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Book: An introduction to infectious disease modelling

Vynnycky, Emilia / White, Richard G.

2010

Author's details	Emilia Vynnycky and Richard White
Keywords	Communicable diseases/Mathematical models ; Epidemiology/Mathematical models
Subject code	616.9015118
Language	English
Size	XXVI, 370 S. : Ill., graph. Darst.
Publisher	Oxford Univ. Press
Publishing place	Oxford u.a.
Publishing country	Great Britain
Document type	Book
Note	Hier auch später erschienene, unveränderte Nachdrucke
HBZ-ID	HT016373502
ISBN	978-0-19-856576-5 ; 0-19-856576-3
Database	Catalogue ZB MED Medicine, Health

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Article ; Online: Estimates of the basic reproduction number for rubella using seroprevalence data and indicator-based approaches.

Papadopoulos, Timos / Vynnycky, Emilia

PLoS computational biology

2022 Volume 18, Issue 3, Page(s) e1008858

Abstract: The basic reproduction number (R0) of an infection determines the impact of its control. For many endemic infections, R0 is often estimated from appropriate country-specific seroprevalence data. Studies sometimes pool estimates from the same region for ... ...

Abstract	The basic reproduction number (R0) of an infection determines the impact of its control. For many endemic infections, R0 is often estimated from appropriate country-specific seroprevalence data. Studies sometimes pool estimates from the same region for settings lacking seroprevalence data, but the reliability of this approach is unclear. Plausibly, indicator-based approaches could predict R0 for such settings. We calculated R0 for rubella for 98 settings and correlated its value against 66 demographic, economic, education, housing and health-related indicators. We also trained a random forest regression algorithm using these indicators as the input and R0 as the output. We used the mean-square error to compare the performances of the random forest, simple linear regression and a regional averaging method in predicting R0 using 4-fold cross validation. R0 was <5, 5-10 and >10 for 81, 14 and 3 settings respectively, with no apparent regional differences and in the limited available data, it was usually lower for rural than urban areas. R0 was most correlated with educational attainment, and household indicators for the Pearson and Spearman correlation coefficients respectively and with poverty-related indicators followed by the crude death rate considering the Maximum Information Coefficient, although the correlation for each was relatively weak (Pearson correlation coefficient: 0.4, 95%CI: (0.24,0.48) for educational attainment). A random forest did not perform better in predicting R0 than simple linear regression, depending on the subsets of training indicators and studies, and neither out-performed a regional averaging approach. R0 for rubella is typically low and using indicators to estimate its value is not straightforward. A regional averaging approach may provide as reliable an estimate of R0 for settings lacking seroprevalence data as one based on indicators. The findings may be relevant for other infections and studies estimating the disease burden and the impact of interventions for settings lacking seroprevalence data.
MeSH term(s)	Basic Reproduction Number ; Humans ; Reproducibility of Results ; Rubella/epidemiology ; Rural Population ; Seroepidemiologic Studies
Language	English
Publishing date	2022-03-03
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.1008858
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Estimates of the basic reproduction number for rubella using seroprevalence data and indicator-based approaches

Timos Papadopoulos / Emilia Vynnycky

PLoS Computational Biology, Vol 18, Iss

2022 Volume 3

Abstract	The basic reproduction number (R0) of an infection determines the impact of its control. For many endemic infections, R0 is often estimated from appropriate country-specific seroprevalence data. Studies sometimes pool estimates from the same region for settings lacking seroprevalence data, but the reliability of this approach is unclear. Plausibly, indicator-based approaches could predict R0 for such settings. We calculated R0 for rubella for 98 settings and correlated its value against 66 demographic, economic, education, housing and health-related indicators. We also trained a random forest regression algorithm using these indicators as the input and R0 as the output. We used the mean-square error to compare the performances of the random forest, simple linear regression and a regional averaging method in predicting R0 using 4-fold cross validation. R0 was <5, 5–10 and >10 for 81, 14 and 3 settings respectively, with no apparent regional differences and in the limited available data, it was usually lower for rural than urban areas. R0 was most correlated with educational attainment, and household indicators for the Pearson and Spearman correlation coefficients respectively and with poverty-related indicators followed by the crude death rate considering the Maximum Information Coefficient, although the correlation for each was relatively weak (Pearson correlation coefficient: 0.4, 95%CI: (0.24,0.48) for educational attainment). A random forest did not perform better in predicting R0 than simple linear regression, depending on the subsets of training indicators and studies, and neither out-performed a regional averaging approach. R0 for rubella is typically low and using indicators to estimate its value is not straightforward. A regional averaging approach may provide as reliable an estimate of R0 for settings lacking seroprevalence data as one based on indicators. The findings may be relevant for other infections and studies estimating the disease burden and the impact of interventions for settings ...
Keywords	Biology (General) ; QH301-705.5
Subject code	310
Language	English
Publishing date	2022-03-01T00:00:00Z
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: Estimates of the basic reproduction number for rubella using seroprevalence data and indicator-based approaches.

