Peter Simmonds
University of Oxford
H-index: 137
Europe-United Kingdom
Description
Peter Simmonds, With an exceptional h-index of 137 and a recent h-index of 71 (since 2020), a distinguished researcher at University of Oxford, specializes in the field of Virology.
His recent articles reflect a diverse array of research interests and contributions to the field:
Parechovirus A Circulation and Testing Capacities in Europe, 2015–2021
Clinical metagenomics for detection of viruses using short-read, long-read and targeted approaches
Genetic diversity of RNA viruses infecting invertebrate pests of rice
Epidemiological and clinical insights into the enterovirus D68 upsurge in Europe 2021/22 and the emergence of novel B3-derived lineages, ENPEN multicentre study
Biomarkers of transfusion transmitted occult hepatitis B virus infection: Where are we and what next?
Blood donation screening for hepatitis B virus core antibodies: The importance of confirmatory testing and initial implication for rare blood donor groups
Absence of detectable monkeypox virus DNA in 11,000 English blood donations during the 2022 outbreak
The roles of nucleic acid editing in adaptation of zoonotic viruses to humans
Professor Information
University | University of Oxford |
---|---|
Position | ___ |
Citations(all) | 70695 |
Citations(since 2020) | 22774 |
Cited By | 58513 |
hIndex(all) | 137 |
hIndex(since 2020) | 71 |
i10Index(all) | 526 |
i10Index(since 2020) | 315 |
University Profile Page | University of Oxford |
Research & Interests List
Virology
Top articles of Peter Simmonds
Parechovirus A Circulation and Testing Capacities in Europe, 2015–2021
Parechovirus infections usually affect neonates and young children; manifestations vary from asymptomatic to life-threatening. We describe laboratory capacity in Europe for assessing parechovirus circulation, seasonality, and epidemiology. We used retrospective anonymized data collected from parechovirus infection case-patients identified in Europe during January 2015–December 2021. Of 21 laboratories from 18 countries that participated in the study, 16 (76%) laboratories with parechovirus detection capacity reported 1,845 positive samples; 12/16 (75%) with typing capability successfully identified 517 samples. Parechovirus A3 was the most common type (n= 278), followed by A1 (153), A6 (50), A4 (13), A5 (22), and A14 (1). Clinical data from 1,269 participants highlighted correlation of types A3, A4, and A5 with severe disease in neonates. We observed a wide capacity in Europe to detect, type, and analyze …
Authors
Laura Bubba,Eeva K Broberg,Thea K Fischer,Peter Simmonds,Heli Harvala,European Non-polio Enterovirus Network working group
Published Date
2024/2
Clinical metagenomics for detection of viruses using short-read, long-read and targeted approaches
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, barriers to broader take-up include the need for high sequencing depths, long turnaround times, and limited sensitivity. Newer metagenomics protocols based on Oxford Nanopore Technologies (ONT) sequencing allow acquisition and analysis of data in real time, potentially reducing the need for high-volume sequencing and enabling point-of-care testing. Furthermore, targeted approaches that selectively amplify known pathogens could improve sensitivity. Methods We evaluated detection of viruses with readily available untargeted metagenomic workflows using Illumina and ONT, and an Illumina-based enrichment approach using the Twist Biosciences Viral Research Panel (VRP), which targets 3153 viruses. We tested samples consisting of a dilution series of a six-virus mock community in a human DNA/RNA background, designed to resemble clinical specimens with low microbial abundance and high host content. Protocols were designed to retain the host transcriptome, since this could help confirm the absence of infectious agents. We further compared the performance of commonly used taxonomic classifiers. Results Capture with the Twist VRP increased sensitivity by at least 10-100-fold over untargeted sequencing, making it suitable for the detection of low viral loads (60 genome copies per ml (gc/ml)), but additional methods may be needed in a diagnostic setting to detect untargeted organisms. While untargeted ONT …
