Fitting to the UK COVID-19 outbreak, short-term forecasts and estimating the reproductive number

Keeling, Matthew James; Dyson, Louise; Guyver‐Fletcher, Glen; Holmes, Alex; Semple, Malcolm G; Investigators, Isaric C; Tildesley, Michael J.; Hill, Edward M.

doi:10.1101/2020.08.04.20163782

Cited by 41 publications

(81 citation statements)

References 39 publications

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“…This allows us to capture household isolation by preventing secondary infections from playing a further role in onward transmission. Model parameters were inferred on a regional basis using regional time series of recorded daily hospitalisation numbers, hospital bed occupancy, ICU occupancy and daily deaths [24].…”

Section: Supporting Information S1 the Mathematical Modelmentioning

confidence: 99%

Vaccination and Non-Pharmaceutical Interventions: When can the UK relax about COVID-19?

Moore

Tildesley

Dyson

2021

Preprint

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SummaryBackgroundThe announcement of efficacious vaccine candidates against SARS-CoV-2 has been met with worldwide acclaim and relief. Many countries already have detailed plans for vaccine targeting based on minimising severe illness, death and healthcare burdens. Normally, relatively simple relationships between epidemiological parameters, vaccine efficacy and vaccine uptake predict the success of any immunisation programme. However, the dynamics of vaccination against SARS-CoV-2 is made more complex by age-dependent factors, changing levels of infection and the potential relaxation of non-pharmaceutical interventions (NPIs) as the perceived risk declines.MethodsIn this study we use an age-structured mathematical model, matched to a range of epidemiological data in the UK, that also captures the roll-out of a two-dose vaccination programme targeted at specific age groups.FindingsWe consider the interaction between the UK vaccination programme and future relaxation (or removal) of NPIs. Our predictions highlight the population-level risks of early relaxation leading to a pronounced wave of infection, hospital admissions and deaths. Only vaccines that offer high infection-blocking efficacy with high uptake in the general population allow relaxation of NPIs without a huge surge in deaths.InterpretationWhile the novel vaccines against SARS-CoV-2 offer a potential exit strategy for this outbreak, this is highly contingent on the infection-blocking (or transmission-blocking) action of the vaccine and the population uptake, both of which need to be carefully monitored as vaccine programmes are rolled out in the UK and other countries.Research in contextEvidence before this studyVaccination has been seen as a key tool in the fight against SARS-CoV-2. The vaccines already developed represent a major technological achievement and have been shown to generate significant immune responses, as well as offering considerable protection against disease. However, to date there is limited information on the degree of infection-blocking these vaccines are likely to induce. Mathematical models have already successfully been used to consider age- and risk-structured targeting of vaccination, highlighting the importance of prioritising older and high-risk individuals.Added value of this studyTranslating current knowledge and uncertainty of vaccine behaviour into meaningful public health messages requires models that fully capture the within-country epidemiology as well as the complex roll-out of a two-dose vaccination programme. We show that under reasonable assumptions for vaccine efficacy and uptake the UK is unlikely to reach herd immunity, which means that non-pharmaceutical interventions cannot be released without generating substantial waves of infection.Implications of all the available evidenceVaccination is likely to provide substantial individual protection to those receiving two doses, but the degree of protection to the wider population is still uncertain. While substantial immunisation of the most vulnerable groups will allow for some relaxation of controls, this must be done gradually to prevent large scale public health consequences.

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Section: Supporting Information S1 the Mathematical Modelmentioning

confidence: 99%

Vaccination and Non-Pharmaceutical Interventions: When can the UK relax about COVID-19?

