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Khales P, Razizadeh MH, Ghorbani S, Moattari A, Sarvari J, Saadati H, Sayyahfar S, Salavatiha Z, Hasanabad MH, Poortahmasebi V, Tavakoli A. Human adenoviruses in children with gastroenteritis: a systematic review and meta-analysis. BMC Infect Dis 2024; 24:478. [PMID: 38724898 PMCID: PMC11084101 DOI: 10.1186/s12879-024-09386-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024] Open
Abstract
PURPOSE Human adenoviruses (HAdVs) have always been suggested as one of the main causes of gastroenteritis in children. However, no comprehensive report on the global epidemiology of these viruses in pediatric gastroenteritis is available. METHODS A systematic search was conducted to obtain published papers from 2003 to 2023 in three main databases PubMed, Scopus, and Web of Science. RESULTS The estimated global pooled prevalence of HAdV infection in children with gastroenteritis was 10% (95% CI: 9-11%), with a growing trend after 2010. The highest prevalence was observed in Africa (20%, 95% CI: 14-26%). The prevalence was higher in inpatients (11%; 95% CI: 8-13%) and patients aged 5 years old and younger (9%; 95% CI: 7-10%). However, no significant difference was observed between male and female patients (P = 0.63). The most prevalent species was found to be the species F (57%; 95% CI: 41-72%). The most common HAdVs observed in children with gastroenteritis were types 40/41, 38, and 2. Analysis of case-control studies showed an association between HAdV and gastroenteritis in children (OR: 2.28, 95% CI; 1.51-3.44). CONCLUSION This study provided valuable insights into the importance of HAdVs in children with gastroenteritis, especially in hospitalized and younger children. The results can be used in future preventive measurements and the development of effective vaccines.
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Affiliation(s)
- Pegah Khales
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Hossein Razizadeh
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Antimicrobial Resistance Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Saied Ghorbani
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Afagh Moattari
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Jamal Sarvari
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hassan Saadati
- Department of Epidemiology and Biostatistics, School of Health, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Shirin Sayyahfar
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Salavatiha
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Morteza Haghighi Hasanabad
- Antimicrobial Resistance Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Vahdat Poortahmasebi
- Department of Bacteriology and Virology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ahmad Tavakoli
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran.
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2
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Lewis MA, Cortés-Penfield NW, Ettayebi K, Patil K, Kaur G, Neill FH, Atmar RL, Ramani S, Estes MK. Standardization of an antiviral pipeline for human norovirus in human intestinal enteroids demonstrates nitazoxanide has no to weak antiviral activity. Antimicrob Agents Chemother 2023; 67:e0063623. [PMID: 37787556 PMCID: PMC10583671 DOI: 10.1128/aac.00636-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/02/2023] [Indexed: 10/04/2023] Open
Abstract
Human noroviruses (HuNoVs) are the leading cause of acute gastroenteritis. In immunocompetent hosts, symptoms usually resolve within 3 days; however, in immunocompromised persons, HuNoV infection can become persistent, debilitating, and sometimes life-threatening. There are no licensed therapeutics for HuNoV due to a near half-century delay in its cultivation. Treatment for chronic HuNoV infection in immunosuppressed patients anecdotally includes nitazoxanide, a broad-spectrum antimicrobial licensed for treatment of parasite-induced gastroenteritis. Despite its off-label use for chronic HuNoV infection, nitazoxanide has not been clearly demonstrated to be an effective treatment. In this study, we standardized a pipeline for antiviral testing using multiple human small intestinal enteroid lines representing different intestinal segments and evaluated whether nitazoxanide inhibits replication of five HuNoV strains in vitro. Nitazoxanide did not exhibit high selective antiviral activity against any HuNoV strain tested, indicating it is not an effective antiviral for HuNoV infection. Human intestinal enteroids are further demonstrated as a model to serve as a preclinical platform to test antivirals against HuNoVs to treat gastrointestinal disease. Abstr.