Authors
Sarah Buddle,Leysa Forrest,Naomi Akinsuyi,Luz Marina Martin Bernal,Tony Brooks,Cristina Venturini,Charles Miller,Julianne R Brown,Nathaniel Storey,Laura Atkinson,Tim Best,Sunando Roy,Sian Goldsworthy,Peter Simmonds,Heli Harvala,Tanya Golubchik,Sergi Castellano,Rachel Williams,Judith Breuer,Sofia Morfopoulou,Oscar Enrique Torres Montaguth
Journal
medRxiv
Published Date
2024
Genetic diversity of RNA viruses infecting invertebrate pests of rice
Invertebrate species are a natural reservoir of viral genetic diversity, and invertebrate pests are widely distributed in crop fields. However, information on viruses infecting invertebrate pests of crops is limited. In this report, we describe the deep metatranscriptomic sequencing of 88 invertebrate samples covering all major invertebrate pests in rice fields. We identified 296 new RNA viruses and 13 known RNA viruses. These viruses clustered within 31 families, with many highly divergent viruses constituting potentially new families and genera. Of the identified viruses, 13 RNA viruses clustered within the Fiersviridae family of bacteriophages, and 48 RNA viruses clustered within families and genera of mycoviruses. We detected known rice viruses in novel invertebrate hosts at high abundances. Furthermore, some novel RNA viruses have genome structures closely matching to known plant viruses and clustered within …
Authors
Haoran Wang,Shufen Chao,Qing Yan,Shu Zhang,Guoqing Chen,Chonghui Mao,Yang Hu,Fengquan Yu,Shuo Wang,Liang Lv,Baojun Yang,Jiachun He,Songbai Zhang,Liangsheng Zhang,Peter Simmonds,Guozhong Feng
Journal
Science China Life Sciences
Published Date
2024/1
Epidemiological and clinical insights into the enterovirus D68 upsurge in Europe 2021/22 and the emergence of novel B3-derived lineages, ENPEN multicentre study
Enterovirus D68 (EV-D68) infections are associated with severe respiratory disease and acute flaccid myelitis (AFM). The European Non-Polio Enterovirus Network (ENPEN) aimed to investigate the epidemiological and genetic characteristics of EV-D68 and its clinical impact during the fall-winter season of 2021/22. From 19 European countries, 58 institutes reported 10,481 (6.8%) EV-positive samples of which 1,004 (9.6%) were identified as EV-D68 (852 respiratory samples). Clinical data was reported for 969 cases. 78.9% of infections were reported in children (0-5 years); 37.9% of cases were hospitalised. Acute respiratory distress was commonly noted (93.1%) followed by fever (49.4%). Neurological problems were observed in 6.4% of cases with six reported with AFM. Phylodynamic/Nextstrain and phylogenetic analyses based on 694 sequences showed the emergence of two novel B3-derived …
Authors
Margarida Pires Simoes,Emma B Hodcroft,Peter Simmonds,Jan Albert,Enagon K Alidjinou,Katia Ambert-Balay,Cristina Andrés,Andrés Antón,Christelle Auvray,Jean-Luc Bailly,Fausto Baldanti,Capser Bastings,Stuart Beard,Carla Berengua Pereira,Natasa Berginc,Mandy Bloemen,Soile Blomqvist,Froukje Bosma,Sindy Böttcher,Laura Bubba,Stafan Buderus,Maria Cabrerizo,Christina Calvo,Christina Celma,Ferruccio Ceriotti,Gemma Clark,Inës Costa,Marianne Coste-Burel,Karen Couderé,Jeroen Cremer,Margarita del Cuerpo Casas,Theo Daehne,Jessica de Beer,Maria de Ceano-Vivas,Cillian De Gascun,Alexis de Rougemont,Johnathan Dean,Jennifer L Dembinski,Sabine Diedrich,Javier Diez-Domingo,Lena Dillner,Dagny H Dorenberg,Alexandra Ducancelle,Susanne