Royal Society Open Science

While case numbers remain low, population-wide control methods combined with efficient tracing, testing, and case isolation, offer the opportunity for New Zealand to contain and eliminate COVID-19. We use a stochastic model to investigate containment and elimination scenarios for COVID-19 in New Zealand, as the country considers the exit from its four week period of strong Level 4 population-wide control measures. In particular we consider how the effectiveness of its case isolation operations i...

The Coronavirus disease-2019 (COVID-19) pandemic has had a significant impact on the world, redefining how we work, respond to public health emergencies and control efforts, and sparking increased research efforts. In this study, we have developed a deterministic, ordinary differential equation multi-risk structured model of the disease outcomes, with a focus on the total number of infections, reported cases, hospitalised individuals, and deaths in the population. The model takes into account so...

Countries around the world are in a state of lockdown to help limit the spread of SARS-CoV-2. However, as the number of new daily confirmed cases begins to decrease, governments must decide how to release their populations from quarantine as efficiently as possible without overwhelming their health services. We applied an optimal control framework to an adapted Susceptible-Exposure-Infection-Recovery (SEIR) model framework to investigate the efficacy of two potential lockdown release strategies,...

AO_SCPLOWBSTRACTC_SCPLOWUnlike other European countries the UK has abandoned widespread testing and tracing of known SARS-CoV-2 carriers in mid-March. The reason given was that the pandemic was out of control and with wide community based spread it would not be possible to contain it by tracing any longer. Like other countries the UK has since relied on a lockdown as the main measure to contain the virus (or more precisely the reproduction number[R] ) at significant economic and social cost. It ...

1We present calculations using the CovidSim code which implements the Imperial College individual-based model of the COVID epidemic. Using the parameterization assumed in March 2020, we reproduce the predictions presented to inform UK government policy in March 2020. We find that CovidSim would have given a good forecast of the subsequent data if a higher initial value of R0 had been assumed. We then investigate further the whole trajectory of the epidemic, presenting results not previously publ...

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 ...

In many countries, demand exceeds supply for elective (non-emergency) hospital treatment, such as hip replacements and cataract removals. The consequence of this is the formation of a waiting list, to which patients join on referral from the family doctor and leave with treatment or renege for other reasons (deconditioning, seeking private healthcare, etc). Adequate performance is commonly incentivised through the imposition of targets on waiting times. In the first study to do so, we develop a...

Prior to lockdown the spread of COVID-19 in UK is found to be exponential, with an exponent =0.207. In case of COVID-19 this spreading behaviour is quantitatively better described with a mobility-driven SIR-SEIR model [2] rather than the homogenous mixing models Lockdown has dramatically slowed down the spread of COVID-19 in UK, and even more significantly, has changed the growth in the total number of infected from exponential to quadratic. This significant change is due to a transition from a ...

BackgroundThe COVID-19 pandemic presents a significant challenge to minimize mortality and hospitalizations due to this disease. Vaccinations have begun to roll-out; however, restriction policies required during and after the rollout remain uncertain. A susceptible-exposed-infected-recovered (SEIR) model was developed for Nova Scotia, and it accounted for the provinces policy interventions, demographics, and vaccine rollout schedule. MethodsA modified SEIR model was developed to simulate the sp...

There was a fury of the pandemic because of novel coronavirus (2019-nCoV/SARS-CoV-2) that happened in Wuhan, Hubei province, in China in December 2019. Since then, many model predictions on the COVID-19 pandemic in Wuhan and other parts of China have been reported. The first incident of coronavirus disease 2019 (COVID-19) in India was reported on 30 January 2020, which was a student from Wuhan. The number of reported cases has started to increase day by day after 30 February 2020. The purpose of...

The rapid rise of antibiotic resistance is a serious threat to global public health. Without further incentives, pharmaceutical companies have little interest in developing antibiotics, since the success probability is low and development costs are huge. The situation is exacerbated by the "antibiotics dilemma": Developing narrow-spectrum antibiotics against resistant bacteria is most beneficial for society, but least attractive for companies since their usage is more limited than for broad-spec...

This study presents a mathematical model for optimal vaccination strategies in interconnected metropolitan areas, considering commuting patterns. It is a compartmental model with a vaccination rate for each city, acting as a control function. The commuting patterns are incorporated through a weighted adjacency matrix and a parameter that selects day and night periods. The optimal control problem is formulated to minimize a functional cost that balances the number of hospitalizations and vaccines...

The effective reproduction ratio r(t) of an epidemic, defined as the average number of secondary infected cases per infectious case in a population in the current state, including both susceptible and non-susceptible hosts, controls the transition between a subcritical threshold regime (r(t) < 1) and a supercritical threshold regime (r(t) > 1). While in subcritical regimes, an index infected case will cause an outbreak that will die out sooner or later, with large fluctuations observed when appr...

We present human mobility data for the United Kingdom collected from the "BBC Pandemic", a public science project linked to the BBC Four television documentary of the same name. Mobile phone GPS trajectories submitted by users and collected over a 24 hour period were aggregated to construct anonymised origin-destination flux matrices at the local administrative district (LAD). We use these data to explore how mobility patterns change with age and employment status - unique stratifications that a...

Contagion happens through heterogeneous interpersonal relations (homophily) which induce contamination clusters. Group testing is increasingly recognized as necessary to fight the asymptomatic transmission of the COVID-19. Still, it is plagued by false negatives. Homophily can be taken into account to design test pools that encompass potential contamination clusters. I show that this makes it possible to overcome the usual information-theoretic limits of group testing, which are based on an impl...

Governments across Europe are preparing for the emergence from lockdown, in phases, to prevent a resurgence in cases of COVID-19. Along with social distancing (SD) measures, contact tracing - find, track, trace and isolate (FTTI) policies are also being implemented. Here, we investigate FTTI policies in terms of their impact on the endemic equilibrium. We used a generative model - the dynamic causal Location, Infection, Symptom and Testing (LIST) model to identify testing, tracing, and quara...

In this paper, we compare the inference regarding the effectiveness of the various non-pharmaceutical interventions (NPIs) for COVID-19 obtained from three SIR models, all developed by the Imperial College COVID-19 Response Team. One model was applied to European countries and published in Nature1 (model 1), concluding that complete lockdown was by far the most effective measure, responsible for 80% of the reduction in Rt, and 3 million deaths were avoided in the examined countries. The Imperial...

The number of active cases in the UK Covid-19 epidemic, the case fatality rate, the susceptible proportion of the population, and how well the lockdown was maintained during April-May 2020 are unknown. These four have a relationship with the shape of the daily mortality curve once one considers the intervals from infection to death or recovery. Without an understanding of this relationship we cannot say that an earlier lockdown would have saved lives. Using a small stochastic model, the lockdown...

Understanding the trajectory of the daily numbers of deaths in people with CoVID-19 is essential to decisions on the response to the CoVID-19 pandemic. Estimating this trajectory from data on numbers of deaths is complicated by the delay between deaths occurring and their being reported to the authorities. In England, Public Health England receives death reports from a number of sources and the reporting delay is typically several days, but can be several weeks. Delayed reporting results in cons...

New Zealand had 1499 cases of COVID-19 before eliminating transmission of the virus. Extensive contract tracing during the outbreak has resulted in a dataset of epidemiologically linked cases. This data contains useful information about the transmission dynamics of the virus, its dependence on factors such as age, and its response to different control measures. We use Monte-Carlo network construction techniques to provide an estimate of the number of secondary cases for every individual infecte...