LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 300

Search options

  1. Article: Steven Riley's discussion contribution to papers in Session 3 of the Royal Statistical Society's Special Topic Meeting on COVID-19 transmission: 11 June 2021.

    Riley, Steven

    Journal of the Royal Statistical Society. Series A, (Statistics in Society)

    2022  Volume 185, Issue Suppl 1, Page(s) S148–S149

    Language English
    Publishing date 2022-12-11
    Publishing country England
    Document type Journal Article
    ZDB-ID 1490715-X
    ISSN 1467-985X ; 0964-1998 ; 0035-9238
    ISSN (online) 1467-985X
    ISSN 0964-1998 ; 0035-9238
    DOI 10.1111/rssa.12981
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  2. Article ; Online: Differences between the true reproduction number and the apparent reproduction number of an epidemic time series.

    Eales, Oliver / Riley, Steven

    Epidemics

    2024  Volume 46, Page(s) 100742

    Abstract: The time-varying reproduction number R(t) measures the number of new infections per infectious individual and is closely correlated with the time series of infection incidence by definition. The timings of actual infections are rarely known, and analysis ...

    Abstract The time-varying reproduction number R(t) measures the number of new infections per infectious individual and is closely correlated with the time series of infection incidence by definition. The timings of actual infections are rarely known, and analysis of epidemics usually relies on time series data for other outcomes such as symptom onset. A common implicit assumption, when estimating R(t) from an epidemic time series, is that R(t) has the same relationship with these downstream outcomes as it does with the time series of incidence. However, this assumption is unlikely to be valid given that most epidemic time series are not perfect proxies of incidence. Rather they represent convolutions of incidence with uncertain delay distributions. Here we define the apparent time-varying reproduction number, R
    MeSH term(s) Humans ; COVID-19/epidemiology ; Time Factors ; SARS-CoV-2 ; Pandemics
    Language English
    Publishing date 2024-01-13
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2467993-8
    ISSN 1878-0067 ; 1755-4365
    ISSN (online) 1878-0067
    ISSN 1755-4365
    DOI 10.1016/j.epidem.2024.100742
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  3. Article ; Online: Is annual vaccination best? A modelling study of influenza vaccination strategies in children.

    Ainslie, Kylie E C / Riley, Steven

    Vaccine

    2022  Volume 40, Issue 21, Page(s) 2940–2948

    Abstract: Introduction: Annual vaccination of children against influenza is a key component of vaccination programs in many countries. However, past infection and vaccination may affect an individual's susceptibility to infection. Little research has evaluated ... ...

    Abstract Introduction: Annual vaccination of children against influenza is a key component of vaccination programs in many countries. However, past infection and vaccination may affect an individual's susceptibility to infection. Little research has evaluated whether annual vaccination is the best strategy. Using the United Kingdom as our motivating example, we developed a framework to assess the impact of different childhood vaccination strategies, specifically annual and biennial (every other year), on attack rate and expected number of infections.
    Methods and findings: We present a multi-annual, individual-based, stochastic, force of infection model that accounts for individual exposure histories and disease/vaccine dynamics influencing susceptibility. We simulate birth cohorts that experience yearly influenza epidemics and follow them until age 18 to determine attack rates and the number of infections during childhood. We perform simulations under baseline conditions, with an assumed vaccination coverage of 44%, to compare annual vaccination to no and biennial vaccination. We relax our baseline assumptions to explore how our model assumptions impact vaccination program performance. At baseline, we observed less than half the number of infections between the ages 2 and 10 under annual vaccination in children who had been vaccinated at least half the time compared to no vaccination. When averaged over all ages 0-18, the number of infections under annual vaccination was 2.07 (2.06, 2.08) compared to 2.63 (2.62, 2.64) under no vaccination, and 2.38 (2.37, 2.40) under biennial vaccination. When we introduced a penalty for repeated exposures, we observed a decrease in the difference in infections between the vaccination strategies. Specifically, the difference in childhood infections under biennial compared to annual vaccination decreased from 0.31 to 0.04 as exposure penalty increased.
    Conclusion: Our results indicate that while annual vaccination averts more childhood infections than biennial vaccination, this difference is small. Our work confirms the value of annual vaccination in children, even with modest vaccination coverage, but also shows that similar benefits of vaccination may be obtained by implementing a biennial vaccination program.
    Author summary: Many countries include annual vaccination of children against influenza in their vaccination programs. In the United Kingdom (UK), annual vaccination of children aged of 2 to 10 against influenza is recommended. However, little research has evaluated whether annual vaccination is the best strategy, while accounting for how past infection and vaccination may affect an individual's susceptibility to infection in the current influenza season. Prior work has suggested that there may be a negative effect of repeated vaccination. In this work we developed a stochastic, individual-based model to assess the impact of repeated vaccination strategies on childhood infections. Specifically, we first compare annual vaccination to no vaccination and then annual vaccination to biennial (every other year) vaccination. We use the UK as our motivating example. We found that an annual vaccination strategy resulted in the fewest childhood infections, followed by biennial vaccination. The difference in number of childhood infections between the different vaccination strategies decreased when we introduced a penalty for repeated exposures. Our work confirms the value of annual vaccination in children, but also shows that similar benefits of vaccination can be obtained by implementing a biennial vaccination program, particularly when there is a negative effect of repeated vaccinations.
    MeSH term(s) Child ; Child, Preschool ; Humans ; Immunization Programs ; Influenza Vaccines/adverse effects ; Influenza, Human/epidemiology ; Influenza, Human/prevention & control ; Seasons ; Vaccination
    Chemical Substances Influenza Vaccines
    Language English
    Publishing date 2022-04-08
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 605674-x
    ISSN 1873-2518 ; 0264-410X
    ISSN (online) 1873-2518
    ISSN 0264-410X
    DOI 10.1016/j.vaccine.2022.03.065
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  4. Article ; Online: Population Monitoring of SARS-CoV-2 Infections via Random Sampling During the COVID-19 Pandemic.

