Louis du Plessis
A5007000185- SARS-CoV-2 and COVID-19 Research
- COVID-19 epidemiological studies
- Genomics and Phylogenetic Studies
- Evolution and Genetic Dynamics
- SARS-CoV-2 detection and testing
- COVID-19 Clinical Research Studies
- Mosquito-borne diseases and control
- Viral Infections and Vectors
- Animal Virus Infections Studies
- Virology and Viral Diseases
- Viral gastroenteritis research and epidemiology
- Plant Virus Research Studies
- Bacteriophages and microbial interactions
- Zoonotic diseases and public health
- Influenza Virus Research Studies
- Genetic diversity and population structure
- Viral Infections and Outbreaks Research
- vaccines and immunoinformatics approaches
- Syphilis Diagnosis and Treatment
- Evolution and Paleontology Studies
- Insect symbiosis and bacterial influences
- Plant and animal studies
- Insect and Pesticide Research
- Forensic and Genetic Research
- Image Retrieval and Classification Techniques
ETH Zurich
2011-2025
SIB Swiss Institute of Bioinformatics
2015-2025
École Nationale Vétérinaire de Toulouse
2023
University of Oxford
2017-2022
Imperial College London
2022
Quadram Institute
2022
Medawar Building for Pathogen Research
2017-2021
University of the Witwatersrand
2009-2011
Biotech (Brazil)
2005
Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances nearly all aspects the joint modelling evolutionary data. It is increasingly appreciated that some questions can only be adequately answered by combining evidence from multiple independent sources data, including genome sequences, sampling dates, phenotypic radiocarbon fossil occurrences, and biogeographic range information among others. Including relevant data into a single...
The ongoing coronavirus disease 2019 (COVID-19) outbreak expanded rapidly throughout China. Major behavioral, clinical, and state interventions were undertaken to mitigate the epidemic prevent persistence of virus in human populations China worldwide. It remains unclear how these unprecedented interventions, including travel restrictions, affected COVID-19 spread We used real-time mobility data from Wuhan detailed case history elucidate role importation transmission cities across ascertain...
Abstract The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. first was associated with a mix of lineages, while the second and third waves were driven Beta (B.1.351) Delta (B.1.617.2) variants, respectively 1–3 . In November 2021, genomic surveillance teams South Botswana detected new variant rapid resurgence infections Gauteng province, Africa. Within days genome being uploaded, it designated concern (Omicron, B.1.1.529) World Health Organization and,...
Abstract The response of the global virus genomics community to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been unprecedented, with significant advances made towards ‘real-time’ generation and sharing SARS-CoV-2 genomic data. rapid growth in genome data production necessitated development new analytical methods that can deal orders magnitude more genomes than previously available. Here, we present describe Phylogenetic Assignment Named Global Outbreak Lineages...
Brazil currently has one of the fastest-growing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemics in world. Because limited available data, assessments impact nonpharmaceutical interventions (NPIs) on this virus spread remain challenging. Using a mobility-driven transmission model, we show that NPIs reduced reproduction number from >3 to 1 1.6 São Paulo and Rio de Janeiro. Sequencing 427 new genomes analysis geographically representative genomic dataset identified >100...
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...
The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed illuminate evolution highly insect societies. Bumblebees also invaluable natural and agricultural pollinators, there widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects bumblebee biology, including susceptibility implicated viability threats.We report high quality draft genome sequences...
The yellow fever virus (YFV) epidemic in Brazil is the largest decades. recent discovery of YFV Brazilian Aedes species mosquitos highlights a need to monitor risk reestablishment urban transmission Americas. We use suite epidemiological, spatial, and genomic approaches characterize transmission. show that age sex distribution human cases characteristic sylvatic Analysis combined with genomes generated locally reveals an early phase spatial expansion toward previously YFV-free areas,...
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome 2 (SARS-CoV-2) has spread globally, with >365,000 cases in California as of 17 July 2020. We investigated the genomic epidemiology SARS-CoV-2 Northern from late January to mid-March 2020, using samples 36 patients spanning nine counties and Grand Princess cruise ship. Phylogenetic analyses revealed cryptic introduction at least seven different lineages into California, including epidemic WA1 strains...