Timos Papadopoulos / Emilia Vynnycky

PLoS Computational Biology, Vol 18, Iss 3, p e

2022 Volume 1008858

Abstract	The basic reproduction number (R0) of an infection determines the impact of its control. For many endemic infections, R0 is often estimated from appropriate country-specific seroprevalence data. Studies sometimes pool estimates from the same region for settings lacking seroprevalence data, but the reliability of this approach is unclear. Plausibly, indicator-based approaches could predict R0 for such settings. We calculated R0 for rubella for 98 settings and correlated its value against 66 demographic, economic, education, housing and health-related indicators. We also trained a random forest regression algorithm using these indicators as the input and R0 as the output. We used the mean-square error to compare the performances of the random forest, simple linear regression and a regional averaging method in predicting R0 using 4-fold cross validation. R0 was <5, 5-10 and >10 for 81, 14 and 3 settings respectively, with no apparent regional differences and in the limited available data, it was usually lower for rural than urban areas. R0 was most correlated with educational attainment, and household indicators for the Pearson and Spearman correlation coefficients respectively and with poverty-related indicators followed by the crude death rate considering the Maximum Information Coefficient, although the correlation for each was relatively weak (Pearson correlation coefficient: 0.4, 95%CI: (0.24,0.48) for educational attainment). A random forest did not perform better in predicting R0 than simple linear regression, depending on the subsets of training indicators and studies, and neither out-performed a regional averaging approach. R0 for rubella is typically low and using indicators to estimate its value is not straightforward. A regional averaging approach may provide as reliable an estimate of R0 for settings lacking seroprevalence data as one based on indicators. The findings may be relevant for other infections and studies estimating the disease burden and the impact of interventions for settings ...
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2022-03-01T00:00:00Z
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: Estimates of the global burden of Congenital Rubella Syndrome, 1996-2019.

Vynnycky, Emilia / Knapp, Jennifer K / Papadopoulos, Timos / Cutts, Felicity T / Hachiya, Masahiko / Miyano, Shinsuke / Reef, Susan E

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases

2023 Volume 137, Page(s) 149–156

Abstract: Objectives: Many countries introduced rubella-containing vaccination (RCV) after 2011, following changes in recommended World Health Organization (WHO) vaccination strategies and external support. We evaluated the impact of these introductions.: ... ...

Abstract	Objectives: Many countries introduced rubella-containing vaccination (RCV) after 2011, following changes in recommended World Health Organization (WHO) vaccination strategies and external support. We evaluated the impact of these introductions. Methods: We estimated the country-specific, region-specific, and global Congenital Rubella Syndrome (CRS) incidence during 1996-2019 using mathematical modeling, including routine and campaign vaccination coverage and seroprevalence data. Results: In 2019, WHO African and Eastern Mediterranean regions had the highest estimated CRS incidence (64 [95% confidence intervals (CI): 24-123] and 27 [95% CI: 4-67] per 100,000 live births respectively), where nearly half of births occur in countries that have introduced RCV. Other regions, where >95% of births occurred in countries that had introduced RCV, had a low estimated CRS incidence (<1 [95% CI: <1 to 8] and <1 [95% CI: <1 to 12] per 100,000 live births in South-East Asia [SEAR] and the Western Pacific [WPR] respectively, and similarly in Europe and the Americas). The estimated number of CRS births globally declined by approximately two-thirds during 2010-2019, from 100,000 (95% CI: 54,000-166,000) to 32,000 (95% CI: 13,000-60,000), representing a 73% reduction since 1996, largely following RCV introductions in WPR and SEAR, where the greatest reductions occurred. Conclusions: Further reductions can occur by introducing RCV in remaining countries and maintaining high RCV coverage.
MeSH term(s)	Humans ; Rubella Syndrome, Congenital/epidemiology ; Rubella Syndrome, Congenital/prevention & control ; Rubella/epidemiology ; Rubella/prevention & control ; Seroepidemiologic Studies ; Vaccination ; World Health Organization ; Rubella Vaccine
Chemical Substances	Rubella Vaccine
Language	English
Publishing date	2023-09-09
Publishing country	Canada
Document type	Journal Article
ZDB-ID	1331197-9
ISSN	1878-3511 ; 1201-9712
ISSN (online)	1878-3511
ISSN	1201-9712
DOI	10.1016/j.ijid.2023.09.003
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Transmission dynamics and control measures of COVID-19 outbreak in China: a modelling study.