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Affiliation(s)
- Miranda A. Lewis
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Nicolás W. Cortés-Penfield
- Department of Medicine, Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Khalil Ettayebi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Ketki Patil
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Gurpreet Kaur
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Frederick H. Neill
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Robert L. Atmar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Mary K. Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
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Johansen RL, Schouw CH, Madsen TV, Nielsen XC, Engberg J. Epidemiology of gastrointestinal infections: lessons learned from syndromic testing, Region Zealand, Denmark. Eur J Clin Microbiol Infect Dis 2023; 42:1091-1101. [PMID: 37468662 PMCID: PMC10427544 DOI: 10.1007/s10096-023-04642-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/09/2023] [Indexed: 07/21/2023]
Abstract
The aim of this study was to investigate the value of syndromic diagnostic testing for a better understanding of the epidemiology of gastrointestinal infections in Denmark. Here we evaluated the QIAstat-Dx® Gastrointestinal (GI) Panel 1 assay on 18,610 fecal samples requested for analysis for enteric pathogens in Region Zealand, Denmark, in 1 year (October 1, 2021, to September 30, 2022). In total, 6905 (37%) samples were detected positive for one or more diarrhoeal bacteria, viruses, and protozoa. The most common bacterial, viral, and parasitic pathogens detected with the QIAstat-Dx® Gastrointestinal Panel 1 were EPEC (in patients ≥ 2 years of age) (n = 1420 (20.6%)), rotavirus (n = 948 (13.7%)), and Cryptosporidium spp. (n = 196 (2.84%)). We identified a large diversity in infections likely reflecting substantial differences in the epidemiology including origin of infections, mode of transmission, seasonality, age-dependent susceptibility to disease, severity, and travel history. All pathogens were detected as both single and coinfections. Viral infections peaked in March with a positive rate of 31.6%, and bacterial infections peaked in August with a positive rate of 35.3%. ETEC, Shigella/EIEC, EAEC, and P. shigelloides were most related to travel activity, and coinfections were frequent. The distribution of Ct values varied significantly between the pathogens, with the lowest Ct values (median 17-18) observed in astrovirus, adenovirus, and rotavirus. Our results highlight the value of providing extensive diagnostic testing on fecal samples for sufficient detection of relevant diarrhoeal pathogens for optimal clinical care.
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Affiliation(s)
- Rikke Lykke Johansen
- The Regional Department of Clinical Microbiology, Zealand University Hospital, Koege, Ingemannsvej 46, DK-4200, Slagelse, Denmark
| | - Christian Højte Schouw
- The Regional Department of Clinical Microbiology, Zealand University Hospital, Koege, Ingemannsvej 46, DK-4200, Slagelse, Denmark
| | - Tina Vasehus Madsen
- The Regional Department of Clinical Microbiology, Zealand University Hospital, Koege, Ingemannsvej 46, DK-4200, Slagelse, Denmark
| | - Xiaohui Chen Nielsen
- The Regional Department of Clinical Microbiology, Zealand University Hospital, Koege, Ingemannsvej 46, DK-4200, Slagelse, Denmark
| | - Jørgen Engberg
- The Regional Department of Clinical Microbiology, Zealand University Hospital, Koege, Ingemannsvej 46, DK-4200, Slagelse, Denmark.
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4
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Farahmand M, Khales P, Salavatiha Z, Sabaei M, Hamidzade M, Aminpanah D, Tavakoli A. Worldwide prevalence and genotype distribution of human astrovirus in gastroenteritis patients: A systematic review and meta-analysis. Microb Pathog 2023:106209. [PMID: 37385570 DOI: 10.1016/j.micpath.2023.106209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/17/2023] [Accepted: 06/18/2023] [Indexed: 07/01/2023]
Abstract
AIM Human astrovirus (HAstV) is an important causative agent of gastroenteritis in humans, which mainly infects young children and the elderly. The goal of this study was to conduct a meta-analytic review of the prevalence of HAstV amongst patients with gastroenteritis, and to shed light on the connection between HAstV infection and gastroenteritis. METHODS Systematic literature searches were conducted to identify all potentially relevant studies recorded up to April 8th, 2022. For study weighting, the inverse variance method was employed and the random-effects model was applied to evaluate data. For case-control studies, the pooled odds ratio (OR) and 95% confidence interval (CI) were calculated to establish the relationship between HAstV infection and gastroenteritis. RESULTS Among 302423 gastroenteritis patients from 69 different countries, the overall pooled prevalence of HAstV infection was 3.48% (95% CI: 3.11%-3.89%). Case-control approach was used in 39 investigations, and the overall prevalence of HAstV infection among the 11342 healthy controls was 2.01% (95% CI: 1.40%-2.89%). Gastroenteritis and HAstV infection were associated with a pooled OR of 2.16 (95% CI: 1.72-2.71; P < 0.0001; I2 = 33.7%). The most commonly found HAstV genotypes in gastroenteritis patients were HAstV1 (62.18%), HAstV7 (33.33%), and HAstV-MLB1 (17.43%). CONCLUSION The frequency of HAstV infection was the highest in children under the age of five, and in developing countries. The prevalence rate of HAstV was not influenced by gender. Semi-nested and nested RT-PCR were highly sensitive assays for detecting HAstV infections.
