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Fu MX, Ingram J, Roberts C, Nurmi V, Watkins E, Dempsey N, Golubchik T, Breuer J, Brailsford S, Irving WL, Andersson M, Simmonds P, Harvala H. Blood donation screening for hepatitis B virus core antibodies: The importance of confirmatory testing and initial implication for rare blood donor groups. Vox Sang 2024; 119:447-459. [PMID: 38419267 DOI: 10.1111/vox.13608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/25/2024] [Accepted: 02/09/2024] [Indexed: 03/02/2024]
Abstract
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 serological testing. Thirty-eight percentage of anti-HBc-positive donors identified as minority ethnic groups compared with 11% representation in anti-HBc-negative donors (p < 0.0001); the frequency of the Ro blood group in anti-HBc-positive donors was 18 times higher in non-white ethnic groups. CONCLUSION Using two anti-HBc assays effectively enabled the identification of HBV-exposed and potentially infectious donors, their deferral and potential clinical follow-up. However, the exclusion of confirmed anti-HBc-positive donors will still impact the supply of rare blood such as Ro.
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Affiliation(s)
- Michael X Fu
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jennifer Ingram
- Donor Testing Department, NHS Blood and Transplant, Manchester, UK
| | | | - Visa Nurmi
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Emma Watkins
- Clinical Services, NHS Blood and Transplant, Birmingham, UK
| | - Nina Dempsey
- Department of Life Sciences, Manchester Metropolitan University, Manchester, UK
| | - Tanya Golubchik
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Sydney Infectious Diseases Institute, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
| | - Su Brailsford
- Microbiology Services, NHS Blood and Transplant, Colindale, UK
| | - William L Irving
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Monique Andersson
- Department of Microbiology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Heli Harvala
- Division of Infection and Immunity, University College London, London, UK
- Microbiology Services, NHS Blood and Transplant, Colindale, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
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Fu MX, Simmonds P, Andersson M, Harvala H. Biomarkers of transfusion transmitted occult hepatitis B virus infection: Where are we and what next? Rev Med Virol 2024; 34:e2525. [PMID: 38375981 DOI: 10.1002/rmv.2525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 02/10/2024] [Accepted: 02/13/2024] [Indexed: 02/21/2024]
Abstract
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 but have low specificity, and titres of anti-surface antibodies that prevent infectivity are poorly defined with suboptimal sensitivity. The challenges associated with these traditional blood HBV markers create an urgent need for alternative biomarkers that would help us better understand the OBI. Emerging viral biomarkers, such as pre-genomic RNA and HBV core-related antigen, immunological HBV biomarkers of T-cell reactivity and cytokine levels, and host biomarkers of microRNA and human leucocyte antigen molecules, present potential advances to gauge intrahepatic activity more accurately. Further studies on these markers may uncover an optimal diagnostic algorithm for OBI using quantification of various novel and traditional blood HBV markers. Addressing critical knowledge gaps identified in this review would decrease the residual risk of transfusion-transmitted HBV infection without compromising the sustainability of blood supplies.
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Affiliation(s)
- Michael X Fu
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Monique Andersson
- Department of Infection, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Heli Harvala
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Microbiology Services, NHS Blood and Transplant, Colindale, UK
- Infection and Immunity, University College London, London, UK
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Bubba L, Broberg EK, Fischer TK, Simmonds P, Harvala H. Parechovirus A Circulation and Testing Capacities in Europe, 2015-2021. Emerg Infect Dis 2024; 30:234-244. [PMID: 38270192 PMCID: PMC10826775 DOI: 10.3201/eid3002.230647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024] Open
Abstract
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 parechovirus data. To enhance surveillance and response for PeV outbreaks, sharing typing protocols and data on parechovirus-positive cases should be encouraged.
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Wang H, Chao S, Yan Q, Zhang S, Chen G, Mao C, Hu Y, Yu F, Wang S, Lv L, Yang B, He J, Zhang S, Zhang L, Simmonds P, Feng G. Genetic diversity of RNA viruses infecting invertebrate pests of rice. Sci China Life Sci 2024; 67:175-187. [PMID: 37946067 DOI: 10.1007/s11427-023-2398-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 06/26/2023] [Indexed: 11/12/2023]
Abstract
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 genera of several plant virus species. Forty-five potential insect pathogenic RNA viruses were detected in invertebrate species. Our analysis revealed that host taxonomy plays a major role and geographical location plays an important role in structuring viral diversity. Cross-species transmission of RNA viruses was detected between invertebrate hosts. Newly identified viral genomes showed extensive variation for invertebrate viral families or genera. Together, the large-scale metatranscriptomic analysis greatly expands our understanding of RNA viruses in rice invertebrate species, the results provide valuable information for developing efficient strategies to manage insect pests and virus-mediated crop diseases.
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Affiliation(s)
- Haoran Wang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shufen Chao
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Qing Yan
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Shu Zhang
- Institute of Plant Protection & Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Guoqing Chen
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Chonghui Mao
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Yang Hu
- Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang, 550000, China
| | - Fengquan Yu
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, China
| | - Shuo Wang
- Sanya Agricultural Technology Extension and Service Centre, Sanya, 572000, China
| | - Liang Lv
- Institute of Plant Protection & Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Baojun Yang
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Jiachun He
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China
| | - Songbai Zhang
- College of Agriculture, Yangtze University, Jingzhou, 434000, China
| | - Liangsheng Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310012, China
| | - Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, OX1 3SY, UK
| | - Guozhong Feng
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 311400, China.
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5
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Christensen KT, Pierard F, Bonsall D, Bowden R, Barnes E, Florence E, Ansari MA, Nguyen D, de Cesare M, Nevens F, Robaeys G, Schrooten Y, Busschots D, Simmonds P, Vandamme AM, Van Wijngaerden E, Dierckx T, Cuypers L, Van Laethem K. Phylogenetic Analysis of Hepatitis C Virus Infections in a Large Belgian Cohort Using Next-Generation Sequencing of Full-Length Genomes. Viruses 2023; 15:2391. [PMID: 38140632 PMCID: PMC10747466 DOI: 10.3390/v15122391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 12/24/2023] Open
Abstract
The hepatitis C virus (HCV) epidemic in Western countries is primarily perpetuated by the sub-populations of men who have sex with men (MSM) and people who inject drugs (PWID). Understanding the dynamics of transmission in these communities is crucial for removing the remaining hurdles towards HCV elimination. We sequenced 269 annotated HCV plasma samples using probe enrichment and next-generation sequencing, obtaining 224 open reading frames of HCV (OR497849-OR498072). Maximum likelihood phylogenies were generated on the four most prevalent subtypes in this study (HCV1a, 1b, 3a, 4d) with a subsequent transmission cluster analysis. The highest rate of clustering was observed for HCV4d samples (13/17 (76.47%)). The second highest rate of clustering was observed in HCV1a samples (42/78 (53.85%)) with significant association with HIV-positive MSM. HCV1b and HCV3a had very low rates of clustering (2/83 (2.41%) and (0/29)). The spread of the prevalent subtype HCV1b appears to have been largely curtailed, and we demonstrate the onwards transmission of HCV1a and HCV4d in the HIV-positive MSM population across municipal borders. More systematic data collection and sequencing is needed to allow a better understanding of the HCV transmission among the community of PWID and overcome the remaining barriers for HCV elimination in Belgium.
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Affiliation(s)
- Kasper T. Christensen
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (F.P.); (Y.S.); (A.-M.V.); (T.D.); (L.C.); (K.V.L.)
| | - Florian Pierard
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (F.P.); (Y.S.); (A.-M.V.); (T.D.); (L.C.); (K.V.L.)
| | - David Bonsall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK;
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; (R.B.); (D.N.); (M.d.C.)
| | - Rory Bowden
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; (R.B.); (D.N.); (M.d.C.)
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK;
- Translational Gastroenterology Unit, University of Oxford, Oxford OX3 9DU, UK
- Oxford NIHR Biomedical Research Centre, University of Oxford, Oxford OX3 9DU, UK
| | - Eric Florence
- Department of General Internal Medicine, Infectious Diseases and Tropical Medicine, Antwerp University Hospital, 2650 Edegem, Belgium;
- Department of Clinical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - M. Azim Ansari
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK;
| | - Dung Nguyen
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; (R.B.); (D.N.); (M.d.C.)
| | - Mariateresa de Cesare
- The Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK; (R.B.); (D.N.); (M.d.C.)
| | - Frederik Nevens
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, 3000 Leuven, Belgium; (F.N.); (G.R.)
| | - Geert Robaeys
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, 3000 Leuven, Belgium; (F.N.); (G.R.)
- Faculty of Medicine and Life Sciences—LCRC, UHasselt, Agoralaan, 3590 Diepenbeek, Belgium;
- Department of Gastroenterology and Hepatology, Ziekenhuis Oost-Limburg, 3600 Genk, Belgium
| | - Yoeri Schrooten
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (F.P.); (Y.S.); (A.-M.V.); (T.D.); (L.C.); (K.V.L.)
- Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Dana Busschots
- Faculty of Medicine and Life Sciences—LCRC, UHasselt, Agoralaan, 3590 Diepenbeek, Belgium;
- Department of Gastroenterology and Hepatology, Ziekenhuis Oost-Limburg, 3600 Genk, Belgium
| | - Peter Simmonds
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Headington, Oxford OX3 7BN, UK;
| | - Anne-Mieke Vandamme
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (F.P.); (Y.S.); (A.-M.V.); (T.D.); (L.C.); (K.V.L.)
- Global Health and Tropical Medicine, Institute of Hygiene and Tropical Medicine, Universidade Nova de Lisboa, Rua da Junqueira 100, 1349-008 Lisbon, Portugal
| | - Eric Van Wijngaerden
- Department of General Internal Medicine, University Hospitals Leuven, 3000 Leuven, Belgium;
| | - Tim Dierckx
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (F.P.); (Y.S.); (A.-M.V.); (T.D.); (L.C.); (K.V.L.)
| | - Lize Cuypers
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (F.P.); (Y.S.); (A.-M.V.); (T.D.); (L.C.); (K.V.L.)
- Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium
- Laboratory of Clinical Microbiology, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Kristel Van Laethem
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium; (F.P.); (Y.S.); (A.-M.V.); (T.D.); (L.C.); (K.V.L.)
- Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium
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6
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Kamau E, Bessaud M, Majumdar M, Martin J, Simmonds P, Harvala H. Estimating prevalence of Enterovirus D111 in human and non-human primate populations using cross-sectional serology. J Gen Virol 2023; 104:001915. [PMID: 37910158 PMCID: PMC10768692 DOI: 10.1099/jgv.0.001915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 10/19/2023] [Indexed: 11/03/2023] Open
Abstract
Enteroviruses primarily affect young children with a varying severity of disease. Recent outbreaks of severe respiratory and neurological disease due to EV-D68 and EV-A71, as well as atypical hand-foot-and-mouth-disease due to CVA6, have brought to light the potency of enteroviruses to emerge as severe human pathogens. Enterovirus D111 (EV-D111) is an enteric pathogen initially detected in Central Africa in human and wildlife samples and was recently detected in environmental samples. The natural history and epidemiology of EV-D111 are poorly studied. Here, the presence of serum neutralizing antibodies to EV-D111 was estimated in human and wildlife samples from five countries. We report high prevalence of neutralizing antibodies measured against EV-D111 in human populations (range, 55-83 %), a proxy for previous infection, which indicates active virus circulation in absence of detection in clinical cases and a high number of undiagnosed infections. Notably, seroprevalence in samples from the UK varied by age and was higher in children and older adults (1-5 and >60 years old), but lower in ages 11-60. EV-D111 seroprevalence in apes and Old World monkeys was 50 % (33-66 %), which also suggests prior exposure and supports existing knowledge of enterovirus circulation in wild and captive apes and Old World monkeys. Generally, reported cases of infection likely underestimate the prevalence of infection particularly when the knowledge of community transmission is limited. Continued serologic surveillance and detection of EV-D111 in clinical and environmental samples will allow for a more robust assessment of EV-D111 epidemiology.
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Affiliation(s)
- Everlyn Kamau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mael Bessaud
- Institut Pasteur-Unité de Biologie des Virus Entériques, Paris, France
- WHO Collaborating Centre for Enteroviruses and Viral Vaccines, Paris, France
| | - Manasi Majumdar
- Science Research and Innovation, Medicines and Healthcare Products Regulatory Agency, South Mimms, UK
| | - Javier Martin
- Science Research and Innovation, Medicines and Healthcare Products Regulatory Agency, South Mimms, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Heli Harvala
- Microbiology Services, NHS Blood Transfusion, London, UK
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7
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Zerbini FM, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Alfenas-Zerbini P, Dempsey DM, Dutilh BE, García ML, Hendrickson RC, Junglen S, Krupovic M, Kuhn JH, Lambert AJ, Łobocka M, Oksanen HM, Robertson DL, Rubino L, Sabanadzovic S, Simmonds P, Smith DB, Suzuki N, Van Doorslaer K, Vandamme AM, Varsani A. Correction to: Changes to virus taxonomy and the ICTV Statutes ratifed by the International Committee on Taxonomy of Viruses (2023). Arch Virol 2023; 168:269. [PMID: 37804442 DOI: 10.1007/s00705-023-05880-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/09/2023]
Affiliation(s)
- Francisco Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
| | - Stuart G Siddell
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Arcady R Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, 2415 Eisenhower Avenue, Alexandria, VA, 22314, USA
| | | | - Poliane Alfenas-Zerbini
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, 36570‑900, Brazil
| | - Donald M Dempsey
- Department of Microbiology, University of Alabama at Birmingham, BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Bas E Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Fürstengraben 1, 07743, Jena, Germany
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, calles 47 y 115 (1900), La Plata, Buenos Aires, Argentina
| | - R Curtis Hendrickson
- Department of Microbiology, University of Alabama at Birmingham, BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 25 rue du Dr Roux, 75015, Paris, France
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Amy J Lambert
- Division of Vector‑Borne Diseases, Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Fort Collins, CO, 80521, USA
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02‑106, Warsaw, Poland
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Luisa Rubino
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Sede Secondaria di Bari, Via Amendola 165/A, 70126, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Old Hwy 12 Mail Stop 9775, Mississippi State, MS, 39762, USA
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Donald B Smith
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710‑0046, Japan
| | - Koenraad Van Doorslaer
- Department of Immunobiology, School of Animal and Comparative Biomedical Sciences, BIO5 Institute, University of Arizona Cancer Center, Tucson, AZ, 85721, USA
| | - Anne-Mieke Vandamme
- Department of Microbiology, Immunology and Transplantation, Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349‑008, Lisbon, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287-4701, USA
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8
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Fu MX, Simmonds P, Andreani J, Baklan H, Webster M, Asadi R, Golubchik T, Breuer J, Ijaz S, Ushiro-Lumb I, Brailsford S, Irving WL, Andersson M, Harvala H. Ultrasensitive PCR system for HBV DNA detection: Risk stratification for occult hepatitis B virus infection in English blood donors. J Med Virol 2023; 95:e29144. [PMID: 37796091 DOI: 10.1002/jmv.29144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023]
Abstract
Occult hepatitis B (HBV) infection (OBI), characterized by low viral loads, accounts for much of the risk of HBV transfusion-transmitted infection. With anticore antibodies (anti-HBc) screening introduced in England, the imperative to identify OBI donors has increased. We aimed to develop an ultra-sensitive PCR system and investigate risk factors for HBV DNA presence in blood donations. Seven extraction methods and three PCR assays were compared. The optimal system was sought to determine HBV DNA presence in anti-HBc-positive donations. Predictors of DNA positivity were subsequently investigated. Extraction from 5 mL of plasma increased sample representation and resulted in HBV DNA detection in low viral load samples (~0.5 IU/mL). Screening of 487 763 donations in 2022 identified two OBI donors and 2042 anti-HBc-positive donors, 412 of the latter with anti-HBs < 100 mIU/mL. Testing of 134 anti-HBc-positive donations utilizing the 5 mL extraction method identified two further HBV DNA-positive donations. Higher anti-HBc titer and anti-HBs negativity were significant predictors of DNA detectability in anti-HBc-positive donations. An ultrasensitive PCR assay identified potentially infectious donations increasing HBV DNA detection in anti-HBc-positive donors from 0.5% to 1.9%. Anti-HBc titers may further complement the risk stratification for DNA positivity in anti-HBc screening and minimize unnecessary donor deferral.
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Affiliation(s)
- Michael X Fu
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Julien Andreani
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Centre Hospitalier Universitaire Grenoble-Alpes, Grenoble, France
| | - Hatice Baklan
- Microbiology Services, NHS Blood and Transplant, Colindale, UK
| | - Mhairi Webster
- Microbiology Services, NHS Blood and Transplant, Colindale, UK
| | - Romisa Asadi
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Tanya Golubchik
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Sydney Infectious Diseases Institute, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
| | - Samreen Ijaz
- Virus Reference Department, Blood Borne Virus Unit, UK Health Security Agency, London, UK
| | | | - Su Brailsford
- Microbiology Services, NHS Blood and Transplant, Colindale, UK
| | - William L Irving
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust, University of Nottingham, Nottingham, UK
| | - Monique Andersson
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- Department of Microbiology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Heli Harvala
- Microbiology Services, NHS Blood and Transplant, Colindale, UK
- Division of Infection and Immunity, University College London, London, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
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9
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Adriaenssens EM, Roux S, Brister JR, Karsch-Mizrachi I, Kuhn JH, Varsani A, Yigang T, Reyes A, Lood C, Lefkowitz EJ, Sullivan MB, Edwards RA, Simmonds P, Rubino L, Sabanadzovic S, Krupovic M, Dutilh BE. Author Correction: Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification. Nat Biotechnol 2023; 41:1346. [PMID: 37608068 DOI: 10.1038/s41587-023-01952-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Affiliation(s)
- Evelien M Adriaenssens
- Quadram Institute Bioscience, Norwich Research Park, Rosalind Franklin Road, Norwich, UK.
| | - Simon Roux
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Ilene Karsch-Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
| | - Tong Yigang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Cédric Lood
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Robert A Edwards
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford, UK
| | - Luisa Rubino
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Bas E Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, CH, the Netherlands
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10
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Raghwani J, Faust CL, François S, Nguyen D, Marsh K, Raulo A, Hill SC, Parag KV, Simmonds P, Knowles SCL, Pybus OG. Seasonal dynamics of the wild rodent faecal virome. Mol Ecol 2023; 32:4763-4776. [PMID: 36367339 PMCID: PMC7614976 DOI: 10.1111/mec.16778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/23/2022] [Accepted: 11/03/2022] [Indexed: 11/13/2022]
Abstract
Viral discovery studies in wild animals often rely on cross-sectional surveys at a single time point. As a result, our understanding of the temporal stability of wild animal viromes remains poorly resolved. While studies of single host-virus systems indicate that host and environmental factors influence seasonal virus transmission dynamics, comparable insights for whole viral communities in multiple hosts are lacking. Utilizing noninvasive faecal samples from a long-term wild rodent study, we characterized viral communities of three common European rodent species (Apodemus sylvaticus, A. flavicollis and Myodes glareolus) living in temperate woodland over a single year. Our findings indicate that a substantial fraction of the rodent virome is seasonally transient and associated with vertebrate or bacteria hosts. Further analyses of one of the most common virus families, Picornaviridae, show pronounced temporal changes in viral richness and evenness, which were associated with concurrent and up to ~3-month lags in host density, ambient temperature, rainfall and humidity, suggesting complex feedbacks from the host and environmental factors on virus transmission and shedding in seasonal habitats. Overall, this study emphasizes the importance of understanding the seasonal dynamics of wild animal viromes in order to better predict and mitigate zoonotic risks.
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Affiliation(s)
- Jayna Raghwani
- Department of BiologyUniversity of OxfordOxfordUK
- Department of Pathobiology and Population SciencesThe Royal Veterinary CollegeLondonUK
| | - Christina L. Faust
- Institute of Biodiversity, Animal Health, and Comparative MedicineUniversity of GlasgowGlasgowUK
| | | | - Dung Nguyen
- Nuffield Department of MedicineUniversity of OxfordOxfordUK
| | - Kirsty Marsh
- School of BiosciencesUniversity of ExeterExeterUK
| | - Aura Raulo
- Department of BiologyUniversity of OxfordOxfordUK
- University of TurkuTurkuFinland
| | - Sarah C. Hill
- Department of Pathobiology and Population SciencesThe Royal Veterinary CollegeLondonUK
| | | | - Peter Simmonds
- Nuffield Department of MedicineUniversity of OxfordOxfordUK
| | | | - Oliver G. Pybus
- Department of BiologyUniversity of OxfordOxfordUK
- Department of Pathobiology and Population SciencesThe Royal Veterinary CollegeLondonUK
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11
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Nurmi V, Knight C, Estcourt L, Hepojoki J, Lamikanra AA, Tsang HP, Roberts DJ, Polack FP, Simmonds P, Hedman K, Alvarez-Paggi D, Harvala H. The Relationship Between SARS-CoV-2 Neutralizing Antibody Titers and Avidity in Plasma Collected From Convalescent Nonvaccinated and Vaccinated Blood Donors. J Infect Dis 2023; 228:245-250. [PMID: 36967714 PMCID: PMC10420400 DOI: 10.1093/infdis/jiad070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 03/24/2023] [Indexed: 08/13/2023] Open
Abstract
Convalescent plasma (CP) treatment of coronavirus disease 2019 (COVID-19) has shown significant therapeutic effect when administered early (eg, Argentinian trial showing reduced hospitalization) but has in general been ineffective (eg, REMAP-CAP trial without improvement during hospitalization). To investigate whether the differences in CP used could explain the different outcomes, we compared neutralizing antibodies, anti-spike IgG, and avidity of CP used in the REMAP-CAP and Argentinian trials and in convalescent vaccinees. We found no difference between the trial plasmas, emphasizing initial patient serostatus as treatment efficacy predictor. By contrast, vaccinee CP showed significantly higher titers and avidity, being preferable for future CP treatment. Clinical Trials Registration. NCT02735707 and NCT04479163.
