A5000526097- HIV Research and Treatment
- SARS-CoV-2 and COVID-19 Research
- HIV/AIDS Research and Interventions
- COVID-19 epidemiological studies
- COVID-19 Clinical Research Studies
- HIV, Drug Use, Sexual Risk
- SARS-CoV-2 detection and testing
- HIV/AIDS drug development and treatment
- Animal Virus Infections Studies
- Genomics and Phylogenetic Studies
- Sex work and related issues
- Hepatitis C virus research
- Evolution and Genetic Dynamics
- COVID-19 and Mental Health
- Liver Disease Diagnosis and Treatment
- vaccines and immunoinformatics approaches
- Viral gastroenteritis research and epidemiology
- Health Systems, Economic Evaluations, Quality of Life
- Data-Driven Disease Surveillance
- Plant Virus Research Studies
- Hepatitis B Virus Studies
- Monoclonal and Polyclonal Antibodies Research
- Healthcare Systems and Reforms
- Vaccine Coverage and Hesitancy
- HIV/AIDS Impact and Responses
Imperial College London
2019-2024
Genomics (United Kingdom)
2022-2023
UK Health Security Agency
2022-2023
University of Chicago
2023
Imperial Valley College
2022
London Centre for Neglected Tropical Disease Research
2019-2021
University of California, San Diego
2017-2021
London School of Hygiene & Tropical Medicine
2020
Medical Research Council
2020
Institut de Recherche Vaccinale
2020
The SARS-CoV-2 lineage B.1.1.7, designated variant of concern (VOC) 202012/01 by Public Health England1, was first identified in the UK late summer to early autumn 20202. Whole-genome sequence data collected from community-based diagnostic testing for COVID-19 show an extremely rapid expansion B.1.1.7 during 2020, suggesting that it has a selective advantage. Here we changes VOC frequency inferred genetic correspond closely S gene target failures (SGTF) PCR testing. Analysis trends SGTF and...
Abstract The SARS-CoV-2 lineage B.1.1.7, now designated Variant of Concern 202012/01 (VOC) by Public Health England, originated in the UK late Summer to early Autumn 2020. We examine epidemiological evidence for this VOC having a transmission advantage from several perspectives. First, whole genome sequence data collected community-based diagnostic testing provides an indication changing prevalence different genetic variants through time. Phylodynamic modelling additionally indicates that...
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%...
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...
WHO has called for increased testing in response to the COVID-19 pandemic, but countries have taken different approaches and effectiveness of alternative strategies is unknown. We aimed investigate potential impact isolation on transmission severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
Abstract Despite its poorly adapted codon usage, HIV-1 replicates and is expressed extremely well in human host cells. has recently been shown to package non-lysyl transfer RNAs (tRNAs) addition the tRNALys needed for priming reverse transcription integration of genome. By comparing usage genes with that host, we found tRNAs decoding codons are highly used by but avoided overrepresented virions. In particular, A-ending codons, required expression HIV's A-rich genome, enriched. Because...
Effective public response to a pandemic relies upon accurate measurement of the extent and dynamics an outbreak. Viral genome sequencing has emerged as powerful approach link seemingly unrelated cases, large-scale surveillance can inform on critical epidemiological parameters. Here, we report analysis 864 SARS-CoV-2 sequences from cases in New York City metropolitan area during COVID-19 outbreak spring 2020. The majority had no recent travel history or known exposure, genetically linked were...
Abstract COVID-19 patients at risk of severe disease may be treated with neutralising monoclonal antibodies (mAbs). To minimise virus escape from neutralisation these are administered as combinations e.g. casirivimab+imdevimab or, for targeting relatively conserved regions, individually sotrovimab. Unprecedented genomic surveillance SARS-CoV-2 in the UK has enabled a genome-first approach to detect emerging drug resistance Delta and Omicron cases sotrovimab respectively. Mutations occur...