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Affiliation(s)
- Mohammad Farahmand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Pegah Khales
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Salavatiha
- Department of Medical Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Milad Sabaei
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Malihe Hamidzade
- Department of Medical Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Danesh Aminpanah
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Ahmad Tavakoli
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran.
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5
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Lewis MA, Cortés-Penfield NW, Ettayebi K, Patil K, Kaur G, Neill FH, Atmar RL, Ramani S, Estes MK. A Standardized Antiviral Pipeline for Human Norovirus in Human Intestinal Enteroids Demonstrates No Antiviral Activity of Nitazoxanide. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.542011. [PMID: 37293103 PMCID: PMC10245936 DOI: 10.1101/2023.05.23.542011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Human noroviruses (HuNoVs) are the leading cause of acute gastroenteritis. In immunocompetent hosts, symptoms usually resolve within three days; however, in immunocompromised persons, HuNoV infection can become persistent, debilitating, and sometimes life-threatening. There are no licensed therapeutics for HuNoV due to a near half-century delay in its cultivation. Treatment for chronic HuNoV infection in immunosuppressed patients anecdotally includes nitazoxanide, a broad-spectrum antimicrobial licensed for treatment of parasite-induced gastroenteritis. Despite its off-label use for chronic HuNoV infection, nitazoxanide has not been clearly demonstrated to be an effective treatment. In this study, we established a standardized pipeline for antiviral testing using multiple human small intestinal enteroid (HIE) lines representing different intestinal segments and evaluated whether nitazoxanide inhibits replication of 5 HuNoV strains in vitro . Nitazoxanide did not exhibit high selective antiviral activity against any HuNoV strains tested, indicating it is not an effective antiviral for norovirus infection. HIEs are further demonstrated as a model to serve as a pre-clinical platform to test antivirals against human noroviruses to treat gastrointestinal disease.
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Affiliation(s)
- Miranda A. Lewis
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030
| | | | - Khalil Ettayebi
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030
| | - Ketki Patil
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030
| | - Gurpreet Kaur
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030
| | - Frederick H. Neill
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030
| | - Robert L. Atmar
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030
| | - Sasirekha Ramani
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030
| | - Mary K. Estes
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX 77030
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030
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6
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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: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [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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7
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Fang B, Lai J, Liu Y, Yu TT, Yu X, Li X, Dong L, Zhang X, Yang W, Yan Q, Sun L, Liu LL. Genetic characterization of human adenoviruses in patients using metagenomic next-generation sequencing in Hubei, China, from 2018 to 2019. Front Microbiol 2023; 14:1153728. [PMID: 37007506 PMCID: PMC10060807 DOI: 10.3389/fmicb.2023.1153728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 02/24/2023] [Indexed: 03/18/2023] Open
Abstract
ObjectivesThis study aimed to characterize the genomic epidemiology of human adenoviruses (HAdVs) in Hubei, China, using metagenomic next-generation sequencing (mNGS).MethodsIn total, 25 HAdV-positive samples collected from 21 pediatric patients were sequenced and subjected to mNGS using the NextSeq 550 and GenoLab M sequencing platforms. The metagenomic data were assembled de novo for molecular typing, phylogenetic and recombination analyzes.ResultsWe assembled 50 HAdV genomes, 88% (22/25) genomes from GenoLab M, and 84% (21/25) genomes from NextSeq 550 have perfect alignments to reference genomes with greater than 90%. The most fully assembled 25 genomes were categorized into 7 HAdV genotypes, the most abundant of which were HAdV-B3 (9/25) and HAdV-C2 (6/25). Phylogenetic analyzes revealed that the newly isolated HAdV-B3 strains diverged into separate clusters according to their genotypes. Vigilance is needed that HAdV-B3 isolates have begun to form new distinct clusters. High nucleotide identity was observed in the whole genome level within the same HAdV genotypes, while marked differences of three capsid genes across HAdV genotypes were noted. The high nucleotide diversity regions were concordant with the reported hypervariable regions. Further, three recombinant strains were identified: S64 and S71 originated from the parental strains HAdV-B14 and HAdV-B11, and S28 originated from HAdV-C1, HAdV-C5, and HAdV-CBJ113. GenoLab M and NextSeq 550 showed comparable performance with respect to data yield, duplication rate, human ratio, and assembly completeness.ConclusionThe sequencing quality and assembly accuracy showed that mNGS assembled genomes can be used for subsequently HAdV genotyping and genomic characterization. The high nucleotide diversity of capsid genes and high frequency of recombination events has highlighted the necessity for HAdV epidemiological surveillance in China.