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Affiliation(s)
- Visa Nurmi
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Chanice Knight
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Lise Estcourt
- Clinical Services, NHS Blood and Transplant, Oxford, United Kingdom
- Radcliffe Department of Medicine and Biomedical Research Centre Haematology Theme, University of Oxford, Oxford, United Kingdom
| | - Jussi Hepojoki
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zürich, Zürich, Switzerland
| | - Abigail A Lamikanra
- Clinical Services, NHS Blood and Transplant, Oxford, United Kingdom
- Radcliffe Department of Medicine and Biomedical Research Centre Haematology Theme, University of Oxford, Oxford, United Kingdom
| | - Hoi P Tsang
- Clinical Services, NHS Blood and Transplant, Oxford, United Kingdom
| | - David J Roberts
- Clinical Services, NHS Blood and Transplant, Oxford, United Kingdom
- Radcliffe Department of Medicine and Biomedical Research Centre Haematology Theme, University of Oxford, Oxford, United Kingdom
| | | | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Klaus Hedman
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Diagnostic Centre, Helsinki University Hospital, Helsinki, Finland
| | | | - Heli Harvala
- Radcliffe Department of Medicine and Biomedical Research Centre Haematology Theme, University of Oxford, Oxford, United Kingdom
- Microbiology Services, NHS Blood and Transplant, Colindale, United Kingdom
- Infection and Immunity, University College of London, London, United Kingdom
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12
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Postler TS, Beer M, Blitvich BJ, Bukh J, de Lamballerie X, Drexler JF, Imrie A, Kapoor A, Karganova GG, Lemey P, Lohmann V, Simmonds P, Smith DB, Stapleton JT, Kuhn JH. Renaming of the genus Flavivirus to Orthoflavivirus and extension of binomial species names within the family Flaviviridae. Arch Virol 2023; 168:224. [PMID: 37561168 DOI: 10.1007/s00705-023-05835-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
This review provides a summary of the recently ratified changes to genus and species nomenclature within the virus family Flaviviridae along with reasons for these changes. First, it was considered that the vernacular terms "flaviviral", "flavivirus", and "flaviviruses" could under certain circumstances be ambiguous due to the same word stem "flavi" in the taxon names Flaviviridae and Flavivirus; these terms could either have referred to all viruses classified in the family Flaviviridae or only to viruses classified in the included genus Flavivirus. To remove this ambiguity, the genus name Flavivirus was changed to Orthoflavivirus by the International Committee on Taxonomy of Viruses (ICTV). Second, all species names in the family were changed to adhere to a newly ICTV-mandated binomial format (e.g., Orthoflavivirus zikaense, Hepacivirus hominis) similar to nomenclature conventions used for species elsewhere in biology. It is important to note, however, that virus names remain unchanged. Here we outline the revised taxonomy of the family Flaviviridae as approved by the ICTV in April 2023.
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Affiliation(s)
- Thomas S Postler
- Vaccine Design and Development Laboratory, International AIDS Vaccine Initiative, Brooklyn, NY, USA
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald, Insel Riems, Germany
| | - Bradley J Blitvich
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
- CO-HEP, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Xavier de Lamballerie
- Unité des Virus Émergents (Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - J Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Allison Imrie
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA, Australia
| | - Amit Kapoor
- Center for Vaccines and Immunity, The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, College of Medicine and Public Health, The Ohio State University, Columbus, OH, USA
| | - Galina G Karganova
- Laboratory of Biology of Arboviruses, FSASI "Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products of RAS" (Chumakov Institute of Poliomyelitis and Viral Encephalitides), Moscow, Russia
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Volker Lohmann
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Donald B Smith
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jack T Stapleton
- Medicine Service, Iowa City Veterans Administration Healthcare, Iowa City, IA, USA
- Departments of Internal Medicine, Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA.
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13
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Adriaenssens EM, Roux S, Brister JR, Karsch-Mizrachi I, Kuhn JH, Varsani A, Yigang T, Reyes A, Lood C, Lefkowitz EJ, Sullivan MB, Edwards RA, Simmonds P, Rubino L, Sabanadzovic S, Krupovic M, Dutilh BE. Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification. Nat Biotechnol 2023; 41:898-902. [PMID: 37430074 PMCID: PMC10526704 DOI: 10.1038/s41587-023-01844-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Affiliation(s)
- Evelien M Adriaenssens
- Quadram Institute Bioscience, Norwich Research Park, Rosalind Franklin Road, Norwich, UK.
| | - Simon Roux
- United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Ilene Karsch-Mizrachi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
| | - Tong Yigang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Alejandro Reyes
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Cédric Lood
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Leuven, Belgium
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Robert A Edwards
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford, UK
| | - Luisa Rubino
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Bas E Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, CH, the Netherlands
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14
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Gates S, Andreani J, Dewar R, Smith DB, Templeton K, Child HT, Breuer J, Golubchik T, Bassano I, Wade MJ, Jeffries AR, Simmonds P, Harvala H. Postpandemic rebound of adeno-associated virus type 2 (AAV2) infections temporally associated with an outbreak of unexplained severe acute hepatitis in children in the United Kingdom. J Med Virol 2023; 95:e28921. [PMID: 37403889 DOI: 10.1002/jmv.28921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/02/2023] [Accepted: 06/07/2023] [Indexed: 07/06/2023]
Abstract
Over 1000 cases of unexplained severe acute hepatitis in children have been reported to date worldwide. An association with adeno-associated virus type 2 (AAV2) infection, a human parvovirus, prompted us to investigate the epidemiology of AAV in the United Kingdom. Three hundred pediatric respiratory samples collected before (April 03, 2009-April 03, 2013) and during (April 03, 2022) the COVID-19 pandemic were obtained. Wastewater samples were collected from 50 locations in London (August 2021-March 2022). Samples were tested for AAV using real-time polymerase chain reaction followed by sequencing. Selected adenovirus (AdV)-positive samples were also sequenced. The detection frequency of AAV2 was a sevenfold higher in 2022 samples compared with 2009-2013 samples (10% vs. 1.4%) and highest in AdV-positive samples compared with negatives (10/37, 27% vs. 5/94, 5.3%, respectively). AAV2-positive samples displayed high genetic diversity. AAV2 sequences were either very low or absent in wastewater collected in 2021 but increased in January 2022 and peaked in March 2022. AAV2 was detected in children in association with AdV of species C, with a highest frequency in 2022. Our findings are consistent with the expansion of the population of children unexposed to AAV2, leading to greater spread of the virus once distancing restrictions were lifted.
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Affiliation(s)
- Shannah Gates
- Microbiology Services, National Health Service (NHS) Blood and Transplant, London, UK
| | - Julien Andreani
- Centre Hospitalier Universitaire (CHU) Grenoble-Alpes, Grenoble, France
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Rebecca Dewar
- Specialist Virology Centre, Royal Infirmary Edinburgh, NHS Lothian, Edinburgh, UK
| | - Donald B Smith
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Kate Templeton
- Specialist Virology Centre, Royal Infirmary Edinburgh, NHS Lothian, Edinburgh, UK
| | - Harry T Child
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Judy Breuer
- Division of Infection and Immunity, University College London, London, UK
| | - Tanya Golubchik
- Faculty of Medicine and Health, Sydney Infectious Diseases Institute, University of Sydney, Sydney, Australia
- Nuffield Department of Medicine, Big Data Institute, Oxford, UK
| | - Irene Bassano
- Analytics & Data Science Directorate, UK Health Security Agency, Nobel House, London, UK
| | - Matthew J Wade
- Analytics & Data Science Directorate, UK Health Security Agency, Nobel House, London, UK
| | - Aaron R Jeffries
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Heli Harvala
- Microbiology Services, National Health Service (NHS) Blood and Transplant, London, UK
- Radcliffe Department of Medicine, Nuffield Division of Clinical Laboratory Sciences, University of Oxford, Oxford, UK
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15
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Zerbini FM, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Alfenas-Zerbini P, Dempsey DM, Dutilh BE, García ML, Hendrickson RC, Junglen S, Krupovic M, Kuhn JH, Lambert AJ, Łobocka M, Oksanen HM, Robertson DL, Rubino L, Sabanadzovic S, Simmonds P, Smith DB, Suzuki N, Van Doorslaer K, Vandamme AM, Varsani A. Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2023). Arch Virol 2023; 168:175. [PMID: 37296227 PMCID: PMC10861154 DOI: 10.1007/s00705-023-05797-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This article reports changes to virus taxonomy and taxon nomenclature that were approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in April 2023. The entire ICTV membership was invited to vote on 174 taxonomic proposals that had been approved by the ICTV Executive Committee in July 2022, as well as a proposed revision of the ICTV Statutes. All proposals and the revised ICTV Statutes were approved by a majority of the voting membership. Of note, the ICTV continued the process of renaming existing species in accordance with the recently mandated binomial format and included gene transfer agents (GTAs) in the classification framework by classifying them as viriforms. In total, one class, seven orders, 31 families, 214 genera, and 858 species were created.
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Affiliation(s)
- Francisco Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
| | - Stuart G Siddell
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Arcady R Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, 2415 Eisenhower Avenue, Alexandria, VA, 22314, USA
| | | | - Poliane Alfenas-Zerbini
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, 36570‑900, Brazil
| | - Donald M Dempsey
- Department of Microbiology, University of Alabama at Birmingham, BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Bas E Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Fürstengraben 1, 07743, Jena, Germany
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, calles 47 y 115 (1900), La Plata, Buenos Aires, Argentina
| | - R Curtis Hendrickson
- Department of Microbiology, University of Alabama at Birmingham, BBRB 276, 845 19th St South, Birmingham, AL, 35294-2170, USA
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 25 rue du Dr Roux, 75015, Paris, France
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Amy J Lambert
- Division of Vector‑Borne Diseases, Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Fort Collins, CO, 80521, USA
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02‑106, Warsaw, Poland
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Luisa Rubino
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Sede Secondaria di Bari, Via Amendola 165/A, 70126, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Old Hwy 12 Mail Stop 9775, Mississippi State, MS, 39762, USA
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Donald B Smith
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710‑0046, Japan
| | - Koenraad Van Doorslaer
- Department of Immunobiology, School of Animal and Comparative Biomedical Sciences, BIO5 Institute, University of Arizona Cancer Center, Tucson, AZ, 85721, USA
| | - Anne-Mieke Vandamme
- Department of Microbiology, Immunology and Transplantation, Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349‑008, Lisbon, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287-4701, USA
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16
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Pons-Salort M, Lambert B, Kamau E, Pebody R, Harvala H, Simmonds P, Grassly NC. Changes in transmission of Enterovirus D68 (EV-D68) in England inferred from seroprevalence data. eLife 2023; 12:76609. [PMID: 37294299 DOI: 10.7554/elife.76609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/29/2023] [Indexed: 06/10/2023] Open
Abstract
The factors leading to the global emergence of Enterovirus D68 (EV-D68) in 2014 as a cause of acute flaccid myelitis (AFM) in children are unknown. To investigate potential changes in virus transmissibility or population susceptibility, we measured the seroprevalence of EV-D68-specific neutralising antibodies in serum samples collected in England in 2006, 2011, and 2017. Using catalytic mathematical models, we estimate an approximately 50% increase in the annual probability of infection over the 10-year study period, coinciding with the emergence of clade B around 2009. Despite such increase in transmission, seroprevalence data suggest that the virus was already widely circulating before the AFM outbreaks and the increase of infections by age cannot explain the observed number of AFM cases. Therefore, the acquisition of or an increase in neuropathogenicity would be additionally required to explain the emergence of outbreaks of AFM. Our results provide evidence that changes in enterovirus phenotypes cause major changes in disease epidemiology.
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Affiliation(s)
- Margarita Pons-Salort
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
| | - Ben Lambert
- Department of Computer Science, University of Oxford, Oxford, United Kingdom
| | - Everlyn Kamau
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Richard Pebody
- Immunization Department, Public Health England, London, United Kingdom
| | - Heli Harvala
- Infection and Immunity, University College of London, London, United Kingdom
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nicholas C Grassly
- MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom
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17
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Morfopoulou S, Buddle S, Torres Montaguth OE, Atkinson L, Guerra-Assunção JA, Moradi Marjaneh M, Zennezini Chiozzi R, Storey N, Campos L, Hutchinson JC, Counsell JR, Pollara G, Roy S, Venturini C, Antinao Diaz JF, Siam A, Tappouni LJ, Asgarian Z, Ng J, Hanlon KS, Lennon A, McArdle A, Czap A, Rosenheim J, Andrade C, Anderson G, Lee JCD, Williams R, Williams CA, Tutill H, Bayzid N, Martin Bernal LM, Macpherson H, Montgomery KA, Moore C, Templeton K, Neill C, Holden M, Gunson R, Shepherd SJ, Shah P, Cooray S, Voice M, Steele M, Fink C, Whittaker TE, Santilli G, Gissen P, Kaufer BB, Reich J, Andreani J, Simmonds P, Alrabiah DK, Castellano S, Chikowore P, Odam M, Rampling T, Houlihan C, Hoschler K, Talts T, Celma C, Gonzalez S, Gallagher E, Simmons R, Watson C, Mandal S, Zambon M, Chand M, Hatcher J, De S, Baillie K, Semple MG, Martin J, Ushiro-Lumb I, Noursadeghi M, Deheragoda M, Hadzic N, Grammatikopoulos T, Brown R, Kelgeri C, Thalassinos K, Waddington SN, Jacques TS, Thomson E, Levin M, Brown JR, Breuer J. Genomic investigations of unexplained acute hepatitis in children. Nature 2023; 617:564-573. [PMID: 36996872 PMCID: PMC10170458 DOI: 10.1038/s41586-023-06003-w] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 03/23/2023] [Indexed: 04/01/2023]
Abstract
Since its first identification in Scotland, over 1,000 cases of unexplained paediatric hepatitis in children have been reported worldwide, including 278 cases in the UK1. Here we report an investigation of 38 cases, 66 age-matched immunocompetent controls and 21 immunocompromised comparator participants, using a combination of genomic, transcriptomic, proteomic and immunohistochemical methods. We detected high levels of adeno-associated virus 2 (AAV2) DNA in the liver, blood, plasma or stool from 27 of 28 cases. We found low levels of adenovirus (HAdV) and human herpesvirus 6B (HHV-6B) in 23 of 31 and 16 of 23, respectively, of the cases tested. By contrast, AAV2 was infrequently detected and at low titre in the blood or the liver from control children with HAdV, even when profoundly immunosuppressed. AAV2, HAdV and HHV-6 phylogeny excluded the emergence of novel strains in cases. Histological analyses of explanted livers showed enrichment for T cells and B lineage cells. Proteomic comparison of liver tissue from cases and healthy controls identified increased expression of HLA class 2, immunoglobulin variable regions and complement proteins. HAdV and AAV2 proteins were not detected in the livers. Instead, we identified AAV2 DNA complexes reflecting both HAdV-mediated and HHV-6B-mediated replication. We hypothesize that high levels of abnormal AAV2 replication products aided by HAdV and, in severe cases, HHV-6B may have triggered immune-mediated hepatic disease in genetically and immunologically predisposed children.
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Affiliation(s)
- Sofia Morfopoulou
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK
- Section for Paediatrics, Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Sarah Buddle
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Oscar Enrique Torres Montaguth
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Laura Atkinson
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - José Afonso Guerra-Assunção
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Mahdi Moradi Marjaneh
- Section for Paediatrics, Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
- Section of Virology, Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Riccardo Zennezini Chiozzi
- University College London Mass Spectrometry Science Technology Platform, Division of Biosciences, University College London, London, UK
| | - Nathaniel Storey
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Luis Campos
- Histopathology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - J Ciaran Hutchinson
- Histopathology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - John R Counsell
- Research Department of Targeted Intervention, Division of Surgery and Interventional Science, University College London, London, UK
| | - Gabriele Pollara
- Division of Infection and Immunity, University College London, London, UK
| | - Sunando Roy
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Cristina Venturini
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Juan F Antinao Diaz
- Research Department of Targeted Intervention, Division of Surgery and Interventional Science, University College London, London, UK
| | - Ala'a Siam
- Research Department of Targeted Intervention, Division of Surgery and Interventional Science, University College London, London, UK
- Gene Transfer Technology Group, EGA-Institute for Women's Health, University College London, London, UK
| | - Luke J Tappouni
- Research Department of Targeted Intervention, Division of Surgery and Interventional Science, University College London, London, UK
| | - Zeinab Asgarian
- Research Department of Targeted Intervention, Division of Surgery and Interventional Science, University College London, London, UK
| | - Joanne Ng
- Gene Transfer Technology Group, EGA-Institute for Women's Health, University College London, London, UK
| | - Killian S Hanlon
- Research Department of Targeted Intervention, Division of Surgery and Interventional Science, University College London, London, UK
| | - Alexander Lennon
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Andrew McArdle
- Section for Paediatrics, Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Agata Czap
- Division of Infection and Immunity, University College London, London, UK
| | - Joshua Rosenheim
- Division of Infection and Immunity, University College London, London, UK
| | - Catarina Andrade
- Histopathology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Glenn Anderson
- Histopathology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Jack C D Lee
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Rachel Williams
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Charlotte A Williams
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Helena Tutill
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Nadua Bayzid
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Luz Marina Martin Bernal
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Hannah Macpherson
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, UK
| | - Kylie-Ann Montgomery
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
- Department of Neurodegenerative Disease, Queen Square Institute of Neurology, University College London, London, UK
| | - Catherine Moore
- Wales Specialist Virology Centre, Public Health Wales Microbiology Cardiff, University Hospital of Wales, Cardiff, UK
| | - Kate Templeton
- Department of Medical Microbiology, Edinburgh Royal Infirmary, Edinburgh, UK
| | - Claire Neill
- Public Health Agency Northern Ireland, Belfast, UK
| | - Matt Holden
- School of Medicine, University of St. Andrews, St. Andrews, UK
- Public Health Scotland, Edinburgh, UK
| | - Rory Gunson
- West of Scotland Specialist Virology Centre, Glasgow, UK
| | | | - Priyen Shah
- Section for Paediatrics, Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Samantha Cooray
- Section for Paediatrics, Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Marie Voice
- Micropathology Ltd, University of Warwick Science Park, Coventry, UK
| | - Michael Steele
- Micropathology Ltd, University of Warwick Science Park, Coventry, UK
| | - Colin Fink
- Micropathology Ltd, University of Warwick Science Park, Coventry, UK
| | - Thomas E Whittaker
- Molecular and Cellular Immunology, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Giorgia Santilli
- Molecular and Cellular Immunology, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Paul Gissen
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | | | - Jana Reich
- Institute of Virology, Freie Universität Berlin, Berlin, Germany
| | - Julien Andreani
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Centre Hospitalier Universitaire (CHU) Grenoble-Alpes, Grenoble, France
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Dimah K Alrabiah
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
- National Centre for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Sergi Castellano
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child Health, University College London, London, UK
- University College London Genomics, University College London, London, UK
| | | | - Miranda Odam
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Tommy Rampling
- Division of Infection and Immunity, University College London, London, UK
- UK Health Security Agency, London, UK
- Hospital for Tropical Diseases, University College London Hospitals NHS Foundation Trust, London, UK
| | - Catherine Houlihan
- Division of Infection and Immunity, University College London, London, UK
- UK Health Security Agency, London, UK
- Department of Clinical Virology, University College London Hospitals, London, UK
| | | | | | | | | | | | | | | | | | | | | | - James Hatcher
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Surjo De
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | | | - Malcolm Gracie Semple
- Pandemic Institute, University of Liverpool, Liverpool, UK
- Respiratory Medicine, Alder Hey Children's Hospital NHS Foundation Trust, Liverpool, UK
| | - Joanne Martin
- Centre for Genomics and Child Health, The Blizard Institute, Queen Mary University of London, London, UK
| | | | - Mahdad Noursadeghi
- Division of Infection and Immunity, University College London, London, UK
| | | | | | | | - Rachel Brown
- Department of Cellular Pathology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Chayarani Kelgeri
- Liver Unit, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Konstantinos Thalassinos
- University College London Mass Spectrometry Science Technology Platform, Division of Biosciences, University College London, London, UK
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
| | - Simon N Waddington
- Gene Transfer Technology Group, EGA-Institute for Women's Health, University College London, London, UK
- Medical Research Council Antiviral Gene Therapy Research Unit, Faculty of Health Sciences, University of the Witswatersrand, Johannesburg, South Africa
| | - Thomas S Jacques
- Histopathology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- Developmental Biology and Cancer Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Emma Thomson
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Michael Levin
- Section for Paediatrics, Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Julianne R Brown
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Judith Breuer
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK.
- Department of Microbiology, Virology and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
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18
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Siddell SG, Smith DB, Adriaenssens E, Alfenas-Zerbini P, Dutilh BE, Garcia ML, Junglen S, Krupovic M, Kuhn JH, Lambert AJ, Lefkowitz EJ, Łobocka M, Mushegian AR, Oksanen HM, Robertson DL, Rubino L, Sabanadzovic S, Simmonds P, Suzuki N, Van Doorslaer K, Vandamme AM, Varsani A, Zerbini FM. Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV). J Gen Virol 2023; 104. [PMID: 37141106 DOI: 10.1099/jgv.0.001840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
The taxonomy of viruses is developed and overseen by the International Committee on Taxonomy of Viruses (ICTV), which scrutinizes, approves and ratifies taxonomic proposals, and maintains a list of virus taxa with approved names (https://ictv.global). The ICTV has approximately 180 members who vote by simple majority. Taxon-specific Study Groups established by the ICTV have a combined membership of over 600 scientists from the wider virology community; they provide comprehensive expertise across the range of known viruses and are major contributors to the creation and evaluation of taxonomic proposals. Proposals can be submitted by anyone and will be considered by the ICTV irrespective of Study Group support. Thus, virus taxonomy is developed from within the virology community and realized by a democratic decision-making process. The ICTV upholds the distinction between a virus or replicating genetic element as a physical entity and the taxon category to which it is assigned. This is reflected by the nomenclature of the virus species taxon, which is now mandated by the ICTV to be in a binomial format (genus + species epithet) and is typographically distinct from the names of viruses. Classification of viruses below the rank of species (such as, genotypes or strains) is not within the remit of the ICTV. This article, authored by the ICTV Executive Committee, explains the principles of virus taxonomy and the organization, function, processes and resources of the ICTV, with the aim of encouraging greater understanding and interaction among the wider virology community.
