Early analysis of the Australian COVID-19 epidemic
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Australia
- Victorian Infectious Diseases Reference Laboratory Epidemiology Unit at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Australia
- Australian Institute of Tropical Health and Medicine, James Cook University, Australia
- Telethon Kids Institute and Curtin University, Australia
- Defence Science and Technology, Department of Defence, Australia
- Kirby Institute for Infection and Immunity, University of New South Wales, Australia
- School of Mathematics and Statistics, University of New South Wales, Australia
- School of Public Health and Community Medicine, University of New South Wales, Australia
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, United Kingdom
- Infection and Immunity Theme, Murdoch Childrenβs Research Institute, The Royal Childrenβs Hospital, Australia
- School of Mathematics and Statistics, The University of Melbourne, Australia
Figures
Figure 1 with 2 supplements
Time series of new daily confirmed cases of COVID-19 in Australia by import status (purple = overseas acquired, blue = locally acquired, green = unknown origin) from 22 January 2020 (first case detected) to 13 April 2020.
Dates of selected key border and social distancing measures implemented by Australian authorities are indicated by annotations above the plotted case counts. These measures were in addition to case β¦
Figure 1βfigure supplement 1
Time series of new daily confirmed cases of COVID-19 in each Australian state/territory by import status (purple = overseas acquired, blue = locally acquired, green = unknown origin) from 22 January 2020 (first case detected) to 13 April 2020.
Details on the epidemiological characteristics of locally and overseas acquired infections are available in the Australian Department of Health fortnightly epidemiological reports (Australian β¦
Figure 1βfigure supplement 2
Timeline of border and social distancing measures implemented in Australia up to 4 April 2020.
These measures were in addition to case targeted interventions, specifically case isolation and quarantine of their contacts. Contact tracing was initiated from 29 January 2020 and was performed by β¦
Figure 2 with 3 supplements
Time-varying estimate of the effective reproduction number () of COVID-19 by Australian state (light blue ribbon = 90% credible interval; dark blue ribbon = 50% credible interval) from 1 March to 5 April 2020, based on data up to and including 13 April 2020.
Confidence in the estimated values is indicated by shading with reduced shading corresponding to reduced confidence. The horizontal dashed line indicates the target value of 1 for the effective β¦
Figure 2βfigure supplement 1
Sensitivity analysis 1 of 3.
Time-varying estimate of the effective reproduction number () of COVID-19 by Australian state (light blue ribbon = 90% credible interval; dark blue ribbon = 50% credible interval) from 1 March to β¦
Figure 2βfigure supplement 2
Sensitivity analysis 2 of 3.
Time-varying estimate of the effective reproduction number () of COVID-19 by Australian state (light blue ribbon = 90% credible interval; dark blue ribbon = 50% credible interval) from 1 March to β¦
Figure 2βfigure supplement 3
Sensitivity analysis 3 of 3.
Time-varying estimate of the effective reproduction number () of COVID-19 by Australian state (light blue ribbon = 90% credible interval; dark blue ribbon = 50% credible interval) from 1 March to β¦
Figure 3 with 1 supplement
Forecasted daily hospital ward (left) and intensive care unit (right) occupancy (dark ribbons = 50% confidence intervals; light ribbons = 95% confidence intervals) from 17 March to 28 April.
Occupancy = the number of beds occupied by COVID-19 patients on a given day. Black dots indicate the reported ward and ICU occupancy available from the Australian national COVID-19 database at the β¦
Figure 3βfigure supplement 1
Time series of new daily confirmed cases of COVID-19 in Australia from 1 March to 13 April 2020 (grey bars) overlaid by daily case counts estimated from the forecasting model up to April 13 and projected forward from 14 to 28 April inclusive.
Inner shading = 50% confidence intervals. Outer shading = 95% confidence intervals. Note that forecasting model estimates prior to 13 April β the last recorded data point at the time of analysis β¦
Tables
Table 1
Age-specific proportions of confirmed cases extracted from the Australian national COVID-19 database and age-specific estimates of the probability of hospitalisation and ICU admission for confirmed cases.
| Age | Proportion of cases | Pr(hospitalisation | confirmed case) | Pr(ICU admission | confirmed case) |
|---|---|---|---|
| 0-9 | 0.0102 | 0.1475 | 0.0000 |
| 10-18 | 0.0186 | 0.1081 | 0.0090 |
| 19-29 | 0.2258 | 0.0504 | 0.0007 |
| 30-39 | 0.1587 | 0.0865 | 0.0074 |
| 40-49 | 0.1291 | 0.0947 | 0.0208 |
| 50-59 | 0.1550 | 0.1112 | 0.0173 |
| 60-69 | 0.1686 | 0.1529 | 0.0318 |
| 70-79 | 0.1050 | 0.2440 | 0.0558 |
| 80+ | 0.0290 | 0.3815 | 0.0462 |
Table 2
Percentage of imported cases assumed to be contributing to transmission over three intervention phases for each sensitivity analysis.
We assume two step changes in the effectiveness of quarantine of overseas arrivals, resulting in three intervention phases: prior to 15 March (self-quarantine of arrivals from selected countries); β¦
| Imported cases contributing to transmission | |||
|---|---|---|---|
| Sensitivity analysis | Prior to 15 March | 15β27 March | 27 Marchβ |
| 1 | 90% | 50% | 1% |
| 2 | 80% | 50% | 1% |
| 3 | 50% | 20% | 1% |
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The results of these three analyses are shown in Figure 2βfigure supplements 1, 2 and 3, respectively.
Table 3
SEEIIR forecasting model parameters.
| Parameter | Definition | Value/Prior distribution |
|---|---|---|
| Ο | Inverse of the mean incubation period | |
| Ξ³ | Inverse of the mean infectious period | |
| Ο | Time of first exposure (days since 2020-01-01) | |
| Probability of observing a case | 0.8 | |
| k | Dispersion parameter on Negative-Binomial | 100 |
| observation model |
Additional files
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Source code 1
Analysis code.
- https://cdn.elifesciences.org/articles/58785/elife-58785-code1-v2.zip
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Transparent reporting form
- https://cdn.elifesciences.org/articles/58785/elife-58785-transrepform-v2.docx