Zhang, Xu-Sheng / Vynnycky, Emilia / Charlett, Andre / De Angelis, Daniela / Chen, Zhengji / Liu, Wei

Scientific reports

2021 Volume 11, Issue 1, Page(s) 2652

Abstract: COVID-19 is reported to have been brought under control in China. To understand the COVID-19 outbreak in China and provide potential lessons for other parts of the world, in this study we apply a mathematical model with multiple datasets to estimate the ... ...

Abstract	COVID-19 is reported to have been brought under control in China. To understand the COVID-19 outbreak in China and provide potential lessons for other parts of the world, in this study we apply a mathematical model with multiple datasets to estimate the transmissibility of the SARS-CoV-2 virus and the severity of the illness associated with the infection, and how both were affected by unprecedented control measures. Our analyses show that before 19th January 2020, 3.5% (95% CI 1.7-8.3%) of infected people were detected; this percentage increased to 36.6% (95% CI 26.1-55.4%) thereafter. The basic reproduction number (R
MeSH term(s)	Basic Reproduction Number ; COVID-19/epidemiology ; COVID-19/transmission ; COVID-19/virology ; China/epidemiology ; Disease Outbreaks ; Humans ; Models, Theoretical ; SARS-CoV-2/isolation & purification
Language	English
Publishing date	2021-01-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-81985-z
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The impact of Measles-Rubella vaccination on the morbidity and mortality from Congenital Rubella Syndrome in 92 countries.

Vynnycky, Emilia / Papadopoulos, Timoleon / Angelis, Konstantinos

Human vaccines & immunotherapeutics

2018 Volume 15, Issue 2, Page(s) 309–316

Abstract: Since 2011, GAVI, The Vaccine Alliance, has funded eligible countries to introduce rubella-containing vaccination (RCV) into their national schedule. Two key indicators used to monitor the impact - the future deaths and DALYs (Disability Adjusted Life ... ...

Abstract	Since 2011, GAVI, The Vaccine Alliance, has funded eligible countries to introduce rubella-containing vaccination (RCV) into their national schedule. Two key indicators used to monitor the impact - the future deaths and DALYs (Disability Adjusted Life Years) averted through vaccination conducted in specific periods - are poorly understood for rubella and Congenital Rubella Syndrome (CRS). We calculate these indicators using an age-structured dynamic transmission model for rubella, with historical vaccination coverage projections during 2001-30 in 92 low and middle-income countries considered most likely to require global support to achieve the Global Vaccine Action Plan's objectives. 131,000 CRS deaths and 12.5 million DALYs may be prevented with immunization campaigns at best-estimate coverage during 2001-30, relative to those without additional support. The impact depended on the time period considered and the method for attributing deaths averted to vaccination in specific periods. The analyses support ongoing activities to reduce CRS-related morbidity and mortality.
MeSH term(s)	Female ; Global Health ; Humans ; Measles-Mumps-Rubella Vaccine/therapeutic use ; Models, Theoretical ; Morbidity ; Poverty ; Pregnancy ; Pregnancy Complications, Infectious/microbiology ; Pregnancy Complications, Infectious/prevention & control ; Quality-Adjusted Life Years ; Rubella Syndrome, Congenital/mortality ; Rubella Syndrome, Congenital/prevention & control ; Vaccination ; Vaccination Coverage
Chemical Substances	Measles-Mumps-Rubella Vaccine
Language	English
Publishing date	2018-10-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2664176-8
ISSN	2164-554X ; 2164-5515
ISSN (online)	2164-554X
ISSN	2164-5515
DOI	10.1080/21645515.2018.1532257
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Positively interacting strains that co-circulate within a network structured population induce cycling epidemics of Mycoplasma pneumoniae.

Zhang, Xu-Sheng / Zhao, Hongxin / Vynnycky, Emilia / Chalker, Vicki

Scientific reports

2019 Volume 9, Issue 1, Page(s) 541

Abstract: Mycoplasma pneumoniae (MP) is considered a common cause of pneumonia, causing about 15-20% of adult community-acquired pneumonia (CAP) and up to 40% of cases in children. It has often been observed that MP epidemics last approximately 1-2 years and occur ...

