Inferring UK COVID‐19 fatal infection trajectories from daily mortality data: were infections already in decline before the UK lockdowns?

The number of daily deaths, reported by Public Health England (PHE) during the UK Covid-19 epidemic, initially omitted out-of-hospital deaths in England. The epidemic has been mitigated by social distancing and the lockdown introduced on 17 and 23 March 2020 respectively. We recently reported a stochastic model of a mitigated epidemic which incorporated changes in social interactions and daily movements and whose simulations were consistent with the initial PHE daily mortality data. However, on 29 April, PHE revised their historic data to include out-of-hospital deaths in England. Out-of-hospital deaths occur sooner than in-hospital deaths. Here we show that if 20% of deaths, representing out-of-hospital deaths, are assigned a shorter illness period, then simulated daily mortality matches the revised PHE mortality at least until 4 May. We now predict that if the lockdown is gently relaxed in late May, whilst maintaining social distancing, there would be a modest second-wave which may be acceptable when weighed against the risks of maintaining the lockdown. Our model complements other more sophisticated work currently guiding national policy but which is not presently in the public domain.

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The Impact of Social Distancing on The Course of The Covid-19 Pandemic in Four European Countries

10.1101/2020.05.03.20089680 ◽

2020 ◽

Author(s):

Andrew Shardlow

Keyword(s):

European Countries ◽

Mortality Data ◽

Daily Mortality ◽

Data Set ◽

Model Type ◽

Social Distancing ◽

Strict Enforcement ◽

The Uk ◽

The Impact ◽

Logistic Functions

In this article the mortality data from four European countries arising from the Covid-19 pandemic is modelled using logistic functions. The countries chosen for examination are Spain, Italy, France and the UK. They have been selected because in each the pandemic is advanced, mortality high and any prospect of containment has passed. They have also been selected because in each social distancing has been used in an attempt to reduce peak daily mortality with relatively strict enforcement following a defined date. The choices of data set and model type is justified. The impact, if any, of social distancing is examined.

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The course of the UK COVID 19 pandemic; no measurable impact of new variants

10.1101/2021.03.16.21253534 ◽

2021 ◽

Author(s):

D Ellis ◽

D Papadopoulos ◽

S Mukherjee ◽

U Ukwu ◽

N Chari ◽

...

Keyword(s):

Pearson Correlation ◽

Time Lag ◽

Reproductive Rate ◽

Viral Transmission ◽

Mortality Data ◽

Daily Mortality ◽

Pearson Coefficient ◽

New Variant ◽

Temperature And Humidity ◽

The Uk

AbstractIntroductionIn November 2020, a new SARS-COV-2 variant or the ‘Kent variant’ emerged in the UK, and became the dominant UK SARS-COV-2 variant, demonstrating faster transmission than the original variant, which rapidly died out. However, it is unknown if this altered the overall course of the pandemic as genomic analysis was not common place at the outset and other factors such as the climate could alter the viral transmission rate over time. We aimed to test the hypothesis that the overall observed viral transmission was not altered by the emergence of the new variant, by testing a model generated earlier in the pandemic based on lockdown stringency, temperature and humidity.MethodsFrom 1/1/20 to 4/2/21, the daily incidence of SARS-COV-2 deaths and the overall stringency of National Lockdown policy on each day was extracted from the Oxford University Government response tracker. The daily average temperature and humidity for London was extracted from Wunderground.com.The viral reproductive rate was calculated on a daily basis from the daily mortality data for each day. The correlation between log10 of viral reproductive rate and lockdown stringency and weather parameters were compared by Pearson correlation to determine the time lag associated with the greatest correlation.A multivariate model for the log10 of viral reproductive rate was constructed using lockdown stringency, temperature and humidity for the period 1/1/20 to 30/9/20. This model was extrapolated forward from 1/10/20 to 4/2/21 and the predicted viral reproductive rate, daily mortality and cumulative mortality were compared with official data.ResultsOn multivariate linear regression, the optimal model had and R2 0f 0.833 for prediction of log10 viral reproductive rate 13 days later in the model construction period, with (coefficient, probability) lockdown stringency (−0.0109, p=0.0000), humidity (0.0038, p=0.0041) and temperature (−0.0035, p=0.0008). When extrapolated to the validation period (1/10/20 to 4/2/21), the model was highly correlated with daily (Pearson coefficient 0.88, p=0.0000) and cumulated SARS-COV-2 mortality (Pearson coefficient 0.99, p=0.0000).ConclusionThe course of the SARS-COV-2 pandemic in the UK seems highly predicted by an earlier model based on the lockdown stringency, humidity and temperature and unaltered by the emergence of a newer viral genotype.

