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Article ; Online: A beta-Poisson model for infectious disease transmission.

Hilton, Joe / Hall, Ian

2024 Volume 20, Issue 2, Page(s) e1011856

Abstract: Outbreaks of emerging and zoonotic infections represent a substantial threat to human health and well-being. These outbreaks tend to be characterised by highly stochastic transmission dynamics with intense variation in transmission potential between ... ...

Abstract	Outbreaks of emerging and zoonotic infections represent a substantial threat to human health and well-being. These outbreaks tend to be characterised by highly stochastic transmission dynamics with intense variation in transmission potential between cases. The negative binomial distribution is commonly used as a model for transmission in the early stages of an epidemic as it has a natural interpretation as the convolution of a Poisson contact process and a gamma-distributed infectivity. In this study we expand upon the negative binomial model by introducing a beta-Poisson mixture model in which infectious individuals make contacts at the points of a Poisson process and then transmit infection along these contacts with a beta-distributed probability. We show that the negative binomial distribution is a limit case of this model, as is the zero-inflated Poisson distribution obtained by combining a Poisson-distributed contact process with an additional failure probability. We assess the beta-Poisson model's applicability by fitting it to secondary case distributions (the distribution of the number of subsequent cases generated by a single case) estimated from outbreaks covering a range of pathogens and geographical settings. We find that while the beta-Poisson mixture can achieve a closer to fit to data than the negative binomial distribution, it is consistently outperformed by the negative binomial in terms of Akaike Information Criterion, making it a suboptimal choice on parsimonious grounds. The beta-Poisson performs similarly to the negative binomial model in its ability to capture features of the secondary case distribution such as overdispersion, prevalence of superspreaders, and the probability of a case generating zero subsequent cases. Despite this possible shortcoming, the beta-Poisson distribution may still be of interest in the context of intervention modelling since its structure allows for the simulation of measures which change contact structures while leaving individual-level infectivity unchanged, and vice-versa.
MeSH term(s)	Humans ; Models, Statistical ; Computer Simulation ; Poisson Distribution ; Binomial Distribution ; Disease Outbreaks
Language	English
Publishing date	2024-02-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1011856
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Estimation of country-level basic reproductive ratios for novel Coronavirus (SARS-CoV-2/COVID-19) using synthetic contact matrices.

Hilton, Joe / Keeling, Matt J

PLoS computational biology

2020 Volume 16, Issue 7, Page(s) e1008031

Abstract: The 2019-2020 pandemic of atypical pneumonia (COVID-19) caused by the virus SARS-CoV-2 has spread globally and has the potential to infect large numbers of people in every country. Estimating the country-specific basic reproductive ratio is a vital first ...

Abstract	The 2019-2020 pandemic of atypical pneumonia (COVID-19) caused by the virus SARS-CoV-2 has spread globally and has the potential to infect large numbers of people in every country. Estimating the country-specific basic reproductive ratio is a vital first step in public-health planning. The basic reproductive ratio (R0) is determined by both the nature of pathogen and the network of human contacts through which the disease can spread, which is itself dependent on population age structure and household composition. Here we introduce a transmission model combining age-stratified contact frequencies with age-dependent susceptibility, probability of clinical symptoms, and transmission from asymptomatic (or mild) cases, which we use to estimate the country-specific basic reproductive ratio of COVID-19 for 152 countries. Using early outbreak data from China and a synthetic contact matrix, we estimate an age-stratified transmission structure which can then be extrapolated to 151 other countries for which synthetic contact matrices also exist. This defines a set of country-specific transmission structures from which we can calculate the basic reproductive ratio for each country. Our predicted R0 is critically sensitive to the intensity of transmission from asymptomatic cases; with low asymptomatic transmission the highest values are predicted across Eastern Europe and Japan and the lowest across Africa, Central America and South-Western Asia. This pattern is largely driven by the ratio of children to older adults in each country and the observed propensity of clinical cases in the elderly. If asymptomatic cases have comparable transmission to detected cases, the pattern is reversed. Our results demonstrate the importance of age-specific heterogeneities going beyond contact structure to the spread of COVID-19. These heterogeneities give COVID-19 the capacity to spread particularly quickly in countries with older populations, and that intensive control measures are likely to be necessary to impede its progress in these countries.
MeSH term(s)	Age Factors ; Asymptomatic Infections/epidemiology ; Betacoronavirus/isolation & purification ; Betacoronavirus/physiology ; COVID-19 ; China/epidemiology ; Computational Biology/methods ; Contact Tracing/methods ; Coronavirus Infections/epidemiology ; Coronavirus Infections/transmission ; Disease Outbreaks/prevention & control ; Forecasting/methods ; Humans ; Models, Statistical ; Pandemics/prevention & control ; Pandemics/statistics & numerical data ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/transmission ; SARS-CoV-2 ; Virus Replication/physiology
Keywords	covid19
Language	English
Publishing date	2020-07-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1008031
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Estimation of country-level basic reproductive ratios for novel Coronavirus (SARS-CoV-2/COVID-19) using synthetic contact matrices.

