Benjamin B. Lindsey
A5002378351- SARS-CoV-2 and COVID-19 Research
- COVID-19 Clinical Research Studies
- Influenza Virus Research Studies
- COVID-19 epidemiological studies
- Respiratory viral infections research
- SARS-CoV-2 detection and testing
- Animal Virus Infections Studies
- Pneumonia and Respiratory Infections
- Viral gastroenteritis research and epidemiology
- vaccines and immunoinformatics approaches
- Vaccine Coverage and Hesitancy
- Immune responses and vaccinations
- Advanced Fluorescence Microscopy Techniques
- Foot and Ankle Surgery
- Animal Disease Management and Epidemiology
- COVID-19 and healthcare impacts
- COVID-19 diagnosis using AI
- Diabetic Foot Ulcer Assessment and Management
- Bacterial Infections and Vaccines
- interferon and immune responses
- Immunotherapy and Immune Responses
- Anodic Oxide Films and Nanostructures
- Sarcoma Diagnosis and Treatment
- CRISPR and Genetic Engineering
- RNA and protein synthesis mechanisms
University of Sheffield
2020-2025
Florey Institute of Neuroscience and Mental Health
2021-2025
MRC Unit the Gambia
2018-2025
Medical Research Council
2025
London School of Hygiene & Tropical Medicine
2021-2025
Imperial College London
2012-2025
Sheffield Teaching Hospitals NHS Foundation Trust
2020-2024
University of Manitoba
2023
Conway Regional Health System
2022
Royal Perth Hospital
2021
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become most prevalent form in global pandemic. Dynamic tracking of frequencies revealed a recurrent pattern G614 increase at multiple geographic levels: national, regional, and municipal. The shift occurred even local epidemics where original D614 was well established prior to introduction variant. consistency this highly statistically significant, suggesting that may have fitness advantage. We found grows higher...
We identify amino acid variants within dominant SARS-CoV-2 T cell epitopes by interrogating global sequence data. Several nucleocapsid and ORF3a have arisen independently in multiple lineages result loss of recognition epitope-specific cells assessed IFN-γ cytotoxic killing assays. Complete responsiveness was seen due to Q213K the A∗01:01-restricted CD8+ epitope FTSDYYQLY207-215; P13L, P13S, P13T B∗27:05-restricted QRNAPRITF9-17; T362I P365S A∗03:01/A∗11:01-restricted KTFPPTEPK361-369. lines...
Genetic variations across the SARS-CoV-2 genome may influence transmissibility of virus and host's anti-viral immune response, in turn affecting frequency variants over time. In this study, we examined adjacent amino acid polymorphisms nucleocapsid (R203K/G204R) that arose on background spike D614G change describe how strains harboring these changes became dominant circulating globally.Deep-sequencing data from public databases clinical samples were analyzed to identify map genetic...
Hospital outbreaks of COVID19 result in considerable mortality and disruption to healthcare services yet little is known about transmission within this setting. We characterise hospital by combining viral genomic epidemiological data using Bayesian modelling amongst 2181 patients workers from a large UK NHS Trust. Transmission events were compared between Wave 1 (1st March 25th J'uly 2020) 2 (30th November 2020 24th January 2021). show that staff-to-staff transmissions reduced 31.6% 12.9%...
We have developed periscope, a tool for the detection and quantification of subgenomic RNA (sgRNA) in SARS-CoV-2 genomic sequence data. The translation genome most open reading frames (ORFs) occurs via intermediates termed "subgenomic RNAs." sgRNAs are produced through discontinuous transcription, which relies on homology between transcription regulatory sequences (TRS-B) upstream ORF start codons that TRS-L, is located 5' UTR. TRS-L immediately preceded by leader sequence. This therefore...
Background: Rapid identification and investigation of healthcare-associated infections (HCAIs) is important for suppression SARS-CoV-2, but the infection source hospital onset COVID-19 (HOCIs) cannot always be readily identified based only on epidemiological data. Viral sequencing data provides additional information regarding potential transmission clusters, low mutation rate SARS-CoV-2 can make interpretation using standard phylogenetic methods difficult. Methods: We developed a novel...
Abstract SARS-CoV-2 lineage B.1.1.7 viruses are more transmissible, may lead to greater clinical severity, and result in modest reductions antibody neutralization. subgenomic RNA (sgRNA) is produced by discontinuous transcription of the genome a crucial step life cycle. Applying our tool (periscope) ARTIC Network Oxford Nanopore genomic sequencing data from 4400 positive samples, we show that normalised sgRNA expression profiles significantly increased infections (n=879). This increase seen...