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Affiliation(s)
- Bin Fang
- Hubei Provincial Center for Disease Control and Prevention, Institute of Health Inspection and Testing, Wuhan, China
| | - Juan Lai
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Yongfeng Liu
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Tian-tian Yu
- School of Public Health, Department of Nutritional Hygiene and Toxicology, Wuhan University of Science and Technology, Wuhan, China
| | - Xiao Yu
- Hubei Provincial Center for Disease Control and Prevention, Institute of Health Inspection and Testing, Wuhan, China
| | - Xiang Li
- Hubei Provincial Center for Disease Control and Prevention, Institute of Health Inspection and Testing, Wuhan, China
| | - Lijun Dong
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Xin Zhang
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Wei Yang
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Qin Yan
- GeneMind Biosciences Company Limited, Shenzhen, China
| | - Lei Sun
- GeneMind Biosciences Company Limited, Shenzhen, China
- *Correspondence: Lei Sun,
| | - Lin-lin Liu
- Hubei Provincial Center for Disease Control and Prevention, Institute of Health Inspection and Testing, Wuhan, China
- Lin-lin Liu,
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8
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Mabasa VV, van Zyl WB, Ismail A, Allam M, Taylor MB, Mans J. Multiple Novel Human Norovirus Recombinants Identified in Wastewater in Pretoria, South Africa by Next-Generation Sequencing. Viruses 2022; 14:v14122732. [PMID: 36560736 PMCID: PMC9788511 DOI: 10.3390/v14122732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/25/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
The genogroup II genotype 4 (GII.4) noroviruses are a major cause of viral gastroenteritis. Since the emergence of the Sydney_2012 variant, no novel norovirus GII.4 variants have been reported. The high diversity of noroviruses and periodic emergence of novel strains necessitates continuous global surveillance. The aim of this study was to assess the diversity of noroviruses in selected wastewater samples from Pretoria, South Africa (SA) using amplicon-based next-generation sequencing (NGS). Between June 2018 and August 2020, 200 raw sewage and final effluent samples were collected fortnightly from two wastewater treatment plants in Pretoria. Viruses were recovered using skimmed milk flocculation and glass wool adsorption-elution virus recovery methods and screened for noroviruses using a one-step real-time reverse-transcription PCR (RT-PCR). The norovirus BC genotyping region (570-579 bp) was amplified from detected norovirus strains and subjected to Illumina MiSeq NGS. Noroviruses were detected in 81% (162/200) of samples. The majority (89%, 89/100) of raw sewage samples were positive for at least one norovirus, compared with 73% (73/100) of final effluent samples. Overall, a total of 89 different GI and GII RdRp-capsid combinations were identified, including 51 putative novel recombinants, 34 previously reported RdRp-capsid combinations, one emerging novel recombinant and three Sanger-sequencing confirmed novel recombinants.