Moore

Tildesley

Dyson

2021

Preprint

Self Cite

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“…We used a compartmental age-structured model, developed to simulate the spread of SARS-CoV-2 within regions of the UK [22], with parameters inferred to generate a good match to deaths, hospitalisations, hospital occupancy and serological testing [13]. It involves an extended SEIR-type framework: susceptibles (S) may become infected and move into a latent exposed (E) state before progressing to become infectious.…”

Section: Model Formulationmentioning

confidence: 99%

Modelling optimal vaccination strategy for SARS-CoV-2 in the UK

Moore

Hill

Dyson

et al. 2020

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The COVID-19 outbreak has highlighted our vulnerability to novel infections. Faced with this threat and no effective treatment, in line with many other countries, the UK adopted enforced social distancing (lockdown) to reduce transmission- successfully reducing the reproductive number, R, below one. However, given the large pool of susceptible individuals that remain, complete relaxation of controls is likely to generate a substantial second wave. Vaccination remains the only foreseeable means of both containing the infection and returning to normal interactions and behaviour. Here, we consider the optimal targeting of vaccination within the UK, with the aim of minimising future deaths or quality adjusted life year (QALY) losses. We show that, for a range of assumptions on the action and efficacy of the vaccine, targeting older age groups first is optimal and can avoid a second wave if the vaccine prevents transmission as well as disease.

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“…We now wish to increase the realism of the modelling framework to more accurately capture the impact of such breaks on the number of hospitalisations and deaths as a result of infection, which requires an age-structured model matched to the wealth of epidemiological data [14, 15]. Even though we have dramatically increased the complexity of the model, the two simple metrics ( B and T R ) remain of key interest.…”

Section: Age-structured Model Descriptionmentioning

confidence: 99%

“…The age-structured model and its matching to the UK data has been described in detail elsewhere [14, 15]. Here, for completeness, we provide a basic review of the main salient points.…”

Section: Age-structured Model Descriptionmentioning

confidence: 99%

Precautionary breaks: planned, limited duration circuit breaks to control the prevalence of COVID-19

Keeling

Guyver‐Fletcher

Holmes

et al. 2020

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The COVID-19 pandemic in the UK has been characterised by periods of exponential growth and decline, as different non-pharmaceutical interventions (NPIs) are brought into play. During the early uncontrolled phase of the outbreak (early March 2020) there was a period of prolonged exponential growth with epidemiological observations such as hospitalisation doubling every 3-4 days (growth rate r≈0.2). The enforcement of strict lockdown measures led to a noticeable decline in all epidemic quantities (r≈-0.06) that slowed during the summer as control measures were relaxed (r≈-0.02). Since August, infections, hospitalisations and deaths have been rising (precise estimation of the cur-rent growth rate is difficult due to extreme regional heterogeneity and temporal lags between the different epidemiological observations) and various NPIs have been applied locally throughout the UK in response. Controlling any rise in infection is a compromise between public health and societal costs, with more stringent NPIs reducing cases but damaging the economy and restricting freedoms. Currently, NPI imposition is made in response to the epidemiological state, are of indefinite length and are often imposed at short notice, greatly increasing the negative impact. An alternative approach is to consider planned, limited duration periods of strict NPIs aiming to purposefully reduce prevalence before such emergency NPIs are required. These 'precautionary breaks' may offer a means of keeping control of the epidemic, while their fixed duration and the forewarning may limit their society impact. Here, using simple analysis and age-structured models matched to the unfolding UK epidemic, we investigate the action of precautionary breaks. In particular we consider their impact on the prevalence of infection, as well as the total number of predicted hospitalisations and deaths. We find that precautionary breaks provide the biggest gains when the growth rate is low, but offer a much needed brake on increasing infection when the growth rate is higher, potentially allowing other measures (such as contact tracing)to regain control.

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Fitting to the UK COVID-19 outbreak, short-term forecasts and estimating the reproductive number

Cited by 41 publications

References 39 publications

Vaccination and Non-Pharmaceutical Interventions: When can the UK relax about COVID-19?

Vaccination and Non-Pharmaceutical Interventions: When can the UK relax about COVID-19?

Modelling optimal vaccination strategy for SARS-CoV-2 in the UK

Precautionary breaks: planned, limited duration circuit breaks to control the prevalence of COVID-19

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