A5021343090- COVID-19 epidemiological studies
- SARS-CoV-2 and COVID-19 Research
- SARS-CoV-2 detection and testing
- COVID-19 Digital Contact Tracing
- Data-Driven Disease Surveillance
- Evolution and Genetic Dynamics
- Mathematical and Theoretical Epidemiology and Ecology Models
- COVID-19 Clinical Research Studies
- Evolutionary Game Theory and Cooperation
- Global Health Care Issues
- COVID-19 and Mental Health
- demographic modeling and climate adaptation
- Healthcare Policy and Management
- Insurance, Mortality, Demography, Risk Management
- Plant Virus Research Studies
- Vaccine Coverage and Hesitancy
- vaccines and immunoinformatics approaches
University of Oxford
2020-2024
Open Data Institute
2020-2024
Centre de Recerca Matemàtica
2019-2020
Universitat Autònoma de Barcelona
2019
Barcelona Graduate School of Mathematics
2019
Institute for Integrative Systems Biology
2019
Universitat de València
2019
The newly emergent human virus SARS-CoV-2 (severe acute respiratory syndrome-coronavirus 2) is resulting in high fatality rates and incapacitated health systems. Preventing further transmission a priority. We analyzed key parameters of epidemic spread to estimate the contribution different routes determine requirements for case isolation contact tracing needed stop epidemic. Although spreading too fast be contained by manual tracing, it could controlled if this process were faster, more...
Abstract The newly emergent human virus SARS-CoV-2 is resulting in high fatality rates and incapacitated health systems. Preventing further transmission a priority. We analysed key parameters of epidemic spread to estimate the contribution different routes determine requirements for case isolation contact-tracing needed stop epidemic. conclude that viral too fast be contained by manual contact tracing, but could controlled if this process was faster, more efficient happened at scale. A App...
SARS-CoV-2 has spread across the world, causing high mortality and unprecedented restrictions on social economic activity. Policymakers are assessing how best to navigate through ongoing epidemic, with computational models being used predict of infection assess impact public health measures. Here, we present OpenABM-Covid19: an agent-based simulation epidemic including detailed age-stratification realistic networks. By default model is parameterised UK demographics calibrated however, it can...
Persistent SARS-CoV-2 infections may act as viral reservoirs that could seed future outbreaks
Abstract The timing of SARS-CoV-2 transmission is a critical factor to understand the epidemic trajectory and impact isolation, contact tracing other non-pharmaceutical interventions on spread COVID-19 epidemics. We examined distribution events with respect exposure onset symptoms. show that for symptomatic individuals, more strongly linked clinical symptoms than time since infection. found it was approximately centered symmetric around symptoms, three quarters occurring in window from 2-3...
Abstract Contact tracing is increasingly used to combat COVID-19, and digital implementations are now being deployed, many based on Apple Google’s Exposure Notification System. These systems utilize non-traditional smartphone-based technology, presenting challenges in understanding possible outcomes. In this work, we create individual-based models of three Washington state counties explore how exposure notifications combined with other non-pharmaceutical interventions influence COVID-19...
Abstract SARS-CoV-2 has spread across the world, causing high mortality and unprecedented restrictions on social economic activity. Policymakers are assessing how best to navigate through ongoing epidemic, with models being used predict of infection assess impact public health measures. Here, we present OpenABM-Covid19: an agent-based simulation epidemic including detailed age-stratification realistic networks. By default model is parameterised UK demographics calibrated however, it can...
Abstract Contact tracing is increasingly being used to combat COVID-19, and digital implementations are now deployed, many of them based on Apple Google’s Exposure Notification System. These systems new smartphone technology that has not traditionally been for this purpose, presenting challenges in understanding possible outcomes. In work, we use individual-based computational models explore how exposure notifications can be conjunction with non-pharmaceutical interventions, such as...
The Office for National Statistics Coronavirus (COVID-19) Infection Survey (ONS-CIS) is the largest surveillance study of SARS-CoV-2 positivity in community, and collected data on United Kingdom (UK) epidemic from April 2020 until March 2023 before being paused. Here, we report epidemiological evolutionary dynamics determined by analysing sequenced samples ONS-CIS during this period. We observed a series sweeps or partial sweeps, with each sweeping lineage having distinct growth advantage...