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Affiliation(s)
- Victor Vusi Mabasa
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
| | - Walda Brenda van Zyl
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
- National Health Laboratory Service, Tshwane Academic Division, Pretoria 0002, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2192, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2192, South Africa
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Maureen Beatrice Taylor
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
| | - Janet Mans
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
- Correspondence: ; Tel.: +27-12-319-2660
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9
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Kõivumägi K, Geller J, Toompere K, Soeorg H, Kallas E, Jõgeda EL, Huik K, Lutsar I. Norovirus strains among children aged 0-18 years hospitalized with acute gastroenteritis in Estonia 2015-2016. J Med Virol 2021; 94:2632-2639. [PMID: 34854093 DOI: 10.1002/jmv.27495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 11/25/2021] [Accepted: 11/30/2021] [Indexed: 11/11/2022]
Abstract
Norovirus (NoV) is the leading cause of acute gastroenteritis (AGE) in many countries that have introduced universal rotavirus mass vaccination. This is the first study to report data on NoV strains in Estonia. We recruited 2249 children aged 0-18 years hospitalized for AGE in Estonian hospitals from February 1, 2015 to August 31, 2016. Norovirus gastroenteritis (NoVGE) was diagnosed in 14.5% (n = 325) cases. Stool sample for RNA extraction and genotyping was available in 86% (n = 280) of NoVGE cases (2015, n = 91; 2016, n = 189). Dominant capsid types detected in 75% (n = 210) samples were, GII.4 (63.8%, n = 134), GII.3 (15.2%, n = 32), GII.17 (6.7%, n = 14), and GII.6 (5.2%, n = 11). Prevailing RNA polymerase types found in 77% (n = 215) samples were GII.P31 (51.1%, n = 110), GII.P21 (17.7%, n = 38), GII.P4 (11.2%, n = 24), and GII.P7 (6.5%, n = 14). Both regions were typeable for 67% (n = 189) of samples. Most prevalent strains were GII.4Sydney_2012[P31] (48.7%, n = 92), GII.3[P21] (15.3%, n = 29), GII.4Sydney_2012[P4] (5.8%, n = 11) and GII.17[P17] (5.8%, n = 11). Simpson's diversity index showed a significant difference between the age groups 1-4 and 5-9 years: D 0.64 (95% confidence interval [CI]: 0.55-0.73) versus 0.83 (95% CI: 0.81-0.86), respectively (p = 0.03). An accurate understanding of NoV strain diversity is important for control and preventive measures, especially in the postrotavirus vaccine era.
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Affiliation(s)
- Kadri Kõivumägi
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.,Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Julia Geller
- The National Institute for Health Development, Tallinn, Estonia
| | - Karolin Toompere
- Institute of Family Medicine and Public Health, University of Tartu, Tartu, Estonia
| | - Hiie Soeorg
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Eveli Kallas
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Ene-Ly Jõgeda
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Kristi Huik
- US National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Irja Lutsar
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
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10
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Razizadeh MH, Khatami A, Zarei M. Global molecular prevalence and genotype distribution of Sapovirus in children with gastrointestinal complications: A systematic review and meta-analysis. Rev Med Virol 2021; 32:e2302. [PMID: 34626019 DOI: 10.1002/rmv.2302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 01/11/2023]
Abstract
Sapovirus (SaV) is an emerging cause of children gastrointestinal complications such as acute gastroenteritis (AGE). The aim of the present systematic review and meta-analysis was to estimate the global prevalence of the SaV in children and association of infection with SaVs and AGE in children based on case-control studies. Four international databases (PubMed, Scopus, Web of Sciences and Google Scholar) were used to retrieve English-language studies published between January 2000 and December 2020. Comprehensive Meta-Analysis software was applied to estimate the overall prevalence, publication bias and heterogeneity index. The pooled prevalence of SaV infection among children with gastroenteritis was 3.4% [95% confidence interval (CI): 2.9%-3.9%] based on a random-effects meta-analysis. Genogroup I was the dominant genogroup of SaV in children with gastroenteritis [2.2% (95% CI: 1.6%-3.0%)], association analysis showed that SaV was associated with gastroenteritis [OR: 1.843 (95% CI: 1.27-2.66)]. Given the significant prevalence of the virus in children, it is necessary to pay more attention to this situation. Therefore, preventive health measures in children should be a priority.