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Affiliation(s)
- Stuart G Siddell
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, University of Bristol, Bristol, UK
| | - Donald B Smith
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | - Bas E Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, Jena, Germany
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Maria Laura Garcia
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET, UNLP, La Plata, Buenos Aires, Argentina
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, USA
| | - Amy J Lambert
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases Centers for Disease Control and Prevention, Fort Collins, Colorado, USA
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham (UAB), Birmingham, Alabama, USA
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland
| | - Arcady R Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, Virginia, USA
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, CNR, SS Bari, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi, USA
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, Department of Immunobiology, BIO5 Institute, Genetics Graduate Interdisciplinary Program, Cancer Biology Graduate Interdisciplinary Program and University of Arizona Cancer Center, Tucson, Arizona, USA
| | - Anne-Mieke Vandamme
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium and Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
| | - F Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
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19
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Sharp CP, Thompson BH, Nash TJ, Diebold O, Pinto RM, Thorley L, Lin YT, Sives S, Wise H, Clohisey Hendry S, Grey F, Vervelde L, Simmonds P, Digard P, Gaunt ER. CpG dinucleotide enrichment in the influenza A virus genome as a live attenuated vaccine development strategy. PLoS Pathog 2023; 19:e1011357. [PMID: 37146066 PMCID: PMC10191365 DOI: 10.1371/journal.ppat.1011357] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 05/17/2023] [Accepted: 04/12/2023] [Indexed: 05/07/2023] Open
Abstract
Synonymous recoding of RNA virus genomes is a promising approach for generating attenuated viruses to use as vaccines. Problematically, recoding typically hinders virus growth, but this may be rectified using CpG dinucleotide enrichment. CpGs are recognised by cellular zinc-finger antiviral protein (ZAP), and so in principle, removing ZAP sensing from a virus propagation system will reverse attenuation of a CpG-enriched virus, enabling high titre yield of a vaccine virus. We tested this using a vaccine strain of influenza A virus (IAV) engineered for increased CpG content in genome segment 1. Virus attenuation was mediated by the short isoform of ZAP, correlated with the number of CpGs added, and was enacted via turnover of viral transcripts. The CpG-enriched virus was strongly attenuated in mice, yet conveyed protection from a potentially lethal challenge dose of wildtype virus. Importantly for vaccine development, CpG-enriched viruses were genetically stable during serial passage. Unexpectedly, in both MDCK cells and embryonated hens' eggs that are used to propagate live attenuated influenza vaccines, the ZAP-sensitive virus was fully replication competent. Thus, ZAP-sensitive CpG enriched viruses that are defective in human systems can yield high titre in vaccine propagation systems, providing a realistic, economically viable platform to augment existing live attenuated vaccines.
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Affiliation(s)
- Colin P. Sharp
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Beth H. Thompson
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Tessa J. Nash
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Ola Diebold
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Rute M. Pinto
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Luke Thorley
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Yao-Tang Lin
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Samantha Sives
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Helen Wise
- Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, United Kingdom
| | - Sara Clohisey Hendry
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Finn Grey
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Lonneke Vervelde
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Paul Digard
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
| | - Eleanor R. Gaunt
- The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, United Kingdom
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20
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Ratcliff J, Simmonds P. The roles of nucleic acid editing in adaptation of zoonotic viruses to humans. Curr Opin Virol 2023; 60:101326. [PMID: 37031485 PMCID: PMC10155873 DOI: 10.1016/j.coviro.2023.101326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 04/11/2023]
Abstract
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 immunodeficiency virus, with compelling bioinformatic evidence also for its mutagenic impact on monkeypox virus and severe acute respiratory syndrome coronavirus 2. ADAR-1 induces adenose-to-inosine (A→I) substitutions in double-stranded ribonucleic acid (RNA); its role in virus adaptation is less clear, as are epigenetic modifications to viral genomes, such as methylation. Nucleic acid editing restricts evolutionary space in which viruses can explore and may restrict viral-host range.
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Affiliation(s)
- Jeremy Ratcliff
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Peter Simmonds
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
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21
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deaths and substantial morbidity worldwide. Intense scientific effort to understand the biology of SARS-CoV-2 has resulted in daunting numbers of genomic sequences. We witnessed evolutionary events that could mostly be inferred indirectly before, such as the emergence of variants with distinct phenotypes, for example transmissibility, severity and immune evasion. This Review explores the mechanisms that generate genetic variation in SARS-CoV-2, underlying the within-host and population-level processes that underpin these events. We examine the selective forces that likely drove the evolution of higher transmissibility and, in some cases, higher severity during the first year of the pandemic and the role of antigenic evolution during the second and third years, together with the implications of immune escape and reinfections, and the increasing evidence for and potential relevance of recombination. In order to understand how major lineages, such as variants of concern (VOCs), are generated, we contrast the evidence for the chronic infection model underlying the emergence of VOCs with the possibility of an animal reservoir playing a role in SARS-CoV-2 evolution, and conclude that the former is more likely. We evaluate uncertainties and outline scenarios for the possible future evolutionary trajectories of SARS-CoV-2.
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Affiliation(s)
- Peter V Markov
- European Commission, Joint Research Centre (JRC), Ispra, Italy.
- London School of Hygiene & Tropical Medicine, University of London, London, UK.
| | - Mahan Ghafari
- Big Data Institute, University of Oxford, Oxford, UK
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Insel Riems, Germany
| | | | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nikolaos I Stilianakis
- European Commission, Joint Research Centre (JRC), Ispra, Italy
- Department of Biometry and Epidemiology, University of Erlangen-Nuremberg, Erlangen, Germany
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22
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Neuberger J, Brailsford SR, Mallinson G, Murphy MF, Simmonds P. Challenges for the maintaining the microbiological safety of the UK blood supply. Clin Med (Lond) 2023; 23:151-156. [PMID: 36806203 PMCID: PMC11046496 DOI: 10.7861/clinmed.2022-0401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The supply of blood, blood products and components in the UK, as elsewhere, is safe, although there is no cause for complacency. Use of blood, blood products and components is not without risk of morbidity and mortality. Transfusion-transmitted infections (TTIs) continue to occur and may severely affect the health and welfare of recipients. As indicated by recent and current inquiries, public interest in these TTIs is huge. The risk of TTI can be mitigated but not abolished. Measures to reduce risk include screening of donors, testing of donations and, where appropriate, treatment of donations. The introduction of newer screening tests might identify some infectious donations but come at a cost, which could exceed a justifiable limit. Thus, the recognition, detection, reporting and investigation of cases of possible TTIs need to be improved. Recipients of blood should understand that, although transfusion in the UK is safe, it is not free of risk and so should be provided with full information so that properly informed consent can be given.
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Affiliation(s)
| | | | - Gary Mallinson
- Joint UK Blood Transfusion and Tissue Transplantation Services Professional Advisory Committee (JPAC), NHS Blood and Transplant, Bristol
| | - Michael F Murphy
- NHS Blood & Transplant, Oxford University Hospitals NHS Foundation Trust and University of Oxford, Oxford
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23
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Knight C, Andreani J, Garrett N, Winter M, Golubchik T, Breuer J, Reynolds C, Brailsford SR, Harvala H, Simmonds P. Absence of detectable monkeypox virus DNA in 11,000 English blood donations during the 2022 outbreak. Transfusion 2023; 63:690-695. [PMID: 36752042 DOI: 10.1111/trf.17266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/03/2023] [Accepted: 01/03/2023] [Indexed: 02/09/2023]
Abstract
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 copies/ml, respectively. 454 minipools produced from 10,896 unique donors were assayed for MPXV DNA by both methods. No positive minipools were detected by either PCR. CONCLUSIONS Although blood donors are unrepresentative of the UK population in terms of MPXV infection risk, the uniformly negative MPXV DNA testing results provide reassurance that MPXV viraemia and potential transmission risk were rare or absent in donors during the outbreak period. Minipools from blood donors allow rapid implementation of large-scale population-based screening for emerging pathogens and represent an important resource for pandemic preparedness.
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Affiliation(s)
- Chanice Knight
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Julien Andreani
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK.,Centre Hospitalier Universitaire (CHU) Grenoble-Alpes, Grenoble, France
| | | | - Mark Winter
- NHSBT Filton Testing/Blood Supply, Bristol, UK
| | - Tanya Golubchik
- Sydney Infectious Diseases Institute, Faculty of Medicine and Health, University of Sydney, Sydney, Australia.,Big Data Institute, Nuffield Department of Medicine, Oxford, UK
| | - Judy Breuer
- Division of Infection and Immunity, University College London, London, UK
| | - Claire Reynolds
- NHS Blood and Transplant/UK Health Security Agency Epidemiology Unit, NHSBT, London, UK
| | - Susan R Brailsford
- NHS Blood and Transplant/UK Health Security Agency Epidemiology Unit, NHSBT, London, UK.,Microbiology Services, National Health Service (NHS) Blood and Transplant, London, UK
| | - Heli Harvala
- Division of Infection and Immunity, University College London, London, UK.,Microbiology Services, National Health Service (NHS) Blood and Transplant, London, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
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24
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Lee BD, Neri U, Roux S, Wolf YI, Camargo AP, Krupovic M, Simmonds P, Kyrpides N, Gophna U, Dolja VV, Koonin EV. Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs. Cell 2023; 186:646-661.e4. [PMID: 36696902 PMCID: PMC9911046 DOI: 10.1016/j.cell.2022.12.039] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/11/2022] [Accepted: 12/20/2022] [Indexed: 01/26/2023]
Abstract
Viroids and viroid-like covalently closed circular (ccc) RNAs are minimal replicators that typically encode no proteins and hijack cellular enzymes for replication. The extent and diversity of viroid-like agents are poorly understood. We developed a computational pipeline to identify viroid-like cccRNAs and applied it to 5,131 metatranscriptomes and 1,344 plant transcriptomes. The search yielded 11,378 viroid-like cccRNAs spanning 4,409 species-level clusters, a 5-fold increase compared to the previously identified viroid-like elements. Within this diverse collection, we discovered numerous putative viroids, satellite RNAs, retrozymes, and ribozy-like viruses. Diverse ribozyme combinations and unusual ribozymes within the cccRNAs were identified. Self-cleaving ribozymes were identified in ambiviruses, some mito-like viruses and capsid-encoding satellite virus-like cccRNAs. The broad presence of viroid-like cccRNAs in diverse transcriptomes and ecosystems implies that their host range is far broader than currently known, and matches to CRISPR spacers suggest that some cccRNAs replicate in prokaryotes.
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Affiliation(s)
- Benjamin D Lee
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Uri Neri
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Antonio Pedro Camargo
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 75015 Paris, France
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Nikos Kyrpides
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Uri Gophna
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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25
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Hill SC, François S, Thézé J, Smith AL, Simmonds P, Perrins CM, van der Hoek L, Pybus OG. Impact of host age on viral and bacterial communities in a waterbird population. ISME J 2023; 17:215-226. [PMID: 36319706 PMCID: PMC9860062 DOI: 10.1038/s41396-022-01334-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022]
Abstract
Wildlife harbour pathogens that can harm human or livestock health and are the source of most emerging infectious diseases. It is rarely considered how changes in wildlife population age-structures or how age-stratified behaviours might alter the level of pathogen detection within a species, or risk of spillover to other species. Micro-organisms that occur in healthy animals can be an important model for understanding and predicting the dynamics of pathogens of greater health concern, which are hard to study in wild populations due to their relative rarity. We therefore used a metagenomic approach to jointly characterise viral and prokaryotic carriage in faeces collected from a healthy wild bird population (Cygnus olor; mute swan) that has been subject to long-term study. Using 223 samples from known individuals allowed us to compare differences in prokaryotic and eukaryotic viral carriage between adults and juveniles at an unprecedented level of detail. We discovered and characterised 77 novel virus species, of which 21% belong putatively to bird-infecting families, and described the core prokaryotic microbiome of C. olor. Whilst no difference in microbiota diversity was observed between juveniles and adult individuals, 50% (4/8) of bird-infecting virus families (picornaviruses, astroviruses, adenoviruses and bornaviruses) and 3.4% (9/267) of prokaryotic families (including Helicobacteraceae, Spirochaetaceae and Flavobacteriaceae families) were differentially abundant and/or prevalent between juveniles and adults. This indicates that perturbations that affect population age-structures of wildlife could alter circulation dynamics and spillover risk of microbes, potentially including pathogens.
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Affiliation(s)
- Sarah C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK.
- Department of Biology, University of Oxford, Oxford, UK.
| | - Sarah François
- Department of Biology, University of Oxford, Oxford, UK.
| | - Julien Thézé
- Department of Biology, University of Oxford, Oxford, UK
- UMR EPIA, Université Clermont Auvergne, INRAE, VetAgro Sup, Saint-Genès-Champanelle, France
| | - Adrian L Smith
- Department of Biology, University of Oxford, Oxford, UK
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, UK
| | | | - Lia van der Hoek
- Amsterdam Institute for Infection and Immunity, Amsterdam, The Netherlands
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC location University of Amsterdam, Amsterdam, The Netherlands
| | - Oliver G Pybus
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK.
- Department of Biology, University of Oxford, Oxford, UK.
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26
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Simmonds P, Adriaenssens EM, Zerbini FM, Abrescia NGA, Aiewsakun P, Alfenas-Zerbini P, Bao Y, Barylski J, Drosten C, Duffy S, Duprex WP, Dutilh BE, Elena SF, García ML, Junglen S, Katzourakis A, Koonin EV, Krupovic M, Kuhn JH, Lambert AJ, Lefkowitz EJ, Łobocka M, Lood C, Mahony J, Meier-Kolthoff JP, Mushegian AR, Oksanen HM, Poranen MM, Reyes-Muñoz A, Robertson DL, Roux S, Rubino L, Sabanadzovic S, Siddell S, Skern T, Smith DB, Sullivan MB, Suzuki N, Turner D, Van Doorslaer K, Vandamme AM, Varsani A, Vasilakis N. Four principles to establish a universal virus taxonomy. PLoS Biol 2023; 21:e3001922. [PMID: 36780432 PMCID: PMC9925010 DOI: 10.1371/journal.pbio.3001922] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., "arboviruses"), infecting a certain type of host (e.g., "mycoviruses," "bacteriophages") or displaying specific pathogenicity (e.g., "human immunodeficiency viruses"), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent.
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Affiliation(s)
- Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - F. Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Nicola G. A. Abrescia
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences—BRTA, Derio, Spain
- Basque Foundation for Science, IKERBASQUE, Bilbao, Spain
| | - Pakorn Aiewsakun
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Yiming Bao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jakub Barylski
- Department of Molecular Virology, Adam Mickiewicz University, Poznan, Poland
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt University, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - W. Paul Duprex
- The Center for Vaccine Research, University of Pittsburgh School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Bas E. Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University, Jena, Germany
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Valencia, Spain
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Maria Laura García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET, UNLP, La Plata, Argentina
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Free University Berlin, Humboldt University, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Aris Katzourakis
- Department of Biology, University of Oxford, Oxford, United Kingdom
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris, France
| | - Jens H. Kuhn
- Integrated Research Facility at Fort Detrick (IRF-Frederick), National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, Maryland, United States of America
| | - Amy J. Lambert
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, United States of America
| | - Elliot J. Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Warsaw, Poland
| | - Cédric Lood
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Jennifer Mahony
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jan P. Meier-Kolthoff
- Department of Bioinformatics and Databases, Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Arcady R. Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, Virginia, United States of America
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Minna M. Poranen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Alejandro Reyes-Muñoz
- Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, Colombia
| | - David L. Robertson
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Simon Roux
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, CNR, UOS Bari, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Stuart Siddell
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Tim Skern
- Medical University of Vienna, Max Perutz Labs, Vienna Biocenter, Vienna, Austria
| | - Donald B. Smith
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Matthew B. Sullivan
- Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, Ohio, United States of America
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Dann Turner
- School of Applied Sciences, College of Health, Science and Society, University of the West of England, Bristol, United Kingdom
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, Department of Immunobiology, BIO5 Institute, and University of Arizona Cancer Center, Tucson, Arizona, United States of America
| | - Anne-Mieke Vandamme
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Leuven, Belgium
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, United States of America
| | - Nikos Vasilakis
- Department of Pathology, Center of Vector-Borne and Zoonotic Diseases, Institute for Human Infection and Immunity and World Reference Center for Emerging Viruses and Arboviruses, The University of Texas Medical Branch, Galveston, Texas, United States of America
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27
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Postler TS, Rubino L, Adriaenssens EM, Dutilh BE, Harrach B, Junglen S, Kropinski AM, Krupovic M, Wada J, Crane A, Kuhn JH, Mushegian A, Rūmnieks J, Sabanadzovic S, Simmonds P, Varsani A, Zerbini FM, Callanan J, Draper LA, Hill C, Stockdale SR. Guidance for creating individual and batch latinized binomial virus species names. J Gen Virol 2022; 103. [PMID: 36748479 DOI: 10.1099/jgv.0.001800] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The International Committee on Taxonomy of Viruses recently adopted, and is gradually implementing, a binomial naming format for virus species. Although full Latinization of these names remains optional, a standardized nomenclature based on Latinized binomials has the advantage of comparability with all other biological taxonomies. As a language without living native speakers, Latin is more culturally neutral than many contemporary languages, and words built from Latin roots are already widely used in the language of science across the world. Conversion of established species names to Latinized binomials or creation of Latinized binomials de novo may seem daunting, but the rules for name creation are straightforward and can be implemented in a formulaic manner. Here, we describe approaches, strategies and steps for creating Latinized binomials for virus species without prior knowledge of Latin. We also discuss a novel approach to the automated generation of large batches of novel genus and species names. Importantly, conversion to a binomial format does not affect virus names, many of which are created from local languages.
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Affiliation(s)
- Thomas S Postler
- Department of Microbiology & Immunology, Vagelos College of Physicians & Surgeons, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Luisa Rubino
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Sede Secondaria di Bari, 70126 Bari, Italy
| | | | - Bas E Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany.,Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, 3584 CH Utrecht, Netherlands
| | - Balázs Harrach
- Veterinary Medical Research Institute, H-1143 Budapest, Hungary
| | - Sandra Junglen
- Institute of Virology, Charité - Universitätsmedizin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Andrew M Kropinski
- Departments of Pathobiology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 75015 Paris, France
| | - Jiro Wada
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Anya Crane
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Arcady Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, Alexandria, VA 22314, USA
| | - Jānis Rūmnieks
- Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Peter Simmonds
- Nuffield Department of Experimental Medicine, University of Oxford, Peter Medawar Building, Oxford, OX1 3SY, UK
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287-4701, USA.,Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - F Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Julie Callanan
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
| | - Lorraine A Draper
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, T12 YT20, Ireland
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28
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Yang J, Liao Q, Luo K, Liu F, Zhou Y, Zou G, Huang W, Yu S, Wei X, Zhou J, Dai B, Qiu Q, Altmeyer R, Hu H, Paireau J, Luo L, Gao L, Nikolay B, Hu S, Xing W, Wu P, van Doorn HR, Horby PW, Simmonds P, Leung GM, Cowling BJ, Cauchemez S, Yu H. Seroepidemiology of enterovirus A71 infection in prospective cohort studies of children in southern China, 2013-2018. Nat Commun 2022; 13:7280. [PMID: 36435844 PMCID: PMC9701185 DOI: 10.1038/s41467-022-34992-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 11/11/2022] [Indexed: 11/28/2022] Open
Abstract
Enterovirus A71 (EV-A71)-related hand, foot, and mouth disease (HFMD) imposes a substantial clinical burden in the Asia Pacific region. To inform policy on the introduction of the EV-A71 vaccine into the National Immunization Programme, we investigated the seroepidemiological characteristics of EV-A71 in two prospective cohorts of children in southern China conducted between 2013 and 2018. Our results show that maternal antibody titres declined rapidly in neonates, with over half becoming susceptible to EV-A71 at 1 month of age. Between 6 months and 2 years of age, over 80% of study participants were susceptible, while one third remained susceptible at 5 years old. The highest incidence of EV-A71 infections was observed in children aged 5-6 months. Our findings support EV-A71 vaccination before 6 months for birth cohorts in southern China, potentially with a one-time catch-up vaccination for children 6 months-5 years old. More regionally representative longitudinal seroepidemiological studies are needed to further validate these findings.
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Affiliation(s)
- Juan Yang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Qiaohong Liao
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
- Key Laboratory of Surveillance and Early-warning on Infectious Disease, Division of Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kaiwei Luo
- Hunan Provincial Center for Disease Control and Prevention (Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences), Changsha, China
| | - Fengfeng Liu
- Key Laboratory of Surveillance and Early-warning on Infectious Disease, Division of Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yonghong Zhou
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Gang Zou
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Wei Huang
- Hunan Provincial Center for Disease Control and Prevention (Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences), Changsha, China
| | - Shuanbao Yu
- Key Laboratory of Surveillance and Early-warning on Infectious Disease, Division of Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xianglin Wei
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Jiaxin Zhou
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Bingbing Dai
- Anhua County Center for Disease Control and Prevention, Yiyang, China
| | - Qi Qiu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China
| | - Ralf Altmeyer
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
- Medusa Therapeutics Limited, Hong Kong Special Administrative Region, Hong Kong, China
| | - Hongan Hu
- Anhua County Center for Disease Control and Prevention, Yiyang, China
| | - Juliette Paireau
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, UMR2000, CNRS, 75015, Paris, France
- Infectious Diseases Department, Santé publique France, Saint-Maurice, France
| | - Li Luo
- Key Laboratory of Surveillance and Early-warning on Infectious Disease, Division of Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lidong Gao
- Hunan Provincial Center for Disease Control and Prevention (Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences), Changsha, China
| | - Birgit Nikolay
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, UMR2000, CNRS, 75015, Paris, France
| | - Shixiong Hu
- Hunan Provincial Center for Disease Control and Prevention (Workstation for Emerging Infectious Disease Control and Prevention, Chinese Academy of Medical Sciences), Changsha, China
| | - Weijia Xing
- Key Laboratory of Surveillance and Early-warning on Infectious Disease, Division of Infectious Disease, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai'an, China
| | - Peng Wu
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Peter W Horby
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Peter Simmonds
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Gabriel M Leung
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, Hong Kong, China
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, UMR2000, CNRS, 75015, Paris, France
| | - Hongjie Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China.
