Kris V. Parag
A5045686938- COVID-19 epidemiological studies
- Influenza Virus Research Studies
- Data-Driven Disease Surveillance
- SARS-CoV-2 and COVID-19 Research
- Evolution and Genetic Dynamics
- Viral Infections and Outbreaks Research
- COVID-19 Pandemic Impacts
- Zoonotic diseases and public health
- SARS-CoV-2 detection and testing
- Mathematical and Theoretical Epidemiology and Ecology Models
- Viral Infections and Vectors
- Genetic diversity and population structure
- Genomics and Phylogenetic Studies
- COVID-19 Clinical Research Studies
- Agricultural risk and resilience
- Gene Regulatory Network Analysis
- Animal Disease Management and Epidemiology
- Virology and Viral Diseases
- Genetic and phenotypic traits in livestock
- COVID-19 and Mental Health
- Genetic Mapping and Diversity in Plants and Animals
- Vaccine Coverage and Hesitancy
- Bioinformatics and Genomic Networks
- Evolution and Paleontology Studies
- Viral gastroenteritis research and epidemiology
Imperial College London
2018-2025
University of Bristol
2022-2025
NIHR Bristol Biomedical Research Centre
2022-2023
London Centre for Neglected Tropical Disease Research
2021-2023
University of Oxford
2015-2021
Medical Research Council
2020
University of Cambridge
2013-2017
SummaryBackgroundCOVID-19 has the potential to cause substantial disruptions health services, due cases overburdening system or response measures limiting usual programmatic activities. We aimed quantify extent which services for HIV, tuberculosis, and malaria in low-income middle-income countries with high burdens of these diseases could lead additional loss life over next 5 years.MethodsAssuming a basic reproduction number 3·0, we constructed four scenarios possible responses COVID-19...
In response to the COVID-19 pandemic, countries have sought control SARS-CoV-2 transmission by restricting population movement through social distancing interventions, thus reducing number of contacts. Mobility data represent an important proxy measure distancing, and here, we characterise relationship between mobility for 52 around world. Transmission significantly decreased with initial reduction in 73% analysed, but found evidence decoupling following relaxation strict measures 80%...
Attack rate in Manaus Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) incidence peaked Manaus, Brazil, May 2020 with a devastating toll on the city's inhabitants, leaving its health services shattered and cemeteries overwhelmed. Buss et al. collected data from blood donors São Paulo, noted when transmission began to fall, estimated final attack rates October (see Perspective by Sridhar Gurdasani). Heterogeneities immune protection, population structure, poverty, modes of public...
Lineage dynamics The scale of genome-sequencing efforts for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unprecedented. United Kingdom has contributed more than 26,000 sequences to this effort. This volume data allowed du Plessis et al. develop a detailed picture the influxes virus reaching U.K. shores as pandemic developed during first months 2020 (see Perspective by Nelson). Before lockdown, high travel volumes and few restrictions on international 1000 lineages become...
Understanding the causes and consequences of emergence severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants concern is crucial to pandemic control yet difficult achieve because they arise in context variable human behavior immunity. We investigated spatial invasion dynamics lineage B.1.1.7 by jointly analyzing UK mobility, virus genomes, community-based polymerase chain reaction data. identified a multistage process which early growth rates were associated with mobility...
Abstract As of 1st June 2020, the US Centres for Disease Control and Prevention reported 104,232 confirmed or probable COVID-19-related deaths in US. This was more than twice number next most severely impacted country. We jointly model epidemic at state-level, using publicly available death data within a Bayesian hierarchical semi-mechanistic framework. For each state, we estimate individuals that have been infected, are currently infectious time-varying reproduction (the average secondary...
Summary Brazil is an epicentre for COVID-19 in Latin America. In this report we describe the Brazilian epidemic using three epidemiological measures: number of infections, deaths and reproduction number. Our modelling framework requires sufficient death data to estimate trends, therefore limit our analysis 16 states that have experienced a total more than fifty deaths. The distribution among highly heterogeneous, with 5 states—Sao Paulo, Rio de Janeiro, Ceara, Pernambuco Amazonas—accounting...
We construct a recursive Bayesian smoother, termed EpiFilter, for estimating the effective reproduction number, R, from incidence of an infectious disease in real time and retrospectively. Our approach borrows Kalman filtering theory, is quick easy to compute, generalisable, deterministic unlike many current methods, requires no change-point or window size assumptions. model R as flexible, hidden Markov state process exactly solve forward-backward algorithms, derive estimates that...
Abstract Summary statistics, often derived from simplified models of epidemic spread, inform public health policy in real time. The instantaneous reproduction number, Rt, is predominant among these measuring the average ability an infection to multiply. However, Rt encodes no temporal information and sensitive modelling assumptions. Consequently, some have proposed growth rate, rt, that is, rate change log-transformed case incidence, as a more temporally meaningful model-agnostic guide. We...
Coronavirus disease 2019 (COVID-19) continues to affect the world, and design of strategies curb outbreaks requires close monitoring their trajectories. We present machine learning methods that leverage internet-based digital traces anticipate sharp increases in COVID-19 activity U.S. counties. In a complementary direction efforts led by Centers for Disease Control Prevention (CDC), our models are designed detect time when an uptrend will occur. Motivated need finer spatial resolution...
The effective reproduction number, Rt, is a key time-varying prognostic for the growth rate of any infectious disease epidemic. Significant changes in Rt can forewarn about new transmissions within population or predict efficacy interventions. Inferring reliably and real-time from observed time-series infected (demographic) data an important problem dynamics. renewal branching process model popular solution that has been applied to Ebola Zika virus outbreaks, among others, currently being...
Italy was the first European country to experience sustained local transmission of COVID-19. As 1st May 2020, Italian health authorities reported 28,238 deaths nationally. To control epidemic, government implemented a suite non-pharmaceutical interventions (NPIs), including school and university closures, social distancing full lockdown involving banning public gatherings non essential movement. In this report, we model effect NPIs on using data average mobility. We estimate that...
Abstract Estimating past population dynamics from molecular sequences that have been sampled longitudinally through time is an important problem in infectious disease epidemiology, ecology, and macroevolution. Popular solutions, such as the skyline skygrid methods, infer effective sizes coalescent event times of phylogenies reconstructed but assume sequence sampling are uninformative about size changes. Recent work has started to question this assumption by exploring how information can aid...
COVID-19 (Disease); Epidemics; Infectious disease; Emerging infectious diseases; Communicable diseases
From the Introduction: The course of COVID-19 [coronavirus disease 2019] epidemic in Low- and Middle-Income Countries (LMICs) will be determined by actions that countries take coming weeks months It is clear taken to reduce size epidemic, delay, or flatten its peak, could lead substantial reductions deaths if doing so allows more patients with severe conditions benefit from supportive care hospital However, impact response it have far reaching consequences - including on other diseases,...