Integrating wastewater and randomised prevalence survey data for national COVID surveillance.

During the COVID-19 pandemic, studies in a number of countries have shown how wastewater can be used as an efficient surveillance tool to detect outbreaks at much lower cost than traditional prevalence surveys. In this study, we consider the utilisation of wastewater data in the post-pandemic setting, in which collection of health data via national randomised prevalence surveys will likely be run at a reduced scale; hence an affordable ongoing surveillance system will need to combine sparse prevalence data with non-traditional disease metrics such as wastewater measurements in order to estimate disease progression in a cost-effective manner. Here, we use data collected during the pandemic to model the dynamic relationship between spatially granular wastewater viral load and disease prevalence. We then use this relationship to nowcast local disease prevalence under the scenario that (i) spatially granular wastewater data continue to be collected; (ii) direct measurements of prevalence are only available at a coarser spatial resolution, for example at national or regional scale. The results from our cross-validation study demonstrate the added value of wastewater data in improving nowcast accuracy and reducing nowcast uncertainty. Our results also highlight the importance of incorporating prevalence data at a coarser spatial scale when nowcasting prevalence at fine spatial resolution, calling for the need to maintain some form of reduced-scale national prevalence surveys in non-epidemic periods. The model framework is disease-agnostic and could therefore be adapted to different diseases and incorporated into a multiplex surveillance system for early detection of emerging local outbreaks.

The effect of immigration policy reform on mental health in people from minoritised ethnic groups in England: an interrupted time series analysis of longitudinal data from the UK Household Longitudinal Study cohort.

BACKGROUND: In 2012, the UK Government announced a series of immigration policy reforms known as the hostile environment policy, culminating in the Windrush scandal. We aimed to investigate the effect of the hostile environment policy on mental health for people from minoritised ethnic backgrounds. We hypothesised that people from Black Caribbean backgrounds would have worse mental health relative to people from White ethnic backgrounds after the Immigration Act 2014 and the Windrush scandal media coverage in 2017, since they were particularly targeted. METHODS: Using data from the UK Household Longitudinal Study, we performed a Bayesian interrupted time series analysis, accounting for fixed effects of confounders (sex, age, urbanicity, relationship status, number of children, education, physical or mental health impairment, housing, deprivation, employment, place of birth, income, and time), and random effects for residual temporal and spatial variation. We measured mental ill health using a widely used, self-administered questionnaire on psychological distress, the 12-item General Health Questionnaire (GHQ-12). We compared mean differences (MDs) and 95% credible intervals (CrIs) in mental ill health among people from minoritised ethnic groups (Black Caribbean, Black African, Indian, Bangladeshi, and Pakistani) relative to people of White ethnicity during three time periods: before the Immigration Act 2014, after the Immigration Act 2014, and after the start of the Windrush scandal media coverage in 2017. FINDINGS: We included 58 087 participants with a mean age of 45·0 years (SD 34·6; range 16-106), including 31 168 (53·6%) female and 26 919 (46·3%) male participants. The cohort consisted of individuals from the following ethnic backgrounds: 2519 (4·3%) Black African, 2197 (3·8%) Black Caribbean, 3153 (5·4%) Indian, 1584 (2·7%) Bangladeshi, 2801 (4·8%) Pakistani, and 45 833 (78·9%) White. People from Black Caribbean backgrounds had worse mental health than people of White ethnicity after the Immigration Act 2014 (MD in GHQ-12 score 0·67 [95% CrI 0·06-1·28]) and after the 2017 media coverage (1·28 [0·34-2·21]). For Black Caribbean participants born outside of the UK, mental health worsened after the Immigration Act 2014 (1·25 [0·11-2·38]), and for those born in the UK, mental health worsened after the 2017 media coverage (2·00 [0·84-3·15]). We did not observe effects in other minoritised ethnic groups. INTERPRETATION: Our finding that the hostile environment policy worsened the mental health of people from Black Caribbean backgrounds in the UK suggests that sufficient, appropriate mental health and social welfare support should be provided to those affected. Impact assessments of new policies on minority mental health should be embedded in all policy making. FUNDING: Wellcome Trust.

Wastewater-based surveillance models for COVID-19: A focused review on spatio-temporal models.

