adeshina Adekunle and Ezra Gayawan have warned that Nigerians should practice “physical” distancing this Easter holiday. They warned that it is important to understand that the travel ban imposed by the Federal Government has prevented or reduced future importations according to their simulation study which found that the effects of the international travel ban imposed by the Australia Government resulted in an 80% reduction in COVID-19 importations. Hence, violating the social distancing intervention strategy could lead to an escalation of cases and all the gains as a result of the international travel ban would be lost.


The outbreak of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) that emerged in the city of Wuhan, China has now spread to every inhabitable continent, but the attention has now shifted from China to other epicenters. The researchers said, “Although the epidemic trajectory in Nigeria has been slow compared to other countries, in part, due to public health interventions being implemented at the early stage, the government must intensify its effort.” We have seen in the USA where COVID-19 cases jumped from 472 on March 10, 2020 to 425, 889 by April 10, 2020.

See full report here

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Plain English explainer about the explainer

6th April 2020

Authors: McBryde ES1, Meehan MT1, Trauer JM2

.1Australian Institute of Tropical Health and Medicine, James Cook University
2School of Public Health and Preventive Medicine, Monash University

When we talk about flattening the curve, there are several interpretations of this. We may make the epidemic longer slower and much less peaked, as shown by the first of the blue curves below. Most efforts to curb COVID in Europe have certainly reduced the infectiousness to levels that will slow the peak but go nowhere near eliminating COVID.

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Flattening the curve is not enough, we need to squash it: An explainer using a simple model

30th March 2020

Authors: McBryde ES1, Meehan MT1, Trauer JM2.

1 Australian Institute of Tropical Health and Medicine, James Cook University
2 School of Public Health and Preventive Medicine, Monash University

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.

Abstract:

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.

See full report here

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Modelling the impact of COVID-19 upon intensive care services in New South Wales

MJA Published online: 30th March 2020

Authors: Gregory J Fox, James M Trauer and Emma McBryde

The known: COVID-19 has been diagnosed in over 1,000 Australians, with the notification rate being the highest in NSW.

The new: This study applies two statistical models to demonstrate the effect of COVID-19 upon critical care services. Even with limited mitigation, the effect is expected to overwhelm existing ICU
capacity.

The implications: Urgent action is required to reduce transmission of COVID-19, and increase the capacity of critical care services.

Abstract:

Background: The Australian healthcare system faces a mounting burden due to COVID-19. Modelling performed in a comparable population in the United Kingdom anticipates a substantial burden for intensive care departments.

Methods: This analysis uses two approaches to estimating intensive care unit (ICU) bed demands associated with COVID-19 in the context of local health districts in NSW. In the first approach, the findings of an individual-based simulation model undertaken in the United Kingdom (UK) was applied to the age distribution of the NSW population. In the second approach, we developed a compartmental model applied to the NSW population. In both models, we estimated the number of hospitalisations and peak ICU demand at the initial peak of the COVID-19 epidemic, under a number of mitigation strategies.

Results: Applying UK-based model to the NSW population, the peak demand for ICU beds was forecast to be 6,965 ICU beds with an intensive mitigation strategy (797% of the ICU capacity prior to COVID-19). The compartmental model estimated that under a strategy that reduced transmission by one third, at least 5,109 ICU beds would be required (584% of the prior ICU capacity).

Conclusions: The burden upon intensive care services due to COVID-19 was forecast to be immense with both modelling approaches. Strategies to mitigate transmission must be accompanied by substantial increases in the capacity of critical care services in advance of peak demand. Modelling is an important tool to assist policymakers and the public to understand the impacts pandemic diseases.

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Economic consequences of the COVID-19 outbreak: the need for epidemic preparedness

27th March 2020

Authors: Anton Pak1,, Oyelola A Adegboye1.*, Adeshina I Adekunle1, Kazi M Rahman2,3, Emma S McBryde1, Damon P Eisen1

1Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Australia

2North Coast Public Health Unit, New South Wales Health, Lismore, NSW 2480, Australia

3The University of Sydney, University Centre for Rural Health, Lismore, NSW 2480, Australia

First authors

*Corresponding author: Oyelola A. Adegboye (oyelola.adegboye@jcu.edu.au)

Keywords: SARS-CoV-2; Global markets; Economy

Abstract

COVID-19 has not only become global pandemic and a public health crisis but also affected the global economy and financial markets. Significant reductions in income, rise of unemployment and disruptions in transportation, service and manufacturing industries are among the consequences of governments’ disease mitigation measures. It has become clear that most governments in the world has underestimated the risks of rapid COVID-19 spread and were mostly reactive in their crisis response. As the disease outbreaks are not likely to disappear in the near future, proactive international actions are required to not only save lives but also protect economic prosperity.