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29
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Walker PJ, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Alfenas-Zerbini P, Dempsey DM, Dutilh BE, García ML, Curtis Hendrickson R, Junglen S, Krupovic M, Kuhn JH, Lambert AJ, Łobocka M, Oksanen HM, Orton RJ, Robertson DL, Rubino L, Sabanadzovic S, Simmonds P, Smith DB, Suzuki N, Van Doorslaer K, Vandamme AM, Varsani A, Zerbini FM. Recent changes to virus taxonomy ratified by the International Committee on Taxonomy of Viruses (2022). Arch Virol 2022; 167:2429-2440. [PMID: 35999326 PMCID: PMC10088433 DOI: 10.1007/s00705-022-05516-5] [Citation(s) in RCA: 102] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This article reports the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2022. The entire ICTV was invited to vote on 174 taxonomic proposals approved by the ICTV Executive Committee at its annual meeting in July 2021. All proposals were ratified by an absolute majority of the ICTV members. Of note, the Study Groups have started to implement the new rule for uniform virus species naming that became effective in 2021 and mandates the binomial 'Genus_name species_epithet' format with or without Latinization. As a result of this ratification, the names of 6,481 virus species (more than 60 percent of all species names currently recognized by ICTV) now follow this format.
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Affiliation(s)
- Peter J Walker
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Stuart G Siddell
- Faculty of Life Sciences, School of Cellular and Molecular Medicine, University of Bristol, University Walk, Bristol, BS8 1TD, UK
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th ST South, Birmingham, AL, 35294-2170, USA
| | - Arcady R Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, 2415 Eisenhower Avenue, Alexandria, VA, 22314, USA.
| | | | - Poliane Alfenas-Zerbini
- Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | - Donald M Dempsey
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th ST South, Birmingham, AL, 35294-2170, USA
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, Room Z-509, 3584 CH, Utrecht, The Netherlands
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Fürstengraben 1, 07743, Jena, Germany
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET - UNLP, calles 47 y 115 (1900), La Plata, Buenos Aires, Argentina
| | - R Curtis Hendrickson
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th ST South, Birmingham, AL, 35294-2170, USA
| | - Sandra Junglen
- Institute of Virology, Charité - Universitätsmedizin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit,, 25 rue du Dr Roux, 75015, Paris, France
| | - Jens H Kuhn
- NIH/NIAID/DCR/Integrated Research Facility at Fort Detrick (IRF-Frederick), B-8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA
| | - Amy J Lambert
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, National Center for Emerging and Zoonotic Infectious Diseases, Fort Collins, CO, 80521, USA
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00014, Helsinki, Finland
| | - Richard J Orton
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow, G61 1QH, UK
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, CNR, UOS Bari, Via Amendola 165/A, 70126, Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Old Hwy 12 Mail Stop 9775, Mississippi State, MS, 39762, USA
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Donald B Smith
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Koenraad Van Doorslaer
- Department of Immunobiology, School of Animal and Comparative Biomedical Sciences, BIO5 Institute, University of Arizona Cancer Center, Tucson, AZ, 85721, USA
| | - Anne-Mieke Vandamme
- KU Leuven, Department of Microbiology, Immunology and TransplantationClinical and Epidemiological VirologyInstitute for the Future, Rega Institute for Medical Research, 3000, Leuven, Belgium
- Center for Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008, Lisbon, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85287-4701, USA
| | - Francisco Murilo Zerbini
- Departamento de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
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30
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Williams S, Ratcliff J, Nguyen D, Simmonds P, Harvala H. Detection frequencies and viral load distribution of parvovirus B19 DNA in blood and plasma donations in England. Transfus Med 2022; 32:402-409. [PMID: 35751630 PMCID: PMC9796365 DOI: 10.1111/tme.12893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/29/2022] [Accepted: 06/08/2022] [Indexed: 01/01/2023]
Abstract
BACKGROUND AND OBJECTIVES Infections with human parvovirus B19 (B19V) are transmissible by blood components and plasma-derived medicines. The European Pharmacopoeia regulates maximum levels of virus allowed in manufacturers' plasma pools. To evaluate contamination risk prior to re-introduction of UK-sourced plasma for manufacturing, we investigated viraemia frequencies of B19V in plasma samples collected from blood donors before and during COVID-enforced lockdown. MATERIALS AND METHODS Quantitative PCR for B19V DNA was used to screen pools of 96 anonymised plasma samples collected in England from 2017 (n = 29 505), 2020 (n = 3360) and 2021 (n = 43 200). Selected positive pools were resolved into individual samples. Data on donor notifications and related lookback investigations were collected from European countries by on-line survey in 2020. RESULTS Screening of 76 065 donations identified 80 B19V-positive pools. While most positive samples had low viral loads (<105 IU ml-1 ), primarily from 2017 (77/29 505; 0.3%), two contained high levels of B19V DNA (1.3 × 108 and 6.3 × 106 IU ml-1 ), both likely to contaminate a final manufacturer's pool and lead to discard. The incidence of B19V infection during lockdown was reduced (1/3360 in 2020; 0/43 200 in 2021). Genomic analysis of positive pools resolved to single samples identified B19V genotype 1 in all nine samples. Seroprevalence of anti-B19V IgG antibodies was 75% (143/192). A survey of B19V screening practices in Europe demonstrated considerable variability. Two blood establishments informed infected blood donors of positive B19V results. CONCLUSION Information on seroprevalence, incidence and viral loads of B19V viraemia is contributory the evaluation of alternative operational screening strategies for plasma testing.
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Affiliation(s)
- Sarah Williams
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen ResearchUniversity of OxfordOxfordUK
| | - Jeremy Ratcliff
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen ResearchUniversity of OxfordOxfordUK
| | - Dung Nguyen
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen ResearchUniversity of OxfordOxfordUK
| | - Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen ResearchUniversity of OxfordOxfordUK
| | - Heli Harvala
- Microbiology Services, NHS Blood and TransplantUK
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31
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Harvala H, Simmonds P. Evaluating the risk of transfusion and transplant-transmitted monkeypox infections. Transfus Med 2022; 32:460-466. [PMID: 36134432 PMCID: PMC10087182 DOI: 10.1111/tme.12918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/17/2022] [Accepted: 09/11/2022] [Indexed: 10/14/2022]
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. Reported infections in the UK have been exponentially increasing over the last 2 months, with 1552 reported cases in the UK by 7th July 2022. This is likely to be considerable underestimate given current limitations in diagnostic capacity and clinical diagnoses hampered by its similar disease presentations to other causes of rash and genitourinary disease. While MPXV infections are currently most widespread in gay, bisexual or other men who have sex with men, wider spread of MPXV outside defined risk groups for infection may prevent identification of infection risk in donors. While typically mild disease outcomes have been reported in UK cases, case fatality rates ranging from 1% to over 10% are reported for different MPXV strains in its source area in sub-Saharan Africa. Recipients of blood components and organs transplant, especially those who are immunosuppressed, may reproduce the greater systemic spread and morbidity of those infected through percutaneous routes. There is a potential risk of MPXV transmission and severe disease outcomes in blood and transplant recipients. In addition to current risk assessments performed in the UK and exclusion of donors with recent MPXV exposure, determining viraemia frequencies in donors and directly evaluating transmission risk would be of considerable value in assessing whether MPXV nucleic acid screening should be implemented.
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Affiliation(s)
- Heli Harvala
- Microbiology Services, NHS Blood and Transplant, London, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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32
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Wellens J, Edmans M, Obolski U, McGregor CG, Simmonds P, Turner M, Jarvis L, Skelly D, Dunachie S, Barnes E, Eyre DW, Colombel JF, Wong SY, Klenerman P, Lindsay JO, Satsangi J, Thompson CP. Combination therapy of infliximab and thiopurines, but not monotherapy with infliximab or vedolizumab, is associated with attenuated IgA and neutralisation responses to SARS-CoV-2 in inflammatory bowel disease. Gut 2022; 71:1919-1922. [PMID: 34911744 DOI: 10.1136/gutjnl-2021-326312] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/06/2021] [Indexed: 12/08/2022]
Affiliation(s)
- Judith Wellens
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium.,Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Matthew Edmans
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK.,Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Uri Obolski
- School of Public Health, Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Porter School of Environmental and Earth Sciences, Faculty of Exact Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | | | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Marc Turner
- National Microbiology Reference Unit, Scottish National Blood Transfusion Service, Edinburgh, Edinburgh, UK
| | - Lisa Jarvis
- National Microbiology Reference Unit, Scottish National Blood Transfusion Service, Edinburgh, Edinburgh, UK
| | - Donal Skelly
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Susanna Dunachie
- Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Eleanor Barnes
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK.,Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - David W Eyre
- Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK.,Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | - Serre-Yu Wong
- The Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Mount Sinai School of Medicine, New York, New York, USA
| | - Paul Klenerman
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK.,Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James O Lindsay
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK
| | - Jack Satsangi
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Craig P Thompson
- Warwick Medical School, University of Warwick, Coventry, UK .,Department of Zoology, University of Oxford, Oxford, UK
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33
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Christensen KT, Pierard F, Beuselinck K, Bonsall D, Bowden R, Lagrou K, Nevens F, Schrooten Y, Simmonds P, Vandamme AM, Van Wijngaerden E, Dierckx T, Cuypers L, Van Laethem K. Full-genome next-generation sequencing of hepatitis C virus to assess the accuracy of genotyping by the commercial assay LiPA and the prevalence of resistance-associated substitutions in a Belgian cohort. J Clin Virol 2022; 155:105252. [DOI: 10.1016/j.jcv.2022.105252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/26/2022] [Accepted: 08/02/2022] [Indexed: 02/07/2023]
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34
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Odon V, Fiddaman SR, Smith AL, Simmonds P. Comparison of CpG- and UpA-mediated restriction of RNA virus replication in mammalian and avian cells and investigation of potential ZAP-mediated shaping of host transcriptome compositions. RNA 2022; 28:1089-1109. [PMID: 35675984 PMCID: PMC9297844 DOI: 10.1261/rna.079102.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
The ability of zinc finger antiviral protein (ZAP) to recognize and respond to RNA virus sequences with elevated frequencies of CpG dinucleotides has been proposed as a functional part of the vertebrate innate immune antiviral response. It has been further proposed that ZAP activity shapes compositions of cytoplasmic mRNA sequences to avoid self-recognition, particularly mRNAs for interferons (IFNs) and IFN-stimulated genes (ISGs) expressed during the antiviral state. We investigated whether restriction of the replication of mutants of influenza A virus (IAV) and the echovirus 7 (E7) replicon with high CpG and UpA frequencies varied in different species of mammals and birds. Cell lines from different bird orders showed substantial variability in restriction of CpG-high mutants of IAV and E7 replicons, whereas none restricted UpA-high mutants, in marked contrast to universal restriction of both mutants in mammalian cells. Dinucleotide representation in ISGs and IFN genes was compared with those of cellular transcriptomes to determine whether potential differences in inferred ZAP activity between species shaped dinucleotide compositions of highly expressed genes during the antiviral state. While mammalian type 1 IFN genes typically showed often profound suppression of CpG and UpA frequencies, there was no oversuppression of either in ISGs in any species, irrespective of their ability to restrict CpG- or UpA-high mutants. Similarly, genome sequences of mammalian and avian RNA viruses were compositionally equivalent, as were IAV strains recovered from ducks, chickens and humans. Overall, we found no evidence for host variability in inferred ZAP function shaping host or viral transcriptome compositions.
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Affiliation(s)
- Valerie Odon
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, United Kingdom
| | - Steven R Fiddaman
- Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, United Kingdom
| | - Adrian L Smith
- Department of Zoology, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, United Kingdom
| | - Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, United Kingdom
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35
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McNaughton AL, Paton RS, Edmans M, Youngs J, Wellens J, Phalora P, Fyfe A, Belij-Rammerstorfer S, Bolton JS, Ball J, Carnell GW, Dejnirattisai W, Dold C, Eyre DW, Hopkins P, Howarth A, Kooblall K, Klim H, Leaver S, Lee LN, López-Camacho C, Lumley SF, Macallan DC, Mentzer AJ, Provine NM, Ratcliff J, Slon-Compos J, Skelly D, Stolle L, Supasa P, Temperton N, Walker C, Wang B, Wyncoll D, Simmonds P, Lambe T, Baillie JK, Semple MG, Openshaw PJ, Obolski U, Turner M, Carroll M, Mongkolsapaya J, Screaton G, Kennedy SH, Jarvis L, Barnes E, Dunachie S, Lourenço J, Matthews PC, Bicanic T, Klenerman P, Gupta S, Thompson CP. Fatal COVID-19 outcomes are associated with an antibody response targeting epitopes shared with endemic coronaviruses. JCI Insight 2022; 7:156372. [PMID: 35608920 PMCID: PMC9310533 DOI: 10.1172/jci.insight.156372] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 05/18/2022] [Indexed: 11/17/2022] Open
Abstract
The role of immune responses to previously seen endemic coronavirus epitopes in severe acute respiratory coronavirus 2 (SARS-CoV-2) infection and disease progression has not yet been determined. Here, we show that a key characteristic of fatal outcomes with coronavirus disease 2019 (COVID-19) is that the immune response to the SARS-CoV-2 spike protein is enriched for antibodies directed against epitopes shared with endemic beta-coronaviruses and has a lower proportion of antibodies targeting the more protective variable regions of the spike. The magnitude of antibody responses to the SARS-CoV-2 full-length spike protein, its domains and subunits, and the SARS-CoV-2 nucleocapsid also correlated strongly with responses to the endemic beta-coronavirus spike proteins in individuals admitted to an intensive care unit (ICU) with fatal COVID-19 outcomes, but not in individuals with nonfatal outcomes. This correlation was found to be due to the antibody response directed at the S2 subunit of the SARS-CoV-2 spike protein, which has the highest degree of conservation between the beta-coronavirus spike proteins. Intriguingly, antibody responses to the less cross-reactive SARS-CoV-2 nucleocapsid were not significantly different in individuals who were admitted to an ICU with fatal and nonfatal outcomes, suggesting an antibody profile in individuals with fatal outcomes consistent with an "original antigenic sin" type response.
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Affiliation(s)
- Anna L. McNaughton
- Peter Medawar Building for Pathogen Research
- Nuffield Department of Medicine, and
| | - Robert S. Paton
- Peter Medawar Building for Pathogen Research
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Matthew Edmans
- Peter Medawar Building for Pathogen Research
- Nuffield Department of Medicine, and
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Jonathan Youngs
- Institute of Infection & Immunity, St George’s University of London, London, United Kingdom
| | - Judith Wellens
- Peter Medawar Building for Pathogen Research
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
- Translational Research for Gastrointestinal Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Prabhjeet Phalora
- Peter Medawar Building for Pathogen Research
- Nuffield Department of Medicine, and
| | - Alex Fyfe
- Peter Medawar Building for Pathogen Research
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Jai S. Bolton
- Peter Medawar Building for Pathogen Research
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Jonathan Ball
- General Intensive Care service, St George’s University Hospital National Health Service (NHS) Trust, London, United Kingdom
| | - George W. Carnell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | | | - David W. Eyre
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Philip Hopkins
- Centre for Human & Applied Physiological Sciences, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King’s College, London, United Kingdom
| | - Alison Howarth
- Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Kreepa Kooblall
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Churchill Hospital, and
| | - Hannah Klim
- Peter Medawar Building for Pathogen Research
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Future of Humanity Institute, Department of Philosophy, and
| | - Susannah Leaver
- General Intensive Care service, St George’s University Hospital National Health Service (NHS) Trust, London, United Kingdom
| | - Lian Ni Lee
- Peter Medawar Building for Pathogen Research
- Nuffield Department of Medicine, and
| | | | - Sheila F. Lumley
- Peter Medawar Building for Pathogen Research
- Nuffield Department of Medicine, and
- Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Derek C. Macallan
- Institute of Infection & Immunity, St George’s University of London, London, United Kingdom
| | | | - Nicholas M. Provine
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Jeremy Ratcliff
- Peter Medawar Building for Pathogen Research
- Nuffield Department of Medicine, and
| | - Jose Slon-Compos
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine
| | - Donal Skelly
- Peter Medawar Building for Pathogen Research
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Lucas Stolle
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Piyada Supasa
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Chatham, United Kingdom
| | - Chris Walker
- Meso Scale Diagnostics, Rockville, Maryland, USA
| | - Beibei Wang
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine
| | - Duncan Wyncoll
- Intensive Care Medicine, Guy’s and St Thomas’ Hospital NHS Foundation Trust, London, United Kingdom
| | | | | | - Peter Simmonds
- Peter Medawar Building for Pathogen Research
- Nuffield Department of Medicine, and
| | - Teresa Lambe
- The Jenner Institute Laboratories, University of Oxford, Oxford, United Kingdom
| | | | - Malcolm G. Semple
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | | | | | - Uri Obolski
- School of Public Health, Faculty of Medicine, and
- Porter School of the Environment and Earth Sciences, Faculty of Exact Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Marc Turner
- National Microbiology Reference Unit, Scottish National Blood Transfusion Service, Edinburgh, United Kingdom
| | - Miles Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine
- National Infection Service, Public Health England (PHE), Salisbury, United Kingdom
| | - Juthathip Mongkolsapaya
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine
- Siriraj Center of Research for Excellence in Dengue & Emerging Pathogens, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, United Kingdom
| | - Gavin Screaton
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, United Kingdom
| | - Stephen H. Kennedy
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Lisa Jarvis
- National Microbiology Reference Unit, Scottish National Blood Transfusion Service, Edinburgh, United Kingdom
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research
- Nuffield Department of Medicine, and
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | - Susanna Dunachie
- Peter Medawar Building for Pathogen Research
- Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - José Lourenço
- Peter Medawar Building for Pathogen Research
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Philippa C. Matthews
- Peter Medawar Building for Pathogen Research
- Nuffield Department of Medicine, and
- Department of Microbiology/Infectious Diseases, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Tihana Bicanic
- Institute of Infection & Immunity, St George’s University of London, London, United Kingdom
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research
- Nuffield Department of Medicine, and
- Translational Research for Gastrointestinal Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Sunetra Gupta
- Peter Medawar Building for Pathogen Research
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Craig P. Thompson
- Peter Medawar Building for Pathogen Research
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
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36
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Smith D, Orton R, Zerbini M, Lefkowitz E, Sabanadzovic S, Simmonds P, Siddell S. Making virus taxonomy accessible. Access Microbiol 2022. [DOI: 10.1099/acmi.ac2021.po0168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The International Committee on Taxonomy of Viruses (ICTV) is responsible for approving changes to the taxonomy of viruses. These changes arise from proposals made to the ICTV, usually by one of its 101 Study Groups, each of which is responsible for a particular virus family or families. The result of this international, voluntary effort is a searchable and structured list of current virus taxonomy that can be accessed on the ICTV website (www.ictv.global). The website also makes available the virus metadata resource (VMR), a spreadsheet with exemplar isolates and GenBank accession numbers for members of each species, as well as the ICTV Report which provides more detail about the taxonomy, structure and biology of each virus family. The online publication mode allows taxonomic changes and relevant research findings to be quickly reflected in the Report, and also means that the sequence alignments and phylogenetic trees, upon which taxonomic decisions often depend, are available as resources for all to use. A two-page summary of each Report chapter is published as an Open Access article by the Journal of General Virology as a Virus Taxonomy Profile. It remains a challenge to make these freely available resources comprehensive because of the pace of taxonomic change; over the last decade the number of virus families has almost doubled from 87 to 168. In meeting this challenge the ICTV will continue to rely on the enthusiasm, expertise and efforts of virologists from around the world.
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Affiliation(s)
- Donald Smith
- University of Edinburgh, United Kingdom
- University of Oxford, United Kingdom
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37
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Harvala H, Nguyen D, Simmonds P, Lamikanra AA, Tsang HP, Otter A, Maes P, Webster M, Clarkson A, Kaloyirou F, Hopkins V, Laidlaw SM, Carroll M, Mora A, Griffiths A, MacLennan S, Estcourt L, Roberts DJ. Convalescent plasma donors show enhanced cross-reactive neutralising antibody response to antigenic variants of SARS-CoV-2 following immunisation. Transfusion 2022; 62:1347-1354. [PMID: 35588314 PMCID: PMC9348319 DOI: 10.1111/trf.16934] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/19/2022] [Accepted: 04/19/2022] [Indexed: 11/30/2022]
Abstract
Background The therapeutic benefit of convalescent plasma (CP) therapy to treat COVID‐19 may derive from neutralizing antibodies (nAbs) to SARS‐CoV‐2. To investigate the effects of antigenic variation on neutralization potency of CP, we compared nAb titers against prototype and recently emerging strains of SARS‐CoV‐2, including Delta and Omicron, in CP donors previously infected with SARS‐CoV‐2 before and after immunization. Methods and Materials Samples were assayed from previously SARS‐CoV‐2 infected donors before (n = 17) and after one (n = 43) or two (n = 71) doses of Astra‐Zeneca or Pfizer vaccinations. Ab titers against Wuhan/wild type (WT), Alpha, Beta, and Delta SARS‐CoV‐2 strains were determined by live virus microneutralization assay while titers to Omicron used a focus reduction neutralization test. Anti‐spike antibody was assayed by Elecsys anti‐SARS‐CoV‐2 quantitative spike assay (Roche). Results Unvaccinated donors showed a geometric mean titer (GMT) of 148 against WT, 80 against Alpha but mostly failed to neutralize Beta, Delta, and Omicron strains. Contrastingly, high GMTs were observed in vaccinated donors against all SARS‐CoV‐2 strains after one vaccine dose (WT:703; Alpha:692; Beta:187; Delta:215; Omicron:434). By ROC analysis, reactivity in the Roche quantitative Elecsys spike assay of 20,000 U/mL was highly predictive of donations with nAb titers of ≥1:640 against Delta (90% sensitivity; 97% specificity) and ≥1:320 against Omicron (89% sensitivity; 81% specificity). Discussion Vaccination of previously infected CP donors induced high levels of broadly neutralizing antibodies against circulating antigenic variants of SARS‐CoV‐2. High titer donations could be reliably identified by automated quantitative anti‐spike antibody assay, enabling large‐scale preselection of high‐titer convalescent plasma.