Abstract	Mycoplasma pneumoniae (MP) is considered a common cause of pneumonia, causing about 15-20% of adult community-acquired pneumonia (CAP) and up to 40% of cases in children. It has often been observed that MP epidemics last approximately 1-2 years and occur every 3-7 years, with the dominant strains alternating between epidemics. However, the underlying mechanism by which these cycles and changes in the dominant strains occur remains unclear. The traditional models for the periodicity of MP epidemics neglected two phenomena: structured contact patterns among people and co-circulating strains of MP. We also believe that the two distinctive aspects of MP epidemics: prevalent serotype shifts among epidemics and incidence cycling of MP, are interconnected. We propose a network transmission model that assumes two strains of MP are transmitted within a network structured population and they can interact as secondary infections with primary infections. Our studies show that multiple strains that co-circulate within a network structured population and interact positively generate the observed patterns of recurrent epidemics of MP. Hence our study provides a possible mechanism for the cycling epidemics of MP, and could provide useful information for future vaccine design and vaccine evaluation/monitoring processes.
MeSH term(s)	Adult ; Child ; Coinfection/epidemiology ; Coinfection/transmission ; Community-Acquired Infections/epidemiology ; Community-Acquired Infections/microbiology ; Community-Acquired Infections/transmission ; Cross Reactions ; Epidemics ; Female ; Humans ; Incidence ; Male ; Models, Biological ; Mycoplasma pneumoniae/immunology ; Periodicity ; Pneumonia, Mycoplasma/epidemiology ; Pneumonia, Mycoplasma/microbiology ; Pneumonia, Mycoplasma/transmission ; Prevalence ; Serogroup
Language	English
Publishing date	2019-01-24
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-018-36325-z
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Transmission dynamics and control measures of COVID-19 outbreak in China

Xu-Sheng Zhang / Emilia Vynnycky / Andre Charlett / Daniela De Angelis / Zhengji Chen / Wei Liu

Scientific Reports, Vol 11, Iss 1, Pp 1-

a modelling study

2021 Volume 12

Abstract: Abstract COVID-19 is reported to have been brought under control in China. To understand the COVID-19 outbreak in China and provide potential lessons for other parts of the world, in this study we apply a mathematical model with multiple datasets to ... ...

Abstract	Abstract COVID-19 is reported to have been brought under control in China. To understand the COVID-19 outbreak in China and provide potential lessons for other parts of the world, in this study we apply a mathematical model with multiple datasets to estimate the transmissibility of the SARS-CoV-2 virus and the severity of the illness associated with the infection, and how both were affected by unprecedented control measures. Our analyses show that before 19th January 2020, 3.5% (95% CI 1.7–8.3%) of infected people were detected; this percentage increased to 36.6% (95% CI 26.1–55.4%) thereafter. The basic reproduction number (R 0) was 2.33 (95% CI 1.96–3.69) before 8th February 2020; then the effective reproduction number dropped to 0.04(95% CI 0.01–0.10). This estimation also indicates that control measures taken since 23rd January 2020 affected the transmissibility about 2 weeks after they were introduced. The confirmed case fatality rate is estimated at 9.6% (95% CI 8.1–11.4%) before 15 February 2020, and then it reduced to 0.7% (95% CI 0.4–1.0%). This shows that SARS-CoV-2 virus is highly transmissible but may be less severe than SARS-CoV-1 and MERS-CoV. We found that at the early stage, the majority of R 0 comes from undetected infectious people. This implies that successful control in China was achieved through reducing the contact rates among people in the general population and increasing the rate of detection and quarantine of the infectious cases.
Keywords	Medicine ; R ; Science ; Q
Subject code	950
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The application of reproduction number concepts to tuberculosis: Vynnycky E, Fine PEM. Epidemiol Infect 1998; 121: 309-324.

Vynnycky, Emilia

Epidemiology and infection

2005 Volume 133 Suppl 1, Page(s) S45–7

MeSH term(s)	Disease Susceptibility/history ; Disease Transmission, Infectious/history ; History, 20th Century ; Humans ; Models, Theoretical ; Tuberculosis, Pulmonary/history ; Tuberculosis, Pulmonary/transmission ; United Kingdom
Language	English
Publishing date	2005-10
Publishing country	England
Document type	Biography ; Classical Article ; Historical Article ; Journal Article
ZDB-ID	632982-2
ISSN	1469-4409 ; 0950-2688
ISSN (online)	1469-4409
ISSN	0950-2688
DOI	10.1017/S0950268805004334
Database	MEDical Literature Analysis and Retrieval System OnLINE

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