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Articles by Peter Simmonds
Virus community views on the possible extension of virus taxonomic assignments to a below-species rank
Article metrics loading... /content/journal/jgv/10.1099/jgv.0.002313 Metrics Download as PowerPoint /deliver/fulltext/jgv/107/8/jgv002313.html?itemId=/content/journal/jgv/10.1099/jgv.0.002313&mimeType=html&fmt=ahah References Adams MJ, Lefkowitz EJ, King AMQ, Harrach B, Harrison RL et al. 50 years of the International Committee on Taxonomy of Viruses: progress and prospects. Arch Virol 2017; 162:1441–1446 [View Article] [Google Scholar] The Master Species List: A Spreadsheet of Current Taxonomy.
Virus taxonomy proposal summaries: a searchable and citable resource to disseminate virus taxonomy advances
Article metrics loading... /content/journal/jgv/10.1099/jgv.0.002079 Download as PowerPoint /deliver/fulltext/jgv/106/7/jgv002079.html?itemId=/content/journal/jgv/10.1099/jgv.0.002079&mimeType=html&fmt=ahah References International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2019; 69:S1–S111 [View Article] [Google Scholar] Cain AJ. Linnaeus’s ordines naturales. Arch Nat Hist 1993; 20:405–415 [Google Scholar] Queiroz K de.
ICTV Virus Taxonomy Summaries
ICTV Virus Taxonomy Summaries are published by the International Committee on Taxonomy of Viruses (ICTV) annually in Journal of General Virology and provide a complete and authoritative record of all ratified taxonomy changes made by the ICTV in the preceding year.
Integrated analysis of protein sequence and structure redefines viral diversity and the taxonomy of the Flaviviridae
Abstract The Flaviviridae are a family of non-segmented positive-sense enveloped RNA viruses containing significant pathogens including hepatitis C virus and yellow fever virus.
C->U transition biases in SARS-CoV-2 – still rampant four years from the start of the COVID-19 pandemic
Abstract The evolution of SARS-CoV2 in the pandemic and post-pandemic periods has been characterised by rapid adaptive changes that confer immune escape and enhanced human-to-human transmissibility. Sequence change is additionally marked by an excess number of C->U transitions suggested as being due to host-mediated genome editing.
Biomarkers of transfusion transmitted occult hepatitis B virus infection: Where are we and what next?
Anti-HBc Antibodies against the hepatitis B virus core antigen Anti-HBe Antibodies against the hepatitis B virus e antigen Anti-HBs Antibodies against the hepatitis B virus surface antigen cccDNA covalently closed circular DNA CHB Chronic hepatitis B virus infection ER endoplasmic reticulum FFP fresh frozen plasma HBcAg Hepatitis B virus core antigen HBcrAg Hepatitis B virus core-related antigen HBeAg Hepatitis B virus e antigen HBsAg Hepatitis B virus surface antigen HBV hepatitis B virus...
Parechovirus A Circulation and Testing Capacities in Europe, 2015-2021
Parechoviruses are small, nonenveloped, single-stranded RNA viruses belonging to the large Picornaviridae family that circulate worldwide; primary infections occur mainly in children <2 years of age (1,2). Parechoviruses are transmitted by fecal-oral and respiratory routes (2,3). Most infections are asymptomatic or have mild general gastrointestinal or respiratory symptoms, but they can occasionally lead to sepsis, meningitis or other neurologic manifestations, or even death (2–6).
Ultrasensitive PCR system for HBV DNA detection: Risk stratification for occult hepatitis B virus infection in English blood donors
1 INTRODUCTION Hepatitis B virus (HBV) infection constitutes a major global health burden, with an estimated 296 million people chronically infected in 2019.1 This DNA virus is highly endemic in geographical areas such as sub-Saharan Africa, South-East Asia, China, and South America.2 HBV infection can be acquired through various routes, including vertical transmission, sexual contact, and unsafe injections.2 HBV is also the most prevalent transfusion-transmitted viral infection despite...
Reconstructing the evolutionary history of human, simian, and prosimian immunodeficiency viruses
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Swine IFI6 confers antiviral effects against Japanese encephalitis virus in vitro and in vivo
Abstract Swine are considered to be an important intermediate host in the cycle of Japanese encephalitis virus (JEV) infection. Most existing antiviral studies of JEV mainly focus on the host factor of the dead-end hosts. However, little research has addressed this in swine. Here, we found that swine interferon alpha-inducible protein 6 (sIFI6) possessed antiviral activity against JEV.
Mechanisms of bunyavirus morphogenesis and egress
Abstract Unlike many segmented negative-sense RNA viruses, most members of the Bunyavirales bud at Golgi membranes, as opposed to the plasma membrane. Central players in this assembly process are the envelope glycoproteins, Gn and Gc, which upon translation undergo proteolytic processing, glycosylation and trafficking to the Golgi, where they interact with ribonucleoprotein genome segments and bud into Golgi-derived compartments.
