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Infectious disease modelling has played an integral part of the scientific evidence used to guide the response to the COVID-19 pandemic. In the UK, modelling evidence used for policy is reported to the Scientific Advisory Group for Emergencies (SAGE) modelling subgroup, SPI-M-O (Scientific Pandemic Influenza Group on Modelling-Operational). This Special Issue contains 20 articles detailing evidence that underpinned advice to the UK government during the SARS-CoV-2 pandemic in the UK between January 2020 and July 2020. Here, we introduce the UK scientific advisory system and how it operates in practice, and discuss how infectious disease modelling can be useful in policy making. We examine the drawbacks of current publishing practices and academic credit and highlight the importance of transparency and reproducibility during an epidemic emergency. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.

• Biodiversity can reduce or increase disease transmission. These divergent effects suggest that community composition rather than diversity per se determines disease transmission. In natural plant communities, little is known about the functional roles of neighbouring plant species in belowground disease transmission. • Here, we experimentally investigated disease transmission of a fungal root pathogen (Rhizoctonia solani) in two focal plant species in combinations with four neighbour species of two ages. We developed stochastic models to test the relative importance of two transmission-modifying mechanisms: (1) infected hosts serve as nutrient supply to increase hyphal growth, so that successful disease transmission is self-reinforcing; and (2) plant resistance increases during plant development. • Neighbouring plants either reduced or increased disease transmission in the focal plants. These effects depended on neighbour age, but could not be explained by a simple dichotomy between hosts and nonhost neighbours. Model selection revealed that both transmission-modifying mechanisms are relevant and that focal host–neighbour interactions changed which mechanisms steered disease transmission rate. • Our work shows that neighbour-induced shifts in the importance of these mechanisms across root networks either make or break disease transmission chains. Understanding how diversity affects disease transmission thus requires integrating interactions between focal and neighbour species and their pathogens.

Background Many European countries experienced outbreaks of mpox in 2022, and there was an mpox outbreak in 2023 in the Democratic Republic of Congo. There were many apparent differences between these outbreaks and previous outbreaks of mpox; the recent outbreaks were observed in men who have sex with men after sexual encounters at common events, whereas earlier outbreaks were observed in a wider population with no identifiable link to sexual contacts. These apparent differences meant that data from previous outbreaks could not reliably be used to parametrise infectious disease models during the 2022 and 2023 mpox outbreaks, and modelling efforts were hampered by uncertainty around key transmission and immunity parameters. Methods We developed a stochastic, discrete-time metapopulation model for mpox that allowed for sexual and non-sexual transmission and the implementation of non-pharmaceutical interventions, specifically contact tracing and pre- and post-exposure vaccinations. We calibrated the model to case data from Berlin and used Sobol sensitivity analysis to identify parameters that mpox transmission is especially sensitive to. We also briefly analysed the sensitivity of the effectiveness of non-pharmaceutical interventions to various efficacy parameters. Results We found that variance in the transmission probabilities due to both sexual and non-sexual transmission had a large effect on mpox transmission in the model, as did the level of immunity to mpox conferred by a previous smallpox vaccination. Furthermore, variance in the number of pre-exposure vaccinations offered was the dominant contributor to variance in mpox dynamics in men who have sex with men. If pre-exposure vaccinations were not available, both the accuracy and timeliness of contact tracing had a large impact on mpox transmission in the model. Conclusions Our results are valuable for guiding epidemiological studies for parameter ascertainment and identifying key factors for success of non-pharmaceutical interventions.

Background Increasing life expectancy and persistently low fertility levels have led to old population age structures in most high-income countries, and population ageing is expected to continue or even accelerate in the coming decades. While older adults on average have few interactions that potentially could lead to disease transmission, their morbidity and mortality due to infectious diseases, respiratory infections in particular, remain substantial. We aim to explore how population ageing affects the future transmission dynamics and mortality burden of emerging respiratory infections. Methods Using longitudinal individual-level data from population registers, we model the Belgian population with evolving age and household structures, and explicitly consider long-term care facilities (LTCFs). Three scenarios are presented for the future proportion of older adults living in LTCFs. For each demographic scenario, we simulate outbreaks of SARS-CoV-2 and a novel influenza A virus in 2020, 2030, 2040 and 2050 and distinguish between household and community transmission. We estimate attack rates by age and household size/type, as well as disease-related deaths and the associated quality-adjusted life-years (QALYs) lost. Results As the population is ageing, small households and LTCFs become more prevalent. Additionally, families with children become smaller (i.e. low fertility, single-parent families). The overall attack rate slightly decreases as the population is ageing, but to a larger degree for influenza than for SARS-CoV-2 due to differential age-specific attack rates. Nevertheless, the number of deaths and QALY losses per 1,000 people is increasing for both infections and at a speed influenced by the share living in LTCFs. Conclusion Population ageing is associated with smaller outbreaks of COVID-19 and influenza, but at the same time it is causing a substantially larger burden of mortality, even if the proportion of LTCF residents were to decrease. These relationships are influenced by age patterns in epidemiological parameters. Not only the shift in the age distribution, but also the induced changes in the household structures are important to consider when assessing the potential impact of population ageing on the transmission and burden of emerging respiratory infections.