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Affiliation(s)
| | - Alireza Khatami
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Mohammad Zarei
- Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
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11
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Adriaenssens EM, Farkas K, McDonald JE, Jones DL, Allison HE, McCarthy AJ. Tracing the fate of wastewater viruses reveals catchment-scale virome diversity and connectivity. WATER RESEARCH 2021; 203:117568. [PMID: 34450465 DOI: 10.1016/j.watres.2021.117568] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
The discharge of wastewater-derived viruses in aquatic environments impacts catchment-scale virome composition. To explore this, we used viromic analysis of RNA and DNA virus-like particles to holistically track virus communities entering and leaving wastewater treatment plants and the connecting river catchment system and estuary. We reconstructed >40 000 partial viral genomes into 10 149 species-level groups, dominated by dsDNA and (+)ssRNA bacteriophages (Caudoviricetes and Leviviricetes) and a small number of genomes that could pose a risk to human health. We found substantial viral diversity and geographically distinct virus communities associated with different wastewater treatment plants. River and estuarine water bodies harboured more diverse viral communities in downstream locations, influenced by tidal movement and proximity to wastewater treatment plants. Shellfish and beach sand were enriched in viral communities when compared with the surrounding water, acting as entrapment matrices for virus particles. Extensive phylogenetic analyses of environmental-derived and reference sequences showed the presence of human-associated sapovirus GII in all sample types, multiple rotavirus A strains in wastewater and a diverse set of picorna-like viruses associated with shellfish. We conclude that wastewater-derived viral genetic material is commonly deposited in the environment and can be traced throughout the freshwater-marine continuum of the river catchment, where it is influenced by local geography, weather events and tidal effects. Our data illustrate the utility of viromic analyses for wastewater- and environment-based ecology and epidemiology, and we present a conceptual model for the circulation of all types of viruses in a freshwater catchment.
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Affiliation(s)
- Evelien M Adriaenssens
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK; Quadram Institute Bioscience, Norwich, NR4 7UQ, UK.
| | - Kata Farkas
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK; School of Ocean Sciences, Bangor University, Bangor, LL59 5AB, UK
| | - James E McDonald
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - David L Jones
- School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK; UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - Heather E Allison
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Alan J McCarthy
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
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12
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Myers CE, Houldcroft CJ, Roy S, Margetts BK, Best T, Venturini C, Guerra-Assunção JA, Williams CA, Williams R, Dunn H, Hartley JC, Rao K, Rolfe KJ, Breuer J. Using Whole Genome Sequences to Investigate Adenovirus Outbreaks in a Hematopoietic Stem Cell Transplant Unit. Front Microbiol 2021; 12:667790. [PMID: 34276599 PMCID: PMC8284422 DOI: 10.3389/fmicb.2021.667790] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/05/2021] [Indexed: 11/18/2022] Open
Abstract
A recent surge in human mastadenovirus (HAdV) cases, including five deaths, amongst a haematopoietic stem cell transplant population led us to use whole genome sequencing (WGS) to investigate. We compared sequences from 37 patients collected over a 20-month period with sequences from GenBank and our own database of HAdVs. Maximum likelihood trees and pairwise differences were used to evaluate genotypic relationships, paired with the epidemiological data from routine infection prevention and control (IPC) records and hospital activity data. During this time period, two formal outbreaks had been declared by IPC, while WGS detected nine monophyletic clusters, seven were corroborated by epidemiological evidence and by comparison of single-nucleotide polymorphisms. One of the formal outbreaks was confirmed, and the other was not. Of the five HAdV-associated deaths, three were unlinked and the remaining two considered the source of transmission. Mixed infection was frequent (10%), providing a sentinel source of recombination and superinfection. Immunosuppressed patients harboring a high rate of HAdV positivity require comprehensive surveillance. As a consequence of these findings, HAdV WGS is being incorporated routinely into clinical practice to influence IPC policy contemporaneously.