Joe Hilton / Matt J Keeling

PLoS Computational Biology, Vol 16, Iss 7, p e

2020 Volume 1008031

Abstract	The 2019-2020 pandemic of atypical pneumonia (COVID-19) caused by the virus SARS-CoV-2 has spread globally and has the potential to infect large numbers of people in every country. Estimating the country-specific basic reproductive ratio is a vital first step in public-health planning. The basic reproductive ratio (R0) is determined by both the nature of pathogen and the network of human contacts through which the disease can spread, which is itself dependent on population age structure and household composition. Here we introduce a transmission model combining age-stratified contact frequencies with age-dependent susceptibility, probability of clinical symptoms, and transmission from asymptomatic (or mild) cases, which we use to estimate the country-specific basic reproductive ratio of COVID-19 for 152 countries. Using early outbreak data from China and a synthetic contact matrix, we estimate an age-stratified transmission structure which can then be extrapolated to 151 other countries for which synthetic contact matrices also exist. This defines a set of country-specific transmission structures from which we can calculate the basic reproductive ratio for each country. Our predicted R0 is critically sensitive to the intensity of transmission from asymptomatic cases; with low asymptomatic transmission the highest values are predicted across Eastern Europe and Japan and the lowest across Africa, Central America and South-Western Asia. This pattern is largely driven by the ratio of children to older adults in each country and the observed propensity of clinical cases in the elderly. If asymptomatic cases have comparable transmission to detected cases, the pattern is reversed. Our results demonstrate the importance of age-specific heterogeneities going beyond contact structure to the spread of COVID-19. These heterogeneities give COVID-19 the capacity to spread particularly quickly in countries with older populations, and that intensive control measures are likely to be necessary to impede its progress in these ...
Keywords	Biology (General) ; QH301-705.5 ; covid19
Language	English
Publishing date	2020-07-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Incorporating household structure and demography into models of endemic disease.

Hilton, Joe / Keeling, Matt J

Journal of the Royal Society, Interface

2019 Volume 16, Issue 157, Page(s) 20190317

Abstract: The spread of infectious diseases is intimately linked with the strength and type of contact between individuals. Multiple observational and modelling studies have highlighted the importance of two forms of social mixing: age structure, where the ... ...

Abstract	The spread of infectious diseases is intimately linked with the strength and type of contact between individuals. Multiple observational and modelling studies have highlighted the importance of two forms of social mixing: age structure, where the likelihood of interaction between two individuals is determined by their ages; and household structure, which recognizes the much stronger contacts and hence transmission potential within the family setting. Age structure has been ubiquitous in predictive models of both endemic and epidemic infections, in part due to the ease of assessing someone's age. By contrast, although household structure is potentially the dominant heterogeneity, it has received less attention, in part due to an absence of the necessary methodology. Here, we develop the modelling framework necessary to predict the behaviour of endemic infections (which necessitates capturing demographic processes) in populations that possess both household and age structure. We compare two childhood infections, with measles-like and mumps-like parameters, and two populations with UK-like and Kenya-like characteristics, which allows us to disentangle the impact of epidemiology and demography. For this high-dimensional model, we predict complex nonlinear dynamics, where the dynamics of within-household outbreaks are tempered by historical waves of infection and the immunity of older individuals.
MeSH term(s)	Communicable Diseases/epidemiology ; Communicable Diseases/transmission ; Endemic Diseases/prevention & control ; Family Characteristics ; Humans ; Models, Biological
Language	English
Publishing date	2019-08-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2156283-0
ISSN	1742-5662 ; 1742-5689
ISSN (online)	1742-5662
ISSN	1742-5689
DOI	10.1098/rsif.2019.0317
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Estimation of country-level basic reproductive ratios for novel Coronavirus (SARS-CoV-2/COVID-19) using synthetic contact matrices

Hilton, Joe / Keeling, Matt J.

PLOS Computational Biology

2020 Volume 16, Issue 7, Page(s) e1008031

Keywords	Ecology ; Modelling and Simulation ; Computational Theory and Mathematics ; Genetics ; Ecology, Evolution, Behavior and Systematics ; Molecular Biology ; Cellular and Molecular Neuroscience ; covid19
Language	English
Publisher	Public Library of Science (PLoS)
Publishing country	us
Document type	Article ; Online
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1008031
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Estimation of country-level basic reproductive ratios for novel Coronavirus (COVID-19) using synthetic contact matrices

Hilton, Joe / Keeling, Matt J

Abstract: The outbreak of novel coronavirus (COVID-19) has the potential for global spread, infecting large numbers in all countries. In this case, estimating the country-specific basic reproductive ratio is a vital first step in public-health planning. The basic ... ...

