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  1. Article ; Online: Waning immunity can drive repeated waves of infections.

    Lai, Desmond Z / Gog, Julia R

    Mathematical biosciences and engineering : MBE

    2024  Volume 21, Issue 2, Page(s) 1979–2003

    Abstract: In infectious disease models, it is known that mechanisms such as births, seasonality in transmission and pathogen evolution can generate oscillations in infection numbers. We show how waning immunity is also a mechanism that is sufficient on its own to ... ...

    Abstract In infectious disease models, it is known that mechanisms such as births, seasonality in transmission and pathogen evolution can generate oscillations in infection numbers. We show how waning immunity is also a mechanism that is sufficient on its own to enable sustained oscillations. When previously infected or vaccinated individuals lose full protective immunity, they become partially susceptible to reinfections. This partial immunity subsequently wanes over time, making individuals more susceptible to reinfections and potentially more infectious if infected. Losses of full and partial immunity lead to a surge in infections, which is the precursor of oscillations. We present a discrete-time Susceptible-Infectious-Immune-Waned-Infectious (SIRWY) model that features the waning of fully immune individuals (as a distribution of time at which individuals lose fully immunity) and the gradual loss of partial immunity (as increases in susceptibility and potential infectiousness over time). A special case of SIRWY is the discrete-time SIRS model with geometric distributions for waning and recovery. Its continuous-time analogue is the classic SIRS with exponential distributions, which does not produce sustained oscillations for any choice of parameters. We show that the discrete-time version can produce sustained oscillations and that the oscillatory regime disappears as discrete-time tends to continuous-time. A different special case of SIRWY is one with fixed times for waning and recovery. We show that this simpler model can also produce sustained oscillations. In conclusion, under certain feature and parameter choices relating to how exactly immunity wanes, fluctuations in infection numbers can be sustained without the need for any additional mechanisms.
    MeSH term(s) Humans ; Reinfection ; Disease Susceptibility ; Systemic Inflammatory Response Syndrome
    Language English
    Publishing date 2024-03-07
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2265126-3
    ISSN 1551-0018 ; 1551-0018
    ISSN (online) 1551-0018
    ISSN 1551-0018
    DOI 10.3934/mbe.2024088
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: The importance of vaccinated individuals to population-level evolution of pathogens.

    Gutierrez, Maria A / Gog, Julia R

    Journal of theoretical biology

    2023  Volume 567, Page(s) 111493

    Abstract: Virus evolution shapes the epidemiological patterns of infectious disease, particularly via evasion of population immunity. At the individual level, host immunity itself may drive viral evolution towards antigenic escape. Using compartmental SIR-style ... ...

    Abstract Virus evolution shapes the epidemiological patterns of infectious disease, particularly via evasion of population immunity. At the individual level, host immunity itself may drive viral evolution towards antigenic escape. Using compartmental SIR-style models with imperfect vaccination, we allow the probability of immune escape to differ in vaccinated and unvaccinated hosts. As the relative contribution to selection in these different hosts varies, the overall effect of vaccination on the antigenic escape pressure at the population level changes. We find that this relative contribution to escape is important for understanding the effects of vaccination on the escape pressure and we draw out some fairly general patterns. If vaccinated hosts do not contribute much more than unvaccinated hosts to the escape pressure, then increasing vaccination always reduces the overall escape pressure. In contrast, if vaccinated hosts contribute significantly more than unvaccinated hosts to the population level escape pressure, then the escape pressure is maximised for intermediate vaccination levels. Past studies find only that the escape pressure is maximal for intermediate levels with fixed extreme assumptions about this relative contribution. Here we show that this result does not hold across the range of plausible assumptions for the relative contribution to escape from vaccinated and unvaccinated hosts. We also find that these results depend on the vaccine efficacy against transmission, particularly through the partial protection against infection. This work highlights the potential value of understanding better how the contribution to antigenic escape pressure depends on individual host immunity.
    MeSH term(s) Humans ; Viruses ; Vaccination ; Population Dynamics
    Language English
    Publishing date 2023-04-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2972-5
    ISSN 1095-8541 ; 0022-5193
    ISSN (online) 1095-8541
    ISSN 0022-5193
    DOI 10.1016/j.jtbi.2023.111493
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: How you can help with COVID-19 modelling.

    Gog, Julia R

    Nature reviews. Physics

    2020  Volume 2, Issue 6, Page(s) 274–275

    Abstract: ... Julia Gog, a mathematical epidemiologist, explains some ways to contribute. ...

    Abstract Many physicists want to use their mathematical modelling skills to study the COVID-19 pandemic. Julia Gog, a mathematical epidemiologist, explains some ways to contribute.
    Language English
    Publishing date 2020-04-08
    Publishing country England
    Document type Journal Article
    ISSN 2522-5820
    ISSN (online) 2522-5820
    DOI 10.1038/s42254-020-0175-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: How you can help with COVID-19 modelling

    Gog, Julia R.