    Elliott, Paul / Ward, Helen / Riley, Steven

    American journal of public health

    2023  Volume 113, Issue 5, Page(s) 514–516

    MeSH term(s) Humans ; COVID-19 ; SARS-CoV-2 ; Pandemics ; Research Design
    Language English
    Publishing date 2023-03-09
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 121100-6
    ISSN 1541-0048 ; 0090-0036 ; 0002-9572
    ISSN (online) 1541-0048
    ISSN 0090-0036 ; 0002-9572
    DOI 10.2105/AJPH.2023.307231
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  5. Book ; Online: Differences between the true reproduction number and the apparent reproduction number of an epidemic time series

    Eales, Oliver / Riley, Steven

    2023  

    Abstract: The time-varying reproduction number $R(t)$ measures the number of new infections per infectious individual and is closely correlated with the time series of infection incidence by definition. The timings of actual infections are rarely known, and ... ...

    Abstract The time-varying reproduction number $R(t)$ measures the number of new infections per infectious individual and is closely correlated with the time series of infection incidence by definition. The timings of actual infections are rarely known, and analysis of epidemics usually relies on time series data for other outcomes such as symptom onset. A common implicit assumption, when estimating $R(t)$ from an epidemic time series, is that $R(t)$ has the same relationship with these downstream outcomes as it does with the time series of incidence. However, this assumption is unlikely to be valid given that most epidemic time series are not perfect proxies of incidence. Rather they represent convolutions of incidence with uncertain delay distributions. Here we define the apparent time-varying reproduction number, $R_A(t)$, the reproduction number calculated from a downstream epidemic time series and demonstrate how differences between $R_A(t)$ and $R(t)$ depend on the convolution function. The mean of the convolution function sets a time offset between the two signals, whilst the variance of the convolution function introduces a relative distortion between them. We present the convolution functions of epidemic time series that were available during the SARS-CoV-2 pandemic. Infection prevalence, measured by random sampling studies, presents fewer biases than other epidemic time series. Here we show that additionally the mean and variance of its convolution function were similar to that obtained from traditional surveillance based on mass-testing and could be reduced using more frequent testing, or by using stricter thresholds for positivity. Infection prevalence studies continue to be a versatile tool for tracking the temporal trends of $R(t)$, and with additional refinements to their study protocol, will be of even greater utility during any future epidemics or pandemics.
    Keywords Quantitative Biology - Populations and Evolution ; Quantitative Biology - Quantitative Methods
    Subject code 612
    Publishing date 2023-07-07
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    More links

    Kategorien

  6. Article ; Online: Epidemiology: Making high-res Zika maps.

    Riley, Steven

    Nature microbiology

    2016  Volume 1, Issue 9, Page(s) 16157

    MeSH term(s) Humans ; Zika Virus ; Zika Virus Infection
    Language English
    Publishing date 2016-08-26
    Publishing country England
    Document type Journal Article ; Comment
    ISSN 2058-5276
    ISSN (online) 2058-5276
    DOI 10.1038/nmicrobiol.2016.157
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  7. Article ; Online: Simulation Study of Surveillance Strategies for Faster Detection of Novel SARS-CoV-2 Variants.

