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The reproduction number R$$ R $$ has been a central metric of the COVID‐19 pandemic response, published weekly by the UK government and regularly reported in the media. Here, we provide a formal definition and discuss the advantages and most common misconceptions around this quantity. We consider the intuition behind different formulations of R$$ R $$, the complexities in its estimation (including the unavoidable lags involved), and its value compared to other indicators (e.g. the growth rate) that can be directly observed from aggregate surveillance data and react more promptly to changes in epidemic trend. As models become more sophisticated, with age and/or spatial structure, formulating R$$ R $$ becomes increasingly complicated and inevitably model‐dependent. We present some models currently used in the UK pandemic response as examples. Ultimately, limitations in the available data streams, data quality and time constraints force pragmatic choices to be made on a quantity that is an average across time, space, social structure and settings. Effectively communicating these challenges is important but often difficult in an emergency. [ABSTRACT FROM AUTHOR]

Infectious disease introduced by non-native species is increasingly cited as a facilitator of native population declines, but direct evidence may be lacking due to inadequate population and disease prevalence data surrounding an outbreak. Previous indirect evidence and theoretical models support squirrelpox virus ( SQPV) as being potentially involved in the decline of red squirrels ( Sciurus vulgaris) following the introduction of the non-native gray squirrel ( Sciurus carolinensis) to the United Kingdom. The red squirrel is a major UK conservation concern and understanding its continuing decline is important for any attempt to mitigate the decline. The red squirrel-gray squirrel system is also exemplary of the interplay between infectious disease (apparent competition) and direct competition in driving the replacement of a native by an invasive species. Time series data from Merseyside are presented on squirrel abundance and squirrelpox disease ( SQPx) incidence, to determine the effect of the pathogen and the non-native species on the native red squirrel populations. Analysis indicates that SQPx in red squirrels has a significant negative impact on squirrel densities and their population growth rate ( PGR). There is little evidence for a direct gray squirrel impact; only gray squirrel presence (but not density) proved to influence red squirrel density, but not red squirrel PGR. The dynamics of red SQPx cases are largely determined by previous red SQPx cases, although previous infection of local gray squirrels also feature, and thus, SQPV-infected gray squirrels are identified as potentially initiating outbreaks of SQPx in red squirrels. Retrospective serology indicates that approximately 8% of red squirrels exposed to SQPV may survive infection during an epidemic. This study further highlights the UK red squirrel - gray squirrel system as a classic example of a native species population decline strongly facilitated by infectious disease introduced by a non-native species. It is therefore paramount that disease prevention and control measures are integral in attempts to conserve red squirrels in the United Kingdom. [ABSTRACT FROM AUTHOR]

Abstract Background Measuring vaccine effectiveness (VE) relies on the use of observational study designs. However, achieving robust estimates of direct and indirect VE is frequently compromised by bias, particularly when using syndromic diagnoses of low-specificity. Methods In order to mitigate confounding between the measured outcome and vaccine uptake, we developed a method to balance comparator populations using individual-level propensity scoring derived from the vaccine-exposed population, and applied it to the unexposed comparator population. Indirect VE was estimated by comparing the unvaccinated vaccine-exposed group with a propensity score-simulated unvaccinated, unexposed group. Direct VE was derived by removing indirect VE from the overall VE. We applied this method to an evaluation of the effectiveness of infant rotavirus vaccination in the UK. Using a general practice cohort of 45,259 live births between May 2010 and December 2015, we calculated indirect and direct VE against consultations for acute gastroenteritis using conventional and vaccination-propensity adjustment comparator populations. Results The overall VE during the rotavirus-season (January-May) calculated using mixed-effects Cox regression was 30% [95% confidence intervals (95% CI: 25,35%)]. Use of conventional comparator populations resulted in implausible VE estimates −14% (95% CI: −41,7%) for direct and 29% (95% CI: 14,42%) for indirect effects. Applying our alternative method, direct VE was 26% (95% CI: 1,45%) and indirect VE was 8% (95% CI: −19,29%). Conclusions Estimating VE using propensity score simulated comparator populations, particularly for studies using routine health data with syndromic, low-specificity endpoints will aid accurate measurement of the broader public health impact of a vaccine programme. [ABSTRACT FROM AUTHOR]

