Peter Simmonds
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View article: Changes to virus taxonomy, the international code of virus classification and nomenclature, and the ICTV statutes ratified by the International Committee on Taxonomy of Viruses (2025)
Changes to virus taxonomy, the international code of virus classification and nomenclature, and the ICTV statutes ratified by the International Committee on Taxonomy of Viruses (2025) Open
The 56th meeting of the Executive Committee (EC) of the International Committee on Taxonomy of Viruses (ICTV) was held in Bari, Italy, in July/August, 2024, and 115 submitted taxonomy proposals were reviewed. A total of 112 were subsequent…
View article: Design and implementation of blood donor sample bioarchives to enhance preparedness for emerging and pandemic pathogens in England
Design and implementation of blood donor sample bioarchives to enhance preparedness for emerging and pandemic pathogens in England Open
New and emerging infections with blood-borne pathogens pose an ongoing threat to the safety of blood transfusions and transplants. Bioarchives of stored blood donor samples represent a valuable pathogen screening resource for both ensuring…
View article: A blood safety perspective on emerging arboviral infections in the United Kingdom
A blood safety perspective on emerging arboviral infections in the United Kingdom Open
A core focus of the blood services is to maintain the blood supply whilst simultaneously being vigilant for potential threats to blood safety. At present, West Nile virus (WNV), Usutu virus (USUV), Dengue virus (DENV) and Tick‐borne enceph…
View article: Design and non-viral delivery of live attenuated virus vaccine to prevent chronic hepacivirus (HCV-like) infection 3916
Design and non-viral delivery of live attenuated virus vaccine to prevent chronic hepacivirus (HCV-like) infection 3916 Open
Description The development of an effective prophylactic vaccine for hepatitis C virus (HCV) is an unmet medical need. We described that rat HCV-like virus (RHV) infection in laboratory rats recapitulates the life-long hepatotropic infecti…
View article: Divergent antibody-mediated population immunity to H5, H7 and H9 subtype potential pandemic influenza viruses
Divergent antibody-mediated population immunity to H5, H7 and H9 subtype potential pandemic influenza viruses Open
Influenza continues to cause significant mortality globally and possesses substantial pandemic potential. Assessing pandemic risk requires a clear understanding of existing population immunity. Leveraging a unique large-scale cohort of hum…
View article: Understanding off-target growth defects introduced to influenza A virus by synonymous recoding
Understanding off-target growth defects introduced to influenza A virus by synonymous recoding Open
CpG dinucleotides are under-represented in the genomes of most RNA viruses. Synonymously increasing CpG content of a range of RNA virus genomes reliably causes replication defects due to the recognition of CpG motifs in RNA by cellular Zin…
View article: Virus taxonomy proposal summaries: a searchable and citable resource to disseminate virus taxonomy advances
Virus taxonomy proposal summaries: a searchable and citable resource to disseminate virus taxonomy advances Open
Taxonomic classification of cellular organisms requires the publication of descriptions and proposed names of species and the deposition of specimens. Virus taxonomy is developed through a different system of annual submission of formal ta…
View article: Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) – General taxonomy proposals, 2025
Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) – General taxonomy proposals, 2025 Open
During the 56th annual meeting of the International Committee on Taxonomy of Viruses (ICTV), held in Bari, Italy, in August 2024, two technical proposals were presented. The first called for amended versions of accepted taxonomic proposals…
View article: Does 'Measure It' measure up? Feasibility and acceptability of a very brief physical activity intervention for cardiac rehabilitation attendees with coronary heart disease
Does 'Measure It' measure up? Feasibility and acceptability of a very brief physical activity intervention for cardiac rehabilitation attendees with coronary heart disease Open
Background Cardiac rehabilitation (CR) attendees with coronary heart disease (CHD) are unlikely to meet recommended physical activity (PA) levels. Time-efficient and easy-to-implement interventions are therefore needed. The ‘Measure It!’ T…
View article: Next-Generation Sequencing Methods for Sensitive Hepatitis B Viral Genome Analysis: A European Study
Next-Generation Sequencing Methods for Sensitive Hepatitis B Viral Genome Analysis: A European Study Open
Objectives This multicentre study investigated the utility of next-generation sequencing (NGS) to detect and generate hepatitis B virus (HBV) genomes in samples of low viral load (from 0.2 to 6207 IU/ml). Methods 23 HBV DNA positive plasma…
View article: RNA binding regulation is a new dimension in the type I IFN response
RNA binding regulation is a new dimension in the type I IFN response Open
The type I interferon (IFN-I) response shapes the intracellular environment to supress virus infection. Historically, this remodelling has been linked to the transcriptional induction of interferon stimulated genes (ISGs). However, IFN-I-d…
View article: Virus species names have been standardized; virus names remain unchanged
Virus species names have been standardized; virus names remain unchanged Open
Virus taxonomy, comprising classification and nomenclature, is regulated by the International Committee on Taxonomy of Viruses (ICTV). Taxon names are standardized to facilitate recognition and communication, with defined suffixes for each…
View article: Nanopore-based hybridization capture approaches for targeted viral metagenomics and whole-genome sequencing
Nanopore-based hybridization capture approaches for targeted viral metagenomics and whole-genome sequencing Open
Hybridization capture approaches can significantly increase the sensitivity of metagenomics. However, their implementation with Oxford Nanopore Technologies (ONT) sequencing has been limited due to the lack of dedicated workflows and the n…
View article: Occult hepatitis B virus infection: risk for a blood supply, but how about individuals’ health?
