Emma B. Hodcroft
A5020801823- SARS-CoV-2 and COVID-19 Research
- COVID-19 epidemiological studies
- SARS-CoV-2 detection and testing
- HIV Research and Treatment
- Animal Virus Infections Studies
- Viral gastroenteritis research and epidemiology
- Viral Infections and Immunology Research
- HIV/AIDS Research and Interventions
- Viral Infections and Outbreaks Research
- COVID-19 Clinical Research Studies
- Genomics and Phylogenetic Studies
- Plant Virus Research Studies
- HIV, Drug Use, Sexual Risk
- Evolution and Genetic Dynamics
- Cytomegalovirus and herpesvirus research
- Virology and Viral Diseases
- Influenza Virus Research Studies
- COVID-19 Pandemic Impacts
- HIV/AIDS drug development and treatment
- RNA and protein synthesis mechanisms
- Respiratory viral infections research
- Data-Driven Disease Surveillance
- Vaccine Coverage and Hesitancy
- Chromosomal and Genetic Variations
- CRISPR and Genetic Engineering
SIB Swiss Institute of Bioinformatics
2018-2025
Institute of Social and Preventive Medicine
2020-2025
University of Bern
2020-2025
University of Basel
2018-2024
University Hospital of Geneva
2024
University of Geneva
2022-2024
Swiss Tropical and Public Health Institute
2024
University of Edinburgh
2013-2018
Institut de Biologia Evolutiva
2015
The variants of concern (VoCs) SARS-CoV-2 have highlighted the need for a global molecular surveillance pathogens via whole genome sequencing.Such sequencing, and other pathogens, is performed by an ever increasing number labs across globe, resulting in increased easy, fast, decentralized analysis initial data.Nextclade aligns viral genomes to reference sequence, calculates several quality control (QC) metrics, assigns sequences clade or variant, identifies changes proteins relative...
This Viewpoint discusses emerging genetic variants of SARS-CoV-2, including new "UK" and "mink" the significance to coronavirus transmissibility, spread, virulence, efforts vaccinate population against COVID-19.
Switzerland is among the countries with highest number of coronavirus disease-2019 (COVID-19) cases per capita in world. There are likely many people undetected SARS-CoV-2 infection because testing efforts currently not detecting all infected people, including some clinical disease compatible COVID-19. Testing on its own will stop spread SARS-CoV-2. part a strategy. The World Health Organization recommends combination measures: rapid diagnosis and immediate isolation cases, rigorous tracking...
As sequence data sets used for the investigation of pathogen transmission patterns increase in size, automated tools and standardized methods cluster analysis have become necessary. We developed an Cluster Picker which identifies monophyletic clades meeting user-input criteria bootstrap support maximum genetic distance within large phylogenetic trees. A second tool, Matcher, automates process linking to epidemiological or clinical data, matches clusters between runs Picker. explore effect...
Following its emergence in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic resulting unprecedented efforts to reduce transmission and develop therapies vaccines (WHO Emergency Committee, 2020; Zhu et al., 2020). Rapidly generated viral genome sequences have allowed the spread of virus be tracked via phylogenetic analysis (Worobey Hadfield 2018; Pybus While globally early 2020 before borders closed, intercontinental travel since been...
After its emergence in Wuhan, China, late November or early December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus rapidly spread globally. Genome sequencing of SARS-CoV-2 allows reconstruction transmission history, although this is contingent on sampling. We analyzed 453 genomes collected between 20 February and 15 March 2020 from infected patients Washington state United States. find that most infections sampled during time derive a single introduction...
A novel coronavirus (SARS-CoV-2) first detected in Wuhan, China, has spread rapidly since December 2019, causing more than 100,000 confirmed infections and 4000 fatalities (as of 10 March 2020). The outbreak been declared a pandemic by the WHO on Mar 11, 2020. Here, we explore how seasonal variation transmissibility could modulate SARS-CoV-2 pandemic. Data from routine diagnostics show strong consistent four endemic coronaviruses (229E, HKU1, NL63, OC43) parameterise our model for using...