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Affiliation(s)
- Heli Harvala
- Microbiology Services, NHS Blood and Transplant, Colindale, UK
| | - Dung Nguyen
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, Roosevelt Drive, Headington, University of Oxford, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | | | - Hoi Pat Tsang
- Clinical Services, NHS Blood and Transplant, Oxford, UK
| | - Ashley Otter
- UK Health Security Agency, Porton Down, Salisbury, UK
| | - Piet Maes
- KU Leuven, Rega Institute, Clinical and Epidemiological Virology, Leuven, Belgium
| | - Mhairi Webster
- Microbiology Services, NHS Blood and Transplant, Colindale, UK
| | - Adam Clarkson
- Microbiology Services, NHS Blood and Transplant, Colindale, UK
| | - Fotini Kaloyirou
- Statistics and Clinical Research, NHS Blood and Transplant, Cambridge, UK
| | - Valerie Hopkins
- Statistics and Clinical Research, NHS Blood and Transplant, Cambridge, UK
| | - Stephen M Laidlaw
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, Roosevelt Drive, Headington, University of Oxford, UK
| | - Miles Carroll
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, Roosevelt Drive, Headington, University of Oxford, UK
| | - Ana Mora
- Statistics and Clinical Research, NHS Blood and Transplant, Cambridge, UK
| | | | | | - Lise Estcourt
- Clinical Services, NHS Blood and Transplant, Oxford, UK.,Radcliffe Department of Medicine and BRC Haematology Theme, University of Oxford, Oxford, UK
| | - David J Roberts
- Clinical Services, NHS Blood and Transplant, Oxford, UK.,Radcliffe Department of Medicine and BRC Haematology Theme, University of Oxford, Oxford, UK
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38
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Zerbini FM, Siddell SG, Mushegian AR, Walker PJ, Lefkowitz EJ, Adriaenssens EM, Alfenas-Zerbini P, Dutilh BE, García ML, Junglen S, Krupovic M, Kuhn JH, Lambert AJ, Łobocka M, Oksanen HM, Robertson DL, Rubino L, Sabanadzovic S, Simmonds P, Suzuki N, Van Doorslaer K, Vandamme AM, Varsani A. Differentiating between viruses and virus species by writing their names correctly. Arch Virol 2022; 167:1231-1234. [PMID: 35043230 PMCID: PMC9020231 DOI: 10.1007/s00705-021-05323-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Following the results of the International Committee on Taxonomy of Viruses (ICTV) Ratification Vote held in March 2021, a standard two-part "binomial nomenclature" is now the norm for naming virus species. Adoption of the new nomenclature is still in its infancy; thus, it is timely to reiterate the distinction between "virus" and "virus species" and to provide guidelines for naming and writing them correctly.
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Affiliation(s)
| | - Stuart G. Siddell
- School of Cellular and Molecular Medicine, Faculty of Life Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Arcady R. Mushegian
- Division of Molecular and Cellular Biosciences, National Science Foundation, 2415 Eisenhower Avenue, Alexandria, VA 22314, USA
| | - Peter J. Walker
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia QLD 4072, Australia
| | - Elliot J. Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham (UAB), BBRB 276, 845 19th St South, Birmingham, AL 35294-2170, USA
| | | | | | - Bas E. Dutilh
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, Jena 07743, Germany,Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - María Laura García
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET, UNLP, calles 47 y 115 (1900), La Plata, Buenos Aires, Argentina
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin, corporate member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Mart Krupovic
- Institut Pasteur, Université de Paris, Archaeal Virology Unit, Paris 75015, France
| | - Jens H. Kuhn
- NIH/NIAID/DCR/Integrated Research Facility at Fort Detrick (IRF-Frederick), B-8200 Research Plaza, Fort Detrick, Frederick, MD 21702, USA
| | - Amy J. Lambert
- Division of Vector-Borne Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, CO 80521, USA
| | - Małgorzata Łobocka
- Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland
| | - David L. Robertson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, CNR, UOS Bari, Via Amendola 165/A, 70126 Bari, Italy
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, 100 Old Hwy 12 Mail Stop 9775, Mississippi State, MS 39762, USA
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford OX1 3SY, UK
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Koenraad Van Doorslaer
- School of Animal and Comparative Biomedical Sciences, Department of Immunobiology, BIO5 Institute, and University of Arizona Cancer Center, Tucson, AZ 85721, USA
| | - Anne-Mieke Vandamme
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Institute for the Future, 3000 Leuven, Belgium,Center for Global Health and Tropical Medicine, Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008 Lisboa, Portugal
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, P.O. Box 874701, Tempe, AZ 85287-4701, USA
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39
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Lee BD, Neri U, Oh CJ, Simmonds P, Koonin EV. ViroidDB: a database of viroids and viroid-like circular RNAs. Nucleic Acids Res 2022; 50:D432-D438. [PMID: 34751403 PMCID: PMC8728161 DOI: 10.1093/nar/gkab974] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/01/2021] [Accepted: 10/06/2021] [Indexed: 12/31/2022] Open
Abstract
We introduce ViroidDB, a value-added database that attempts to collect all known viroid and viroid-like circular RNA sequences into a single resource. Spanning about 10 000 unique sequences, ViroidDB includes viroids, retroviroid-like elements, small circular satellite RNAs, ribozyviruses, and retrozymes. Each sequence's secondary structure, ribozyme content, and cluster membership are predicted via a custom pipeline optimized for handling circular RNAs. The data can be explored via a purpose-built user interface that features visualizations, multiple sequence alignments, and a portal for downloading bulk data. Users can browse the data by sequence type, taxon, or typo-tolerant search of metadata fields. The database is freely accessible at https://viroids.org.
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MESH Headings
- Base Sequence
- Databases, Nucleic Acid
- Internet
- Metadata
- Nucleic Acid Conformation
- Plant Diseases/virology
- Plants/virology
- RNA, Catalytic/chemistry
- RNA, Catalytic/classification
- RNA, Catalytic/genetics
- RNA, Catalytic/metabolism
- RNA, Circular/chemistry
- RNA, Circular/classification
- RNA, Circular/genetics
- RNA, Circular/metabolism
- RNA, Viral/chemistry
- RNA, Viral/classification
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Sequence Alignment
- Software
- Viroids/classification
- Viroids/genetics
- Viroids/metabolism
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Affiliation(s)
- Benjamin D Lee
- National Center for Biotechnology Information, National Library of Medicine, National Institutes Health, Bethesda, MD 20894, USA
- Nuffield Department of Medicine, University of Oxford, Oxford OX1, UK
| | - Uri Neri
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel
| | | | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford OX1, UK
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes Health, Bethesda, MD 20894, USA
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40
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Iselin L, Palmalux N, Kamel W, Simmonds P, Mohammed S, Castello A. Uncovering viral RNA-host cell interactions on a proteome-wide scale. Trends Biochem Sci 2022; 47:23-38. [PMID: 34509361 PMCID: PMC9187521 DOI: 10.1016/j.tibs.2021.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/12/2021] [Accepted: 08/06/2021] [Indexed: 01/14/2023]
Abstract
RNA viruses interact with a wide range of cellular RNA-binding proteins (RBPs) during their life cycle. The prevalence of these host-virus interactions has been highlighted by new methods that elucidate the composition of viral ribonucleoproteins (vRNPs). Applied to 11 viruses so far, these approaches have revealed hundreds of cellular RBPs that interact with viral (v)RNA in infected cells. However, consistency across methods is limited, raising questions about methodological considerations when designing and interpreting these studies. Here, we discuss these caveats and, through comparing available vRNA interactomes, describe RBPs that are consistently identified as vRNP components and outline their potential roles in infection. In summary, these novel approaches have uncovered a new universe of host-virus interactions holding great therapeutic potential.
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Affiliation(s)
- Louisa Iselin
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, OX1 3SY, UK,Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK
| | - Natasha Palmalux
- MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, (UK)
| | - Wael Kamel
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK,MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, (UK)
| | - Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, OX1 3SY, UK
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK,Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK,The Rosalind Franklin Institute, Oxfordshire, OX11 0FA, UK
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU, Oxford, UK,MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61 1QH, Scotland, (UK),Correspondence:
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41
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Kuhn JH, Adkins S, Agwanda BR, Kubrusli RA, Alkhovsky (Aльxoвcкий Cepгeй Bлaдимиpoвич) SV, Amarasinghe GK, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Basler CF, Bavari S, Beer M, Bejerman N, Bennett AJ, Bente DA, Bergeron É, Bird BH, Blair CD, Blasdell KR, Blystad DR, Bojko J, Borth WB, Bradfute S, Breyta R, Briese T, Brown PA, Brown JK, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Büttner C, Calisher CH, Cao (曹孟籍) M, Casas I, Chandran K, Charrel RN, Cheng Q, Chiaki (千秋祐也) Y, Chiapello M, Choi IR, Ciuffo M, Clegg JCS, Crozier I, Bó ED, de la Torre JC, de Lamballerie X, de Swart RL, Debat H, Dheilly NM, Di Cicco E, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Dolnik O, Drebot MA, Drexler JF, Dundon WG, Duprex WP, Dürrwald R, Dye JM, Easton AJ, Ebihara (海老原秀喜) H, Elbeaino T, Ergünay K, Ferguson HW, Fooks AR, Forgia M, Formenty PBH, Fránová J, Freitas-Astúa J, Fu (付晶晶) J, Fürl S, Gago-Zachert S, Gāo GF, García ML, García-Sastre A, Garrison AR, Gaskin T, Gonzalez JPJ, Griffiths A, Goldberg TL, Groschup MH, Günther S, Hall RA, Hammond J, Han (韩彤) T, Hepojoki J, Hewson R, Hong (洪健) J, Hong (洪霓) N, Hongo S, Horie (堀江真行) M, Hu JS, Hu T, Hughes HR, Hüttner F, Hyndman TH, Ilyas M, Jalkanen R, Jiāng (姜道宏) D, Jonson GB, Junglen S, Kadono (上遠野冨士夫) F, Kaukinen KH, Kawate M, Klempa B, Klingström J, Kobinger G, Koloniuk I, Kondō (近藤秀樹) H, Koonin EV, Krupovic M, Kubota (久保田健嗣) K, Kurath G, Laenen L, Lambert AJ, Langevin SL, Lee B, Lefkowitz EJ, Leroy EM, Li (李邵蓉) S, Li (李龙辉) L, Lǐ (李建荣) J, Liu (刘华珍) H, Lukashevich IS, Maes P, de Souza WM, Marklewitz M, Marshall SH, Marzano SYL, Massart S, McCauley JW, Melzer M, Mielke-Ehret N, Miller KM, Ming TJ, Mirazimi A, Mordecai GJ, Mühlbach HP, Mühlberger E, Naidu R, Natsuaki (夏秋知英) T, Navarro JA, Netesov (Heтёcoв Cepгeй Bиктopoвич) SV, Neumann G, Nowotny N, Nunes MRT, Olmedo-Velarde A, Palacios G, Pallás V, Pályi B, Papa (Άννα Παπά) A, Paraskevopoulou (Παρασκευοπούλου Σοφία) S, Park AC, Parrish CR, Patterson DA, Pauvolid-Corrêa A, Pawęska JT, Payne S, Peracchio C, Pérez DR, Postler TS, Qi (亓立莹) L, Radoshitzky SR, Resende RO, Reyes CA, Rima BK, Luna GR, Romanowski V, Rota P, Rubbenstroth D, Rubino L, Runstadler JA, Sabanadzovic S, Sall AA, Salvato MS, Sang R, Sasaya (笹谷孝英) T, Schulze AD, Schwemmle M, Shi (施莽) M, Shí (石晓宏) X, Shí (石正丽) Z, Shimomoto (下元祥史) Y, Shirako Y, Siddell SG, Simmonds P, Sironi M, Smagghe G, Smither S, Song (송진원) JW, Spann K, Spengler JR, Stenglein MD, Stone DM, Sugano J, Suttle CA, Tabata A, Takada (高田礼人) A, Takeuchi (竹内繁治) S, Tchouassi DP, Teffer A, Tesh RB, Thornburg NJ, Tomitaka (冨高保弘) Y, Tomonaga (朝長啓造) K, Tordo N, Torto B, Towner JS, Tsuda (津田新哉) S, Tu (涂长春) C, Turina M, Tzanetakis I, Uchida J, Usugi (宇杉富雄) T, Vaira AM, Vallino M, van den Hoogen B, Varsani A, Vasilakis (Νίκος Βασιλάκης) N, Verbeek M, von Bargen S, Wada J, Wahl V, Walker PJ, Wang (王林发) LF, Wang (王国平) G, Wang (王雁翔) Y, Wang (王亚琴) YQ, Waqas M, Wèi (魏太云) T, Wen (温少华) S, Whitfield AE, Williams JV, Wolf YI, Wu (吴建祥) JX, Xu (徐雷) L, Yanagisawa (栁澤広宣) H, Yang (杨彩霞) C, Yang (杨作坤) Z, Zerbini FM, Zhai (翟立峰) L, Zhang YZ, Zhang (张松) S, Zhang (张靖国) J, Zhang (张哲) Z, Zhou (周雪平) X. Correction to: 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Arch Virol 2021; 166:3567-3579. [PMID: 34786611 PMCID: PMC11078012 DOI: 10.1007/s00705-021-05266-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Jens H. Kuhn
- Integrated Research Facility at Fort Detrick, National
Institute of Allergy and Infectious Diseases, National Institutes of Health,
Frederick, MD, USA
| | - Scott Adkins
- United States Department of Agriculture, Agricultural
Research Service, US Horticultural Research Laboratory, Fort Pierce, FL, USA
| | - Bernard R. Agwanda
- Zoology Department, National Museums of Kenya, Nairobi,
Kenya
- Jomo Kenyatta University of Agriculture &
Technology, Nairobi, Kenya
| | - Rim Al Kubrusli
- Division Phytomedicine, Faculty of Life Sciences,
Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Gaya K. Amarasinghe
- Department of Pathology and Immunology, Washington
University School of Medicine, St. Louis, MO, USA
| | | | - María A. Ayllón
- Centro de Biotecnología y Genómica de
Plantas, Universidad Politécnica de Madrid—Instituto Nacional de
Investigación y Tecnología Agraria y Alimentaria, Campus de
Montegancedo, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología
Vegetal, Escuela Técnica Superior de Ingeniería Agronómica,
Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid,
Spain
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Department of
Infectious Diseases, Department of Epidemiology and Biostatistics, Insitute of
Bioinformatics, University of Georgia, Athens, GA, USA
| | - Anne Balkema-Buschmann
- Institute of Novel and Emerging Infectious Diseases,
Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health,
Greifswald-Insel Riems, Germany
| | - Matthew J. Ballinger
- Department of Biological Sciences, Mississippi State
University, Mississippi State, MS, USA
| | - Christopher F. Basler
- Center for Microbial Pathogenesis, Institute for
Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Sina Bavari
- Edge BioInnovation Consulting and Mgt, Frederick, MD,
USA
| | - Martin Beer
- Institute of Diagnostic Virology,
Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | | | - Andrew J. Bennett
- Genomics and Bioinformatics Department, Biological
Defense Research Directorate, Naval Medical Research Center–Frederick, Fort
Detrick, Frederick, MD, USA
| | | | - Éric Bergeron
- Viral Special Pathogens Branch, Division of
High-Consequence Pathogens and Pathology, Centers for Disease Control and
Prevention, Atlanta, GA, USA
| | - Brian H. Bird
- School of Veterinary Medicine, One Health Institute,
University of California, Davis, Davis, CA, USA
| | - Carol D. Blair
- Department of Microbiology, Immunology and Pathology,
Colorado State University, Fort Collins, CO, USA
| | - Kim R. Blasdell
- Commonwealth Scientific and Industrial Research
Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, VIC,
Australia
| | | | - Jamie Bojko
- School of Health and Life Sciences, Teesside University,
Middlesbrough TS1 3BX, UK
- National Horizons Centre, Teesside University,
Darlington DL1 1HG, UK
| | | | - Steven Bradfute
- University of New Mexico Health Sciences Center,
Albuquerque, NM, USA
| | - Rachel Breyta
- University of Washington, Seattle, WA, USA
- US Geological Survey, Western Fisheries Research
Center, Seattle, WA, USA
| | - Thomas Briese
- Center for Infection and Immunity, and Department of
Epidemiology, Mailman School of Public Health, Columbia University, New York, NY,
USA
| | - Paul A. Brown
- Laboratory of Ploufragan-Plouzané-Niort, French
Agency for Food, Environmental and Occupational Heath Safety ANSES, Ploufragan,
France
| | - Judith K. Brown
- School of Plant Sciences, University of Arizona, Tucson,
AZ, USA
| | - Ursula J. Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases,
National Institute of Allergy and Infectious Diseases, National Institutes of
Health, Bethesda, MD, USA
| | - Michael J. Buchmeier
- Department of Molecular Biology and Biochemistry,
University of California, Irvine, Irvine, CA, USA
| | - Alexander Bukreyev
- Galveston National Laboratory, The University of Texas
Medical Branch at Galveston, Galveston, TX, USA
| | - Felicity Burt
- Division of Virology, National Health Laboratory Service
and Division of Virology, University of the Free State, Bloemfontein, Republic of
South Africa
| | - Carmen Büttner
- Division Phytomedicine, Faculty of Life Sciences,
Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Mengji Cao (曹孟籍)
- National Citrus Engineering and Technology Research
Center, Citrus Research Institute, Southwest University, Beibei, Chongqing,
People’s Republic of China
| | - Inmaculada Casas
- Respiratory Virus and Influenza Unit, National
Microbiology Center, Instituto de Salud Carlos III, Madrid, Spain
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert
Einstein College of Medicine, Bronx, NY, USA
| | - Rémi N. Charrel
- Unité des Virus Emergents (Aix-Marseille Univ, IRD
190, Inserm 1207, IHU Méditerranée Infection), Marseille, France
| | - Qi Cheng
- State Key Laboratory of Rice Biology, Institute of
Biotechnology, Zhejiang University, Hangzhou, People’s Republic of
China
| | - Yuya Chiaki (千秋祐也)
- Grape and Persimmon Research Station, Institute of Fruit
tree and Tea Science, NARO, Higashihiroshima, Hiroshima, Japan
| | - Marco Chiapello
- Institute for Sustainable Plant Protection, National
Research Council of Italy (CNR), Strada delle Cacce 73, 10135 Turin, Italy
| | - Il-Ryong Choi
- Plant Breeding Genetics and Biotechnology Division and
International Rice Research Institute, Los Baños, Philippines
| | - Marina Ciuffo
- Institute for Sustainable Plant Protection, National
Research Council of Italy (CNR), Strada delle Cacce 73, 10135 Turin, Italy
| | | | - Ian Crozier
- Clinical Monitoring Research Program Directorate,
Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Elena Dal Bó
- CIDEFI, Facultad de Ciencias Agrarias y Forestales,
Universidad de La Plata, La Plata, Argentina
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology IMM-6, The
Scripps Research Institute, La Jolla, CA, USA
| | - Xavier de Lamballerie
- Unité des Virus Emergents (Aix-Marseille Univ, IRD
190, Inserm 1207, IHU Méditerranée Infection), Marseille, France
| | - Rik L. de Swart
- Department Viroscience, Erasmus MC, University Medical
Centre Rotterdam, Rotterdam, The Netherlands
| | - Humberto Debat
- Centro de Investigaciones Agropecuarias, Instituto
Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba,
Argentina
- Unidad de Fitopatología y Modelización
Agrícola, Consejo Nacional de Investigaciones Científicas y
Técnicas (UFYMA-CONICET), Córdoba, Argentina
| | - Nolwenn M. Dheilly
- UMR 1161 Virology ANSES/INRAE/ENVA, ANSES Animal Health
Laboratory, 94704 Maisons-Alfort, France
| | | | - Nicholas Di Paola
- United States Army Medical Research Institute of
Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante,
Consiglio Nazionale delle Ricerche, Turin, Italy
| | - Ralf G. Dietzgen
- Queensland Alliance for Agriculture and Food Innovation,
The University of Queensland, St. Lucia, QLD, Australia
| | - Michele Digiaro
- CIHEAM, Istituto Agronomico Mediterraneo di Bari,
Valenzano, Italy
| | - Olga Dolnik
- Institute of Virology, Philipps University Marburg,
Marburg, Germany
| | - Michael A. Drebot
- Zoonotic Diseases and Special Pathogens, National
Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - J. Felix Drexler
- Institute of Virology,
Charité-Universitätsmedizin Berlin, Corporate Member of Freie
Universität Berlin, Humboldt Universität Berlin, Berlin, Germany
| | - William G. Dundon
- Animal Production and Health Laboratory, Joint FAO/IAEA
Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear
Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - W. Paul Duprex
- School of Medicine, University of Pittsburgh, Pittsburgh,
PA, USA
| | | | - John M. Dye
- United States Army Medical Research Institute of
Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | | | | | | | - Koray Ergünay
- Virology Unit, Department of Medical Microbiology,
Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Hugh W. Ferguson
- School of Veterinary Medicine, St. George’s
University, True Blue, Grenada
| | | | - Marco Forgia
- Institute for sustainable plant protection, CNR, Turin,
Italy
| | | | - Jana Fránová
- Plant Virology Department, Institute of Plant Molecular
Biology, Biology Centre CAS, Ceske Budejovice, Czech Republic
| | | | - Jingjing Fu (付晶晶)
- College of Life Science and Engineering, Shenyang
University, Shenyang, Liaoning, People’s Republic of China
| | - Stephanie Fürl
- Albrecht Daniel Thaer-Institute for Crop and Animal
Sciences, Division Phytomedicine, Humboldt-Universität zu Berlin, Berlin,
Germany
| | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Martin
Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - George Fú Gāo
- National Institute for Viral Disease Control and
Prevention, Chinese Center for Disease Control and Prevention, Beijing,
People’s Republic of China
| | - María Laura García
- nstituto de Biotecnología y Biología
Molecular, Facultad de Ciencias Exactas, I, CONICET UNLP, La Plata, Argentina
| | | | - Aura R. Garrison
- United States Army Medical Research Institute of
Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Thomas Gaskin
- Division Phytomedicine, Faculty of Life Sciences,
Humboldt-Universität zu Berlin, Berlin, Germany
- Landwirtschaft und Flurneuordnung, Landesamt für
ländliche Entwicklung, Frankfurt (Oder), Germany
| | - Jean-Paul J. Gonzalez
- Department of Microbiology and Immunology, Division of
Biomedical Graduate Research Organization, School of Medicine, Georgetown
University, Washington, DC 20057, USA
- Centaurus Biotechnologies, CTP, Manassas, VA, USA
| | - Anthony Griffiths
- Department of Microbiology and National Emerging
Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA,
USA
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, School of
Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Martin H. Groschup
- Institute of Novel and Emerging Infectious Diseases,
Friedric h-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Stephan Günther
- WHO Collaborating Centre for Arboviruses and Hemorrhagic