    Patel, Selina / Cumming, Fergus / Mayers, Carl / Charlett, André / Riley, Steven

    Emerging infectious diseases

    2023  Volume 29, Issue 11, Page(s) 2292–2297

    Abstract: Earlier global detection of novel SARS-CoV-2 variants gives governments more time to respond. However, few countries can implement timely national surveillance, resulting in gaps in monitoring. The United Kingdom implemented large-scale community and ... ...

    Abstract Earlier global detection of novel SARS-CoV-2 variants gives governments more time to respond. However, few countries can implement timely national surveillance, resulting in gaps in monitoring. The United Kingdom implemented large-scale community and hospital surveillance, but experience suggests it might be faster to detect new variants through testing England arrivals for surveillance. We developed simulations of emergence and importation of novel variants with a range of infection hospitalization rates to the United Kingdom. We compared time taken to detect the variant though testing arrivals at England borders, hospital admissions, and the general community. We found that sampling 10%-50% of arrivals at England borders could confer a speed advantage of 3.5-6 weeks over existing community surveillance and 1.5-5 weeks (depending on infection hospitalization rates) over hospital testing. Directing limited global capacity for surveillance to highly connected ports could speed up global detection of novel SARS-CoV-2 variants.
    MeSH term(s) Humans ; COVID-19/diagnosis ; SARS-CoV-2/genetics ; England/epidemiology ; United Kingdom/epidemiology
    Language English
    Publishing date 2023-11-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1380686-5
    ISSN 1080-6059 ; 1080-6040
    ISSN (online) 1080-6059
    ISSN 1080-6040
    DOI 10.3201/eid2911.230492
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  8. Article: Is annual vaccination best? A modelling study of influenza vaccination strategies in children

    Ainslie, Kylie E.C. / Riley, Steven

    Vaccine. 2022 May 09, v. 40, no. 21

    2022  

    Abstract: Annual vaccination of children against influenza is a key component of vaccination programs in many countries. However, past infection and vaccination may affect an individual’s susceptibility to infection. Little research has evaluated whether annual ... ...

    Abstract Annual vaccination of children against influenza is a key component of vaccination programs in many countries. However, past infection and vaccination may affect an individual’s susceptibility to infection. Little research has evaluated whether annual vaccination is the best strategy. Using the United Kingdom as our motivating example, we developed a framework to assess the impact of different childhood vaccination strategies, specifically annual and biennial (every other year), on attack rate and expected number of infections. We present a multi-annual, individual-based, stochastic, force of infection model that accounts for individual exposure histories and disease/vaccine dynamics influencing susceptibility. We simulate birth cohorts that experience yearly influenza epidemics and follow them until age 18 to determine attack rates and the number of infections during childhood. We perform simulations under baseline conditions, with an assumed vaccination coverage of 44%, to compare annual vaccination to no and biennial vaccination. We relax our baseline assumptions to explore how our model assumptions impact vaccination program performance. At baseline, we observed less than half the number of infections between the ages 2 and 10 under annual vaccination in children who had been vaccinated at least half the time compared to no vaccination. When averaged over all ages 0–18, the number of infections under annual vaccination was 2.07 (2.06, 2.08) compared to 2.63 (2.62, 2.64) under no vaccination, and 2.38 (2.37, 2.40) under biennial vaccination. When we introduced a penalty for repeated exposures, we observed a decrease in the difference in infections between the vaccination strategies. Specifically, the difference in childhood infections under biennial compared to annual vaccination decreased from 0.31 to 0.04 as exposure penalty increased. Our results indicate that while annual vaccination averts more childhood infections than biennial vaccination, this difference is small. Our work confirms the value of annual vaccination in children, even with modest vaccination coverage, but also shows that similar benefits of vaccination may be obtained by implementing a biennial vaccination program. Many countries include annual vaccination of children against influenza in their vaccination programs. In the United Kingdom (UK), annual vaccination of children aged of 2 to 10 against influenza is recommended. However, little research has evaluated whether annual vaccination is the best strategy, while accounting for how past infection and vaccination may affect an individual’s susceptibility to infection in the current influenza season. Prior work has suggested that there may be a negative effect of repeated vaccination. In this work we developed a stochastic, individual-based model to assess the impact of repeated vaccination strategies on childhood infections. Specifically, we first compare annual vaccination to no vaccination and then annual vaccination to biennial (every other year) vaccination. We use the UK as our motivating example. We found that an annual vaccination strategy resulted in the fewest childhood infections, followed by biennial vaccination. The difference in number of childhood infections between the different vaccination strategies decreased when we introduced a penalty for repeated exposures. Our work confirms the value of annual vaccination in children, but also shows that similar benefits of vaccination can be obtained by implementing a biennial vaccination program, particularly when there is a negative effect of repeated vaccinations.
    Keywords childhood ; influenza ; influenza vaccination ; models ; vaccines ; United Kingdom
    Language English
    Dates of publication 2022-0509
    Size p. 2940-2948.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 605674-x
    ISSN 1873-2518 ; 0264-410X
    ISSN (online) 1873-2518
    ISSN 0264-410X
    DOI 10.1016/j.vaccine.2022.03.065
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