Objective: To determine and identify distance patterns in the movements of medical students and junior doctors between their training locations., Design: A retrospective cohort study of UK medical students from 2002 to 2015 (UKMED data)., Setting: All UK medical schools, foundations and specialty training organisation., Participants: All UK medical students from 2002 to 2015, for a total of 97 932 participants., Outcome Measures: Individual movements and number of movements by county of students from family home to medical school training, from medical school to foundation training and from foundation to specialty training., Methods: Leslie matrix, principal components analysis, Gini coefficient, χ 2 test, generalised linear models and variable selection methods were employed to explore the different facets of students' and junior doctors' movements from the family home to medical school and for the full pathway (from family home to specialty training)., Results: The majority of the movements between the different stages of the full pathway were restricted to a distance of up to 50 km; although the proportion of movements changed from year-to-year, with longer movements during 2007-2008. At the individual level, ethnicity, socioeconomic class of the parent(s) and the deprivation score of the family home region were found to be the most important factors associated with the length of the movements from the family home to medical school. Similar results were found when movements were aggregated at the county level, with the addition of factors such as gender and qualification at entry (to medical school) being statistically associated with the number of new entrant students moving between counties., Conclusion: Our findings show that while future doctors do not move far from their family home or training location, this pattern is not homogeneous over time. Distances are influenced by demographics, socioeconomic status and deprivation. These results may contribute in designing interventions aimed at solving the chronic problems of maldistribution and underdoctoring in the UK., Competing Interests: Competing interests: CM is a medical director and director of education and standards at the General Medical Council. Views expressed in this article do not necessarily reflect those of the General Medical Council., (© Author(s) (or their employer(s)) 2024. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Longitudinal, community-based sampling is important for understanding prevalence and transmission of respiratory pathogens. Using a minimally invasive sampling method, the FAMILY Micro study monitored the oral, nasal and hand microbiota of families for 6 months. Here, we explore participant experiences and opinions. A mixed methods approach was utilised. A quantitative questionnaire was completed after every sampling timepoint to report levels of discomfort and pain, as well as time taken to collect samples. Participants were also invited to discuss their experiences in a qualitative structured exit interview. We received questionnaires from 36 families. Most adults and children >5y experienced no pain (94% and 70%) and little discomfort (73% and 47% no discomfort) regardless of sample type, whereas children ≤5y experienced variable levels of pain and discomfort (48% no pain but 14% hurts even more, whole lot or worst; 38% no discomfort but 33% moderate, severe, or extreme discomfort). The time taken for saliva and hand sampling decreased over the study. We conducted interviews with 24 families. Families found the sampling method straightforward, and adults and children >5y preferred nasal sampling using a synthetic absorptive matrix over nasopharyngeal swabs. It remained challenging for families to fit sampling into their busy schedules. Adequate fridge/freezer space and regular sample pick-ups were found to be important factors for feasibility. Messaging apps proved extremely effective for engaging with participants. Our findings provide key information to inform the design of future studies, specifically that self-sampling at home using minimally invasive procedures is feasible in a family context., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 German et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Objectives: To quantify contact patterns of UK home delivery drivers and identify protective measures adopted during the pandemic., Methods: We conducted a cross-sectional online survey to measure the interactions of 170 UK delivery drivers during a working shift between 7 December 2020 and 31 March 2021., Results: Delivery drivers had a mean number of 71.6 (95% CI 61.0 to 84.1) customer contacts per shift and 15.0 (95% CI 11.2 to 19.2) depot contacts per shift. Maintaining physical distancing with customers was more common than at delivery depots. Prolonged contact (more than 5 min) with customers was reported by 5.4% of drivers on their last shift. We found 3.0% of drivers had tested positive for SARS-CoV-2 since the start of the pandemic and 16.8% of drivers had self-isolated due to a suspected or confirmed case of COVID-19. In addition, 5.3% (95% CI 2.3% to 10.2%) of participants reported having worked while ill with COVID-19 symptoms, or with a member of their household having a suspected or confirmed case of COVID-19., Conclusion: Delivery drivers had a large number of face-to-face customer and depot contacts per shift compared with other working adults during this time. However, transmission risk may be curtailed as contact with customers was of short duration. Most drivers were unable to maintain physical distance with customers and at depots at all times. Usage of protective items such as face masks and hand sanitiser was widespread., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2023. Re-use permitted under CC BY. Published by BMJ.)

Objectives: To quantify and characterise non-household contact and to identify the effect of shielding and isolating on contact patterns., Design: Cross-sectional study., Setting and Participants: Anyone living in the UK was eligible to take part in the study. We recorded 5143 responses to the online questionnaire between 28 July 2020 and 14 August 2020., Outcome Measures: Our primary outcome was the daily non-household contact rate of participants. Secondary outcomes were propensity to leave home over a 7 day period, whether contacts had occurred indoors or outdoors locations visited, the furthest distance travelled from home, ability to socially distance and membership of support bubble., Results: The mean rate of non-household contacts per person was 2.9 d -1 . Participants attending a workplace (adjusted incidence rate ratio (aIRR) 3.33, 95% CI 3.02 to 3.66), self-employed (aIRR 1.63, 95% CI 1.43 to 1.87) or working in healthcare (aIRR 5.10, 95% CI 4.29 to 6.10) reported significantly higher non-household contact rates than those working from home. Participants self-isolating as a precaution or following Test and Trace instructions had a lower non-household contact rate than those not self-isolating (aIRR 0.58, 95% CI 0.43 to 0.79). We found limited evidence that those shielding had reduced non-household contacts compared with non-shielders., Conclusion: The daily rate of non-household interactions remained lower than prepandemic levels measured by other studies, suggesting continued adherence to social distancing guidelines. Individuals attending a workplace in-person or employed as healthcare professionals were less likely to maintain social distance and had a higher non-household contact rate, possibly increasing their infection risk. Shielding and self-isolating individuals required greater support to enable them to follow the government guidelines and reduce non-household contact and therefore their risk of infection., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY. Published by BMJ.)

In the absence of a vaccine, severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) transmission has been controlled by preventing person-to-person interactions via social distancing measures. In order to re-open parts of society, policy-makers need to consider how combinations of measures will affect transmission and understand the trade-offs between them. We use age-specific social contact data, together with epidemiological data, to quantify the components of the COVID-19 reproduction number. We estimate the impact of social distancing policies on the reproduction number by turning contacts on and off based on context and age. We focus on the impact of re-opening schools against a background of wider social distancing measures. We demonstrate that pre-collected social contact data can be used to provide a time-varying estimate of the reproduction number ( R ). We find that following lockdown (when R = 0.7, 95% CI 0.6, 0.8), opening primary schools has a modest impact on transmission ( R = 0.89, 95% CI 0.82-0.97) as long as other social interactions are not increased. Opening secondary and primary schools is predicted to have a larger impact ( R = 1.22, 95% CI 1.02-1.53). Contact tracing and COVID security can be used to mitigate the impact of increased social mixing to some extent; however, social distancing measures are still required to control transmission. Our approach has been widely used by policy-makers to project the impact of social distancing measures and assess the trade-offs between them. Effective social distancing, contact tracing and COVID security are required if all age groups are to return to school while controlling transmission. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.