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Delaying the COVID-19 epidemic in Australia: Evaluating the effectiveness of international travel bans

24th March 2020

Authors: Adeshina I. Adekunle1, 2*, Michael Meehan1, Diana Rojas3, James Trauer4, Emma McBryde1

1Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Australia.

2Decision Sciences Program Victoria University, Melbourne, Australia

3College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia.

4Department of Epidemiology and Biostatistics, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia

corresponding author: adeshina.adekunle@jcu.edu.au

Summary: Following the outbreak of novel Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) or COVID-19 in Wuhan, China late 2019, different countries have put in place interventions such as travel ban, proper hygiene, and social distancing to slow the spread of this novel virus. We evaluated the effects of travel bans in the Australia context and projected the epidemic until May 2020. Our modelling results closely align with observed cases in Australia indicating the need for maintaining or improving on the control measures to slow down the virus.

Introduction: As of 18th March 2020, COVID-19 has caused almost 200,000 cases, 8,000 deaths and spread to over 150 countries (1). Declared a pandemic on 12th March (2), it is clear that the world has lost the opportunity to contain the virus SARS-CoV2 as it managed to for SARS-CoV. With 565 confirmed cases (3) and still counting, COVID-19 now looks certain to cause sustained local transmission within Australia. Therefore, at this time it is reasonable to reflect on the value of travel restrictions imposed to date, and to consider the benefit of ongoing travel restrictions in the coming weeks and months, when community transmission starts to increase. We answer these questions using OAG-travel data and a meta-population model for disease transmission. First we examine the counterfactuals: what would have happened had the travel ban from Wuhan/China not been implemented. Similarly we examine the impacts of bans to other emerging epicentres including Iran, Italy, and South Korea. We then examine the impacts for the future and compare the cases expected through community transmission, and from importation over the next 2 months.

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Change in outbreak epicenter and its impact on the importation risks of COVID-19 progression: a modelling study

15th March 2020

Authors: Oyelola A Adegboye1*, Adeshina I Adekunle1, Anton Pak1, Ezra Gayawan2, Denis HY Leung3, Diana P Rojas4, Faiz Elfaki5, Emma S McBryde1, Damon P Eisen1

1Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Australia
2Biostatistics and Spatial Statistics Research Group, Department of Statistics, Federal 
University of Technology, Akure, Nigeria.
3School of Economics, Singapore Management University, Singapore, Singapore
4College of Public Health. Medical and Veterinary Sciences, James Cook University, Townsville, Australia
5Department of Mathematics, Statistics and Physics, Qatar University, Doha, Qatar

*Corresponding author: Oyelola A. Adegboye, Email: oyelola.adegboye@jcu.edu.au, Phone: +61 7 4781 5707.

Abstract:

The outbreak of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) that originated in the city of Wuhan, China has now spread to every inhabitable continent, but now the attention has shifted from China to other epicenters, especially Italy. This study explored the influence of spatial proximities and travel patterns from Italy on the further spread of SARS-CoV-2 around the globe. We showed that as the epicenter changes, the dynamics of SARS-CoV-2 spread change to reflect spatial proximities.

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The value of early transmission dynamic studies in emerging infectious diseases

The Lancet published online: 11th March 2020
Author: Emma McBryde

The world is braced for a public health emergency of international concern caused by a novel emerging infectious disease, a coronavirus with similarities to severe acute respiratory syndrome coronavirus (SARS-CoV). Person-to-person transmission of SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19), started in December, 2019, in Wuhan, China and has spread to become a global pandemic, with, as of Feb 26, 2020, community transmission in Italy, Iran, and South Korea.

Modelling studies have aided understanding of COVID-19 dynamics from the first announcement of the epidemic and publication of the genetic sequence of the causative virus. Initial phylogenetic analysis of closely related viruses suggested highly linked person-to-person spread of SARS-CoV-2 originating from mid-November to early December, 2019., Following this, modellers provided simple calculations that identified a mismatch between reported cases in China and reported importations of cases from travellers. Based on travel volumes, modellers inferred  that cases in Wuhan were underestimated by a factor of 40—a crucially important finding. Further calculations, again based on travel volumes, suggested that some countries would be expected to have many more travel-related cases than had been notified,  drawing attention to the possibility of undetected cases and community transmission in several countries.

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