A review of reptile virus experimental infection studies
Abstract Despite recent advances in molecular techniques, infection studies remain an important tool for biosecurity, veterinary and conservation medicines. Experimental infection studies are performed for many reasons: to investigate causal links between pathogens and disease, to study host species susceptibility, to study immune response to inoculation, to investigate pathogen transmission and to investigate methods for infection control.
Digoxin is a potent inhibitor of Bunyamwera virus infection in cell culture
Abstract Drug repurposing is a valuable source of new antivirals because many compounds used to treat a variety of pathologies can also inhibit viral infections. In this work, we have tested the antiviral capacity of four repurposed drugs to treat Bunyamwera virus (BUNV) infection in cell cultures. BUNV is the prototype of the Bunyavirales order, a large group of RNA viruses that includes important pathogens for humans, animals and plants.
Four principles to establish a universal virus taxonomy
Principle 3. An evolutionary taxonomy is but one of many possible means to classify viruses We recognize that classifications of viruses by clinicians, veterinarians, agronomists, and regulators may differ from a virus taxonomy that is grounded in evolutionary relationships. Numerous widely used clinical or veterinary virus designations cannot be supported by taxonomic assignments but often better serve clinical and regulatory purposes.
A pleasant surprise may be in store for consumers this Christmas
A pleasant surprise may be in store for consumers this Christmas, Opinion - THE BUSINESS TIMES
Evaluating the risk of transfusion and transplant‐transmitted monkeypox infections
Funding information: National Institute of Health Research, Grant/Award Number: NIHR203338 Abstract The recent emergence of monkeypox virus (MPXV) in the UK and elsewhere is of urgent public health concern. Several aspects of MPXV epidemiology and pathogenesis, including its systemic spread and viraemia during acute infection, furthermore represent an important potential threat to the safety of blood transfusion and organ transplantation.
A mechanistic evolutionary model explains the time-dependent pattern of substitution rates in viruses
Highlights • Chronological saturation of sites creates a power-law rate decay with slope −0.65 • Our model can be used to correctly estimate the rate decay and viral ages • Humanity may have been exposed to sarbecoviruses since the Paleolithic period • The origins of HCV date back before human migration out of Africa Summary Estimating viral timescales is fundamental in understanding the evolutionary biology of viruses.
The importance of enterovirus surveillance in a post-polio world
Summary Poliovirus is known to most people in the world as the cause of polio, a devastating paralytic disease from the past. Success in polio eradication has understandably translated into stricter containment plans for poliovirus, coordinated by WHO. In this Personal View, we discuss the impact of recent biosafety level 3+ guidelines for handling potential poliovirus-containing diagnostic specimens, which has resulted in closure of many national WHO poliovirus reference laboratories.
Prisoner of War dynamics explains the time-dependent pattern of substitution rates in viruses
New Results Mahan Ghafari, View ORCID ProfilePeter Simmonds, Oliver Pybus, Aris Katzourakis doi: https://doi.org/10.1101/2021.02.09.430479 Abstract Molecular clock dating is widely used to estimate timescales of phylogenetic histories and to infer rates at which species evolve. One of the major challenges with inferring rates of molecular evolution is the observation of a strong correlation between estimated rates and the timeframe of their measurements.
The First Nonmammalian Pegivirus Demonstrates Efficient In Vitro Replication and High Lymphotropism
Pathogenesis and Immunity Zhen Wu, Yuanyuan Wu, Wei Zhang, Andres Merits, Peter Simmonds, Mingshu Wang, Renyong Jia, Dekang Zhu, Mafeng Liu, Xinxin Zhao, Qiao Yang, Ying Wu, ShaQiu Zhang, Juan Huang, Xumin Ou, Sai Mao, YunYa Liu, Ling Zhang, YanLing Yu, Bin Tian, Leichang Pan, Mujeeb Ur Rehman, Shun Chen, Anchun Cheng Colin R.
Molecular epidemiology and clinical impact of rhinovirus infections in adults during three epidemic seasons in 11 European countries (2007-2010)
Molecular epidemiology and clinical impact of rhinovirus infections in adults during three epidemic seasons in 11 European countries (2007–2010) Kalina T Zlateva1, http://orcid.org/0000-0002-0551-5543Anneloes L van Rijn1, Peter Simmonds2, Frank E J Coenjaerts3, Anton M van Loon3, Theo J M Verheij4, Jutte J C de Vries1, http://orcid.org/0000-0003-3664-1873Paul Little5, Christopher C Butler6, Erik W van Zwet7, Herman Goossens8, Margareta Ieven8, Eric C J Claas1 on behalf of the GRACE Study...