Background Mathematical models are valuable tools for guiding public health policy decisions to combat the spread of infectious diseases. Nevertheless, a lack of appropriate quality assessment tools and reporting guidelines hinders the comprehensibility, transparency, and credibility of infectious disease modelling studies and the ability to assess their quality. In a first step towards addressing the need for reporting guidelines and quality assessment tools specific to infectious disease modelling, this scoping review identified common themes in existing reporting and quality assessment guidance for infectious disease modelling studies and adjacent fields. Methods We conducted temporally-unrestricted searches on Medline (via Ovid), Web of Science, medRxiv, and bioRxiv in January 2024 to find articles that provide guidance on writing or assessing modelling studies within infectious disease modelling and adjacent fields including but not limited to healthcare and, more specifically, health economics. Articles were double-screened for eligibility via title-and-abstract screening and full-text screening. Recommendations made by eligible articles were classified into 31 subdimensions which were categorised into seven overarching dimensions ( 1. applicability ; 2. model structure ; 3. parameterisation and calibration ; 4. validity ; 5. uncertainty ; 6. interpretation ; 7. reproducibility , clarity , and transparency ). We followed the PRISMA extension for reporting scoping reviews. Results Our final review included 53 articles. All dimensions except for interpretation were covered by most articles (81%-98%). However, we found substantial heterogeneity in the frequency with which subdimensions were addressed (11%-96%). Subdimensions pertaining to parameter uncertainty and transparency about parameter values were mentioned in most articles (91%-96%); conversely, discussions about auxiliary publication details and software implementation were covered less frequently (11%-23%). Conclusions This review shows that many recommendations made by reporting guidelines and quality assessment tools have thematic similarities and address common topics that are also relevant to infectious disease modelling. These identified themes and recommendations can be used as a starting point to inform the development of standardised guidelines for infectious disease modelling. Registration DOI https://doi.org/10.17605/OSF.IO/AB6D3 . Clinical trial number Not applicable.

Background In Germany, primary vaccination against invasive meningococcal disease (IMD) serogroup C aims to reduce the highest burden of IMD in infants aged 12–23 month. Due to another IMD-peak in adolescents, we modelled the potential impact of introducing adolescent boosters with conjugate meningococcal C or ACWY (MenC/MenACWY) vaccines. Methods We built an age- and serogroup-structured dynamic-transmission model for Germany, which we calibrated to national surveillance data in 2005–2019. We simulated five vaccination scenarios of either continuing with the current MenC primary vaccination (scenario 1), or additionally introducing MenC or MenACWY boosters at age 13 years (scenarios 2–3) or 16 years (scenarios 4–5). We performed comprehensive sensitivity analyses, including on the protection against carriage and serogroup replacement. Results The calibrated model projected for scenario 1 an annual mean of 243 (95%-uncertainty interval: 220–258) expected IMD cases over a 10-year period. Introducing the MenC booster prevented an estimated 5 (3.9–6.7) and the MenACWY booster 8 (6.7–9.1) IMD cases per year on average (scenario 2 and 3). The number-needed-to-vaccinate (NNVs) to prevent one IMD case were 140,000 (100,000-180,000) and 91,000 (76,000-100,000), respectively. To prevent one sequela or death, NNVs were higher (i.e., less efficient). Results were broadly similar for scenarios 4–5. Simulations suggested relevant serogroup replacement starting eight-to-ten years after introducing the MenACWY booster. Conclusions Introducing adolescent MenC or MenACWY boosters marginally reduces the expected IMD burden in Germany. Effectiveness and efficiency of evaluated strategies depend on future incidence. The magnitude of future serogroup replacement for the MenACWY vaccine is highly uncertain.