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Impact of Relaxing Covid-19 Social Distancing Measures on Rural North Wales: A Simulation Analysis

Frontiers in Public Health ◽

10.3389/fpubh.2020.562473 ◽

2020 ◽

Vol 8 ◽

Author(s):

Rhodri P. Hughes ◽

Dyfrig A. Hughes

Keyword(s):

Simulation Analysis ◽

Model Averaging ◽

Incidence Rates ◽

Mortality Data ◽

Rural Regions ◽

Social Distancing ◽

North Wales ◽

The Uk ◽

Sigmoidal Growth ◽

Related Mortality

Background: Social distancing policies aimed to limit Covid-19 across the UK were gradually relaxed between May and August 2020, as peak incidences passed. Population density is an important driver of national incidence rates; however peak incidences in rural regions may lag national figures by several weeks. We aimed to forecast the timing of peak Covid-19 mortality rate in rural North Wales.Methods: Covid-19 related mortality data up to 7/5/2020 were obtained from Public Health Wales and the UK Government. Sigmoidal growth functions were fitted by non-linear least squares and model averaging used to extrapolate mortality to 24/8/2020. The dates of peak mortality incidences for North Wales, Wales and the UK; and the percentage of predicted mortality at 24/8/2020 were calculated.Results: The peak daily death rates in Wales and the UK were estimated to have occurred on the 14/04/2020 and 15/04/2020, respectively. For North Wales, this occurred on the 07/05/2020, corresponding to the date of analysis. The number of deaths reported in North Wales on 07/05/2020 represents 33% of the number predicted to occur by 24/08/2020, compared with 74 and 62% for Wales and the UK, respectively.Conclusion: Policies governing the movement of people in the gradual release from lockdown are likely to impact significantly on areas–principally rural in nature–where cases of Covid-19, deaths and immunity are likely to be much lower than in populated areas. This is particularly difficult to manage across jurisdictions, such as between England and Wales, and in popular holiday destinations.

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Bayesian inference across multiple models suggests a strong increase in lethality of COVID-19 in late 2020 in the UK

PLoS ONE ◽

10.1371/journal.pone.0258968 ◽

2021 ◽

Vol 16 (11) ◽

pp. e0258968

Author(s):

Patrick Pietzonka ◽

Erik Brorson ◽

William Bankes ◽

Michael E. Cates ◽

Robert L. Jack ◽

...

Keyword(s):

Bayesian Inference ◽

Time Window ◽

Fold Increase ◽

Strong Increase ◽

Mortality Data ◽

New Variant ◽

Model Evidence ◽

Age Structured ◽

The Uk ◽

Inference Methods

We apply Bayesian inference methods to a suite of distinct compartmental models of generalised SEIR type, in which diagnosis and quarantine are included via extra compartments. We investigate the evidence for a change in lethality of COVID-19 in late autumn 2020 in the UK, using age-structured, weekly national aggregate data for cases and mortalities. Models that allow a (step-like or graded) change in infection fatality rate (IFR) have consistently higher model evidence than those without. Moreover, they all infer a close to two-fold increase in IFR. This value lies well above most previously available estimates. However, the same models consistently infer that, most probably, the increase in IFR preceded the time window during which variant B.1.1.7 (alpha) became the dominant strain in the UK. Therefore, according to our models, the caseload and mortality data do not offer unequivocal evidence for higher lethality of a new variant. We compare these results for the UK with similar models for Germany and France, which also show increases in inferred IFR during the same period, despite the even later arrival of new variants in those countries. We argue that while the new variant(s) may be one contributing cause of a large increase in IFR in the UK in autumn 2020, other factors, such as seasonality, or pressure on health services, are likely to also have contributed.

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The new automated daily mortality surveillance system in Portugal

Eurosurveillance ◽

10.2807/ese.15.13.19529-en ◽

2010 ◽

Vol 15 (13) ◽

Author(s):

P J Nogueira ◽

A Machado ◽

E Rodrigues ◽

B Nunes ◽

L Sousa ◽

...

Keyword(s):

Information Acquisition ◽

Surveillance System ◽

Warning System ◽

Automated System ◽

Mortality Data ◽

Fast Method ◽

Daily Mortality ◽

Public Health Action ◽

The Impact ◽

Mortality Surveillance

The experience reported in an earlier Eurosurveillance issue on a fast method to evaluate the impact of the 2003 heatwave on mortality in Portugal, generated a daily mortality surveillance system (VDM) that has been operating ever since jointly with the Portuguese Heat Health Watch Warning System. This work describes the VDM system and how it evolved to become an automated system operating year-round, and shows briefly its potential using mortality data from January 2006 to June 2009 collected by the system itself. The new system has important advantages such as: rapid information acquisition, completeness (the entire population is included), lightness (very little information is exchanged, date of death, age, sex, place of death registration). It allows rapid detection of impacts (within five days) and allows a quick preliminary quantification of impacts that usually took several years to be done. These characteristics make this system a powerful tool for public health action. The VDM system also represents an example of inter-institutional cooperation, bringing together organisations from two different ministries, Health and Justice, aiming at improving knowledge about the mortality in the population.