Fever Reference and Research, Department of Virology, Bernhard-Nocht Institute for
Tropical Medicine, Hamburg, Germany
| | - Roy A. Hall
- Australian Infectious Diseases Research Centre, School of
Chemistry and Molecular Biosciences, The University of Queensland, Brisbane,
Australia
| | - John Hammond
- Floral and Nursery Plants Research Unit, United States
Department of Agriculture, Agricultural Research Service, USNA, Beltsville, MD,
USA
| | - Tong Han (韩彤)
- College of Life Science and Engineering, Shenyang
University, Shenyang, Liaoning, People’s Republic of China
| | - Jussi Hepojoki
- Department of Virology, University of Helsinki, Medicum,
Helsinki, Finland
- Institute of Veterinary Pathology, Vetsuisse Faculty,
University of Zurich, Zurich, Switzerland
| | - Roger Hewson
- London School of Hygeine and Tropical Medicine, London,
UK
| | - Jiang Hong (洪健)
- Analysis Center of Agrobiology and Environmental
Sciences, Zhejiang University, Hangzhou, People’s Republic of China
| | - Ni Hong (洪霓)
- Key Lab of Plant Pathology of Hubei Province, College of
Plant Science and Technology, Huazhong Agricultural University, Wuhan,
People’s Republic of China
| | - Seiji Hongo
- Department of Infectious Diseases, Yamagata University
Faculty of Medicine, Yamagata, Japan
| | - Masayuki Horie (堀江真行)
- Hakubi Center for Advanced Research, Kyoto University,
Kyoto, Japan
- Division of Veterinary Sciences, Graduate School of
Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Japan
| | | | - Tao Hu
- State Key Laboratory of Rice Biology, Institute of
Biotechnology, Zhejiang University, Hangzhou, People’s Republic of
China
| | - Holly R. Hughes
- Centers for Disease Control and Prevention, Fort Collins,
CO, USA
| | - Florian Hüttner
- Division Phytomedicine, Faculty of Life Sciences,
Humboldt-Universität zu Berlin, Berlin, Germany
| | - Timothy H. Hyndman
- School of Veterinary Medicine, Murdoch University,
Murdoch, WA, Australia
| | - M. Ilyas
- Entomology and Plant Pathology, North Carolina State
University, Raleigh, NC, USA
| | | | - Dàohóng Jiāng (姜道宏)
- State Key Laboratory of Agricultural Microbiology,
Huazhong Agricultural University, Wuhan, Hubei Province, People’s Republic of
China
| | - Gilda B. Jonson
- Rice Breeding Innovations Platform, International Rice
Research Institute, Los Baños, Laguna, Philippines
| | - Sandra Junglen
- Institute of Virology,
Charité-Universitätsmedizin Berlin, Corporate Member of Free
University Berlin, Humboldt-University Berlin, and Berlin Institute of Health,
Berlin, Germany
- German Centre for Infection Research, Berlin,
Germany
| | - Fujio Kadono (上遠野冨士夫)
- Department of Clinical Plant Science, Faculty of
Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo, Japan
| | - Karia H. Kaukinen
- Pacific Biological Station, Fisheries and Oceans Canada,
Nanaimo, BC, Canada
| | | | - Boris Klempa
- Institute of Virology, Biomedical Research Center, Slovak
Academy of Sciences, Bratislava, Slovakia
| | - Jonas Klingström
- Center for Infectious Medicine, Department of Medicine
Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm,
Sweden
| | - Gary Kobinger
- Department of Microbiology, Immunology and Infectious
Diseases, Université Laval, Quebec City, Canada
| | - Igor Koloniuk
- Plant Virology Department, Institute of Plant Molecular
Biology, Biology Centre CAS, Ceske Budejovice, Czech Republic
| | - Hideki Kondō (近藤秀樹)
- Institute of Plant Science and Resources, Okayama
University, Kurashiki, Japan
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National
Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris,
France
| | | | - Gael Kurath
- US Geological Survey Western Fisheries Research Center,
Seattle, WA, USA
| | - Lies Laenen
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases
unit, Leuven, Belgium
- Department of Laboratory Medicine, University Hospitals
Leuven, Leuven, Belgium
| | - Amy J. Lambert
- Centers for Disease Control and Prevention, Fort Collins,
CO, USA
| | | | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at
Mount Sinai, New York, NY, USA
| | | | - Eric M. Leroy
- MIVEGEC (IRD-CNRS-Montpellier university) Unit, French
National Research Institute for Sustainable Development (IRD), Montpellier,
France
| | - Shaorong Li (李邵蓉)
- Fisheries and Oceans Canada, Pacific Biological
Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - Longhui Li (李龙辉)
- Key Lab of Plant Pathology of Hubei Province, College of
Plant Science and Technology, Huazhong Agricultural University, Wuhan,
People’s Republic of China
| | - Jiànróng Lǐ (李建荣)
- Department of Veterinary Biosciences, College of
Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Huazhen Liu (刘华珍)
- Key Lab of Plant Pathology of Hubei Province, College of
Plant Science and Technology, Huazhong Agricultural University, Wuhan,
People’s Republic of China
| | - Igor S. Lukashevich
- Department of Pharmacology and Toxicology, School of
Medicine, and the Center for Predictive Medicine for Biodefense and Emerging
Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Piet Maes
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases
unit, Leuven, Belgium
| | | | - Marco Marklewitz
- Institute of Virology,
Charité-Universitätsmedizin Berlin, Corporate Member of Free
University Berlin, Humboldt-University Berlin, and Berlin Institute of Health,
Berlin, Germany
- German Center for Infection Research (DZIF), Berlin,
Germany
| | - Sergio H. Marshall
- Pontificia Universidad Católica de
Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Shin-Yi L. Marzano
- United States Department of Agriculture, Agricultural
Research Service, Washington, USA
| | - Sebastien Massart
- Gembloux Agro-Bio Tech, TERRA, Plant Pathology
Laboratory, Liège University, Liege, Belgium
| | | | - Michael Melzer
- Plant and Environmental Protection Sciences, University
of Hawai’i at Mānoa, Honolulu, HI, USA
| | | | - Kristina M. Miller
- Pacific Biological Station, Fisheries and Oceans Canada,
Nanaimo, BC, Canada
| | - Tobi J. Ming
- Molecular Genetics, Pacific Biological Station,
Department of Fisheries and Oceans, Nanaimo, Canada
| | | | - Gideon J. Mordecai
- Department of Medicine, Univeristy of British Columbia,
Vancouver, Canada
| | | | - Elke Mühlberger
- Department of Microbiology and National Emerging
Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA,
USA
| | - Rayapati Naidu
- Department of Plant Pathology, Irrigated Agricultural
Research and Extension Center, Washington State University, Prosser, WA, USA
| | | | - José A. Navarro
- Instituto de Biología Molecular y Celular de
Plantas, Universitat Politècnica de València-Consejo Superior de
Investigaciones Científicas, Valencia, Spain
| | | | - Gabriele Neumann
- Influenza Research Institute, Department of
Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary
Medicine Vienna, Vienna, Austria
- College of Medicine, Mohammed Bin Rashid University of
Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | | | - Gustavo Palacios
- United States Army Medical Research Institute of
Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Vicente Pallás
- Instituto de Biología Molecular y Celular de
Plantas (IBMCP), Consejo Superior de Investigaciones Cientificas-Universidad
Politécnica de Valencia, Valencia, Spain
| | - Bernadett Pályi
- National Biosafety Laboratory, National Public Health
Center, Budapest, Hungary
| | - Anna Papa (Άννα Παπά)
- National Reference Centre for Arboviruses and
Haemorrhagic Fever Viruses, Department of Microbiology, Medical School, Aristotle
University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Paraskevopoulou (Παρασκευοπούλου Σοφία)
- Institute of Virology,
Charité-Universitätsmedizin Berlin, corporate member of Freie
Universität Berlin, Humboldt-Universität zu Berlin, and Berlin
Institute of Health, Berlin, Germany
| | - Adam C. Park
- University of Hawaii, Honolulu, HI, USA
- Hawaii Department of Agriculture, Honolulu, HI,
USA
| | - Colin R. Parrish
- Baker Institute for Animal Health, College of
Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - David A. Patterson
- Fisheries and Oceans Canada, Resource and Environmental
Management, Simon Fraser University, Burnaby, BC, Canada
| | - Alex Pauvolid-Corrêa
- Department of Veterinary Integrated Biosciences and
Department of Entomology, Texas A&M University, College Station, USA
- Laboratory of Respiratory Viruses and Measles, Fiocruz,
Rio de Janeiro, Brazil
| | - Janusz T. Pawęska
- Center for Emerging Zoonotic and Parasitic Diseases,
National Institute for Communicable Diseases of the National Health Laboratory
Service, Sandringham-Johannesburg, Gauteng, South Africa
| | - Susan Payne
- Department of Veterinary Pathobiology, College of
Veterinary Medicine and Biomedical Sciences, Texas A&M University, College
Station, TX, USA
| | - Carlotta Peracchio
- Institute for Sustainable Plant Protection, National
Research Council of Italy (CNR), Strada delle Cacce 73, 10135 Turin, Italy
| | - Daniel R. Pérez
- Department of Population Health, College of Veterinary
Medicine, University of Georgia, Athens, GA, USA
| | - Thomas S. Postler
- Department of Microbiology and Immunology, Vagelos
College of Physicians and Surgeons, Columbia University Irving Medical Center, New
York, NY 10032, USA
| | - Liying Qi (亓立莹)
- Jiangxi Academy of Agricultural Sciences, Nanchang,
Jiangxi, People’s Republic of China
| | | | - Renato O. Resende
- Departamento de Biologia Celular, Universidade de
Brasília, Brasília, Brazil
| | - Carina A. Reyes
- Instituto de Biotecnología y Biología
Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Bertus K. Rima
- Centre for Experimental Medicine, School of Medicine,
Dentistry and Biomedical Sciences, The Queen’s University of Belfast,
Belfast, Northern Ireland, UK
| | - Gabriel Robles Luna
- Instituto de Biotecnología y Biología
Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Víctor Romanowski
- Instituto de Biotecnología y Biología
Molecular, Centro Cientifico Technológico-La Plata, Consejo Nacional de
Investigaciones Científico Tecnológico—Universidad Nacional de
La Plata, La Plata, Argentina
| | - Paul Rota
- National Center for Immunization and Respiratory
Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dennis Rubbenstroth
- Institute of Diagnostic Virology,
Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Luisa Rubino
- Consiglio Nazionale delle Ricerche, Istituto per la
Protezione Sostenibile delle Piante, Bari, Italy
| | - Jonathan A. Runstadler
- Department of Infectious Disease and Global Health,
Tufts University Cummings School of Veterinary Medicine, 200 Westboro Road, North
Grafton, MA 01536, USA
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology,
Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS,
USA
| | | | - Maria S. Salvato
- Institute of Human Virology, University of Maryland
School of Medicine, Baltimore, MA, USA
| | - Rosemary Sang
- International Centre of Insect Physiology and Ecology,
Nairobi, Kenya
| | - Takahide Sasaya (笹谷孝英)
- Western Region Agricultural Research Center, National
Agriculture and Food Research Organization, Fukuyama, Japan
| | - Angela D. Schulze
- Molecular Genetics Lab, Pacific Biological Station,
Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Martin Schwemmle
- Faculty of Medicine, University Medical
Center-University Freiburg, Freiburg, Germany
| | - Mang Shi (施莽)
- Sun Yat-sen University, Shenzhen, People’s
Republic of China
| | - Xiǎohóng Shí (石晓宏)
- MRC-University of Glasgow Centre for Virus Research,
Glasgow, Scotland, UK
| | - Zhènglì Shí (石正丽)
- CAS Key Laboratory of Special Pathogens, Wuhan
Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of
Sciences, Wuhan, Hubei, People’s Republic of China
| | | | - Yukio Shirako
- Asian Center for Bioresources and Environmental
Sciences, University of Tokyo, Tokyo, Japan
| | - Stuart G. Siddell
- School of Cellular and Molecular Medicine, University
of Bristol, Bristol, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford,
Oxford, UK
| | - Manuela Sironi
- Bioinformatics Unit, Scientific Institute IRCCS
“E. Medea”, Bosisio Parini, Italy
| | - Guy Smagghe
- Faculty of Bioscience Engineering, Department of Plant
and Crops, Ghent University, Ghent, Belgium
| | - Sophie Smither
- CBR Division, DSTL, Porton Down, Salisbury, Wiltshire,
UK
| | - Jin-Won Song (송진원)
- Department of Microbiology, College of Medicine, Korea
University, Seoul, Republic of Korea
| | - Kirsten Spann
- School of Biomedical Sciences, Faculty of Health,
Queensland University of Technology, Brisbane, QLD, Australia
| | - Jessica R. Spengler
- Viral Special Pathogens Branch, Division of
High-Consequence Pathogens and Pathology, Centers for Disease Control and
Prevention, Atlanta, USA
| | - Mark D. Stenglein
- Department of Microbiology, Immunology, and Pathology,
College of Veterinary Medicine and Biomedical Sciences, Colorado State University,
Fort Collins, CO, USA
| | - David M. Stone
- Centre for Environment, Fisheries and Aquaculture
Science, Weymouth, Dorset, UK
| | | | - Curtis A. Suttle
- Departments of Earth, Ocean and Atmospheric Sciences,
Microbiology and Immunology, and Botany, and the Institute for Oceans and Fisheries,
University of British Columbia, Vancouver, Canada
| | - Amy Tabata
- Pacific Biological Station, Fisheries and Oceans Canada,
Nanaimo, BC, Canada
| | - Ayato Takada (高田礼人)
- Division of Global Epidemiology, Research Center for
Zoonosis Control, Hokkaido University, Sapporo, Japan
| | | | | | - Amy Teffer
- Department of Forest Sciences, University of British
Columbia, Vancouver, Canada
| | - Robert B. Tesh
- The University of Texas Medical Branch, Galveston, TX,
USA
| | | | | | - Keizō Tomonaga (朝長啓造)
- Institute for Frontier Life and Medical Sciences
(inFront), Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Unité des Stratégies Antivirales, WHO
Collaborative Centre for Viral Haemorrhagic Fevers and Arboviruses, OIE Reference
Laboratory for RVFV & CCHFV, Institut Pasteur, Paris, France
| | - Baldwyn Torto
- International Centre of Insect Physiology and Ecology,
Nairobi, Kenya
| | - Jonathan S. Towner
- Viral Special Pathogens Branch, Division of
High-Consequence Pathogens Pathology, National Center for Emerging and Zoonotic
Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA,
USA
- Institut Pasteur de Guinée, Conakry,
Guinea
| | - Shinya Tsuda (津田新哉)
- Department of Clinical Plant Science, Faculty of
Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo, Japan
| | - Changchun Tu (涂长春)
- Changchun Veterinary Research Institute, Chinese
Academy of Agricultural Sciences, Changchun, Jilin Province, People’s
Republic of China
| | - Massimo Turina
- National Institute of Optics, National Research Council
of Italy (INO-CNR), Via Branze 45, 25123Brescia, Italy
| | - Ioannis Tzanetakis
- Department of Entomology and Plant Pathology, Division
of Agriculture, University of Arkansas System,, Fayetteville, AR 72701, USA
| | | | - Tomio Usugi (宇杉富雄)
- Central Region Agricultural Research Center, NARO,
Tsukuba, Ibaraki, Japan
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National
Research Council of Italy (CNR), Strada delle Cacce 73, 10135 Turin, Italy
| | - Marta Vallino
- Institute for Sustainable Plant Protection, National
Research Council of Italy (CNR), Strada delle Cacce 73, 10135 Turin, Italy
| | - Bernadette van den Hoogen
- Department of Viroscience, Erasmus MC, University
Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied
Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona
State University, Tempe, AZ, USA
- Structural Biology Research Unit, Department of
Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South
Africa
| | | | - Martin Verbeek
- Wageningen University and Research, Biointeractions and
Plant Health, Wageningen, The Netherlands
| | - Susanne von Bargen
- Division Phytomedicine, Faculty of Life Sciences,
Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jiro Wada
- Integrated Research Facility at Fort Detrick, National
Institute of Allergy and Infectious Diseases, National Institutes of Health,
Frederick, MD, USA
| | - Victoria Wahl
- National Biodefense Analysis and Countermeasures
Center, Fort Detrick, Frederick, MD, USA
| | - Peter J. Walker
- School of Chemistry and Molecular Biosciences,
University of Queensland, St. Lucia, QLD, Australia
| | - Lin-Fa Wang (王林发)
- Programme in Emerging Infectious Diseases, Duke-NUS
Medical School, Singapore, Singapore
| | - Guoping Wang (王国平)
- Key Lab of Plant Pathology of Hubei Province, College of
Plant Science and Technology, Huazhong Agricultural University, Wuhan,
People’s Republic of China
| | - Yanxiang Wang (王雁翔)
- Key Lab of Plant Pathology of Hubei Province, College of
Plant Science and Technology, Huazhong Agricultural University, Wuhan,
People’s Republic of China
| | - Ya-qin Wang (王亚琴)
- State Key Laboratory of Rice Biology, Institute of
Biotechnology, Zhejiang University, Hangzhou, People’s Republic of
China
| | - Muhammad Waqas
- Key Laboratory of Crop Disease Monitoring and Safety
Control in Hubei Province, College of Plant Science and Technology, Huazhong
Agricultural University, Wuhan, Hubei, People’s Republic of China
| | - Tàiyún Wèi (魏太云)
- Fujian Province Key Laboratory of Plant Virology,
Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou,
Fujian, People’s Republic of China
| | - Shaohua Wen (温少华)
- Key Lab of Plant Pathology of Hubei Province, College of
Plant Science and Technology, Huazhong Agricultural University, Wuhan,
People’s Republic of China
| | - Anna E. Whitfield
- Department of Entomology and Plant Pathology, North
Carolina State University, Raleigh, NC, USA
| | - John V. Williams
- School of Medicine, University of Pittsburgh,
Pittsburgh, PA, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National
Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jiang-xiang Wu (吴建祥)
- State Key Laboratory of Rice Biology, Institute of
Biotechnology, Zhejiang University, Hangzhou, People’s Republic of
China
| | - Lei Xu (徐雷)
- Jiangxi Academy of Agricultural Sciences, Nanchang,
Jiangxi, People’s Republic of China
| | | | - Caixia Yang (杨彩霞)
- College of Life Science and Engineering, Shenyang
University, Shenyang, Liaoning, People’s Republic of China
| | - Zuokun Yang (杨作坤)
- Key Lab of Plant Pathology of Hubei Province, College of
Plant Science and Technology, Huazhong Agricultural University, Wuhan,
People’s Republic of China
| | - F. Murilo Zerbini
- epartamento de Fitopatologia, Instituto de
Biotecnologia Aplicada à Agropecuária, Universidade Federal de
Viçosa, Viçosa, Minas Gerais, Brazil
| | - Lifeng Zhai (翟立峰)
- Key Laboratory of Horticultural Plant Biology, Ministry
of Education, Wuhan 430070, Hubei, People’s Republic of China
| | - Yong-Zhen Zhang
- National Institute for Communicable Disease Control and
Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing,
People’s Republic of China
- Shanghai Public Health Clinical Center & Institutes
of Biomedical Sciences, Fudan University, Shanghai, People’s Republic of
China
| | - Song Zhang (张松)
- National Citrus Engineering and Technology Research
Center, Citrus Research Institute, Southwest University, Beibei, Chongqing,
People’s Republic of China
| | - Jinguo Zhang (张靖国)
- National Sand Pear Germplasm Repository in Wuchang,
Research Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan,
Hubei, People’s Republic of China
| | - Zhe Zhang (张哲)
- Key Lab of Plant Pathology of Hubei Province, College of
Plant Science and Technology, Huazhong Agricultural University, Wuhan,
People’s Republic of China
| | - Xueping Zhou (周雪平)
- State Key Laboratory for Biology of Plant Diseases and
Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural
Sciences, Beijing, People’s Republic of China
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Kuhn JH, Adkins S, Agwanda BR, Al Kubrusli R, Alkhovsky SV, Amarasinghe GK, Avšič-Županc T, Ayllón MA, Bahl J, Balkema-Buschmann A, Ballinger MJ, Basler CF, Bavari S, Beer M, Bejerman N, Bennett AJ, Bente DA, Bergeron É, Bird BH, Blair CD, Blasdell KR, Blystad DR, Bojko J, Borth WB, Bradfute S, Breyta R, Briese T, Brown PA, Brown JK, Buchholz UJ, Buchmeier MJ, Bukreyev A, Burt F, Büttner C, Calisher CH, Cao M, Casas I, Chandran K, Charrel RN, Cheng Q, Chiaki Y, Chiapello M, Choi IR, Ciuffo M, Clegg JCS, Crozier I, Dal Bó E, de la Torre JC, de Lamballerie X, de Swart RL, Debat H, Dheilly NM, Di Cicco E, Di Paola N, Di Serio F, Dietzgen RG, Digiaro M, Dolnik O, Drebot MA, Drexler JF, Dundon WG, Duprex WP, Dürrwald R, Dye JM, Easton AJ, Ebihara H, Elbeaino T, Ergünay K, Ferguson HW, Fooks AR, Forgia M, Formenty PBH, Fránová J, Freitas-Astúa J, Fu J, Fürl S, Gago-Zachert S, Gāo GF, García ML, García-Sastre A, Garrison AR, Gaskin T, Gonzalez JPJ, Griffiths A, Goldberg TL, Groschup MH, Günther S, Hall RA, Hammond J, Han T, Hepojoki J, Hewson R, Hong J, Hong N, Hongo S, Horie M, Hu JS, Hu T, Hughes HR, Hüttner F, Hyndman TH, Ilyas M, Jalkanen R, Jiāng D, Jonson GB, Junglen S, Kadono F, Kaukinen KH, Kawate M, Klempa B, Klingström J, Kobinger G, Koloniuk I, Kondō H, Koonin EV, Krupovic M, Kubota K, Kurath G, Laenen L, Lambert AJ, Langevin SL, Lee B, Lefkowitz EJ, Leroy EM, Li S, Li L, Lǐ J, Liu H, Lukashevich IS, Maes P, de Souza WM, Marklewitz M, Marshall SH, Marzano SYL, Massart S, McCauley JW, Melzer M, Mielke-Ehret N, Miller KM, Ming TJ, Mirazimi A, Mordecai GJ, Mühlbach HP, Mühlberger E, Naidu R, Natsuaki T, Navarro JA, Netesov SV, Neumann G, Nowotny N, Nunes MRT, Olmedo-Velarde A, Palacios G, Pallás V, Pályi B, Papa A, Paraskevopoulou S, Park AC, Parrish CR, Patterson DA, Pauvolid-Corrêa A, Pawęska JT, Payne S, Peracchio C, Pérez DR, Postler TS, Qi L, Radoshitzky SR, Resende RO, Reyes CA, Rima BK, Luna GR, Romanowski V, Rota P, Rubbenstroth D, Rubino L, Runstadler JA, Sabanadzovic S, Sall AA, Salvato MS, Sang R, Sasaya T, Schulze AD, Schwemmle M, Shi M, Shí X, Shí Z, Shimomoto Y, Shirako Y, Siddell SG, Simmonds P, Sironi M, Smagghe G, Smither S, Song JW, Spann K, Spengler JR, Stenglein MD, Stone DM, Sugano J, Suttle CA, Tabata A, Takada A, Takeuchi S, Tchouassi DP, Teffer A, Tesh RB, Thornburg NJ, Tomitaka Y, Tomonaga K, Tordo N, Torto B, Towner JS, Tsuda S, Tu C, Turina M, Tzanetakis IE, Uchida J, Usugi T, Vaira AM, Vallino M, van den Hoogen B, Varsani A, Vasilakis N, Verbeek M, von Bargen S, Wada J, Wahl V, Walker PJ, Wang LF, Wang G, Wang Y, Wang Y, Waqas M, Wèi T, Wen S, Whitfield AE, Williams JV, Wolf YI, Wu J, Xu L, Yanagisawa H, Yang C, Yang Z, Zerbini FM, Zhai L, Zhang YZ, Zhang S, Zhang J, Zhang Z, Zhou X. 2021 Taxonomic update of phylum Negarnaviricota (Riboviria: Orthornavirae), including the large orders Bunyavirales and Mononegavirales. Arch Virol 2021; 166:3513-3566. [PMID: 34463877 PMCID: PMC8627462 DOI: 10.1007/s00705-021-05143-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In March 2021, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, and Gammarhabdovirinae), 42 genera, and 200 species. Thirty-nine species were renamed and/or moved and seven species were abolished. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.