The evident shedding of the SARS-CoV-2 RNA particles from infected individuals into the wastewater opened up a tantalizing array of possibilities for prediction of COVID-19 prevalence prior to symptomatic case identification through community testing. Many countries have therefore explored the use of wastewater metrics as a surveillance tool, replacing traditional direct measurement of prevalence with cost-effective approaches based on SARS-CoV-2 RNA concentrations in wastewater samples. Two important aspects in building prediction models are: time over which the prediction occurs and space for which the predicted case numbers is shown. In this review, our main focus was on finding mathematical models which take into the account both the time-varying and spatial nature of wastewater-based metrics into account. We used six main characteristics as our assessment criteria: i) modelling approach; ii) temporal coverage; iii) spatial coverage; iv) sample size; v) wastewater sampling method; and vi) covariates included in the modelling. The majority of studies in the early phases of the pandemic recognized the temporal association of SARS-CoV-2 RNA concentration level in wastewater with the number of COVID-19 cases, ignoring their spatial context. We examined 15 studies up to April 2023, focusing on models considering both temporal and spatial aspects of wastewater metrics. Most early studies correlated temporal SARS-CoV-2 RNA levels with COVID-19 cases but overlooked spatial factors. Linear regression and SEIR models were commonly used (n = 10, 66.6 % of studies), along with machine learning (n = 1, 6.6 %) and Bayesian approaches (n = 1, 6.6 %) in some cases. Three studies employed spatio-temporal modelling approach (n = 3, 20.0 %). We conclude that the development, validation and calibration of further spatio-temporally explicit models should be done in parallel with the advancement of wastewater metrics before the potential of wastewater as a surveillance tool can be fully realised.

Community factors and excess mortality in the COVID-19 pandemic in England, Italy and Sweden.

BACKGROUND: Analyses of coronavirus disease 19 suggest specific risk factors make communities more or less vulnerable to pandemic-related deaths within countries. What is unclear is whether the characteristics affecting vulnerability of small communities within countries produce similar patterns of excess mortality across countries with different demographics and public health responses to the pandemic. Our aim is to quantify community-level variations in excess mortality within England, Italy and Sweden and identify how such spatial variability was driven by community-level characteristics. METHODS: We applied a two-stage Bayesian model to quantify inequalities in excess mortality in people aged 40 years and older at the community level in England, Italy and Sweden during the first year of the pandemic (March 2020-February 2021). We used community characteristics measuring deprivation, air pollution, living conditions, population density and movement of people as covariates to quantify their associations with excess mortality. RESULTS: We found just under half of communities in England (48.1%) and Italy (45.8%) had an excess mortality of over 300 per 100 000 males over the age of 40, while for Sweden that covered 23.1% of communities. We showed that deprivation is a strong predictor of excess mortality across the three countries, and communities with high levels of overcrowding were associated with higher excess mortality in England and Sweden. CONCLUSION: These results highlight some international similarities in factors affecting mortality that will help policy makers target public health measures to increase resilience to the mortality impacts of this and future pandemics.

Aircraft noise and cardiovascular morbidity and mortality near Heathrow Airport: A case-crossover study.

Aircraft noise causes annoyance and sleep disturbance and there is some evidence of associations between long-term exposures and cardiovascular disease (CVD). We investigated short-term associations between previous day aircraft noise and cardiovascular events in a population of 6.3 million residing near Heathrow Airport using a case-crossover design and exposure data for different times of day and night. We included all recorded hospitalisations (n = 442,442) and deaths (n = 49,443) in 2014-2018 due to CVD. Conditional logistic regression was used to estimate the ORs and adjusted for NO2 concentration, temperature, and holidays. We estimated an increase in risk for 10 dB increment in noise during the previous evening (Leve OR = 1.007, 95% CI 0.999-1.015), particularly from 22:00-23:00 h (OR = 1.007, 95% CI 1.000-1.013), and the early morning hours 04:30-06:00 h (OR = 1.012, 95% CI 1.002-1.021) for all CVD admissions, but no significant associations with day-time noise. There was effect modification by age-sex, ethnicity, deprivation, and season, and some suggestion that high noise variability at night was associated with higher risks. Our findings are consistent with proposed mechanisms for short-term impacts of aircraft noise at night on CVD from experimental studies, including sleep disturbance, increases in blood pressure and stress hormone levels and impaired endothelial function.