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Risk of ischemic stroke in asymptomatic atrial fibrillation incidentally-detected in primary care compared with other clinical presentations

Thrombosis and Haemostasis ◽

10.1055/a-1541-3885 ◽

2021 ◽

Author(s):

Christopher Wallenhorst ◽

Carlos Martinez ◽

Ben FREEDMAN

Keyword(s):

Atrial Fibrillation ◽

Primary Care ◽

Ischemic Stroke ◽

Stroke Risk ◽

Practice Research ◽

Mortality Data ◽

Clinical Practice Research Datalink ◽

Primary Hospital ◽

Ischemic Stroke Risk ◽

The Uk

Background: It is uncertain whether stroke risk of asymptomatic ambulatory atrial fibrillation (AA-AF) incidentally-detected in primary care is comparable with other clinical AF presentations in primary care or hospital. Methods: The stoke risk of 22,035 patients with incident non-valvular AF from the UK primary care Clinical Practice Research Datalink with linkage to hospitalization and mortality data, was compared to 23,605 controls without AF (age and sex-matched 5:1 to 5,409 AA-AF patients). Incident AF included 5,913 with symptomatic ambulatory AF (SA-AF); 4,989 with Primary and 5,724 with non-Primary Hospital AF discharge diagnosis (PH-AF and Non-PH-AF); and 5,409 with AA-AF. Ischemic stroke adjusted subhazard ratios (aSHR) within 3 years of AA-AF were compared with SA-AF, PH-AF, Non-PH-AF and controls, accounting for mortality as competing risk and adjusted for ischemic stroke risk factors. Results: There were 1026 ischemic strokes in 49,544 person-years in patients with incident AF (crude incidence rate 2.1 ischemic strokes/100 person-years). Ischemic stroke aSHR over 3 years showed no differences between AA-AF, and SA-AF, PH-AF and nonPH-AF groups (aSHR 0.87-1.01 vs AA-AF). All AF groups showed a significantly higher aSHR compared to controls. (subhazard rate ratio 0.40 [0.34 - 0.47]. Conclusion: Ischemic stroke risk in patients with AA-AF incidentally-detected in primary care is far from benign, and not less than incident AF presenting clinically in general practice or hospital. This provides justification for identification of previously undetected AF, e.g. by opportunistic screening, and subsequent stroke prevention with thromboprophylaxis, to reduce the approximately 10% of ischemic strokes related to unrecognized AF.

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Estimating within-flock transmission rate parameter for H5N2 highly pathogenic avian influenza virus in Minnesota turkey flocks during the 2015 epizootic

Epidemiology and Infection ◽

10.1017/s0950268819000633 ◽

2019 ◽

Vol 147 ◽

Cited By ~ 1

Author(s):

A. Ssematimba ◽

S. Malladi ◽

T. J. Hagenaars ◽

P. J. Bonney ◽

J. T. Weaver ◽

...

Keyword(s):

Avian Influenza ◽

Highly Pathogenic Avian Influenza ◽

Transmission Rate ◽

Mortality Data ◽

Rate Parameter ◽

Daily Mortality ◽

Highly Pathogenic ◽

Pathogenic Avian Influenza ◽

Generalised Linear Mixed Model ◽

Back Calculation

AbstractBetter control of highly pathogenic avian influenza (HPAI) outbreaks requires deeper understanding of within-flock virus transmission dynamics. For such fatal diseases, daily mortality provides a proxy for disease incidence. We used the daily mortality data collected during the 2015 H5N2 HPAI outbreak in Minnesota turkey flocks to estimate the within-flock transmission rate parameter (β). The number of birds in Susceptible, Exposed, Infectious and Recovered compartments was inferred from the data and used in a generalised linear mixed model (GLMM) to estimate the parameters. Novel here was the correction of these data for normal mortality before use in the fitting process. We also used mortality threshold to determine HPAI-like mortality to improve the accuracy of estimates from the back-calculation approach. The estimated β was 3.2 (95% confidence interval (CI) 2.3–4.3) per day with a basic reproduction number of 12.8 (95% CI 9.2–17.2). Although flock-level estimates varied, the overall estimate was comparable to those from other studies. Sensitivity analyses demonstrated that the estimated β was highly sensitive to the bird-level latent period, emphasizing the need for its precise estimation. In all, for fatal poultry diseases, the back-calculation approach provides a computationally efficient means to obtain reasonable transmission parameter estimates from mortality data.