  9. Article ; Online: Phylogenetic evidence for a mild H1 pandemic in the early 1900s.

    Riley, Steven

    Proceedings of the National Academy of Sciences of the United States of America

    2014  Volume 111, Issue 22, Page(s) 7892–7893

    MeSH term(s) Animals ; Humans ; Influenza A virus/genetics ; Influenza A virus/immunology ; Influenza Pandemic, 1918-1919/mortality ; Influenza, Human/mortality ; Influenza, Human/virology ; Reassortant Viruses/genetics
    Keywords covid19
    Language English
    Publishing date 2014-05-27
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1406869111
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

  10. Article ; Online: Consistent pattern of epidemic slowing across many geographies led to longer, flatter initial waves of the COVID-19 pandemic.

    Ben-Nun, Michal / Riley, Pete / Turtle, James / Riley, Steven

    PLoS computational biology

    2022  Volume 18, Issue 8, Page(s) e1010375

    Abstract: To define appropriate planning scenarios for future pandemics of respiratory pathogens, it is important to understand the initial transmission dynamics of COVID-19 during 2020. Here, we fit an age-stratified compartmental model with a flexible underlying ...

    Abstract To define appropriate planning scenarios for future pandemics of respiratory pathogens, it is important to understand the initial transmission dynamics of COVID-19 during 2020. Here, we fit an age-stratified compartmental model with a flexible underlying transmission term to daily COVID-19 death data from states in the contiguous U.S. and to national and sub-national data from around the world. The daily death data of the first months of the COVID-19 pandemic was qualitatively categorized into one of four main profile types: "spring single-peak", "summer single-peak", "spring/summer two-peak" and "broad with shoulder". We estimated a reproduction number R as a function of calendar time tc and as a function of time since the first death reported in that population (local pandemic time, tp). Contrary to the diversity of categories and range of magnitudes in death incidence profiles, the R(tp) profiles were much more homogeneous. We found that in both the contiguous U.S. and globally, the initial value of both R(tc) and R(tp) was substantial: at or above two. However, during the early months, pandemic time R(tp) decreased exponentially to a value that hovered around one. This decrease was accompanied by a reduction in the variance of R(tp). For calendar time R(tc), the decrease in magnitude was slower and non-exponential, with a smaller reduction in variance. Intriguingly, similar trends of exponential decrease and reduced variance were not observed in raw death data. Our findings suggest that the combination of specific government responses and spontaneous changes in behaviour ensured that transmissibility dropped, rather than remaining constant, during the initial phases of a pandemic. Future pandemic planning scenarios should include models that assume similar decreases in transmissibility, which lead to longer epidemics with lower peaks when compared with models based on constant transmissibility.
    MeSH term(s) COVID-19/epidemiology ; Forecasting ; Government ; Humans ; Pandemics ; Seasons
    Language English
    Publishing date 2022-08-15
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, U.S. Gov't, P.H.S.
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1010375
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

To top