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Affiliation(s)
- Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA.
| | - Scott Adkins
- United States Department of Agriculture, Agricultural Research Service, US Horticultural Research Laboratory, Fort Pierce, FL, USA
| | - Bernard R Agwanda
- Zoology Department, National Museums of Kenya, Nairobi, Kenya
- Jomo Kenyatta University of Agriculture & Technology, Nairobi, Kenya
| | - Rim Al Kubrusli
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sergey V Alkhovsky
- D.I. Ivanovsky Institute of Virology of N.F. Gamaleya National Center on Epidemiology and Microbiology of Ministry of Health of Russian Federation, Moscow, Russia
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | | | - María A Ayllón
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, Department of Epidemiology and Biostatistics, Insitute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Anne Balkema-Buschmann
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany
| | - Matthew J Ballinger
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Christopher F Basler
- Center for Microbial Pathogenesis, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Sina Bavari
- Edge BioInnovation Consulting and Mgt, Frederick, MD, USA
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | | | - Andrew J Bennett
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD, USA
| | | | - Éric Bergeron
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Brian H Bird
- School of Veterinary Medicine, One Health Institute, University of California, Davis, Davis, CA, USA
| | - Carol D Blair
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Kim R Blasdell
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australian Centre for Disease Preparedness, Geelong, VIC, Australia
| | | | - Jamie Bojko
- School of Health and Life Sciences, Teesside University, Middlesbrough, TS1 3BX, UK
- National Horizons Centre, Teesside University, Darlington, DL1 1HG, UK
| | | | - Steven Bradfute
- University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Rachel Breyta
- University of Washington, Seattle, WA, USA
- US Geological Survey, Western Fisheries Research Center, Seattle, WA, USA
| | - Thomas Briese
- Center for Infection and Immunity, and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Paul A Brown
- Laboratory of Ploufragan-Plouzané-Niort, French Agency for Food, Environmental and Occupational Heath Safety ANSES, Ploufragan, France
| | - Judith K Brown
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Ursula J Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael J Buchmeier
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, USA
| | - Alexander Bukreyev
- Galveston National Laboratory, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Felicity Burt
- Division of Virology, National Health Laboratory Service and Division of Virology, University of the Free State, Bloemfontein, Republic of South Africa
| | - Carmen Büttner
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, People's Republic of China
| | - Inmaculada Casas
- Respiratory Virus and Influenza Unit, National Microbiology Center, Instituto de Salud Carlos III, Madrid, Spain
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rémi N Charrel
- Unité des Virus Emergents (Aix-Marseille Univ, IRD 190, Inserm 1207, IHU Méditerranée Infection), Marseille, France
| | - Qi Cheng
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Yuya Chiaki
- Grape and Persimmon Research Station, Institute of Fruit tree and Tea Science, NARO, Higashihiroshima, Hiroshima, Japan
| | - Marco Chiapello
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Il-Ryong Choi
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Baños, Philippines
| | - Marina Ciuffo
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | | | - Ian Crozier
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Elena Dal Bó
- CIDEFI, Facultad de Ciencias Agrarias y Forestales, Universidad de La Plata, La Plata, Argentina
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology IMM-6, The Scripps Research Institute, La Jolla, CA, USA
| | - Xavier de Lamballerie
- Unité des Virus Emergents (Aix-Marseille Univ, IRD 190, Inserm 1207, IHU Méditerranée Infection), Marseille, France
| | - Rik L de Swart
- Department Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Humberto Debat
- Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnología Agropecuaria (IPAVE-CIAP-INTA), Córdoba, Argentina
- Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas (UFYMA-CONICET), Córdoba, Argentina
| | - Nolwenn M Dheilly
- UMR 1161 Virology ANSES/INRAE/ENVA, ANSES Animal Health Laboratory, 94704, Maisons-Alfort, France
| | | | - Nicholas Di Paola
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Michele Digiaro
- CIHEAM, Istituto Agronomico Mediterraneo di Bari, Valenzano, Italy
| | - Olga Dolnik
- Institute of Virology, Philipps University Marburg, Marburg, Germany
| | - Michael A Drebot
- Zoonotic Diseases and Special Pathogens, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - J Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität Berlin, Berlin, Germany
| | - William G Dundon
- Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Department of Nuclear Sciences and Applications, International Atomic Energy Agency, Vienna, Austria
| | - W Paul Duprex
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - John M Dye
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Andrew J Easton
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hideki Ebihara
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | - Koray Ergünay
- Virology Unit, Department of Medical Microbiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Hugh W Ferguson
- School of Veterinary Medicine, St. George's University, True Blue, Grenada
| | | | - Marco Forgia
- Institute for sustainable plant protection, CNR, Turin, Italy
| | | | - Jana Fránová
- Plant Virology Department, Institute of Plant Molecular Biology, Biology Centre CAS, Ceske Budejovice, Czech Republic
| | | | - Jingjing Fu
- College of Life Science and Engineering, Shenyang University, Shenyang, Liaoning, People's Republic of China
| | - Stephanie Fürl
- Albrecht Daniel Thaer-Institute for Crop and Animal Sciences, Division Phytomedicine, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Selma Gago-Zachert
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - George Fú Gāo
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - María Laura García
- nstituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, I, CONICET UNLP, La Plata, Argentina
| | | | - Aura R Garrison
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Thomas Gaskin
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
- Landwirtschaft und Flurneuordnung, Landesamt für ländliche Entwicklung, Frankfurt (Oder), Germany
| | - Jean-Paul J Gonzalez
- Department of Microbiology and Immunology, Division of Biomedical Graduate Research Organization, School of Medicine, Georgetown University, Washington, DC, 20057, USA
- Centaurus Biotechnologies, CTP, Manassas, VA, USA
| | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Martin H Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Stephan Günther
- WHO Collaborating Centre for Arboviruses and Hemorrhagic Fever Reference and Research, Department of Virology, Bernhard-Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Roy A Hall
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - John Hammond
- Floral and Nursery Plants Research Unit, United States Department of Agriculture, Agricultural Research Service, USNA, Beltsville, MD, USA
| | - Tong Han
- College of Life Science and Engineering, Shenyang University, Shenyang, Liaoning, People's Republic of China
| | - Jussi Hepojoki
- Department of Virology, University of Helsinki, Medicum, Helsinki, Finland
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Roger Hewson
- London School of Hygeine and Tropical Medicine, London, UK
| | - Jiang Hong
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou, People's Republic of China
| | - Ni Hong
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Seiji Hongo
- Department of Infectious Diseases, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Masayuki Horie
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
- Division of Veterinary Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Japan
| | - John S Hu
- University of Hawaii, Honolulu, HI, USA
| | - Tao Hu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Holly R Hughes
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | - Florian Hüttner
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Timothy H Hyndman
- School of Veterinary Medicine, Murdoch University, Murdoch, WA, Australia
| | - M Ilyas
- Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | | | - Dàohóng Jiāng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei Province, People's Republic of China
| | - Gilda B Jonson
- Rice Breeding Innovations Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Sandra Junglen
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
- German Centre for Infection Research, Berlin, Germany
| | - Fujio Kadono
- Department of Clinical Plant Science, Faculty of Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo, Japan
| | - Karia H Kaukinen
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | | | - Boris Klempa
- Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jonas Klingström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Gary Kobinger
- Department of Microbiology, Immunology and Infectious Diseases, Université Laval, Quebec City, Canada
| | - Igor Koloniuk
- Plant Virology Department, Institute of Plant Molecular Biology, Biology Centre CAS, Ceske Budejovice, Czech Republic
| | - Hideki Kondō
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Paris, France
| | - Kenji Kubota
- Central Region Agricultural Research Center, NARO, Tsukuba, Ibaraki, Japan
| | - Gael Kurath
- US Geological Survey Western Fisheries Research Center, Seattle, WA, USA
| | - Lies Laenen
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases unit, Leuven, Belgium
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Amy J Lambert
- Centers for Disease Control and Prevention, Fort Collins, CO, USA
| | | | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Eric M Leroy
- MIVEGEC (IRD-CNRS-Montpellier university) Unit, French National Research Institute for Sustainable Development (IRD), Montpellier, France
| | - Shaorong Li
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC, V9T 6N7, Canada
| | - Longhui Li
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Jiànróng Lǐ
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Huazhen Liu
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Igor S Lukashevich
- Department of Pharmacology and Toxicology, School of Medicine, and the Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - Piet Maes
- KU Leuven, Rega Institute, Zoonotic Infectious Diseases unit, Leuven, Belgium
| | | | - Marco Marklewitz
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Free University Berlin, Humboldt-University Berlin, and Berlin Institute of Health, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
| | - Sergio H Marshall
- Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Shin-Yi L Marzano
- United States Department of Agriculture, Agricultural Research Service , Washington, USA
| | - Sebastien Massart
- Gembloux Agro-Bio Tech, TERRA, Plant Pathology Laboratory, Liège University, Liege, Belgium
| | - John W McCauley
- Worldwide Influenza Centre, Francis Crick Institute, London, UK
| | - Michael Melzer
- Plant and Environmental Protection Sciences, University of Hawai'i at Mānoa, Honolulu, HI, USA
| | | | - Kristina M Miller
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Tobi J Ming
- Molecular Genetics, Pacific Biological Station, Department of Fisheries and Oceans, Nanaimo, Canada
| | | | - Gideon J Mordecai
- Department of Medicine, Univeristy of British Columbia, Vancouver, Canada
| | | | - Elke Mühlberger
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA, USA
| | - Rayapati Naidu
- Department of Plant Pathology, Irrigated Agricultural Research and Extension Center, Washington State University, Prosser, WA, USA
| | - Tomohide Natsuaki
- School of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, Japan
| | - José A Navarro
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Sergey V Netesov
- Novosibirsk State University, Novosibirsk, Novosibirsk Oblast, Russia
| | - Gabriele Neumann
- Influenza Research Institute, Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Norbert Nowotny
- Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | | | - Gustavo Palacios
- United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Vicente Pallás
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Cientificas-Universidad Politécnica de Valencia, Valencia, Spain
| | - Bernadett Pályi
- National Biosafety Laboratory, National Public Health Center, Budapest, Hungary
| | - Anna Papa
- National Reference Centre for Arboviruses and Haemorrhagic Fever Viruses, Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sofia Paraskevopoulou
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Adam C Park
- University of Hawaii, Honolulu, HI, USA
- Hawaii Department of Agriculture, Honolulu, HI, USA
| | - Colin R Parrish
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - David A Patterson
- Fisheries and Oceans Canada, Resource and Environmental Management, Simon Fraser University, Burnaby, BC, Canada
| | - Alex Pauvolid-Corrêa
- Department of Veterinary Integrated Biosciences and Department of Entomology, Texas A&M University, College Station, USA
- Laboratory of Respiratory Viruses and Measles, Fiocruz, Rio de Janeiro, Brazil
| | - Janusz T Pawęska
- Center for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham-Johannesburg, Gauteng, South Africa
| | - Susan Payne
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Carlotta Peracchio
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Daniel R Pérez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Thomas S Postler
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Liying Qi
- Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, People's Republic of China
| | | | - Renato O Resende
- Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brazil
| | - Carina A Reyes
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Bertus K Rima
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, Northern Ireland, UK
| | - Gabriel Robles Luna
- Instituto de Biotecnología y Biología Molecular, CCT-La Plata, CONICET-UNLP, La Plata, Buenos Aires, Argentina
| | - Víctor Romanowski
- Instituto de Biotecnología y Biología Molecular, Centro Cientifico Technológico-La Plata, Consejo Nacional de Investigaciones Científico Tecnológico-Universidad Nacional de La Plata, La Plata, Argentina
| | - Paul Rota
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dennis Rubbenstroth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Luisa Rubino
- Consiglio Nazionale delle Ricerche, Istituto per la Protezione Sostenibile delle Piante, Bari, Italy
| | - Jonathan A Runstadler
- Department of Infectious Disease and Global Health, Tufts University Cummings School of Veterinary Medicine, 200 Westboro Road, North Grafton, MA, 01536, USA
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | | | - Maria S Salvato
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MA, USA
| | - Rosemary Sang
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Takahide Sasaya
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Angela D Schulze
- Molecular Genetics Lab, Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Martin Schwemmle
- Faculty of Medicine, University Medical Center-University Freiburg, Freiburg, Germany
| | - Mang Shi
- Sun Yat-sen University, Shenzhen, People's Republic of China
| | - Xiǎohóng Shí
- MRC-University of Glasgow Centre for Virus Research, Glasgow, Scotland, UK
| | - Zhènglì Shí
- CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| | | | - Yukio Shirako
- Asian Center for Bioresources and Environmental Sciences, University of Tokyo, Tokyo, Japan
| | - Stuart G Siddell
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Manuela Sironi
- Bioinformatics Unit, Scientific Institute IRCCS "E. Medea", Bosisio Parini, Italy
| | - Guy Smagghe
- Faculty of Bioscience Engineering, Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Sophie Smither
- CBR Division, DSTL, Porton Down, Salisbury, Wiltshire, UK
| | - Jin-Won Song
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Kirsten Spann
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Jessica R Spengler
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, USA
| | - Mark D Stenglein
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - David M Stone
- Centre for Environment, Fisheries and Aquaculture Science, Weymouth, Dorset, UK
| | | | - Curtis A Suttle
- Departments of Earth, Ocean and Atmospheric Sciences, Microbiology and Immunology, and Botany, and the Institute for Oceans and Fisheries, University of British Columbia, Vancouver, Canada
| | - Amy Tabata
- Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, BC, Canada
| | - Ayato Takada
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Shigeharu Takeuchi
- Japan Plant Protection Association Kochi Experiment Station, Konan, Kochi, Japan
| | - David P Tchouassi
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Amy Teffer
- Department of Forest Sciences, University of British Columbia, Vancouver, Canada
| | - Robert B Tesh
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | | | - Yasuhiro Tomitaka
- Kyushu Okinawa Agricultural Research Center, NARO, Koshi, Kumamoto, Japan
| | - Keizō Tomonaga
- Institute for Frontier Life and Medical Sciences (inFront), , Kyoto University, Kyoto, Japan
| | - Noël Tordo
- Unité des Stratégies Antivirales, WHO Collaborative Centre for Viral Haemorrhagic Fevers and Arboviruses, OIE Reference Laboratory for RVFV & CCHFV, Institut Pasteur, Paris, France
| | - Baldwyn Torto
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Jonathan S Towner
- Viral Special Pathogens Branch, Division of High-Consequence Pathogens Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Institut Pasteur de Guinée, Conakry, Guinea
| | - Shinya Tsuda
- Department of Clinical Plant Science, Faculty of Bioscience and Applied Chemistry, Hosei University, Koganei, Tokyo, Japan
| | - Changchun Tu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin Province, People's Republic of China
| | - Massimo Turina
- National Institute of Optics, National Research Council of Italy (INO-CNR), Via Branze 45, 25123Brescia, Italy
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System,, Fayetteville, AR, 72701, USA
| | | | - Tomio Usugi
- Central Region Agricultural Research Center, NARO, Tsukuba, Ibaraki, Japan
| | - Anna Maria Vaira
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Marta Vallino
- Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Strada delle Cacce 73, 10135, Turin, Italy
| | - Bernadette van den Hoogen
- Department of Viroscience, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Nikos Vasilakis
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Martin Verbeek
- Wageningen University and Research, Biointeractions and Plant Health, Wageningen, The Netherlands
| | - Susanne von Bargen
- Division Phytomedicine, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jiro Wada
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, USA
| | - Victoria Wahl
- National Biodefense Analysis and Countermeasures Center, Fort Detrick, Frederick, MD, USA
| | - Peter J Walker
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD, Australia
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Guoping Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yanxiang Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Muhammad Waqas
- Key Laboratory of Crop Disease Monitoring and Safety Control in Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People's Republic of China
| | - Tàiyún Wèi
- Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, People's Republic of China
| | - Shaohua Wen
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - John V Williams
- School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Jiangxiang Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Lei Xu
- Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, People's Republic of China
| | | | - Caixia Yang
- College of Life Science and Engineering, Shenyang University, Shenyang, Liaoning, People's Republic of China
| | - Zuokun Yang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - F Murilo Zerbini
- Departamento de Fitopatologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Lifeng Zhai
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Wuhan, 430070, Hubei , People's Republic of China
| | - Yong-Zhen Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, People's Republic of China
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
| | - Song Zhang
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, People's Republic of China
| | - Jinguo Zhang
- National Sand Pear Germplasm Repository in Wuchang, Research Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, Hubei, People's Republic of China
| | - Zhe Zhang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
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Dutilh BE, Varsani A, Tong Y, Simmonds P, Sabanadzovic S, Rubino L, Roux S, Muñoz AR, Lood C, Lefkowitz EJ, Kuhn JH, Krupovic M, Edwards RA, Brister JR, Adriaenssens EM, Sullivan MB. Perspective on taxonomic classification of uncultivated viruses. Curr Opin Virol 2021; 51:207-215. [PMID: 34781105 DOI: 10.1016/j.coviro.2021.10.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 12/19/2022]
Abstract
Historically, virus taxonomy has been limited to describing viruses that were readily cultivated in the laboratory or emerging in natural biomes. Metagenomic analyses, single-particle sequencing, and database mining efforts have yielded new sequence data on an astounding number of previously unknown viruses. As metagenomes are relatively free of biases, these data provide an unprecedented insight into the vastness of the virosphere, but to properly value the extent of this diversity it is critical that the viruses are taxonomically classified. Inclusion of uncultivated viruses has already improved the process as well as the understanding of the taxa, viruses, and their evolutionary relationships. The continuous development and testing of computational tools will be required to maintain a dynamic virus taxonomy that can accommodate the new discoveries.