Spatiotemporal bayesian modelling of scorpionism and its risk factors in the state of São Paulo, Brazil.

BACKGROUND: Scorpion stings in Brazil represent a major public health problem due to their incidence and their potential ability to lead to severe and often fatal clinical outcomes. A better understanding of scorpionism determinants is essential for a precise comprehension of accident dynamics and to guide public policy. Our study is the first to model the spatio-temporal variability of scorpionism across municipalities in São Paulo (SP) and to investigate its relationship with demographic, socioeconomic, environmental, and climatic variables. METHODOLOGY: This ecological study analyzed secondary data on scorpion envenomation in SP from 2008 to 2021, using the Integrated Nested Laplace Approximation (INLA) to perform Bayesian inference for detection of areas and periods with the most suitable conditions for scorpionism. PRINCIPAL FINDINGS: From the spring of 2008 to 2021, the relative risk (RR) increased eight times in SP, from 0.47 (95%CI 0.43-0.51) to 3.57 (95%CI 3.36-3.78), although there has been an apparent stabilization since 2019. The western, northern, and northwestern parts of SP showed higher risks; overall, there was a 13% decrease in scorpionism during winters. Among the covariates considered, an increase of one standard deviation in the Gini index, which captures income inequality, was associated with a 11% increase in scorpion envenomation. Maximum temperatures were also associated with scorpionism, with risks doubling for temperatures above 36°C. Relative humidity displayed a nonlinear association, with a 50% increase in risk for 30-32% humidity and reached a minimum of 0.63 RR for 75-76% humidity. CONCLUSIONS: Higher temperatures, lower humidity, and social inequalities were associated with a higher risk of scorpionism in SP municipalities. By capturing local and temporal relationships across space and time, authorities can design more effective strategies that adhere to local and temporal considerations.

A dependent Bayesian Dirichlet process model for source apportionment of particle number size distribution.

The relationship between particle exposure and health risks has been well established in recent years. Particulate matter (PM) is made up of different components coming from several sources, which might have different level of toxicity. Hence, identifying these sources is an important task in order to implement effective policies to improve air quality and population health. The problem of identifying sources of particulate pollution has already been studied in the literature. However, current methods require an a priori specification of the number of sources and do not include information on covariates in the source allocations. Here, we propose a novel Bayesian nonparametric approach to overcome these limitations. In particular, we model source contribution using a Dirichlet process as a prior for source profiles, which allows us to estimate the number of components that contribute to particle concentration rather than fixing this number beforehand. To better characterize them we also include meteorological variables (wind speed and direction) as covariates within the allocation process via a flexible Gaussian kernel. We apply the model to apportion particle number size distribution measured near London Gatwick Airport (UK) in 2019. When analyzing this data, we are able to identify the most common PM sources, as well as new sources that have not been identified with the commonly used methods.

Asthma hospitalisations and heat exposure in England: a case-crossover study during 2002-2019.

BACKGROUND: Previous studies have reported an association between warm temperature and asthma hospitalisation. They have reported different sex-related and age-related vulnerabilities; nevertheless, little is known about how this effect has changed over time and how it varies in space. This study aims to evaluate the association between asthma hospitalisation and warm temperature and investigate vulnerabilities by age, sex, time and space. METHODS: We retrieved individual-level data on summer asthma hospitalisation at high temporal (daily) and spatial (postcodes) resolutions during 2002-2019 in England from the NHS Digital. Daily mean temperature at 1 km×1 km resolution was retrieved from the UK Met Office. We focused on lag 0-3 days. We employed a case-crossover study design and fitted Bayesian hierarchical Poisson models accounting for possible confounders (rainfall, relative humidity, wind speed and national holidays). RESULTS: After accounting for confounding, we found an increase of 1.11% (95% credible interval: 0.88% to 1.34%) in the asthma hospitalisation risk for every 1°C increase in the ambient summer temperature. The effect was highest for males aged 16-64 (2.10%, 1.59% to 2.61%) and during the early years of our analysis. We also found evidence of a decreasing linear trend of the effect over time. Populations in Yorkshire and the Humber and East and West Midlands were the most vulnerable. CONCLUSION: This study provides evidence of an association between warm temperature and hospital admission for asthma. The effect has decreased over time with potential explanations including temporal differences in patterns of heat exposure, adaptive mechanisms, asthma management, lifestyle, comorbidities and occupation.

