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1.
Journal of the Royal Statistical Society: Series C (Applied Statistics) ; n/a(n/a), 2022.
Article in English | Wiley | ID: covidwho-1807261

##### ABSTRACT

Obtaining up to date information on the number of UK COVID-19 regional infections is hampered by the reporting lag in positive test results for people with COVID-19 symptoms. In the UK, for ?Pillar 2? swab tests for those showing symptoms, it can take up to five days for results to be collated. We make use of the stability of the under reporting process over time to motivate a statistical temporal model that infers the final total count given the partial count information as it arrives. We adopt a Bayesian approach that provides for subjective priors on parameters and a hierarchical structure for an underlying latent intensity process for the infection counts. This results in a smoothed time-series representation nowcasting the expected number of daily counts of positive tests with uncertainty bands that can be used to aid decision making. Inference is performed using sequential Monte Carlo.

2.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-315862

##### ABSTRACT

The Covid-19 pandemic has resulted in a variety of approaches for managing infection outbreaks in international populations. One example is mobile phone applications, which attempt to alert infected individuals and their contacts by automatically inferring two key components of infection risk: the proximity to an individual who may be infected, and the duration of proximity. The former component, proximity, relies on Bluetooth Low Energy (BLE) Received Signal Strength Indicator(RSSI) as a distance sensor, and this has been shown to be problematic;not least because of unpredictable variations caused by different device types, device location on-body, device orientation, the local environment and the general noise associated with radio frequency propagation. In this paper, we present an approach that infers posterior probabilities over distance given sequences of RSSI values. Using a single-dimensional Unscented Kalman Smoother (UKS) for non-linear state space modelling, we outline several Gaussian process observation transforms, including: a generative model that directly captures sources of variation;and a discriminative model that learns a suitable observation function from training data using both distance and infection risk as optimisation objective functions. Our results show that good risk prediction can be achieved in $\mathcal{O}(n)$ time on real-world data sets, with the UKS outperforming more traditional classification methods learned from the same training data.

3.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-307317

##### ABSTRACT

We consider how the NHS COVID-19 application will initially calculate a risk score for an individual based on their recent contact with people who report that they have coronavirus symptoms.

4.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-313320

##### ABSTRACT

Obtaining up to date information on the number of UK COVID-19 regional infections is hampered by the reporting lag in positive test results for people with COVID-19 symptoms. In the UK, for "Pillar 2" swab tests for those showing symptoms, it can take up to five days for results to be collated. We make use of the stability of the under reporting process over time to motivate a statistical temporal model that infers the final total count given the partial count information as it arrives. We adopt a Bayesian approach that provides for subjective priors on parameters and a hierarchical structure for an underlying latent intensity process for the infection counts. This results in a smoothed time-series representation now-casting the expected number of daily counts of positive tests with uncertainty bands that can be used to aid decision making. Inference is performed using sequential Monte Carlo.

5.
Lancet Reg Health Eur ; 15: 100322, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1676851

##### ABSTRACT

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.

6.
Nature Machine Intelligence ; 2(10):554-556, 2020.
Article in English | ProQuest Central | ID: covidwho-1635248

##### ABSTRACT

For machine learning developers, the use of prediction tools in real-world clinical settings can be a distant goal. Recently published guidelines for reporting clinical research that involves machine learning will help connect clinical and computer science communities, and realize the full potential of machine learning tools.

7.
Nat Microbiol ; 7(1): 97-107, 2022 01.
Article in English | MEDLINE | ID: covidwho-1596437

##### ABSTRACT

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.

##### Subject(s)
COVID-19/epidemiology , Models, Statistical , SARS-CoV-2/isolation & purification , Basic Reproduction Number , Bias , COVID-19/diagnosis , COVID-19/transmission , COVID-19 Testing/statistics & numerical data , Forecasting , Humans , Prevalence , Reproducibility of Results , SARS-CoV-2/genetics , Spatio-Temporal Analysis , United Kingdom/epidemiology
8.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-295610

##### ABSTRACT

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 spatial-temporal coronavirus disease 2019 (COVID-19) prevalence and reproduction numbers in England.