Abstract Little is known about SARS-CoV-2 infection risk in African countries with high levels of infection-driven immunity and low vaccine coverage. We conducted a prospective cohort study 349 participants from 52 households The Gambia between March 2021 June 2022, routine weekly RT-PCR 6-monthly serology. Attack rates 45% 57% were seen during Delta Omicron BA.1 waves respectively. Eighty-four percent RT-PCR-positive infections asymptomatic. Children under 5-years had lower incidence than...
B.1.1.7 lineage SARS-CoV-2 is more transmissible, leads to greater clinical severity, and results in modest reductions antibody neutralization. Subgenomic RNA (sgRNA) produced by discontinuous transcription of the genome. Applying our tool (periscope) ARTIC Network Oxford Nanopore Technologies genomic sequencing data from 4400 positive samples, we show that normalised sgRNA significantly increased (alpha) infections (n = 879). This increase seen over previous dominant UK, B.1.177 943), which...
Abstract Background Genetic variations across the SARS-CoV-2 genome may influence transmissibility of virus and host’s anti-viral immune response, in turn affecting frequency variants over-time. In this study, we examined adjacent amino acid polymorphisms nucleocapsid (R203K/G204R) that arose on background spike D614G change describe how strains harboring these changes became dominant circulating globally. Methods Deep sequencing data from public databases clinical samples were analyzed to...
Predicting individual vaccine responses remains a significant challenge due to the complexity and variability of immune processes. To address this gap, we developed immunaut , an open-source, data-driven framework implemented as R package specifically designed for all systems vaccinologists seeking analyze predict immunological outcomes across diverse vaccination settings. Leveraging one most comprehensive live attenuated influenza (LAIV) datasets date - 244 Gambian children enrolled in...
The reported number of SARS-CoV-2 cases and deaths are lower in Africa compared to many high-income countries. However, African cohorts, detailed characterisation mucosal T cell immunity limited. We assessed the SARS-CoV-2-specific immune landscape Gambia during presence pre-Delta variant July 2021. A cross-sectional assessment 349 unvaccinated individuals from 52 Gambian households was performed between March-June spike (S) nucleocapsid (N) specific binding antibodies were measured by...
<ns3:p><ns3:bold>Background:</ns3:bold> We aimed to measure SARS-CoV-2 seroprevalence in a cohort of healthcare workers (HCWs) during the first UK wave COVID-19 pandemic, explore risk factors associated with infection, and investigate impact antibody titres on assay sensitivity.</ns3:p><ns3:p> </ns3:p><ns3:p> <ns3:bold>Methods:</ns3:bold> HCWs at Sheffield Teaching Hospitals NHS Foundation Trust were prospectively enrolled sampled two time points. developed an in-house ELISA for testing...
Background: Knowledge regarding the prevalence, clinical features and etiology of pediatric influenza-like illness (ILI) remains limited in African settings. Furthermore, it is likely that many children presenting with ILI receive antibiotics unnecessarily. More data are required to develop antimicrobial stewardship practice guide effective vaccine strategies. We undertook a 1-year prospective study Gambia. Methods: Children <5 years age from March 2018 2019 were recruited. Clinical...
<ns3:p><ns3:bold>Background:</ns3:bold> We aimed to measure SARS-CoV-2 seroprevalence in a cohort of healthcare workers (HCWs) during the first UK wave COVID-19 pandemic, explore risk factors associated with infection, and investigate impact antibody titres on assay sensitivity.</ns3:p><ns3:p> <ns3:bold>Methods:</ns3:bold> HCWs at Sheffield Teaching Hospitals NHS Foundation Trust were prospectively enrolled sampled two time points. antibodies tested using an in-house for IgG IgA reactivity...
Background: In order to understand the molecular epidemiology of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Sri Lanka, since March 2020, we carried out genomic sequencing overlaid on available epidemiological data until April 2021. Methods: Whole genome was diagnostic sputum or nasopharyngeal swabs from 373 patients with COVID-19. Molecular clock phylogenetic analysis undertaken further explore dominant lineages. Results: The B.1.411 lineage most prevalent, which...
We identify amino acid variants within dominant SARS-CoV-2 T-cell epitopes by interrogating global sequence data. Several nucleocapsid and ORF3a have arisen independently in multiple lineages result loss of recognition epitope-specific T-cells assessed IFN-γ cytotoxic killing assays. These data demonstrate the potential for evasion highlight need ongoing surveillance capable escaping as well humoral immunity.Funding: This work is supported UK Medical Research Council (MRC); Chinese Academy...
Abstract Directly measuring evidence of influenza infections is difficult, especially in low-surveillance settings such as sub-Saharan Africa. Using a Bayesian model, we estimated unobserved infection times and underlying antibody responses to A/H3N2, using cross-sectional serum 4 strains children aged 24–60 months. Among the 242 individuals, variable seasonal attack rate found that most had ≥1 before 2 years age. Our results are consistent with previously published high rates children. The...