A decade of child pedestrian safety in England: a bayesian spatio-temporal analysis.

BACKGROUND: Child pedestrian injury is a public health and health equality challenge worldwide, including in high-income countries. However, child pedestrian safety is less-understood, especially over long time spans. The intent of this study is to understand factors affecting child pedestrian safety in England over the period 2011-2020. METHODS: We conducted an area-level study using a Bayesian space-time interaction model to understand the association between the number of road crashes involving child pedestrians in English Local Authorities and a host of socio-economic, transport-related and built-environment variables. We investigated spatio-temporal trends in child pedestrian safety in England over the study period and identified high-crash local authorities. RESULTS: We found that child pedestrian crash frequencies increase as child population, unemployment-related claimants, road density, and the number of schools increase. Nevertheless, as the number of licensed vehicles per capita and zonal-level walking/cycling increase, child pedestrian safety increases. Generally, child pedestrian safety has improved in England since 2011. However, the socio-economic inequality gap in child pedestrian safety has not narrowed down. In addition, we found that after adjusting for the effect of covariates, the rate of decline in crashes varies between local authorities. The presence of localised risk factors/mitigation measures contributes to variation in the spatio-temporal patterns of child pedestrian safety. CONCLUSIONS: Overall, southern England has experienced more improvement in child pedestrian safety over the last decade than the northern regions. Our study revealed socio-economic inequality in child pedestrian safety in England. To better inform safety and public health policy, our findings support the importance of a targeted system approach, considering the identification of high-crash areas while keeping track of how child pedestrian safety evolves over time.

A spatio-temporal framework for modelling wastewater concentration during the COVID-19 pandemic.

The potential utility of wastewater-based epidemiology as an early warning tool has been explored widely across the globe during the current COVID-19 pandemic. Methods to detect the presence of SARS-CoV-2 RNA in wastewater were developed early in the pandemic, and extensive work has been conducted to evaluate the relationship between viral concentration and COVID-19 case numbers at the catchment areas of sewage treatment works (STWs) over time. However, no attempt has been made to develop a model that predicts wastewater concentration at fine spatio-temporal resolutions covering an entire country, a necessary step towards using wastewater monitoring for the early detection of local outbreaks. We consider weekly averages of flow-normalised viral concentration, reported as the number of SARS-CoV-2N1 gene copies per litre (gc/L) of wastewater available at 303 STWs over the period between 1 June 2021 and 30 March 2022. We specify a spatially continuous statistical model that quantifies the relationship between weekly viral concentration and a collection of covariates covering socio-demographics, land cover and virus associated genomic characteristics at STW catchment areas while accounting for spatial and temporal correlation. We evaluate the model's predictive performance at the catchment level through 10-fold cross-validation. We predict the weekly viral concentration at the population-weighted centroid of the 32,844 lower super output areas (LSOAs) in England, then aggregate these LSOA predictions to the Lower Tier Local Authority level (LTLA), a geography that is more relevant to public health policy-making. We also use the model outputs to quantify the probability of local changes of direction (increases or decreases) in viral concentration over short periods (e.g. two consecutive weeks). The proposed statistical framework can predict SARS-CoV-2 viral concentration in wastewater at high spatio-temporal resolution across England. Additionally, the probabilistic quantification of local changes can be used as an early warning tool for public health surveillance.

A framework for estimating and visualising excess mortality during the COVID-19 pandemic.

COVID-19 related deaths underestimate the pandemic burden on mortality because they suffer from completeness and accuracy issues. Excess mortality is a popular alternative, as it compares observed with expected deaths based on the assumption that the pandemic did not occur. Expected deaths had the pandemic not occurred depend on population trends, temperature, and spatio-temporal patterns. In addition to this, high geographical resolution is required to examine within country trends and the effectiveness of the different public health policies. In this tutorial, we propose a framework using R to estimate and visualise excess mortality at high geographical resolution. We show a case study estimating excess deaths during 2020 in Italy. The proposed framework is fast to implement and allows combining different models and presenting the results in any age, sex, spatial and temporal aggregation desired. This makes it particularly powerful and appealing for online monitoring of the pandemic burden and timely policy making.