We propose a novel, non-discriminatory classification of monkeypox virus diversity. Together with the World Health Organization, we named three clades (I, IIa and IIb) in order detection. Within IIb, cause current global outbreak, identified multiple lineages (A.1, A.2, A.1.1 B.1) to support real-time genomic surveillance.
We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries outline potential genomic surveillance objectives. applied three nomenclature systems to all sequence data from World Health Organization European Region available until 10 July 2020. highlight importance real-time sequencing dissemination in a pandemic situation, compare nomenclatures lay foundation for future SARS-CoV-2.
With the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants that may increase transmissibility and/or cause escape from immune responses, there is an urgent need for targeted surveillance circulating lineages. It was found B.1.1.7 (also 501Y.V1) variant, first detected in United Kingdom, could be serendipitously by Thermo Fisher TaqPath COVID-19 PCR assay because a key deletion these viruses, spike Δ69-70, would "spike gene target failure" (SGTF) result....
The analysis of human pathogens requires a diverse collection bioinformatics tools.These tools include standard genomic and phylogenetic software custom developed to handle the relatively numerous short genomes viruses bacteria.Researchers increasingly depend on outputs these infer transmission dynamics diseases make actionable recommendations public health officials (Black et al., 2020;Gardy 2015).In order enable real-time analyses pathogen evolution, must scale rapidly with number samples...
A novel coronavirus (SARS-CoV-2) first detected in Wuhan, China, has spread rapidly since December 2019, causing more than 80,000 confirmed infections and 2,700 fatalities (as of Feb 27, 2020). Imported cases transmission clusters various sizes have been reported globally suggesting a pandemic is likely. Here, we explore how seasonal variation transmissibility could modulate SARS-CoV-2 pandemic. Data from routine diagnostics show strong consistent the four endemic coronaviruses (229E, HKU1,...
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein (S) plays critical roles in host cell entry. Non-synonymous substitutions affecting S are not uncommon and have become fixed a number of SARS-CoV-2 lineages. A subset such mutations enable escape from neutralizing antibodies or thought to enhance transmission through mechanisms as increased affinity for the entry receptor, angiotensin-converting enzyme (ACE2). Independent genomic surveillance programs based New...
The evolutionary mechanisms by which SARS-CoV-2 viruses adapt to mammalian hosts and, potentially, undergo antigenic evolution depend on the ways genetic variation is generated and selected within between individual hosts. Using domestic cats as a model, we show that consensus sequences remain largely unchanged over time hosts, while dynamic sub-consensus diversity reveals processes of drift weak purifying selection. We further identify notable variant at amino acid position 655 in Spike...
Tissue-resident memory CD8 + T cells in unexposed oropharyngeal lymphoid tissue exhibit specificity for SARS-CoV-2.
Worldwide outbreaks of enterovirus D68 (EV-D68) in 2014 and 2016 have caused serious respiratory neurological disease. We collected samples from several European countries during the 2018 outbreak determined 53 near full-length genome ('whole genome') sequences. These sequences were combined with 718 whole 1,987 VP1-gene publicly available In 2018, circulating strains clustered into multiple subgroups B3 A2 subclades, different phylogenetic origins. Clusters subclade emerged primarily US...
Pre-existing SARS-CoV-2-reactive T cells have been identified in SARS-CoV-2-unexposed individuals, potentially modulating COVID-19 and vaccination outcomes. Here, we provide evidence that functional cross-reactive memory CD4 + cell immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is established early childhood, mirroring seroconversion with seasonal human OC43. Humoral cellular immune responses OC43 SARS-CoV-2 were assessed children (paired samples at age two...
Abstract Enterovirus D68 (EV-D68) infections are associated with severe respiratory disease and acute flaccid myelitis (AFM). The European Non-Polio Network (ENPEN) aimed to investigate the epidemiological genetic characteristics of EV-D68 its clinical impact during fall-winter season 2021–2022. From 19 countries, 58 institutes reported 10 481 (6.8%) EV-positive samples which 1004 (9.6%) were identified as (including 852 samples). Clinical data for 969 cases; 78.9% in children (0–5 years);...