9.
Nature ; 594(7863): 408-412, 2021 06.
Article in English | MEDLINE | ID: covidwho-1225509

##### ABSTRACT

The COVID-19 pandemic has seen the emergence of digital contact tracing to help to prevent the spread of the disease. A mobile phone app records proximity events between app users, and when a user tests positive for COVID-19, their recent contacts can be notified instantly. Theoretical evidence has supported this new public health intervention1-6, but its epidemiological impact has remained uncertain7. Here we investigate the impact of the National Health Service (NHS) COVID-19 app for England and Wales, from its launch on 24 September 2020 to the end of December 2020. It was used regularly by approximately 16.5 million users (28% of the total population), and sent approximately 1.7 million exposure notifications: 4.2 per index case consenting to contact tracing. We estimated that the fraction of individuals notified by the app who subsequently showed symptoms and tested positive (the secondary attack rate (SAR)) was 6%, similar to the SAR for manually traced close contacts. We estimated the number of cases averted by the app using two complementary approaches: modelling based on the notifications and SAR gave an estimate of 284,000 (central 95% range of sensitivity analyses 108,000-450,000), and statistical comparison of matched neighbouring local authorities gave an estimate of 594,000 (95% confidence interval 317,000-914,000). Approximately one case was averted for each case consenting to notification of their contacts. We estimated that for every percentage point increase in app uptake, the number of cases could be reduced by 0.8% (using modelling) or 2.3% (using statistical analysis). These findings support the continued development and deployment of such apps in populations that are awaiting full protection from vaccines.

##### Subject(s)
COVID-19/epidemiology , COVID-19/prevention & control , Contact Tracing/instrumentation , Contact Tracing/methods , Mobile Applications/statistics & numerical data , Basic Reproduction Number , COVID-19/mortality , COVID-19/transmission , England/epidemiology , Humans , Mortality , National Health Programs , Quarantine , Wales/epidemiology
10.
Kidney Int ; 99(6): 1492-1494, 2021 06.
Article in English | MEDLINE | ID: covidwho-1193420
11.
Lancet Digit Health ; 2(12): e658-e666, 2020 12.
Article in English | MEDLINE | ID: covidwho-857316

##### ABSTRACT

Background: In May 2020, the UK National Health Service (NHS) Test and Trace programme was launched in England in response to the COVID-19 pandemic. The programme was first rolled out on the Isle of Wight and included version 1 of the NHS contact tracing app. The aim of the study was to make a preliminary assessment of the epidemiological impact of the Test and Trace programme using publicly available data. Methods: We used COVID-19 daily case data from Public Health England to infer incidence of new infections and estimate the reproduction number (R) for each of the 150 Upper-Tier Local Authorities (UTLAs) in England and nationally, before and after the launch of the Test and Trace programme on the Isle of Wight. We used Bayesian and maximum-likelihood methods to estimate R and compared the Isle of Wight with other UTLAs using a synthetic control method. Findings: We observed significant decreases in incidence and R on the Isle of Wight immediately after the launch of the Test and Trace programme. The Isle of Wight had a marked reduction in R, from 1·3 before the Test and Trace programme to 0·5 after by one of our measures, and went from having the third highest R before the Test and Trace programme, to the twelfth lowest afterwards compared with other UTLAs. Interpretation: Our results show that the epidemic on the Isle of Wight was controlled quickly and effectively after the launch of Test and Trace. Our findings highlight the need for further research to determine the causes of the reduction in the spread of the disease, as these could be translated into local and national non-pharmaceutical intervention strategies in the period before a treatment or vaccination for COVID-19 becomes available. Funding: Li Ka Shing Foundation and UK Economic and Social Research Council.