Spatiotemporal bayesian modelling of scorpionism and its risk factors in the state of São Paulo, Brazil

Background Scorpion stings in Brazil represent a major public health problem due to their incidence and their potential ability to lead to severe and often fatal clinical outcomes. A better understanding of scorpionism determinants is essential for a precise comprehension of accident dynamics and to guide public policy. Our study is the first to model the spatio-temporal variability of scorpionism across municipalities in São Paulo (SP) and to investigate its relationship with demographic, socioeconomic, environmental, and climatic variables. Methodology This ecological study analyzed secondary data on scorpion envenomation in SP from 2008 to 2021, using the Integrated Nested Laplace Approximation (INLA) to perform Bayesian inference for detection of areas and periods with the most suitable conditions for scorpionism. Principal findings From the spring of 2008 to 2021, the relative risk (RR) increased eight times in SP, from 0.47 (95%CI 0.43–0.51) to 3.57 (95%CI 3.36–3.78), although there has been an apparent stabilization since 2019. The western, northern, and northwestern parts of SP showed higher risks; overall, there was a 13% decrease in scorpionism during winters. Among the covariates considered, an increase of one standard deviation in the Gini index, which captures income inequality, was associated with a 11% increase in scorpion envenomation. Maximum temperatures were also associated with scorpionism, with risks doubling for temperatures above 36°C. Relative humidity displayed a nonlinear association, with a 50% increase in risk for 30–32% humidity and reached a minimum of 0.63 RR for 75–76% humidity. Conclusions Higher temperatures, lower humidity, and social inequalities were associated with a higher risk of scorpionism in SP municipalities. By capturing local and temporal relationships across space and time, authorities can design more effective strategies that adhere to local and temporal considerations.

Community-level characteristics of COVID-19 vaccine hesitancy in England: A nationwide cross-sectional study.

One year after the start of the COVID-19 vaccination programme in England, more than 43 million people older than 12 years old had received at least a first dose. Nevertheless, geographical differences persist, and vaccine hesitancy is still a major public health concern; understanding its determinants is crucial to managing the COVID-19 pandemic and preparing for future ones. In this cross-sectional population-based study we used cumulative data on the first dose of vaccine received by 01-01-2022 at Middle Super Output Area level in England. We used Bayesian hierarchical spatial models and investigated if the geographical differences in vaccination uptake can be explained by a range of community-level characteristics covering socio-demographics, political view, COVID-19 health risk awareness and targeting of high risk groups and accessibility. Deprivation is the covariate most strongly associated with vaccine uptake (Odds Ratio 0.55, 95%CI 0.54-0.57; most versus least deprived areas). The most ethnically diverse areas have a 38% (95%CI 36-40%) lower odds of vaccine uptake compared with those least diverse. Areas with the highest proportion of population between 12 and 24 years old had lower odds of vaccination (0.87, 95%CI 0.85-0.89). Finally increase in vaccine accessibility is associated with COVID-19 vaccine coverage (OR 1.07, 95%CI 1.03-1.12). Our results suggest that one year after the start of the vaccination programme, there is still evidence of inequalities in uptake, affecting particularly minorities and marginalised groups. Strategies including prioritising active outreach across communities and removing practical barriers and factors that make vaccines less accessible are needed to level up the differences.

Interoperability of statistical models in pandemic preparedness: principles and reality.

We present interoperability as a guiding framework for statistical modelling to assist policy makers asking multiple questions using diverse datasets in the face of an evolving pandemic response. Interoperability provides an important set of principles for future pandemic preparedness, through the joint design and deployment of adaptable systems of statistical models for disease surveillance using probabilistic reasoning. We illustrate this through case studies for inferring and characterising spatial-temporal prevalence and reproduction numbers of SARS-CoV-2 infections in England.

Towards healthy school neighbourhoods: A baseline analysis in Greater London.