The ongoing pandemic spread of a novel human coronavirus, SARS-COV-2, associated with severe pneumonia disease (COVID-19), has resulted in the generation thousands virus genome sequences. rate is unprecedented, yet there currently no coherent nor accepted scheme for naming expanding phylogenetic diversity SARS-CoV-2. We present rational and dynamic nomenclature that uses framework to identify those lineages contribute most active spread. Our system made tractable by constraining number depth...
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...
The first SARS-CoV-2 variant of concern (VOC) to be designated was lineage B.1.1.7, later labelled by the World Health Organization as Alpha. Originating in early autumn but discovered December 2020, it spread rapidly and caused large waves infections worldwide. Alpha is notable for being defined a long ancestral phylogenetic branch with an increased evolutionary rate, along which only two sequences have been sampled. genomes comprise well-supported monophyletic clade within rate typical...
The SARS-CoV-2 Delta (Pango lineage B.1.617.2) variant of concern spread globally, causing resurgences COVID-19 worldwide1,2. emergence the in UK occurred on background a heterogeneous landscape immunity and relaxation non-pharmaceutical interventions. Here we analyse 52,992 genomes from England together with 93,649 rest world to reconstruct quantify its introduction regional dissemination across context changing travel social restrictions. Using analysis human movement, contact tracing...
The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. first was associated with a mix of lineages, while the second and third waves were driven Beta (B.1.351) Delta (B.1.617.2) variants, respectively1–3. In November 2021, genomic surveillance teams South Botswana detected new variant rapid resurgence infections Gauteng province, Africa. Within days genome being uploaded, it designated concern (Omicron, B.1.1.529) World Health Organization and, within...
Abstract Background Sociality has many rewards, but can also be dangerous, as high population density and low genetic diversity, common in social insects, is ideal for parasite transmission. Despite this risk, honeybees other sequenced insects have far fewer canonical immune genes relative to solitary insects. Social protection from infection, including behavioral responses, may explain depauperate repertoire. Here, based on full genome sequences, we describe the repertoire of two...
With high-throughput technologies providing vast amounts of data, it has become more important to provide systematic, quality annotations. The Gene Ontology (GO) project is the largest resource for cataloguing gene function. Nonetheless, its use not yet ubiquitous and still fraught with pitfalls. In this review, we a short primer GO bioinformaticians. We summarize aspects structure ontology, describe sources types functional annotations, survey measures annotation similarity, review typical...
Significance Some genotypes of parasites can infect some hosts but not others, whereas also vary in susceptibility to a given parasite genotype. Variation genes important for defenses against could produce this specificity. Here, we find that variation gene expression depended on both the genotype host and parasite. Moreover, found bumblebees were exposed infectious trypanosome had low immune upregulation control expression. A poorly infecting genotype, however, induced genes. These results...
Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in Near East, and mitochondrial DNA (mtDNA) suggests pigs arrived Europe alongside farmers ∼8,500 BP. A few thousand years after introduction of Eastern into Europe, however, their characteristic mtDNA signature disappeared was replaced haplotypes associated with European wild boars. This turnover could be accounted for substantial gene flow from local boars, although it is also possible...
Abstract The ongoing COVID-19 outbreak has expanded rapidly throughout China. Major behavioral, clinical, and state interventions are underway currently to mitigate the epidemic prevent persistence of virus in human populations China worldwide. It remains unclear how these unprecedented interventions, including travel restrictions, have affected spread We use real-time mobility data from Wuhan detailed case history elucidate role importation on transmission cities across ascertain impact...
Phylogenetics and phylodynamics are central topics in modern evolutionary biology. Phylogenetic methods reconstruct the relationships among organisms, whereas phylodynamic approaches reveal underlying diversification processes that lead to observed relationships. These two fields have many practical applications disciplines as diverse epidemiology, developmental biology, palaeontology, ecology, linguistics. The combination of increasingly large genetic data sets increases computing power is...
The Zika virus (ZIKV) epidemic in the Americas established ZIKV as a major public health threat and uncovered its association with severe diseases, including microcephaly. However, genetic epidemiology some at-risk regions, particularly Central America Mexico, remains limited. We report 61 genomes from this region, generated using metagenomic sequencing ZIKV-specific enrichment, combine phylogenetic, epidemiological, environmental data to reconstruct transmission. These analyses revealed...