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Affiliation(s)
- Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands; Institute of Bioloversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, 07743, Jena, Germany.
| | - Arvind Varsani
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA; Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, 7925, Cape Town, South Africa
| | - Yigang Tong
- Beijing Advanced Innovation Centre for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Peter Medawar Building, South Parks Road, Oxford, OX1 3SY, UK
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, MS 39762, USA
| | - Luisa Rubino
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alejandro Reyes Muñoz
- Max Planck Tandem Group in Computational Biology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Cédric Lood
- Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 23, 3001, Leuven, Belgium; Department of Biosystems, KU Leuven, Willem de Croylaan 42, 3001, Leuven, Belgium
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, USA
| | - Mart Krupovic
- Institut Pasteur, Université de Paris, Archaeal Virology Unit, F-75015, Paris, France
| | - Robert A Edwards
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda MD 20894, USA
| | | | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH, USA
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44
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Benschop KS, Albert J, Anton A, Andrés C, Aranzamendi M, Armannsdóttir B, Bailly JL, Baldanti F, Baldvinsdóttir GE, Beard S, Berginc N, Böttcher S, Blomqvist S, Bubba L, Calvo C, Cabrerizo M, Cavallero A, Celma C, Ceriotti F, Costa I, Cottrell S, Del Cuerpo M, Dean J, Dembinski JL, Diedrich S, Diez-Domingo J, Dorenberg D, Duizer E, Dyrdak R, Fanti D, Farkas A, Feeney S, Flipse J, De Gascun C, Galli C, Georgieva I, Gifford L, Guiomar R, Hönemann M, Ikonen N, Jeannoël M, Josset L, Keeren K, López-Labrador FX, Maier M, McKenna J, Meijer A, Mengual-Chuliá B, Midgley SE, Mirand A, Montes M, Moore C, Morley U, Murk JL, Nikolaeva-Glomb L, Numanovic S, Oggioni M, Palminha P, Pariani E, Pellegrinelli L, Piralla A, Pietsch C, Piñeiro L, Rabella N, Rainetova P, Uceda Renteria SC, Romero MP, Reynders M, Roorda L, Savolainen-Kopra C, Schuffenecker I, Soynova A, Swanink CM, Ursic T, Verweij JJ, Vila J, Vuorinen T, Simmonds P, Fischer TK, Harvala H. Re-emergence of enterovirus D68 in Europe after easing the COVID-19 lockdown, September 2021. ACTA ACUST UNITED AC 2021; 26. [PMID: 34763750 PMCID: PMC8646978 DOI: 10.2807/1560-7917.es.2021.26.45.2100998] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We report a rapid increase in enterovirus D68 (EV-D68) infections, with 139 cases reported from eight European countries between 31 July and 14 October 2021. This upsurge is in line with the seasonality of EV-D68 and was presumably stimulated by the widespread reopening after COVID-19 lockdown. Most cases were identified in September, but more are to be expected in the coming months. Reinforcement of clinical awareness, diagnostic capacities and surveillance of EV-D68 is urgently needed in Europe.
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Affiliation(s)
- Kimberley Sm Benschop
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Jan Albert
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Andres Anton
- Respiratory Virus Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Cristina Andrés
- Respiratory Virus Unit, Microbiology Department, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Maitane Aranzamendi
- Microbiology Department, Donostia University Hospital and Biodonostia Health Research Institute, San Sebastián, Spain
| | | | - Jean-Luc Bailly
- Université d'Auvergne, LMGE UMR CNRS 6023, Equipe EPIE - Epidémiologie et physiopathologie des infections à entérovirus, Faculté de Médecine, Clermont-Ferrand, France.,CHU Clermont-Ferrand, National Reference Centre for enteroviruses and parechoviruses - Associated laboratory, Clermont-Ferrand, France
| | - Fausto Baldanti
- Department of Clinical Surgical Diagnostic and Pediatric Sciences, Università degli Studi di Pavia, Pavia, Italy.,Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Italy
| | | | - Stuart Beard
- UK Health Security Agency, Colindale, United Kingdom
| | - Natasa Berginc
- National laboratory of health, environment and food, Laboratory for public health virology, Ljubljana, Slovenia
| | - Sindy Böttcher
- National Reference Center for Poliomyelitis and Enteroviruses, Robert-Koch Institute, Berlin, Germany
| | - Soile Blomqvist
- National Institute for Health and Welfare, Helsinki, Finland
| | - Laura Bubba
- Department of Biomedical Sciences of Health, University of Milan, Milan, Italy
| | | | - Maria Cabrerizo
- National Centre for Microbiology, Instituto de Salud Carlos III, Enterovirus and Viral Gastroenteritis Unit/Polio National Lab, Madrid, Spain
| | - Annalisa Cavallero
- Laboratory of Microbiology, ASST Monza, San Gerardo Hospital, Monza (MB), Italy
| | | | - Ferruccio Ceriotti
- Virology Unit, Division of Clinical Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Inês Costa
- National Institute of Health (INSA), Lisbon, Portugal
| | | | - Margarita Del Cuerpo
- Microbiology Department Hospital Universitari de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jonathan Dean
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | | | - Sabine Diedrich
- National Reference Center for Poliomyelitis and Enteroviruses, Robert-Koch Institute, Berlin, Germany
| | - Javier Diez-Domingo
- Center for Public Health Research (FISABIO-Public Health), Generalitat Valenciana, Valencia, Spain
| | | | - Erwin Duizer
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Robert Dyrdak
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Diana Fanti
- Chemical-clinical and Microbiological Analyses, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Agnes Farkas
- National Public Health Center, Budapest, Hungary
| | - Susan Feeney
- Regional Virus Laboratory, Belfast Health and Social Care Trust (BHSCT, Royal Victoria Hospital, Belfast, United Kingdom
| | - Jacky Flipse
- Laboratory for Medical Microbiology and Immunology, Rijnstate, Velp, the Netherlands
| | - Cillian De Gascun
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Cristina Galli
- Department of Biomedical Sciences of Health, University of Milan, Milan, Italy
| | - Irina Georgieva
- National Reference Laboratory for Enteroviruses, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | | | | | - Mario Hönemann
- Institute of Medical Microbiology and Virology, University of Leipzig, Leipzig, Germany
| | - Niina Ikonen
- National Institute for Health and Welfare, Helsinki, Finland
| | - Marion Jeannoël
- National Reference Center for Enteroviruses and Parechoviruses, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Laurence Josset
- National Reference Center for Enteroviruses and Parechoviruses, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Kathrin Keeren
- Secretary of the commission for Polio Eradication in Germany, Robert-Koch Institute, Berlin, Germany
| | - F Xavier López-Labrador
- CIBERESP, Instituto de Salud Carlos III, Madrid, Spain.,Center for Public Health Research (FISABIO-Public Health), Generalitat Valenciana, Valencia, Spain
| | - Melanie Maier
- Institute of Medical Microbiology and Virology, University of Leipzig, Leipzig, Germany
| | - James McKenna
- Regional Virus Laboratory, Belfast Health and Social Care Trust (BHSCT, Royal Victoria Hospital, Belfast, United Kingdom
| | - Adam Meijer
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Beatriz Mengual-Chuliá
- Center for Public Health Research (FISABIO-Public Health), Generalitat Valenciana, Valencia, Spain
| | - Sofie E Midgley
- The Danish WHO National Reference Laboratory for Poliovirus, Statens Serum Institut, Copenhagen, Denmark
| | - Audrey Mirand
- Université d'Auvergne, LMGE UMR CNRS 6023, Equipe EPIE - Epidémiologie et physiopathologie des infections à entérovirus, Faculté de Médecine, Clermont-Ferrand, France.,CHU Clermont-Ferrand, National Reference Centre for enteroviruses and parechoviruses - Associated laboratory, Clermont-Ferrand, France
| | - Milagrosa Montes
- Microbiology Department, Donostia University Hospital and Biodonostia Health Research Institute, San Sebastián, Spain
| | | | - Ursula Morley
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - Jean-Luc Murk
- Elisabeth Tweesteden Hospital, Tilburg, the Netherlands
| | - Lubomira Nikolaeva-Glomb
- National Reference Laboratory for Enteroviruses, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Sanela Numanovic
- Department of Virology, Norwegian Institute of Public Health, Oslo, Norway
| | - Massimo Oggioni
- Virology Unit, Division of Clinical Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Elena Pariani
- Department of Biomedical Sciences of Health, University of Milan, Milan, Italy
| | - Laura Pellegrinelli
- Department of Biomedical Sciences of Health, University of Milan, Milan, Italy
| | - Antonio Piralla
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Italy
| | - Corinna Pietsch
- Institute of Medical Microbiology and Virology, University of Leipzig, Leipzig, Germany
| | - Luis Piñeiro
- Microbiology Department, Donostia University Hospital and Biodonostia Health Research Institute, San Sebastián, Spain
| | - Núria Rabella
- Microbiology Department Hospital Universitari de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Sara Colonia Uceda Renteria
- Virology Unit, Division of Clinical Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - María P Romero
- Department of Biomedical Sciences of Health, University of Milan, Milan, Italy
| | | | | | | | - Isabelle Schuffenecker
- National Reference Center for Enteroviruses and Parechoviruses, Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Aysa Soynova
- National Reference Laboratory for Enteroviruses, National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Caroline Ma Swanink
- Laboratory for Medical Microbiology and Immunology, Rijnstate, Velp, the Netherlands
| | - Tina Ursic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | | | - Jorgina Vila
- Pediatric Hospitalization Unit, Department of Pediatrics, Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Tytti Vuorinen
- Clinical Microbiology, Turku University Hospital and Institute of Biomedicine, University of Turku, Turku, Finland
| | | | - Thea K Fischer
- Nordsjaellands Hospital, Hillerod, Denmark.,University of Sothern Denmark, Odense, Denmark
| | - Heli Harvala
- University College London (UCL), Department of infection and Immunity, London, United Kingdom.,NHS Blood and Transplant, Microbiology Services, Colindale, United Kingdom
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45
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Cunningham L, Kimber I, Basketter D, Simmonds P, McSweeney S, Tziotzios C, McFadden JP. Perforin, COVID-19 and a possible pathogenic auto-inflammatory feedback loop. Scand J Immunol 2021; 94:e13102. [PMID: 34755902 PMCID: PMC8646999 DOI: 10.1111/sji.13102] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/31/2021] [Accepted: 09/07/2021] [Indexed: 12/23/2022]
Abstract
During COVID‐19 infection, reduced function of natural killer (NK) cells can lead to both compromised viral clearance and dysregulation of the immune response. Such dysregulation leads to overproduction of cytokines, a raised neutrophil/lymphocyte ratio and monocytosis. This in turn increases IL‐6 expression, which promotes scar and thrombus formation. Excess IL‐6 also leads to a further reduction in NK function through downregulation of perforin expression, therefore forming a pathogenic auto‐inflammatory feedback loop. The perforin/granzyme system of cytotoxicity is the main mechanism through which NK cells and cytotoxic T lymphocytes eliminate virally infected host cells, as well as being central to their role in regulating immune responses to microbial infection. Here, we present epidemiological evidence suggesting an association between perforin expression and resistance to COVID‐19. In addition, we outline the manner in which a pathogenic auto‐inflammatory feedback loop could operate and the relationship of this loop to genes associated with severe COVID‐19. Such an auto‐inflammatory loop may be amenable to synergistic multimodal therapy.
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Affiliation(s)
- Louise Cunningham
- St. John's Institute of Dermatology, Guy's and St Thomas' Hospital, London, UK
| | - Ian Kimber
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | | | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sheila McSweeney
- St. John's Institute of Dermatology, Guy's and St Thomas' Hospital, London, UK
| | - Christos Tziotzios
- St. John's Institute of Dermatology, Guy's and St Thomas' Hospital, London, UK
| | - John P McFadden
- St. John's Institute of Dermatology, Guy's and St Thomas' Hospital, London, UK
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46
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Nguyen D, Xiao J, Simmonds P, Lamikanra A, Odon V, Ratcliff J, Townsend A, Roberts DJ, Harvala H. Effects of SARS-CoV-2 strain variation on virus neutralisation titres: therapeutic use of convalescent plasma. J Infect Dis 2021; 225:971-976. [PMID: 34751775 PMCID: PMC8689936 DOI: 10.1093/infdis/jiab563] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Abstract
We compared neutralising antibody titres of convalescent samples collected before and after the emergence of novel strains of SARS-CoV-2, against the wild-type virus (WT), Alpha (B.1.1.7) and Beta (B.1.351) variants. Plasma collected in 2020 before emergence of variants showed reduced titres against the Alpha variants, and both sets of samples demonstrated significantly reduced titres against Beta. Comparison of microneutralisation titres to those obtained with pseudotype and HAT assays showed a good correlation of titres and effects of strain variation, supporting the use of these simpler assays for assessment of convalescent plasma potency against currently circulating and emerging strains of SARS-CoV-2.
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Affiliation(s)
- Dung Nguyen
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Julie Xiao
- MRC Human Immunology Unit, MRC Weatherall Institute, Radcliffe Department of Medicine, John Radcliffe Hospital, Oxford, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | | | - Valerie Odon
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Jeremy Ratcliff
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Alain Townsend
- MRC Human Immunology Unit, MRC Weatherall Institute, Radcliffe Department of Medicine, John Radcliffe Hospital, Oxford, UK.,Chinese Academy of Medical Science, Oxford Institute, University of Oxford, Oxford, UK
| | - David J Roberts
- Clinical Services, NHS Blood and Transplant, Oxford, UK.,Radcliffe Department of Medicine and BRC Haematology Theme, University of Oxford, Oxford, UK
| | - Heli Harvala
- Chinese Academy of Medical Science, Oxford Institute, University of Oxford, Oxford, UK.,Microbiology Services, NHS Blood and Transplant, Colindale, UK
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47
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Ghafari M, Simmonds P, Pybus OG, Katzourakis A. A mechanistic evolutionary model explains the time-dependent pattern of substitution rates in viruses. Curr Biol 2021; 31:4689-4696.e5. [PMID: 34478645 PMCID: PMC8585505 DOI: 10.1016/j.cub.2021.08.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/02/2021] [Accepted: 08/05/2021] [Indexed: 01/16/2023]
Abstract
Estimating viral timescales is fundamental in understanding the evolutionary biology of viruses. Molecular clocks are widely used to reveal the recent evolutionary histories of viruses but may severely underestimate their longer-term origins because of the inverse correlation between inferred rates of evolution and the timescale of their measurement. Here, we provide a predictive mechanistic model that readily explains the rate decay phenomenon over a wide range of timescales and recapitulates the ubiquitous power-law rate decay with a slope of -0.65. We show that standard substitution models fail to correctly estimate divergence times once the most rapidly evolving sites saturate, typically after hundreds of years in RNA viruses and thousands of years in DNA viruses. Our model successfully recreates the observed pattern of decay and explains the evolutionary processes behind the time-dependent rate phenomenon. We then apply our model to re-estimate the date of diversification of genotypes of hepatitis C virus to 423,000 (95% highest posterior density [HPD]: 394,000-454,000) years before present, a time preceding the dispersal of modern humans out of Africa, and show that the most recent common ancestor of sarbecoviruses dates back to 21,000 (95% HPD: 19,000-22,000) years ago, nearly thirty times older than previous estimates. This creates a new perspective for our understanding of the origins of these viruses and also suggests that a substantial revision of evolutionary timescales of other viruses can be similarly achieved.
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Affiliation(s)
- Mahan Ghafari
- Department of Zoology, University of Oxford, Oxford, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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48
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Liu Y, Demina TA, Roux S, Aiewsakun P, Kazlauskas D, Simmonds P, Prangishvili D, Oksanen HM, Krupovic M. Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes. PLoS Biol 2021; 19:e3001442. [PMID: 34752450 PMCID: PMC8651126 DOI: 10.1371/journal.pbio.3001442] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 12/07/2021] [Accepted: 10/17/2021] [Indexed: 11/19/2022] Open
Abstract
The archaeal tailed viruses (arTV), evolutionarily related to tailed double-stranded DNA (dsDNA) bacteriophages of the class Caudoviricetes, represent the most common isolates infecting halophilic archaea. Only a handful of these viruses have been genomically characterized, limiting our appreciation of their ecological impacts and evolution. Here, we present 37 new genomes of haloarchaeal tailed virus isolates, more than doubling the current number of sequenced arTVs. Analysis of all 63 available complete genomes of arTVs, which we propose to classify into 14 new families and 3 orders, suggests ancient divergence of archaeal and bacterial tailed viruses and points to an extensive sharing of genes involved in DNA metabolism and counterdefense mechanisms, illuminating common strategies of virus-host interactions with tailed bacteriophages. Coupling of the comparative genomics with the host range analysis on a broad panel of haloarchaeal species uncovered 4 distinct groups of viral tail fiber adhesins controlling the host range expansion. The survey of metagenomes using viral hallmark genes suggests that the global architecture of the arTV community is shaped through recurrent transfers between different biomes, including hypersaline, marine, and anoxic environments.
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Affiliation(s)
- Ying Liu
- Institut Pasteur, Université de Paris, Archaeal Virology Unit, Paris, France
| | - Tatiana A. Demina
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Pakorn Aiewsakun
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Darius Kazlauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - David Prangishvili
- Institut Pasteur, Université de Paris, Archaeal Virology Unit, Paris, France
- Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Mart Krupovic
- Institut Pasteur, Université de Paris, Archaeal Virology Unit, Paris, France
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49
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Smith DA, Fernandez-Antunez C, Magri A, Bowden R, Chaturvedi N, Fellay J, McLauchlan J, Foster GR, Irving WL, Simmonds P, Pedergnana V, Ramirez S, Bukh J, Barnes E, Ansari MA. Viral genome wide association study identifies novel hepatitis C virus polymorphisms associated with sofosbuvir treatment failure. Nat Commun 2021; 12:6105. [PMID: 34671027 PMCID: PMC8528821 DOI: 10.1038/s41467-021-25649-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/11/2021] [Indexed: 12/12/2022] Open
Abstract
Persistent hepatitis C virus (HCV) infection is a major cause of chronic liver disease, worldwide. With the development of direct-acting antivirals, treatment of chronically infected patients has become highly effective, although a subset of patients responds less well to therapy. Sofosbuvir is a common component of current de novo or salvage combination therapies, that targets the HCV NS5B polymerase. We use pre-treatment whole-genome sequences of HCV from 507 patients infected with HCV subtype 3a and treated with sofosbuvir containing regimens to detect viral polymorphisms associated with response to treatment. We find three common polymorphisms in non-targeted HCV NS2 and NS3 proteins are associated with reduced treatment response. These polymorphisms are enriched in post-treatment HCV sequences of patients unresponsive to treatment. They are also associated with lower reductions in viral load in the first week of therapy. Using in vitro short-term dose-response assays, these polymorphisms do not cause any reduction in sofosbuvir potency, suggesting an indirect mechanism of action in decreasing sofosbuvir efficacy. The identification of polymorphisms in NS2 and NS3 proteins associated with poor treatment outcomes emphasises the value of systematic genome-wide analyses of viruses in uncovering clinically relevant polymorphisms that impact treatment.
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Affiliation(s)
- David A Smith
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 1SY, UK
| | - Carlota Fernandez-Antunez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrea Magri
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 1SY, UK
| | - Rory Bowden
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Nimisha Chaturvedi
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Precision Medicine Unit, University Hospital and University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - John McLauchlan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, G61 1QH, UK
| | - Graham R Foster
- Barts Liver Centre, Blizard Institute, Queen Mary University of London, London, UK
| | - William L Irving
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, UK
| | - Peter Simmonds
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 1SY, UK
| | | | - Santseharay Ramirez
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Eleanor Barnes
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 1SY, UK
| | - M Azim Ansari
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 1SY, UK.
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
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50
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Clemens SAC, Folegatti PM, Emary KRW, Weckx LY, Ratcliff J, Bibi S, De Almeida Mendes AV, Milan EP, Pittella A, Schwarzbold AV, Sprinz E, Aley PK, Bonsall D, Fraser C, Fuskova M, Gilbert SC, Jenkin D, Kelly S, Kerridge S, Lambe T, Marchevsky NG, Mujadidi YF, Plested E, Ramasamy MN, Simmonds P, Golubchik T, Voysey M, Pollard AJ. Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil. Nat Commun 2021; 12:5861. [PMID: 34615860 PMCID: PMC8494913 DOI: 10.1038/s41467-021-25982-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/13/2021] [Indexed: 11/09/2022] Open
Abstract
Several COVID-19 vaccines have shown good efficacy in clinical trials, but there remains uncertainty about the efficacy of vaccines against different variants. Here, we investigate the efficacy of ChAdOx1 nCoV-19 (AZD1222) against symptomatic COVID-19 in a post-hoc exploratory analysis of a Phase 3 randomised trial in Brazil (trial registration ISRCTN89951424). Nose and throat swabs were tested by PCR in symptomatic participants. Sequencing and genotyping of swabs were performed to determine the lineages of SARS-CoV-2 circulating during the study. Protection against any symptomatic COVID-19 caused by the Zeta (P.2) variant was assessed in 153 cases with vaccine efficacy (VE) of 69% (95% CI 55, 78). 49 cases of B.1.1.28 occurred and VE was 73% (46, 86). The Gamma (P.1) variant arose later in the trial and fewer cases (N = 18) were available for analysis. VE was 64% (-2, 87). ChAdOx1 nCoV-19 provided 95% protection (95% CI 61%, 99%) against hospitalisation due to COVID-19. In summary, we report that ChAdOx1 nCoV-19 protects against emerging variants in Brazil despite the presence of the spike protein mutation E484K.
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Affiliation(s)
- Sue Ann Costa Clemens
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- Institute of Global Health, University of Siena, Siena, Italy
| | - Pedro M Folegatti
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Katherine R W Emary
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Lily Yin Weckx
- Department of Pediatrics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Jeremy Ratcliff
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Sagida Bibi
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Ana Verena De Almeida Mendes
- Escola Bahiana de Medicina e Saúde Pública, Brazil and ID'OR, Salvador, Brazil
- Hospital São Rafael, Salvador, Brazil
| | | | - Ana Pittella
- Hospital Quinta D'Or, Rio de Janeiro, Brazil
- Instituto D'Or de Pesquisa e Ensino (IDOR), Rio de Janeiro, Brazil
- Universidade Unigranrio, Rio de Janeiro, Brazil
| | - Alexandre V Schwarzbold
- Clinical Research Unit, Department of Clinical Medicine, Universidade Federal de Santa Maria, Santa Maria, Brazil
| | - Eduardo Sprinz
- Infectious Diseases Service, Hospital de Clinicas de Porto Alegre, Porto Alegre, Brazil
- Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Parvinder K Aley
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - David Bonsall
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Christophe Fraser
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Michelle Fuskova
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sarah C Gilbert
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daniel Jenkin
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sarah Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Simon Kerridge
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Teresa Lambe
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Natalie G Marchevsky
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Yama F Mujadidi
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Emma Plested
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Maheshi N Ramasamy
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Tanya Golubchik
- Oxford Viral Sequencing Group, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Merryn Voysey
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
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