HIV-1 subtype B infections are associated with MSM in the UK. Yet, around 13% of found those reporting heterosexual contact as transmission route. Using phylogenetics, we explored possible misclassification sexual exposure among men diagnosed HIV UK.Viral gene sequences linked to patient-derived information were used identify phylogenetic chains.A total 22,481 pol sampled between 1996 and 2008 analysed. Dated phylogenies reconstructed clusters identified clades at least two a maximum genetic...
We compared the behavior of two approaches (Cluster Picker and HIV-TRACE) at varying genetic distances to identify transmission clusters. used three HIV gp41 sequence datasets originating from Rakai Community Cohort Study: (1) next-generation (NGS) data nine linked couples; (2) NGS longitudinal sampling 14 individuals; (3) Sanger consensus sequences a cross-sectional dataset (n = 1,022) containing 91 epidemiologically heterosexual couples. calculated optimal distance threshold separate...
Abstract Motivation The ability to simulate epidemics as a function of model parameters allows insights that are unobtainable from real datasets. Further, reconstructing transmission networks for fast-evolving viruses like Human Immunodeficiency Virus (HIV) may have the potential greatly enhance epidemic intervention, but network reconstruction methods been inadequately studied, largely because it is difficult obtain ‘truth’ sets on which test them and properly measure their performance....
Harm reduction has dramatically reduced HIV incidence among people who inject drugs (PWID). In Glasgow, Scotland, <10 infections/year have been diagnosed PWID since the mid-1990s. However, in 2015 a sharp rise diagnoses was noted PWID; many were subtype C with 2 identical drug-resistant mutations and some displayed low avidity, suggesting infections linked recent.We collected Scottish pol sequences identified closely related from public databases. Genetic linkage ascertained 228 Scottish,...
Background. The United Kingdom human immunodeficiency virus (HIV) epidemic was historically dominated by HIV subtype B transmission among men who have sex with (MSM). Now 50% of diagnoses and prevalent infections are heterosexual individuals mainly involve non-B subtypes. Between 2002 2010, the prevalence MSM increased from 5.4% to 17%, this study focused on drivers change.
COVID-19 (Disease); Epidemics; Infectious disease; Emerging infectious diseases; Communicable diseases
It has been reported that the increase in human immunodeficiency virus (HIV) sequence diversity drug resistance surveillance specimens may be used to classify duration of HIV infection as <1 or >1 year. We describe a mixed base classifier (MBC) optimized categorize subtype B infections <6 >6 months on basis sequences for and compared MBC findings with those serologic methods.The behavior was examined across range thresholds calling bases. performance then evaluated using either complete pol...
HIV prevalence has decreased in Uganda since the 1990s, but remains substantial within high-risk groups. Here, we reconstruct history and spread of subtypes A1 D explore transmission dynamics populations. We analysed pol sequences from female sex workers Kampala (n = 42), Lake Victoria fisher-folk 46) a rural clinical cohort 74), together with publicly available adjacent regions 412) newly generated samples taken 1986 12). Of three Ugandan populations, 60 (37.1 %) were classified as subtype...
Abstract Effective public response to a pandemic relies upon accurate measurement of the extent and dynamics an outbreak. Viral genome sequencing has emerged as powerful approach link seemingly unrelated cases, large-scale surveillance can inform on critical epidemiological parameters. Here, we report analysis 864 SARS-CoV-2 sequences from cases in New York City metropolitan area during COVID-19 outbreak Spring 2020. The majority had no recent travel history or known exposure, genetically...
Abstract Unprecedented public health interventions including travel restrictions and national lockdowns have been implemented to stem the COVID-19 epidemic, but effectiveness of non-pharmaceutical is still debated. We carried out a phylogenetic analysis more than 29,000 publicly available whole genome SARS-CoV-2 sequences from 57 locations estimate time that epidemic originated in different places. These estimates were examined relation dates most stringent each location as well number...
Objective: Through the application of simple, accessible, molecular epidemiology tools, we aimed to resolve phylogenetic relationships that best predicted patterns cluster growth using longitudinal population level drug resistance genotype data. Methods: Analysis was performed on 971 specimens from naïve, first time HIV positive subjects collected in British Columbia between 2002 and 2005. A 1240bp fragment pol gene amplified sequenced with among subtype B sequences inferred...