Abstract	The outbreak of novel coronavirus (COVID-19) has the potential for global spread, infecting large numbers in all countries. In this case, estimating the country-specific basic reproductive ratio is a vital first step in public-health planning. The basic reproductive ratio (R0) is determined by both the nature of pathogen and the network of contacts through which the disease can spread - with this network determined by socio-demographics including age-structure and household composition. Here we focus on the age-structured transmission within the population, using data from China to inform age-dependent susceptibility and synthetic age-mixing matrices to inform the contact network. This allows us to determine the country-specific basic reproductive ratio as a multiplicative scaling of the value from China. We predict that R0 will be highest across Eastern Europe and Japan, and lowest across Africa, Central America and South-Western Asia. This pattern is largely driven by the ratio of children to older adults in each country and the observed propensity of clinical cases in the elderly.
Keywords	covid19
Publisher	MedRxiv; WHO
Document type	Article ; Online
DOI	10.1101/2020.02.26.20028167
Database	COVID19

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Article ; Online: Estimation of country-level basic reproductive ratios for novel Coronavirus (COVID-19) using synthetic contact matrices

Hilton, Joe / Keeling, Matt J

medRxiv

Abstract	The outbreak of novel coronavirus (COVID-19) has the potential for global spread, infecting large numbers in all countries. In this case, estimating the country-specific basic reproductive ratio is a vital first step in public-health planning. The basic reproductive ratio (R<sub>0</sub>) is determined by both the nature of pathogen and the network of contacts through which the disease can spread - with this network determined by socio-demographics including age-structure and household composition. Here we focus on the age-structured transmission within the population, using data from China to inform age-dependent susceptibility and synthetic age-mixing matrices to inform the contact network. This allows us to determine the country-specific basic reproductive ratio as a multiplicative scaling of the value from China. We predict that R<sub>0</sub> will be highest across Eastern Europe and Japan, and lowest across Africa, Central America and South-Western Asia. This pattern is largely driven by the ratio of children to older adults in each country and the observed propensity of clinical cases in the elderly.
Keywords	covid19
Language	English
Publishing date	2020-02-27
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.02.26.20028167
Database	COVID19

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Article: Estimation of country-level basic reproductive ratios for novel Coronavirus (SARS-CoV-2/COVID-19) using synthetic contact matrices

Hilton, Joe / Keeling, Matt J

PLoS Comput Biol

Abstract	The 2019-2020 pandemic of atypical pneumonia (COVID-19) caused by the virus SARS-CoV-2 has spread globally and has the potential to infect large numbers of people in every country. Estimating the country-specific basic reproductive ratio is a vital first step in public-health planning. The basic reproductive ratio (R0) is determined by both the nature of pathogen and the network of human contacts through which the disease can spread, which is itself dependent on population age structure and household composition. Here we introduce a transmission model combining age-stratified contact frequencies with age-dependent susceptibility, probability of clinical symptoms, and transmission from asymptomatic (or mild) cases, which we use to estimate the country-specific basic reproductive ratio of COVID-19 for 152 countries. Using early outbreak data from China and a synthetic contact matrix, we estimate an age-stratified transmission structure which can then be extrapolated to 151 other countries for which synthetic contact matrices also exist. This defines a set of country-specific transmission structures from which we can calculate the basic reproductive ratio for each country. Our predicted R0 is critically sensitive to the intensity of transmission from asymptomatic cases; with low asymptomatic transmission the highest values are predicted across Eastern Europe and Japan and the lowest across Africa, Central America and South-Western Asia. This pattern is largely driven by the ratio of children to older adults in each country and the observed propensity of clinical cases in the elderly. If asymptomatic cases have comparable transmission to detected cases, the pattern is reversed. Our results demonstrate the importance of age-specific heterogeneities going beyond contact structure to the spread of COVID-19. These heterogeneities give COVID-19 the capacity to spread particularly quickly in countries with older populations, and that intensive control measures are likely to be necessary to impede its progress in these countries.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #624431
Database	COVID19

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Article ; Online: Estimation of country-level basic reproductive ratios for novel Coronavirus (SARS-CoV-2/COVID-19) using synthetic contact matrices

Hilton, Joe / Keeling, Matt J.