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Outcome after conservatively managed intracapsular fractures of the femoral neck

Annals of The Royal College of Surgeons of England ◽

10.1308/003588415x14181254788809 ◽

2015 ◽

Vol 97 (4) ◽

pp. 279-282 ◽

Cited By ~ 12

Author(s):

LS Moulton ◽

NL Green ◽

T Sudahar ◽

NK Makwana ◽

JP Whittaker

Keyword(s):

Hip Fracture ◽

Femoral Neck ◽

Mortality Data ◽

Study Cohort ◽

Infection Pressure ◽

Number Of Patients ◽

Admission Status ◽

American Society ◽

One Year ◽

The Uk

Introduction In 2012, 2.6% of hip-fracture patients in the UK were treated conservatively. There is little data on outcome for these patients. However, one study demonstrated that though 30-day mortality is higher, mortality over the rest of the year is comparable with that in surgical groups. Therefore, we assessed conservatively managed patients in our unit. Methods Patients with intracapsular fractures of the femoral neck treated by conservative means between 2010 and 2012 inclusive were identified. Data were collected: American Society of Anaesthesiologists (ASA) grade, Nottingham Hip Fracture Score (NHFS), mobility, mortality (30 days and one year) and pain levels. Results Thirty-two patients formed the study cohort. Mean age was 85.6 years. Median ASA grade was 4. Mortality at 30 days and one year was 31.3% and 56.3%, respectively. There was one case of pneumonia and one of infection. Pressure sores or venous thromboembolism were not documented. Three patients underwent surgery once their health improved. In general, mobility was decreased, but 30.8% of patients could mobilise with two aids or a frame. Only two cases had ongoing problems with pain. Conclusions Our data are similar to those published previously. Our patients were likely to have higher mortality data due to selection bias. Thirty-day mortality was significantly higher than the national average, but patients surviving 30 days had a prevalence of mortality similar to those managed by surgical means. Despite mobility decreasing from the pre-admission status, a considerable number of patients were free of pain and could mobilise. These data suggest that conservative management of intracapsular fractures of the femoral neck can produce acceptable results.

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Fatal Self-poisoning in the UK and the Paracetamol/Dextropropoxyphene Combination

Human Toxicology ◽

10.1177/096032718400300115 ◽

1984 ◽

Vol 3 (1_suppl) ◽

pp. 145s-174S ◽

Cited By ~ 9

Author(s):

P.S. Dwyer ◽

I.F. Jones

Keyword(s):

Northern Ireland ◽

Causes Of Death ◽

Mortality Data ◽

Specific Reference ◽

Combination Product ◽

Analgesic Drugs ◽

Wide Range ◽

Wide Variability ◽

The Uk ◽

Direct Investigation

1 Coroners' files have been examined to ascertain the numbers of deaths involving self-poisoning with analgesic drugs with specific reference to the paracetamol/dextropropoxyphene combination. The period of study was 1976-1980. This report concentrates on cases in England, although reference is made to similar deaths occurring in Scotland and Northern Ireland. 2 Data have been collected extensively on a wide range of issues concerning fatal self-poisonings mainly by visiting coroners' offices in England to make direct investigation of records. 3 The total number of cases where the paracetamol/dextropropoxyphene combination can be considered as ingested in the self-poisoning episode is underestimated. The number of cases involving alcohol and/or other drugs taken together with the combination product is particularly underestimated. 4 Involvement of people aged 30 years and below comprises 32% of all cases. 5 'Gesture' overdoses comprise an estimated 14% of all cases in England. 6 An analysis of fatalities from cases where quantities in post-mortem blood of dextropropoxyphene < 1 μg/ml and paracetamol < 50 μg/ml are found and of cases where death occurs within 2 h of ingestion of the overdose has been carried out. The results are inconclusive. In most cases alcohol and/or other drugs are found to be involved. Critical inspection of coroners' files shows relatively few of these cases where the combination product is ingested on its own. 7 There is wide variability in the data available in coroners' files. In many cases data of value to this research are not recorded. Medical history and quantitative levels of drugs suspected (particularly dextropropoxyphene) are particular examples of factors which may not be recorded. 8 Office of Population, Censuses and Surveys (OPCS) mortality data are based on certified causes of death. Because of the underestimate of the involvement of this combination product and the under-reporting of other drug and/or alcohol ingestion with the combination, care must be exercised in quoting or drawing conclusions from OPCS statistics.

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