Inference of COVID-19 epidemiological distributions from Brazilian hospital data
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Published version
Author(s)
Type
Journal Article
Abstract
Knowing COVID-19 epidemiological distributions, such as the time from patient admission to death, is directly relevant to effective primary and secondary care planning, and moreover, the mathematical modelling of the pandemic generally. We determine epidemiological distributions for patients hospitalized with COVID-19 using a large dataset (N = 21 000 − 157 000) from the Brazilian Sistema de Informação de Vigilância Epidemiológica da Gripe database. A joint Bayesian subnational model with partial pooling is used to simultaneously describe the 26 states and one federal district of Brazil, and shows significant variation in the mean of the symptom-onset-to-death time, with ranges between 11.2 and 17.8 days across the different states, and a mean of 15.2 days for Brazil. We find strong evidence in favour of specific probability density function choices: for example, the gamma distribution gives the best fit for onset-to-death and the generalized lognormal for onset-to-hospital-admission. Our results show that epidemiological distributions have considerable geographical variation, and provide the first estimates of these distributions in a low and middle-income setting. At the subnational level, variation in COVID-19 outcome timings are found to be correlated with poverty, deprivation and segregation levels, and weaker correlation is observed for mean age, wealth and urbanicity.
Date Issued
2020
Date Acceptance
2020-10-26
Citation
Journal of The Royal Society Interface, 2020, 17, pp.20200596-20200596
ISSN
1742-5662
Publisher
The Royal Society
Start Page
20200596
End Page
20200596
Journal / Book Title
Journal of The Royal Society Interface
Volume
17
Issue
172
Copyright Statement
© 2020 The Authors.
Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.
Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.
Sponsor
Medical Research Council (MRC)
Medical Research Council (MRC)
Bill & Melinda Gates Foundation
Imperial College Healthcare NHS Trust- BRC Funding
The Academy of Medical Sciences
Bill & Melinda Gates Foundation
National Institute for Health Research
UK Research and Innovation
Identifier
https://royalsocietypublishing.org/doi/10.1098/rsif.2020.0596
Grant Number
MR/R015600/1
MR/K010174/1B
1606H5002/JH6
RDA02
SBF004/1080
RES- -62388
NIHR200908
MR/V038109/1
Subjects
COVID-19
Brazil
symptom-onset-to-death
admission-to-death
model selection
General Science & Technology
Publication Status
Published
Article Number
172
Date Publish Online
2020-11-25