Creating healthy environments around schools is important to promote healthy childhood development and is a critical component of public health. In this paper we present a tool to characterize exposure to multiple urban environment features within 400 m (5-10 min walking distance) of schools in Greater London. We modelled joint exposure to air pollution (NO2 and PM2.5), access to public greenspace, food environment, and road safety for 2,929 schools, employing a Bayesian non-parametric approach based on the Dirichlet Process Mixture modelling. We identified 12 latent clusters of schools with similar exposure profiles and observed some spatial clustering patterns. Socioeconomic and ethnicity disparities were manifested with respect to exposure profiles. Specifically, three clusters (containing 645 schools) showed the highest joint exposure to air pollution, poor food environment, and unsafe roads and were characterized with high deprivation. The neighbourhood of the most deprived cluster of schools had a median of 2.5 ha greenspace, 29.0 µg/m3 of NO2, 19.3 µg/m3 of PM2.5, 20 fast food retailers, and five child pedestrian crashes over a three-year period. The neighbourhood of the least deprived cluster of schools had a median of 21.8 ha greenspace, 15.6 µg/m3 of NO2, 15.1 µg/m3 of PM2.5, 2 fast food retailers, and one child pedestrian crash over a three-year period. To have a school-level understanding of exposure levels, we then benchmarked schools based on the probability of exceeding the median exposure to various features of interest. Our study accounts for multiple exposures, enabling us to highlight spatial distribution of exposure profile clusters, and to identify predominant exposure to urban environment features for each cluster of schools. Our findings can help relevant stakeholders, such as schools and public health authorities, to compare schools based on their exposure levels, prioritize interventions, and design local policies that target the schools most in need.

Ambient heat exposure and COPD hospitalisations in England: a nationwide case-crossover study during 2007-2018.

BACKGROUND: There is emerging evidence suggesting a link between ambient heat exposure and chronic obstructive pulmonary disease (COPD) hospitalisations. Individual and contextual characteristics can affect population vulnerabilities to COPD hospitalisation due to heat exposure. This study quantifies the effect of ambient heat on COPD hospitalisations and examines population vulnerabilities by age, sex and contextual characteristics. METHODS: Individual data on COPD hospitalisation at high geographical resolution (postcodes) during 2007-2018 in England was retrieved from the small area health statistics unit. Maximum temperature at 1 km ×1 km resolution was available from the UK Met Office. We employed a case-crossover study design and fitted Bayesian conditional Poisson regression models. We adjusted for relative humidity and national holidays, and examined effect modification by age, sex, green space, average temperature, deprivation and urbanicity. RESULTS: After accounting for confounding, we found 1.47% (95% Credible Interval (CrI) 1.19% to 1.73%) increase in the hospitalisation risk for every 1°C increase in temperatures above 23.2°C (lags 0-2 days). We reported weak evidence of an effect modification by sex and age. We found a strong spatial determinant of the COPD hospitalisation risk due to heat exposure, which was alleviated when we accounted for contextual characteristics. 1851 (95% CrI 1 576 to 2 079) COPD hospitalisations were associated with temperatures above 23.2°C annually. CONCLUSION: Our study suggests that resources should be allocated to support the public health systems, for instance, through developing or expanding heat-health alerts, to challenge the increasing future heat-related COPD hospitalisation burden.

Time varying association between deprivation, ethnicity and SARS-CoV-2 infections in England: A population-based ecological study.