Molecular epidemiology and clinical impact of rhinovirus infections in adults during three epidemic seasons in 11 European countries (2007-2010)
Molecular epidemiology and clinical impact of rhinovirus infections in adults during three epidemic seasons in 11 European countries (2007–2010) Kalina T Zlateva1, http://orcid.org/0000-0002-0551-5543Anneloes L van Rijn1, Peter Simmonds2, Frank E J Coenjaerts3, Anton M van Loon3, Theo J M Verheij4, Jutte J C de Vries1, http://orcid.org/0000-0003-3664-1873Paul Little5, Christopher C Butler6, Erik W van Zwet7, Herman Goossens8, Margareta Ieven8, Eric C J Claas1 on behalf of the GRACE Study...
Perforin and resistance to SARS coronavirus 2
Louise Cunningham, MB Louise Cunningham Correspondence Corresponding author: Dr Louise Cunningham, C/O: St. John’s Institute of Dermatology, Guy’s and St Thomas’ Hospital, London, United Kingdom. +447789368407 Affiliations St. John’s Institute of Dermatology, Guy’s and St Thomas’ Hospital, London, UK Search for articles by this author Peter Simmonds, PhD Ian Kimber, PhD David Arthur Basketter, FRCPath John Paul McFadden, DM
Sero-Prevalence and Incidence of A/H1N1 2009 Influenza Infection in Scotland in Winter 2009-2010
Loading metrics Open Access Peer-reviewed Research Article Nigel J. McLeish, Peter Simmonds, Chris Robertson, Ian Handel, Mark McGilchrist, Brajendra K. Singh, Shona Kerr, Margo E. Chase-Topping, Katy Sinka, Mark Bronsvoort, David J. Porteous, William Carman, James McMenamin, Andrew Leigh-Brown, Mark E. J. Woolhouse Nigel J. McLeish, Peter Simmonds, Chris Robertson, Ian Handel, Mark McGilchrist, Brajendra K. Singh, Shona Kerr, Margo E.
Plant Virus Genome Is Shaped by Specific Dinucleotide Restrictions That Influence Viral Infection
Research Article | Host-Microbe Biology Alfonso González de Prádena, Adrián Sánchez Jimenez, David San León, Peter Simmonds, Juan Antonio García, Adrián A. Valli Nisha K. Duggal, Editor DOI: 10.1128/mBio.02818-19 ABSTRACT The presence of CpG and UpA dinucleotides is restricted in the genomes of animal RNA viruses to avoid specific host defenses. We wondered whether a similar phenomenon exists in nonanimal RNA viruses.
Reply to ‘Evolutionary stasis of viruses?’
Our Opinion article (Prisoners of war — host adaptation and its constraints on virus evolution. Nat. Rev. Microbiol. https://doi.org/10.1038/s41579-018-0120-2 (2018))1 describes host adaptation and its potential role in shaping long-term evolution of viruses. Holmes and Duchêne’s correspondence (Evolutionary stasis of viruses? Nat. Rev. Microbiol.
Prisoners of war - host adaptation and its constraints on virus evolution
1. Jenkins, G. M., Rambaut, A., Pybus, O. G. & Holmes, E. C. Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. J. Mol. Evol. 54, 156–165 (2002). 2. Lemey, P., Rambaut, A. & Pybus, O. G. HIV evolutionary dynamics within and among hosts. AIDS Rev. 8, 125–140 (2006). 3. Sanjuan, R. From molecular genetics to phylodynamics: evolutionary relevance of mutation rates across viruses. PLOS Pathog. 8, e1002685 (2012). 4. Hanada, K., Suzuki, Y. & Gojobori, T.
Strategies to improve detection and management of human parechovirus infection in young infants
Human parechovirus infections are the second most common cause of viral meningitis in children. These infections are most frequently seen in infants younger than 90 days. Clinical manifestations include encephalitis, meningitis, myocarditis, and sepsis, which can lead to serious neurodevelopmental sequelae in young infants.
Bodas de Sangre
Federico Garcia Lorca’s celebrated Spanish-language play tells the tale of a wedding day that descends into tragedy. This simple but powerful tale criticises the divisive and close-mindedness of traditional, rural Spanish culture. It is a theme that resonated with Lorca’s life as he struggled to reconcile his homosexuality amongst the prejudice of the time. This was a vibrant and exciting performance from Edinburgh University’s Spanish students.
Consensus statement: Virus taxonomy in the age of metagenomics
The workshop reached a consensus view on classifying viruses solely on the basis of metagenomic sequence data and, consequently, developed a set of proposals (Box 1; Supplementary information S1 (box)). These proposals are diagrammatically summarized in Fig. 3. Basis of classification. Classifying viruses that are identified only from metagenomic data will advance virus taxonomy, dependent on appropriate checks on data integrity and following the standard procedures of assignment.
Consensus statement: Virus taxonomy in the age of metagenomics
The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV).
Journal of General Virology
The Microbiology Society's founding journal, Microbiology, is now fully Open Access (OA). Find out more about the transformation here. Journal of General Virology has been publishing peer-reviewed research for more than 50 years. We recognise the importance of virology as a unique discipline within microbiology, and actively collaborate with partners such as the International Committee on Taxonomy of Viruses (ICTV) to support the global virology community.
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