2020

Abstract	The 2019-2020 pandemic of atypical pneumonia (COVID-19) caused by the virus SARS-CoV-2 has spread globally and has the potential to infect large numbers of people in every country. Estimating the country-specific basic reproductive ratio is a vital first step in public-health planning. The basic reproductive ratio (R0) is determined by both the nature of pathogen and the network of human contacts through which the disease can spread, which is itself dependent on population age structure and household composition. Here we introduce a transmission model combining age-stratified contact frequencies with age-dependent susceptibility, probability of clinical symptoms, and transmission from asymptomatic (or mild) cases, which we use to estimate the country-specific basic reproductive ratio of COVID-19 for 152 countries. Using early outbreak data from China and a synthetic contact matrix, we estimate an age-stratified transmission structure which can then be extrapolated to 151 other countries for which synthetic contact matrices also exist. This defines a set of country-specific transmission structures from which we can calculate the basic reproductive ratio for each country. Our predicted R0 is critically sensitive to the intensity of transmission from asymptomatic cases; with low asymptomatic transmission the highest values are predicted across Eastern Europe and Japan and the lowest across Africa, Central America and South-Western Asia. This pattern is largely driven by the ratio of children to older adults in each country and the observed propensity of clinical cases in the elderly. If asymptomatic cases have comparable transmission to detected cases, the pattern is reversed. Our results demonstrate the importance of age-specific heterogeneities going beyond contact structure to the spread of COVID-19. These heterogeneities give COVID-19 the capacity to spread particularly quickly in countries with older populations, and that intensive control measures are likely to be necessary to impede its progress in these countries.
Keywords	QR355 Virology ; covid19
Publishing date	2020-07-02
Publisher	Public Library of Science
Publishing country	uk
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Estimation of country-level basic reproductive ratios for novel Coronavirus (SARS-CoV-2/COVID-19) using synthetic contact matrices

Hilton, Joe / Keeling, Matt

PLoS Computational Biology, 16(7):e1008031

2020

Abstract	The 2019-2020 pandemic of atypical pneumonia (COVID-19) caused by the virus SARS-CoV-2 has spread globally and has the potential to infect large numbers of people in every country. Estimating the country-specific basic reproductive ratio is a vital first step in public-health planning. The basic reproductive ratio (R0) is determined by both the nature of pathogen and the network of human contacts through which the disease can spread, which is itself dependent on population age structure and household composition. Here we introduce a transmission model combining age-stratified contact frequencies with age-dependent susceptibility, probability of clinical symptoms, and transmission from asymptomatic (or mild) cases, which we use to estimate the country-specific basic reproductive ratio of COVID-19 for 152 countries. Using early outbreak data from China and a synthetic contact matrix, we estimate an age-stratified transmission structure which can then be extrapolated to 151 other countries for which synthetic contact matrices also exist. This defines a set of country-specific transmission structures from which we can calculate the basic reproductive ratio for each country. Our predicted R0 is critically sensitive to the intensity of transmission from asymptomatic cases; with low asymptomatic transmission the highest values are predicted across Eastern Europe and Japan and the lowest across Africa, Central America and South-Western Asia. This pattern is largely driven by the ratio of children to older adults in each country and the observed propensity of clinical cases in the elderly. If asymptomatic cases have comparable transmission to detected cases, the pattern is reversed. Our results demonstrate the importance of age-specific heterogeneities going beyond contact structure to the spread of COVID-19. These heterogeneities give COVID-19 the capacity to spread particularly quickly in countries with older populations, and that intensive control measures are likely to be necessary to impede its progress in these countries. AUTHOR SUMMARY: Over 100 countries have reported laboratory-confirmed cases of atypical pneumonia caused by 2019 novel coronavirus (COVID-19). Cases are largely reported in older age groups, suggesting a strong age-dependent component to either transmission or the probability of developing symptoms and thus being detected. We introduce a mathematical model for COVID-19 transmission in which contact behaviour, susceptibility, detection probability, and transmission from undetected cases all vary with age. We fit our model to epidemiological data from the outbreak in China for the special case where asymptomatic transmission is negligible, and compare it to a null model where only contact behaviour varies with age. Our fitted model suggests that contacts involving older individuals are particularly likely to generate new detected cases, intensifying the spread of infection in countries with older populations. We estimate the basic reproductive ratio (a measure of a pathogen’s capacity for spread) of COVID-19 in 152 countries under both models, and find that estimates of the basic reproductive ratio are highly dependent on the assumed underlying transmission structure; our more complex model predicts higher values in Japan and much of Europe and lower values in much of Africa, in comparison to the contact frequency-based model where this pattern is reversed.
Keywords	Epidemiology ; COVID-19 ; Infectious disease epidemiology ; Italy ; China ; Japan ; Mathematical models ; Europe ; covid19
Language	English
Publishing country	de
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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