A5013810794- COVID-19 epidemiological studies
- Viral Infections and Outbreaks Research
- Data-Driven Disease Surveillance
- Genetic diversity and population structure
- SARS-CoV-2 and COVID-19 Research
- Genetic and phenotypic traits in livestock
- Influenza Virus Research Studies
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Phylogenetic Studies
- Ecology and Vegetation Dynamics Studies
- Vaccine Coverage and Hesitancy
- COVID-19 Clinical Research Studies
- COVID-19 and healthcare impacts
- Disaster Response and Management
- Evolution and Paleontology Studies
- Evolution and Genetic Dynamics
- Gene expression and cancer classification
- Data Analysis with R
- Viral Infections and Vectors
- Scientific Computing and Data Management
- Salmonella and Campylobacter epidemiology
- Species Distribution and Climate Change
- COVID-19 Pandemic Impacts
- Respiratory viral infections research
- Mosquito-borne diseases and control
Imperial College London
2016-2025
London School of Hygiene & Tropical Medicine
2018-2024
University of London
2019-2022
London Centre for Neglected Tropical Disease Research
2019-2021
Medical Research Council
2014-2021
University of Cambridge
2021
Public Health England
2020-2021
World Health Organization
2021
Gates Foundation
2020
University of Hong Kong
2020
The package adegenet for the R software is dedicated to multivariate analysis of genetic markers. It extends ade4 methods by implementing formal classes and functions manipulate analyse Data can be imported from common population genetics exported other packages. also implements standard tools along with more original approaches spatial hybridization.Stable version available CRAN: http://cran.r-project.org/mirrors.html. Development website: http://adegenet.r-forge.r-project.org/. Both...
The dramatic progress in sequencing technologies offers unprecedented prospects for deciphering the organization of natural populations space and time. However, size datasets generated also poses some daunting challenges. In particular, Bayesian clustering algorithms based on pre-defined population genetics models such as STRUCTURE or BAPS software may not be able to cope with this amount data. Thus, there is a need less computer-intensive approaches. Multivariate analyses seem particularly...
While the R software is becoming a standard for analysis of genetic data, classical population genetics tools are being challenged by increasing availability genomic sequences. Dedicated needed harnessing large amount information generated next-generation sequencing technologies. We introduce new implemented in adegenet 1.3-1 package handling and analyzing genome-wide single nucleotide polymorphism (SNP) data. Using bit-level coding scheme SNP data parallelized computation, enables SNPs...
Summary 1. Phylogenetic signal is the tendency of related species to resemble each other more than drawn at random from same tree. This pattern considerable interest in a range ecological and evolutionary research areas, various indices have been proposed for quantifying it. Unfortunately, these often lead contrasting results, guidelines choosing most appropriate index are lacking. 2. Here, we compare performance four commonly used using simulated data. Data were generated with numerical...
BackgroundNon-pharmaceutical interventions have been implemented to reduce transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the UK. Projecting size an unmitigated epidemic and potential effect different control measures has crucial support evidence-based policy making during early stages epidemic. This study assesses impact for mitigating burden COVID-19 UK.MethodsWe used a stochastic age-structured model explore range intervention scenarios, tracking 66·4...
We present a global analysis of the spread recently emerged SARS-CoV-2 variants and estimate changes in effective reproduction numbers at country-specific level using sequence data from GISAID. Nearly all investigated countries demonstrated rapid replacement previously circulating lineages by World Health Organization-designated concern, with estimated transmissibility increases 29% (95% CI: 24-33), 25% 20-30), 38% 29-48) 97% 76-117), respectively, for B.1.1.7, B.1.351, P.1 B.1.617.2.
Species spatial distributions are the result of population demography, behavioral traits, and species interactions in spatially heterogeneous environmental conditions. Hence composition assemblages is an integrative response variable, its variability can be explained by complex interplay among several structuring factors. The thorough analysis variation may help infer processes shaping ecological communities. We suggest that studies would benefit from combined use classical statistical...
Accurate estimation of the parameters characterising infectious disease transmission is vital for optimising control interventions during epidemics. A valuable metric assessing current threat posed by an outbreak time-dependent reproduction number, i.e. expected number secondary cases caused each infected individual. This quantity can be estimated using data on numbers observed new at successive times epidemic and distribution serial interval (the time between symptomatic in a chain). Some...
Abstract Summary: adephylo is a package for the R software dedicated to analysis of comparative evolutionary data. Phylogenetic methods initially aimed at accounting or removing effects phylogenetic signal in biological traits. However, recent approaches have shown that considerable information can be gathered from study signal. In particular, close examination structures unveil interesting patterns. For this purpose, we developed provides tools quantifying and describing implements tests...
SummaryBackgroundNational immunisation programmes globally are at risk of suspension due to the severe health system constraints and physical distancing measures in place mitigate ongoing COVID-19 pandemic. We aimed compare benefits sustaining routine childhood Africa with acquiring acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection through visiting vaccination service delivery points.MethodsWe considered a high-impact scenario low-impact approximate child deaths that could be...
Recent years have seen progress in the development of statistically rigorous frameworks to infer outbreak transmission trees (“who infected whom”) from epidemiological and genetic data. Making use pathogen genome sequences such analyses remains a challenge, however, with variety heuristic approaches having been explored date. We introduce statistical method exploiting both collection dates unravel dynamics densely sampled outbreaks. Our approach identifies likely events infers infections,...
Recent years have seen the development of numerous methodologies for reconstructing transmission trees in infectious disease outbreaks from densely sampled whole genome sequence data. However, a fundamental and as yet poorly addressed limitation such approaches is requirement genetic diversity to arise on epidemiological timescales. Specifically, position infected individuals tree can only be resolved by data if mutations accumulated between pathogen genomes. To quantify compare useful...
Abstract Background Asymptomatic or subclinical SARS-CoV-2 infections are often unreported, which means that confirmed case counts may not accurately reflect underlying epidemic dynamics. Understanding the level of ascertainment (the ratio symptomatic cases to true number individuals) and undetected progression is crucial informing COVID-19 response planning, including introduction relaxation control measures. Estimating over time allows for accurate estimates specific outcomes such as...