BACKGROUND: Ethnically diverse and socio-economically deprived communities have been differentially affected by the COVID-19 pandemic in the UK. METHOD: Using a multilevel regression model we assessed the time-varying association between SARS-CoV-2 infections and areal level deprivation and ethnicity from 1st of June 2020 to the 19th of September 2021. We separately considered weekly test positivity rate and estimated debiased prevalence at the Lower Tier Local Authority (LTLA) level, adjusting for confounders and spatio-temporal correlation structure. FINDINGS: Comparing the least deprived and predominantly White areas with most deprived and predominantly non-White areas over the whole study period, the weekly positivity rate increases from 2·977% (95% CrI 2.913%-3.029%) to 3·347% (95% CrI 3.300%-3.402%). Similarly, prevalence increases from 0·369% (95% CrI 0.361%-0.375%) to 0·405% (95% CrI 0.399%-0.412%). Deprivation has a stronger effect until October 2020, while the effect of ethnicity becomes more pronounced at the peak of the second wave and then again in May-June 2021. In the second wave of the pandemic, LTLAs with large South Asian populations were the most affected, whereas areas with large Black populations did not show increased values for either outcome during the entire period under analysis. INTERPRETATION: Deprivation and proportion of non-White populations are both associated with an increased COVID-19 burden in terms of disease spread and monitoring, but the strength of association varies over the course of the pandemic and for different ethnic subgroups. The consistency of results across the two outcomes suggests that deprivation and ethnicity have a differential impact on disease exposure or susceptibility rather than testing access and habits. FUNDINGS: EPSRC, MRC, The Alan Turing Institute, NIH, UKHSA, DHSC.

Improving local prevalence estimates of SARS-CoV-2 infections using a causal debiasing framework.

Global and national surveillance of SARS-CoV-2 epidemiology is mostly based on targeted schemes focused on testing individuals with symptoms. These tested groups are often unrepresentative of the wider population and exhibit test positivity rates that are biased upwards compared with the true population prevalence. Such data are routinely used to infer infection prevalence and the effective reproduction number, Rt, which affects public health policy. Here, we describe a causal framework that provides debiased fine-scale spatiotemporal estimates by combining targeted test counts with data from a randomized surveillance study in the United Kingdom called REACT. Our probabilistic model includes a bias parameter that captures the increased probability of an infected individual being tested, relative to a non-infected individual, and transforms observed test counts to debiased estimates of the true underlying local prevalence and Rt. We validated our approach on held-out REACT data over a 7-month period. Furthermore, our local estimates of Rt are indicative of 1-week- and 2-week-ahead changes in SARS-CoV-2-positive case numbers. We also observed increases in estimated local prevalence and Rt that reflect the spread of the Alpha and Delta variants. Our results illustrate how randomized surveys can augment targeted testing to improve statistical accuracy in monitoring the spread of emerging and ongoing infectious disease.

Differential impact of government lockdown policies on reducing air pollution levels and related mortality in Europe.

Previous studies have reported a decrease in air pollution levels following the enforcement of lockdown measures during the first wave of the COVID-19 pandemic. However, these investigations were mostly based on simple pre-post comparisons using past years as a reference and did not assess the role of different policy interventions. This study contributes to knowledge by quantifying the association between specific lockdown measures and the decrease in NO2, O3, PM2.5, and PM10 levels across 47 European cities. It also estimated the number of avoided deaths during the period. This paper used new modelled data from the Copernicus Atmosphere Monitoring Service (CAMS) to define business-as-usual and lockdown scenarios of daily air pollution trends. This study applies a spatio-temporal Bayesian non-linear mixed effect model to quantify the changes in pollutant concentrations associated with the stringency indices of individual policy measures. The results indicated non-linear associations with a stronger decrease in NO2 compared to PM2.5 and PM10 concentrations at very strict policy levels. Differences across interventions were also identified, specifically the strong effects of actions linked to school/workplace closure, limitations on gatherings, and stay-at-home requirements. Finally, the observed decrease in pollution potentially resulted in hundreds of avoided deaths across Europe.

Regional excess mortality during the 2020 COVID-19 pandemic in five European countries.

The impact of the COVID-19 pandemic on excess mortality from all causes in 2020 varied across and within European countries. Using data for 2015-2019, we applied Bayesian spatio-temporal models to quantify the expected weekly deaths at the regional level had the pandemic not occurred in England, Greece, Italy, Spain, and Switzerland. With around 30%, Madrid, Castile-La Mancha, Castile-Leon (Spain) and Lombardia (Italy) were the regions with the highest excess mortality. In England, Greece and Switzerland, the regions most affected were Outer London and the West Midlands (England), Eastern, Western and Central Macedonia (Greece), and Ticino (Switzerland), with 15-20% excess mortality in 2020. Our study highlights the importance of the large transportation hubs for establishing community transmission in the first stages of the pandemic. Here, we show that acting promptly to limit transmission around these hubs is essential to prevent spread to other regions and countries.