Alex Keeley

Alex Keeley
The University of Sheffield | Sheffield · Department of Infection and Immunity

About

23
Publications
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Publications

Publications (23)
Article
Full-text available
B.1.1.7 lineage SARS-CoV-2 is more transmissible, leads to greater clinical severity, and results in modest reductions in antibody neutralization. Subgenomic RNA (sgRNA) is produced by discontinuous transcription of the SARS-CoV-2 genome. Applying our tool (periscope) to ARTIC Network Oxford Nanopore Technologies genomic sequencing data from 4400 S...
Article
Full-text available
The measurement of antibodies to vaccine antigens is crucial for research towards a safe and effective vaccine for Streptococcus pyogenes (Strep A). We describe the establishment and detailed characterisation of a four-plex assay to measure IgG to the Strep A vaccine antigens SpyCEP, Slo, SpyAD and GAC using the Luminex multiplex platform. A standa...
Article
Full-text available
Background Group A Streptococcus (GAS) is a major human pathogen and an important cause of maternal and neonatal sepsis. Asymptomatic bacterial colonization is considered a necessary step towards sepsis. Intra-partum azithromycin may reduce GAS carriage. Methods A posthoc analysis of a double-blind, placebo-controlled randomized-trial was performe...
Preprint
Full-text available
Streptococcus pyogenes is a leading cause of human morbidity and mortality, especially in resource limited settings. The World Health Organisation has recently made a vaccine for S. pyogenes a global health priority to reduce the burden of the post-infection rheumatic heart disease. For a vaccine to be active against all relevant strains in each re...
Article
Full-text available
Background: Genetic variations across the SARS-CoV-2 genome may influence transmissibility of the virus and the host's anti-viral immune response, in turn affecting the frequency of variants over time. In this study, we examined the adjacent amino acid polymorphisms in the nucleocapsid (R203K/G204R) of SARS-CoV-2 that arose on the background of th...
Preprint
Full-text available
Objectives To characterise within-hospital SARS-CoV-2 transmission across two waves of the COVID-19 pandemic. Design A retrospective Bayesian modelling study to reconstruct transmission chains amongst 2181 patients and healthcare workers using combined viral genomic and epidemiological data. Setting A large UK NHS Trust with over 1400 beds and em...
Article
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Background: Rapid identification and investigation of healthcare-associated infections (HCAIs) is important for suppression of SARS-CoV-2, but the infection source for hospital onset COVID-19 infections (HOCIs) cannot always be readily identified based only on epidemiological data. Viral sequencing data provides additional information regarding pot...
Preprint
Full-text available
SARS-CoV-2 lineage B.1.1.7 viruses are more transmissible, may lead to greater clinical severity, and result in modest reductions in antibody neutralization. subgenomic RNA (sgRNA) is produced by discontinuous transcription of the SARS-CoV-2 genome and is a crucial step in the SARS-CoV-2 life cycle. Applying our tool (periscope) to ARTIC Network Ox...
Preprint
Full-text available
Background Group A Streptococcus (GAS) is a major human pathogen and an important cause of maternal and neonatal sepsis. Methods We performed a posthoc analysis of a double-blind, placebo-controlled randomized-trial (ratio 1:1) carried out in The Gambia to determine the impact of one oral dose (2g) of intra-partum azithromycin on maternal and neon...
Article
We have developed periscope, a tool for the detection and quantification of sub-genomic RNA (sgRNA) in SARS-CoV-2 genomic sequence data. The translation of the SARS-CoV-2 RNA genome for most open reading frames (ORFs) occurs via RNA intermediates termed “sub-genomic RNAs”. sgRNAs are produced through discontinuous transcription which relies on homo...
Article
Full-text available
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional and municipal. The shift occurred even in local epidemics where the original D614 f...
Article
Full-text available
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional, and municipal. The shift occurred even in local epidemics where the original D614...
Research
Full-text available
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional and municipal. The shift occurred even in local epidemics where the original D614 f...
Article
Paradoxical reactions, including immune reconstitution inflammatory syndrome (IRIS), are common in patients co-infected with human immunodeficiency virus (HIV) and tuberculosis (TB). Paradoxical reactions may confer substantial morbidity and mortality, especially in cases of central nervous system (CNS) TB, or through protracted usage of corticoste...
Article
Full-text available
Healthcare workers (HCW) are potentially at increased risk of infection with coronavirus disease (COVID-19) and may transmit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to vulnerable patients. We present results from staff testing at Sheffield Teaching Hospitals NHS Foundation Trust, United Kingdom. Between 16 and 29 March 2020, 1,...
Article
Background Paradoxical inflammatory reactions are well known to complicate tuberculosis (TB) and are observed with greater frequency in patients who are co-infected with HIV. Immune reconstitution inflammatory syndrome (IRIS) is a paradoxical inflammatory reaction following early immune system recovery after initiation of antiretroviral therapy. IR...
Article
Full-text available
Lyme disease (LD) is the most common tick-borne infectious disease in the Northern hemisphere. LD can present with a wide range of symptoms depending on time since infection; from localised skin reactions such as erythema migrans, to widespread multi-system involvement. There may be non-specific symptoms of malaise, aching joints and muscles, and c...
Article
Full-text available
Meningococcal pericarditis is classically divided into three separate entities: isolated meningococcal pericarditis, disseminated meningococcal disease with pericarditis, and reactive (immunopathic) meningococcal pericarditis. We present the case of a 74-year-old woman with meningococcal septicaemia with meningococcal myopericarditis, which demonst...
Article
Full-text available
We present a successful conservative management strategy for a frail elderly patient with a cardiac resynchronisation pacemaker who presented with evidence of an Enterobacter cloacae pacemaker pocket infection. A device washout and debridement procedure was performed, with reburial of the device in a new prepectoral pocket and creation of a closed-...
Article
Full-text available
Background Untreated, miliary tuberculosis (TB) has a mortality approaching 100%. As it is uncommon there is little specific data to guide its management. We report detailed data from a UK cohort of patients with miliary tuberculosis and the associations and predictive ability of admission blood tests with clinical outcomes. Methods Routinely coll...