Early case detection is critical to preventing onward transmission of COVID-19 by enabling prompt isolation of index infections, and identification and quarantining of contacts. Timeliness and completeness of ascertainment depend on the surveillance strategy employed. This paper presents modelling used to inform workplace testing strategies for the Australian government in early 2021. We use rapid prototype modelling to quickly investigate the effectiveness of testing strategies to aid decision making. Models are developed with a focus on providing relevant results to policy makers, and these models are continually updated and improved as new questions are posed. Developed to support the implementation of testing strategies in high risk workplace settings in Australia, our modelling explores the effects of test frequency and sensitivity on outbreak detection. We start with an exponential growth model, which demonstrates how outbreak detection changes depending on growth rate, test frequency and sensitivity. From the exponential model, we learn that low sensitivity tests can produce high probabilities of detection when testing occurs frequently. We then develop a more complex Agent Based Model, which was used to test the robustness of the results from the exponential model, and extend it to include intermittent workplace scheduling. These models help our fundamental understanding of disease detectability through routine surveillance in workplaces and evaluate the impact of testing strategies and workplace characteristics on the effectiveness of surveillance. This analysis highlights the risks of particular work patterns while also identifying key testing strategies to best improve outbreak detection in high risk workplaces.

Background Day-to-day variability in social contacts can shape transmission dynamics yet is rarely quantified. We aimed to quantify intraindividual variability (IIV) in non-household contacts during the COVID-19 pandemic in Germany and to assess its associations with sociodemographic characteristics, vaccination, and policy stringency. Methods We analyzed longitudinal contact survey data with 33 waves between April 2020 and December 2021, including 7,845 participants and 59,462 observations. Pearson residuals from a mixed-effects negative binomial model were used to derive the within-person standard deviation (riSD) for participants with at least two observations, as a proxy of IIV. Gamma regression models with log link were fitted to estimate mean ratios (MR). Results Children and adolescents aged 0–17 years showed higher riSD than other age groups (MR = 1.13, 95% CI 1.09–1.16). Participants living in households with three or more members had higher riSD than those living alone (1.05, 95% CI 1.02–1.07). Retired individuals, homemakers, the unemployed, and students exhibited lower riSD than employed participants. Regarding COVID-19 vaccination, compared with the pre-vaccination window (− 100 to 0 days), riSD was higher in the post-vaccination window (1 to 100 days after the first COVID-19 vaccination dose) (1.13, 95% CI 1.06–1.20). Weaker policy stringency was strongly associated with higher riSD (1.36, 95% CI 1.32–1.39). Conclusions IIV in non-household contacts was shaped by age, household composition, employment status, vaccination status, and policy context. Analyses relying solely on average contact numbers may misrepresent transmission risk when contact behavior is highly variable. Incorporating IIV alongside mean contact levels may improve infectious disease models and inform public health policies.

Almost all models used in analysis of infectious disease outbreaks contain some notion of population size, usually taken as the census population size of the community in question. In many settings, however, the census population is not equivalent to the population likely to be exposed, for example if there are population structures, outbreak controls or other heterogeneities. Although these factors may be taken into account in the model: adding compartments to a compartmental model, variable mixing rates and so on, this makes fitting more challenging, especially if the population complexities are not fully known. In this work we consider the concept of effective population size in outbreak modelling, which we define as the size of the population involved in an outbreak, as an alternative to use of more complex models. Effective population size is an important quantity in genetics for estimation of genetic diversity loss in populations, but it has not been widely applied in epidemiology. Through simulation studies and application to data from outbreaks of COVID-19 in China, we find that simple SIR models with effective population size can provide a good fit to data which are not themselves simple or SIR.

Background Respiratory syncytial virus (RSV) is the most common cause of acute lower respiratory infections in children worldwide. The highest incidence of severe disease is in the first 6 months of life, with infants born preterm at greatest risk for severe RSV infections. The licensure of new RSV therapeutics (a long-acting monoclonal antibody and a maternal vaccine) in Europe, USA, UK and most recently in Australia, has driven the need for strategic decision making on the implementation of RSV immunisation programs. Data driven approaches, considering the local RSV epidemiology, are critical to advise on the optimal use of these therapeutics for effective RSV control. Methods We developed a dynamic compartmental model of RSV transmission fitted to individually-linked population-based laboratory, perinatal and hospitalisation data for 2000–2012 from metropolitan Western Australia (WA), stratified by age and prior exposure. We account for the differential risk of RSV-hospitalisation in full-term and preterm infants (defined as < 37 weeks gestation). We formulated a function relating age, RSV exposure history, and preterm status to the risk of RSV-hospitalisation given infection. Results The age-to-risk function shows that risk of hospitalisation, given RSV infection, declines quickly in the first 12 months of life for all infants and is 2.6 times higher in preterm compared with term infants. The hospitalisation risk, given infection, declines to < 10% of the risk at birth by age 7 months for term infants and by 9 months for preterm infants. Conclusions The dynamic model, using the age-to-risk function, characterises RSV epidemiology for metropolitan WA and can now be extended to predict the impact of prevention measures. The stratification of the model by preterm status will enable the comparative assessment of potential strategies in the extended model that target this RSV risk group relative to all-population approaches. Furthermore, the age-to-risk function developed in this work has wider relevance to the epidemiological characterisation of RSV.