Whole pathogen genome sequencing, phylogenetics and modelling in viral diagnostics
Lead Research Organisation:
UNIVERSITY COLLEGE LONDON
Department Name: Great Ormond St. Instit of Child Health
Abstract
Using Bioinformatics to analyse whole genome pathogen sequences from patients in GOSH & wider, starting with norovirus & adenovirus. Aim to drive improvements in diagnostics for personalised medical care, better handle transmission in outbreaks and study effects of experimental drugs.
Organisations
People |
ORCID iD |
| Oscar Charles (Student) |
Publications
Meng B
(2022)
Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts infectivity and fusogenicity.
in Nature
Mlcochova P
(2021)
SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion.
in Nature
Patella F
(2021)
Shrinking Weibel-Palade bodies prevents high platelet recruitment in assays using thrombotic thrombocytopenic purpura plasma.
in Research and practice in thrombosis and haemostasis
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| MR/N013867/1 | 30/09/2016 | 29/09/2025 | |||
| 2074328 | Studentship | MR/N013867/1 | 30/09/2018 | 30/12/2022 | Oscar Charles |
| NE/W502716/1 | 31/03/2021 | 30/03/2022 | |||
| 2074328 | Studentship | NE/W502716/1 | 30/09/2018 | 30/12/2022 | Oscar Charles |
| Title | cmvdrg - Human Cytomegalovirus Drug Resistance Genotyping database and application |
| Description | The first Comprehensive database of Human Cytomegalovirus Drug Resistance Mutations to All clinically relevant drugs. Ganciclovir, Cidofovir, Foscarnet, Letermovir, Tomeglovir. - Text database - R package - Web server - Only open source verifiable dataset Processes sequence and variant data, allowing use of minor variant frequencies known to be crucial for analysis of immunosuppressed patients. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | - Now the GOSH standard - Although still in pre-print it receives ~5 downloads a week and the web server has been used in 10 countries. - Was required for an upcoming paper in the lab (confidential) on longitudinal patient sequencing and prognosis. - Was required for an upcoming paper on Machine Learning to predict Resistance Mutations in the herpesviruses in general. |
| URL | https://github.com/ucl-pathgenomics/cmvdrg |