Dudman,Robert Dyrdak,Anna-Maria Eis-Huebinger,Iker Falces-Romero,Agnes Farkas,Susan Feeney,Maria D Fernandez-Garcia,Jacky Flipse,Kristina T Franck,Cristina Galli,Isabelle Garrigue,Felix Geeraedts,Irina Georgieva,Federica Giardina,Raquel Guiomar,Elenor Hauzenberger,Esther Heikens,Cécille Henquell,Didier Hober,Amrio Hönemann,Hannah Howson-Wells,Željka Hruškar,Niina Ikonen,Berthemarie Imbert,Arjan R Jansz,Marion Jeannoël,Helena Jiřincová,Laurence Josset,Kathrin Keeren,Naomie Kramer-Lindhout,Sidsel Krokstad,Mouna Lazrek,Hélène Le Guillou-Guillemette,Caroline Lefeuvre,Andreas Lind,Maja M Lunar,Melanie Maier,Stéphanie Marque-Juillet,C Patrick McClure,James McKenna,Adam Meijer,Ana Menasalvas Ruiz,Beatriz Mengual-Chuliá,Sofie Midgley,Audrey Mirand,Richard Molenkamp,Milagrosa Montes,Antonio Moreno-Docón,Ursula Morley,Jean-Luc Murk,Ana Navascués-Ortega,Roel Nijhuis,Lubomira Nikolaeva-Glomb,Svein A Nordbø,Sanela Numanovic,Massimo Oggioni,Eider Oñate Vergara,Jordi Pacaud,Marie L Pacreau,Marcus Panning,Elena Pariani,Lili Pekova,Laura Pellegrinelli,Miroslav Petrovec,Corinna Pietsch,Léa Pilorge,Luis Piñeiro,Antonio Piralla,Mario Poljak,Birgit Prochazka,Nuria Rabella,Janette C Rahamat-Langendoen,petra Rainetova,Marijke Reynders,Annelies Riezebos-Brilman,Lieuwe Roorda,Carita Savolainen-Kopra,Isabelle Schuffenecker,Leo C Smeets,Ayse Stoyanova,Karl Stefic,Caroline Swanink,Irena Tabain,Jeroen Tjhie,Luc Thouault,Camille Tumiotto,Sara Uceda Renteria,Tina Uršič,Sophie Vallet,Marc Van Ranst,Peter Van Wunnik,Jaco J Verweij,Jorgina Vila,Bas Wintermans,Elke Wollants,Katja C Wolthers,F Xavier López-Labrado,Thea Kolsen Fischer,Heli Harvala,Kimberley SM Benschop
Journal
The Journal of infectious diseases
Published Date
2024/3/28
Biomarkers of transfusion transmitted occult hepatitis B virus infection: Where are we and what next?
Blood transfusion is a vital procedure, where transfusion‐transmitted infection of hepatitis B virus (HBV) remains an important issue, especially from blood donors with occult hepatitis B virus infection (OBI). Occult hepatitis B virus infection is a complex entity to detect using surrogate blood biomarkers for intrahepatic viral transcriptional activity, requiring a continually refined battery of tests utilised for screening. This review aims to critically evaluate the latest advances in the current blood biomarkers to guide the identification of OBI donors and discuss novel HBV markers that could be introduced in future diagnostic practice. Challenges in detecting low HBV surface antigen levels, mutants, and complexes necessitate ultrasensitive multivalent dissociation assays, whilst HBV DNA testing requires improved sensitivity but worsens inaccessibility. Anti‐core antibody assays defer almost all potentially infectious donations …
Authors
Michael X Fu,Peter Simmonds,Monique Andersson,Heli Harvala
Published Date
2024/3
Blood donation screening for hepatitis B virus core antibodies: The importance of confirmatory testing and initial implication for rare blood donor groups
Background and Objectives Exclusion of blood donors with hepatitis B virus (HBV) core antibodies (anti‐HBc) prevents transfusion‐transmitted HBV infection but can lead to significant donor loss. As isolated anti‐HBc positivity does not always indicate true past HBV infection, we have investigated the effectiveness of confirmatory anti‐HBc testing and the representation of rare blood groups in anti‐HBc‐positive donors. Materials and Methods Three hundred ninety‐seven HBV surface antigen‐negative and anti‐HBc initially reactive blood donor samples were tested by five different anti‐HBc assays. Results Eighty percentage of samples reactive in Architect anti‐HBc assay were positive by the Murex assay and anti‐HBc neutralization. Eleven out of 397 samples showed discordant results in supplementary testing from the Murex confirmatory test result, and five remained undetermined following extensive …