Occult hepatitis B virus infection: risk for a blood supply, but how about individuals’ health? Open
The implementation of effective blood donation screening for hepatitis B virus (HBV) anti-core antibodies with highly sensitive molecular HBV DNA detection in low-endemic countries like the United Kingdom has improved blood safety. However…
View article: Integrated analysis of protein sequence and structure redefines viral diversity and the taxonomy of the <i>Flaviviridae</i>
Integrated analysis of protein sequence and structure redefines viral diversity and the taxonomy of the <i>Flaviviridae</i> Open
The Flaviviridae are a family of non-segmented positive-sense enveloped RNA viruses containing significant pathogens including hepatitis C virus and yellow fever virus. Recent large-scale metagenomic surveys have identified many diverse RN…
View article: Seroprevalence of Borrelia burgdorferi sensu lato antibodies in English adult blood donors: A nationwide cross-sectional study, 2021–2022
Seroprevalence of Borrelia burgdorferi sensu lato antibodies in English adult blood donors: A nationwide cross-sectional study, 2021–2022 Open
The seroprevalence of Borrelia burgdorferi sensu lato-specific IgG in the English adult population (2021 - 2022), determined using two-tier testing was estimated at 0.49 % (95 % CI 0.36 - 0.65). This is lower than neighbouring UK nation Sc…
View article: Quantifying the impact of a novel virus on the economic value of pathogen reduction technology for platelets
Quantifying the impact of a novel virus on the economic value of pathogen reduction technology for platelets Open
Background Pathogen reduction technology (PRT) is an intervention designed to proactively reduce the amount of known and unknown pathogens in donated blood. As current screening for known pathogens is highly effective, some previous evalua…
View article: C→U transition biases in SARS-CoV-2: still rampant 4 years from the start of the COVID-19 pandemic
C→U transition biases in SARS-CoV-2: still rampant 4 years from the start of the COVID-19 pandemic Open
The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the pandemic and post-pandemic periods has been characterized by rapid adaptive changes that confer immune escape and enhanced human-to-human transmissibility…
View article: Intra-host genomic diversity and integration landscape of human tissue-resident DNA virome
Intra-host genomic diversity and integration landscape of human tissue-resident DNA virome Open
The viral intra-host genetic diversities and interactions with the human genome during decades of persistence remain poorly characterized. In this study, we analyzed the variability and integration sites of persisting viruses in nine organ…
View article: International review of blood donation screening for anti‐HBc and occult hepatitis B virus infection
International review of blood donation screening for anti‐HBc and occult hepatitis B virus infection Open
Background Hepatitis B core antibody (anti‐HBc) screening has been implemented in many blood establishments to help prevent transmission of hepatitis B virus (HBV), including from donors with occult HBV infection (OBI). We review HBV scree…
View article: Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data
Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data Open
Motivation Target enrichment strategies generate genomic data from multiple pathogens in a single process, greatly improving sensitivity over metagenomic sequencing and enabling cost-effective, high-throughput surveillance and clinical app…
View article: GRAViTy-V2: a grounded viral taxonomy application
GRAViTy-V2: a grounded viral taxonomy application Open
Taxonomic classification of viruses is essential for understanding their evolution. Genomic classification of viruses at higher taxonomic ranks, such as order or phylum, is typically based on alignment and comparison of amino acid sequence…
View article: Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses
Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses Open
Background Metagenomics is a powerful approach for the detection of unknown and novel pathogens. Workflows based on Illumina short-read sequencing are becoming established in diagnostic laboratories. However, high sequencing depth requirem…