Background: The timing of SARS-CoV-2 transmission is a critical factor to understand the epidemic trajectory and impact isolation, contact tracing other non-pharmaceutical interventions on spread COVID-19 epidemics. Methods: We examined distribution event times with respect exposure onset symptoms. analysed 119 pairs known date symptoms for both index secondary cases partial information their intervals exposure. inferred generation time from by maximum likelihood. modelled different...
The first year of the COVID-19 pandemic put considerable strain on healthcare systems worldwide. In order to predict effect local epidemic hospital capacity in England, we used a variety data streams inform construction and parameterisation progression model, EpiBeds, which was coupled model generalised epidemic. this individuals progress through different pathways (e.g. may recover, die, or intensive care recover die) from partially complete patient-pathway line-list provide initial...
In this study, we evaluated the impact of viral variant, in addition to other variables, on within-host burden, by analysing cycle threshold (Ct) values derived from nose and throat swabs, collected as part UK COVID-19 Infection Survey. Because burden distributions determined community survey data can be biased due variant epidemiology time-since-infection samples, developed a method explicitly adjust observed Ct value account for expected bias. By adjusted using partial least squares...
Abstract The Office for National Statistics COVID-19 Infection Survey (ONS-CIS) is the largest surveillance study of SARS-CoV-2 positivity in community, and collected data on United Kingdom (UK) epidemic from April 2020 until March 2023 before being paused. Here, we report epidemiological evolutionary dynamics determined by analysing sequenced samples ONS-CIS during this period. We observed a series sweeps or partial sweeps, with each sweeping lineage having distinct growth advantage...
Abstract Persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections may act as viral reservoirs that could seed future outbreaks 1–5 , give rise to highly divergent lineages 6–8 and contribute cases with post-acute Coronavirus disease 2019 (COVID-19) sequelae (Long Covid) 9,10 . However, the population prevalence of persistent infections, their load kinetics, evolutionary dynamics over course remain largely unknown. We identified 381 lasting at least 30 days, which 54...
We investigate the dynamics of a wild-type viral strain which generates mutant strains differing in phenotypic properties for infectivity, virulence and mutation rates. study, by means mathematical model bifurcation analysis, conditions under viruses, compete same host cells, can coexist. The coexistence are formulated terms basic reproductive numbers strains, maximum value rate pathogens. analysis reveals that parameter space be divided into five regions, each with distinct dynamics,...
Abstract Quarantining close contacts of individuals infected with SARS-CoV-2 for 10 to 14 days is a key strategy in reducing transmission. However, quarantine requirements are often unpopular, low adherence, especially when large fraction the population has been vaccinated. Daily contact testing (DCT), which required isolate only if they test positive, an alternative mitigating risk transmission from traced contacts. In this study, we developed integrated model COVID-19 dynamics and compared...
In this work, we have investigated the evolutionary dynamics of a generalist pathogen, e.g., virus population, that evolves toward specialization in an environment with multiple host types. We particularly explored under which conditions viral strains may rise frequency and coexist specialist or even dominate population. By means nonlinear mathematical model bifurcation analysis, determined theoretical for stability nine identified equilibria provided biological interpretation terms...
Abstract In this study, we evaluated the impact of viral variant, in addition to other variables, on within-host burdens, by analysing cycle threshold (Ct) values derived from nose and throat swabs, collected as part UK COVID-19 Infection Survey. Because burden distributions determined community survey data can be biased due variant epidemiology time-since-infection samples, developed a method explicitly adjust observed Ct value account for expected bias. Analysing adjusted using partial...
The first year of the COVID-19 pandemic put considerable strain on national healthcare system in England. In order to predict effect local epidemic hospital capacity England, we used a variety data streams inform construction and parameterisation progression model, which was coupled model generalised epidemic. We named this EpiBeds. Data from partially complete patient-pathway line-list provide initial estimates mean duration that individuals spend different compartments. then fitted EpiBeds...