Authors
Michael X Fu,Jennifer Ingram,Courtney Roberts,Visa Nurmi,Emma Watkins,Nina Dempsey,Tanya Golubchik,Judith Breuer,Su Brailsford,William L Irving,Monique Andersson,Peter Simmonds,Heli Harvala
Journal
Vox Sanguinis
Published Date
2024/2/28
Absence of detectable monkeypox virus DNA in 11,000 English blood donations during the 2022 outbreak
Background A large, worldwide outbreak of mpox (formerly referred to as monkeypox) involving mainly men who have sex with men commenced in May 2022. We evaluated the frequency of positivity for the causative agent, monkeypox virus (MPXV), in blood donations collected in August 2022, during the outbreak period in Southern England. Methods/Materials The sensitivity and specificity of an MPXV‐specific PCR and a generic non‐variola orthopoxvirus (NVO) PCR were evaluated using samples from mpox cases and synthetic DNA standards. Residual minipools from nucleic acid testing were obtained from 10,896 blood donors in Southern England, with 21% from London. Results MPXV and NVO PCRs were both capable of detection of single copies of target sequence with calculated limits of detection (LOD)90 s of 2.3 and 2.1 DNA copies and analytical sample sensitivities of 46 and 42 MPXV DNA …
Authors
Chanice Knight,Julien Andreani,Neil Garrett,Mark Winter,Tanya Golubchik,Judy Breuer,Claire Reynolds,Susan R Brailsford,Heli Harvala,Peter Simmonds
Journal
Transfusion
Published Date
2023/4
The roles of nucleic acid editing in adaptation of zoonotic viruses to humans
HighlightsMammalian APOBEC3 proteins induce C→ U transitions in viral genomes.ADAR introduces A→ I transitions in the double-stranded replicative form of RNA viruses.Viral adaptation to a new host may involve elaboration of countermeasures to cellular antiviral RNA editing pathways.Following spillover, viruses must adapt to new selection pressures exerted by antiviral responses in their new hosts. In mammals, cellular defense mechanisms often include viral nucleic acid editing pathways mediated through protein families apolipoprotein-B mRNA-editing complex (APOBEC) and Adenosine Deaminase Acting on ribonucleic acid (ADAR). APOBECs induce C→ U transitions in viral genomes; the APOBEC locus is highly polymorphic with variable numbers of APOBEC3 paralogs and target preferences in humans and other mammals. APOBEC3 paralogs have shaped the evolutionary history of human …
Authors
Jeremy Ratcliff,Peter Simmonds
Published Date
2023/6/1
Professor FAQs
What is Peter Simmonds's h-index at University of Oxford?
The h-index of Peter Simmonds has been 71 since 2020 and 137 in total.
What are Peter Simmonds's top articles?
The articles with the titles of
Parechovirus A Circulation and Testing Capacities in Europe, 2015–2021
Clinical metagenomics for detection of viruses using short-read, long-read and targeted approaches
Genetic diversity of RNA viruses infecting invertebrate pests of rice
Epidemiological and clinical insights into the enterovirus D68 upsurge in Europe 2021/22 and the emergence of novel B3-derived lineages, ENPEN multicentre study
Biomarkers of transfusion transmitted occult hepatitis B virus infection: Where are we and what next?
Blood donation screening for hepatitis B virus core antibodies: The importance of confirmatory testing and initial implication for rare blood donor groups
Absence of detectable monkeypox virus DNA in 11,000 English blood donations during the 2022 outbreak
The roles of nucleic acid editing in adaptation of zoonotic viruses to humans
...
are the top articles of Peter Simmonds at University of Oxford.
What are Peter Simmonds's research interests?
The research interests of Peter Simmonds are: Virology
What is Peter Simmonds's total number of citations?
Peter Simmonds has 70,695 citations in total.