##### Subject(s)
COVID-19 Testing/methods , COVID-19/epidemiology , Contact Tracing/methods , Islands/epidemiology , Adolescent , Adult , Age Factors , Aged , COVID-19/diagnosis , COVID-19/prevention & control , COVID-19 Testing/statistics & numerical data , Child , Child, Preschool , Contact Tracing/statistics & numerical data , England/epidemiology , Humans , Infant , Infant, Newborn , Likelihood Functions , Middle Aged , State Medicine , Thiocarbamates , United Kingdom/epidemiology , Young Adult
12.
Lancet ; 395(10238): 1715-1725, 2020 05 30.
Article in English | MEDLINE | ID: covidwho-245277

##### ABSTRACT

BACKGROUND: The medical, societal, and economic impact of the coronavirus disease 2019 (COVID-19) pandemic has unknown effects on overall population mortality. Previous models of population mortality are based on death over days among infected people, nearly all of whom thus far have underlying conditions. Models have not incorporated information on high-risk conditions or their longer-term baseline (pre-COVID-19) mortality. We estimated the excess number of deaths over 1 year under different COVID-19 incidence scenarios based on varying levels of transmission suppression and differing mortality impacts based on different relative risks for the disease. METHODS: In this population-based cohort study, we used linked primary and secondary care electronic health records from England (Health Data Research UK-CALIBER). We report prevalence of underlying conditions defined by Public Health England guidelines (from March 16, 2020) in individuals aged 30 years or older registered with a practice between 1997 and 2017, using validated, openly available phenotypes for each condition. We estimated 1-year mortality in each condition, developing simple models (and a tool for calculation) of excess COVID-19-related deaths, assuming relative impact (as relative risks [RRs]) of the COVID-19 pandemic (compared with background mortality) of 1·5, 2·0, and 3·0 at differing infection rate scenarios, including full suppression (0·001%), partial suppression (1%), mitigation (10%), and do nothing (80%). We also developed an online, public, prototype risk calculator for excess death estimation. FINDINGS: We included 3â862â012 individuals (1â957â935 [50·7%] women and 1â904â077 [49·3%] men). We estimated that more than 20% of the study population are in the high-risk category, of whom 13·7% were older than 70 years and 6·3% were aged 70 years or younger with at least one underlying condition. 1-year mortality in the high-risk population was estimated to be 4·46% (95% CI 4·41-4·51). Age and underlying conditions combined to influence background risk, varying markedly across conditions. In a full suppression scenario in the UK population, we estimated that there would be two excess deaths (vs baseline deaths) with an RR of 1·5, four with an RR of 2·0, and seven with an RR of 3·0. In a mitigation scenario, we estimated 18â374 excess deaths with an RR of 1·5, 36â749 with an RR of 2·0, and 73â498 with an RR of 3·0. In a do nothing scenario, we estimated 146â996 excess deaths with an RR of 1·5, 293â991 with an RR of 2·0, and 587â982 with an RR of 3·0. INTERPRETATION: We provide policy makers, researchers, and the public a simple model and an online tool for understanding excess mortality over 1 year from the COVID-19 pandemic, based on age, sex, and underlying condition-specific estimates. These results signal the need for sustained stringent suppression measures as well as sustained efforts to target those at highest risk because of underlying conditions with a range of preventive interventions. Countries should assess the overall (direct and indirect) effects of the pandemic on excess mortality. FUNDING: National Institute for Health Research University College London Hospitals Biomedical Research Centre, Health Data Research UK.

##### Subject(s)
Coronavirus Infections/epidemiology , Mortality/trends , Pneumonia, Viral/epidemiology , Adult , Aged , Aged, 80 and over , COVID-19 , Cohort Studies , Coronavirus Infections/complications , Female , Humans , Male , Middle Aged , Models, Statistical , Multimorbidity , Pandemics , Pneumonia, Viral/complications , Risk Factors , United Kingdom/epidemiology