    Nature Reviews Physics

    2020  Volume 2, Issue 6, Page(s) 274–275

    Keywords covid19
    Language English
    Publisher Springer Science and Business Media LLC
    Publishing country us
    Document type Article ; Online
    ISSN 2522-5820
    DOI 10.1038/s42254-020-0175-7
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Book ; Online: How you can help with COVID-19 modelling.

    Gog, Julia R.

    essn: 2522-5820

    2020  

    Abstract: ... Julia Gog, a mathematical epidemiologist, explains some ways to contribute. ...

    Abstract Many physicists want to use their mathematical modelling skills to study the COVID-19 pandemic. Julia Gog, a mathematical epidemiologist, explains some ways to contribute.
    Keywords Scientific Community ; Infectious-disease Epidemiology ; covid19
    Language English
    Publishing date 2020-05-14T00:24:56Z
    Publisher Nature Reviews Physics
    Publishing country uk
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Epidemic interventions: insights from classic results.

    Gog, Julia R / Hollingsworth, T Déirdre

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences

    2021  Volume 376, Issue 1829, Page(s) 20200263

    Abstract: Analytical expressions and approximations from simple models have performed a pivotal role in our understanding of infectious disease epidemiology. During the current COVID-19 pandemic, while there has been proliferation of increasingly complex models, ... ...

    Abstract Analytical expressions and approximations from simple models have performed a pivotal role in our understanding of infectious disease epidemiology. During the current COVID-19 pandemic, while there has been proliferation of increasingly complex models, still the most basic models have provided the core framework for our thinking and interpreting policy decisions. Here, classic results are presented that give insights into both the role of transmission-reducing interventions (such as social distancing) in controlling an emerging epidemic, and also what would happen if insufficient control is applied. Though these are simple results from the most basic of epidemic models, they give valuable benchmarks for comparison with the outputs of more complex modelling approaches. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.
    MeSH term(s) COVID-19/epidemiology ; COVID-19/virology ; Humans ; Models, Theoretical ; Pandemics ; Physical Distancing ; SARS-CoV-2/pathogenicity ; Travel ; United Kingdom/epidemiology
    Language English
    Publishing date 2021-05-31
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 208382-6
    ISSN 1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
    ISSN (online) 1471-2970
    ISSN 0080-4622 ; 0264-3839 ; 0962-8436
    DOI 10.1098/rstb.2020.0263
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Pease (1987): The evolutionary epidemiology of influenza A.

    Andreasen, Viggo / Gog, Julia R

    Theoretical population biology

    2020  Volume 133, Page(s) 29–32

    MeSH term(s) Biological Evolution ; Evolution, Molecular ; Humans ; Influenza A virus/genetics ; Influenza, Human/epidemiology ; Phylogeny
    Language English
    Publishing date 2020-01-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3948-2
    ISSN 1096-0325 ; 0040-5809
    ISSN (online) 1096-0325
    ISSN 0040-5809
    DOI 10.1016/j.tpb.2019.12.006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: A novel approach to finding conserved features in low-variability gene alignments characterises RNA motifs in SARS-CoV and SARS-CoV-2.

    Skittrall, Jordan P / Irigoyen, Nerea / Brierley, Ian / Gog, Julia R

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 12079

    Abstract: Collections of genetic sequences belonging to related organisms contain information on the evolutionary constraints to which the organisms have been subjected. Heavily constrained regions can be investigated to understand their roles in an organism's ... ...

    Abstract Collections of genetic sequences belonging to related organisms contain information on the evolutionary constraints to which the organisms have been subjected. Heavily constrained regions can be investigated to understand their roles in an organism's life cycle, and drugs can be sought to disrupt these roles. In organisms with low genetic diversity, such as newly-emerged pathogens, it is key to obtain this information early to develop new treatments. Here, we present methods that ensure we can leverage all the information available in a low-signal, low-noise set of sequences, to find contiguous regions of relatively conserved nucleic acid. We demonstrate the application of these methods by analysing over 5 million genome sequences of the recently-emerged RNA virus SARS-CoV-2 and correlating these results with an analysis of 119 genome sequences of SARS-CoV. We propose the precise location of a previously described packaging signal, and discuss explanations for other regions of high conservation.
    MeSH term(s) Humans ; SARS-CoV-2/genetics ; COVID-19/genetics ; Nucleotide Motifs ; Sequence Alignment ; Genome, Viral ; Severe acute respiratory syndrome-related coronavirus/genetics
    Language English
    Publishing date 2023-07-26
    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/s41598-023-39207-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: SARS-CoV-2 incidence and vaccine escape.

    Thompson, Robin N / Hill, Edward M / Gog, Julia R

    The Lancet. Infectious diseases

    2021  Volume 21, Issue 7, Page(s) 913–914

    MeSH term(s) COVID-19 ; Humans ; Incidence ; SARS-CoV-2 ; Vaccines
    Chemical Substances Vaccines
    Language English
    Publishing date 2021-04-13
    Publishing country United States
    Document type Letter ; Comment
    ZDB-ID 2061641-7
    ISSN 1474-4457 ; 1473-3099
    ISSN (online) 1474-4457
    ISSN 1473-3099
    DOI 10.1016/S1473-3099(21)00202-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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