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Affiliation(s)
- Chloe E Myers
- Cambridge Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, United Kingdom
| | | | - Sunando Roy
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Ben K Margetts
- Division of Infection, Immunity and Inflammation, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Timothy Best
- Department of Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children National Health Service Foundation Trust, London, United Kingdom
| | - Cristina Venturini
- Division of Infection and Immunity, University College London, London, United Kingdom
| | | | - Charlotte A Williams
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Rachel Williams
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Helen Dunn
- Department of Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children National Health Service Foundation Trust, London, United Kingdom
| | - John C Hartley
- Department of Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children National Health Service Foundation Trust, London, United Kingdom
| | - Kanchan Rao
- Department of Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children National Health Service Foundation Trust, London, United Kingdom
| | - Kathryn J Rolfe
- Cambridge Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, United Kingdom
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, United Kingdom.,Department of Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children National Health Service Foundation Trust, London, United Kingdom
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13
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Abstract
Viral acute gastroenteritis (AGE) is common and afflicts people of all ages. Nonviral causes of AGE are less common. Norovirus is a leading cause of sporadic cases and outbreaks of AGE across all ages. Universal rotavirus vaccination of infants has reduced frequency and severity of rotavirus AGE cases in children and indirectly reduced cases in older adults. Severe illness is more likely in persons at age extremes or with immunocompromising conditions. Viral causes of AGE can lead to protracted diarrheal illness in immunocompromised persons. Nucleic acid amplification tests are changing diagnostic testing algorithms.
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Affiliation(s)
- Jeffery L Meier
- Division of Infectious Diseases, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City Veterans Affairs Healthcare System, SW34 GH, 200 Hawkins Dr., Iowa City, IA 52242, USA.
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14
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Farahmand M, Moghoofei M, Dorost A, Shoja Z, Ghorbani S, Kiani SJ, Khales P, Esteghamati A, Sayyahfar S, Jafarzadeh M, Minaeian S, Khanaliha K, Naghdalipour M, Tavakoli A. Global prevalence and genotype distribution of norovirus infection in children with gastroenteritis: A meta-analysis on 6 years of research from 2015 to 2020. Rev Med Virol 2021; 32:e2237. [PMID: 33793023 DOI: 10.1002/rmv.2237] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/10/2021] [Accepted: 03/15/2021] [Indexed: 12/12/2022]
Abstract
In the post rotavirus vaccine era, norovirus (NoV) plays an increasingly important role in epidemic and sporadic gastroenteritis among children. This study was designed to provide an updated meta-analytic review of the prevalence of NoV among paediatric patients with gastroenteritis and to clarify the relationship between NoV infection and gastroenteritis. Systematic searches of the literature for potentially relevant studies were carried out from 1 January 2015 to 29 May 2020. The inverse variance method was chosen for weighting of the studies, and the random-effects model was used to analyse data. To determine the association between NoV infection and gastroenteritis in children, pooled odds ratio (OR) and its 95% confidence interval (CI) were computed for case-control studies. The pooled prevalence of NoV infection among 12,0531 children with gastroenteritis from 45 countries across the world was 17.7% (95% CI: 16.3%-19.2%). There were 28 studies with a case-control design, and the pooled prevalence of NoV infection among 11,954 control subjects was 6.7% (95% CI: 5.1%-8.8%). The pooled OR of the association of NoV infection and gastroenteritis was 2.7 (95% CI: 2.2-3.4). The most common NoV genotypes were GII.4 (59.3%) and GII.3 (14.9%). The highest frequency of NoV was found in the age group below 1 year. Our findings indicated a substantial burden of gastroenteritis caused by NoV globally, with GII.4 and GII.3 the major genotypes responsible for the majority of NoV-associated gastroenteritis cases among children. Younger age and male sex can be considered risk factors for NoV-associated gastroenteritis among children.
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Affiliation(s)
- Mohammad Farahmand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohsen Moghoofei
- Department of Microbiology, Faculty of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Abolfazl Dorost
- Department of Health Economics and Management, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Saied Ghorbani
- Department of Medical Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Jalal Kiani
- Department of Medical Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Pegah Khales
- Department of Medical Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Student Research Committee, Iran University of Medical Sciences, Tehran, Iran
| | - Abdoulreza Esteghamati
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Shirin Sayyahfar
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Mehrzad Jafarzadeh
- Institute of Endocrinology and Metabolism Research and Training Center, Iran University of Medical Sciences, Tehran, Iran
| | - Sara Minaeian
- Antimicrobial Resistance Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Khadijeh Khanaliha
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Mehri Naghdalipour
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Ahmad Tavakoli
- Department of Medical Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.,Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
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15
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Li Y, Handley SA, Baldridge MT. The dark side of the gut: Virome-host interactions in intestinal homeostasis and disease. J Exp Med 2021; 218:211916. [PMID: 33760921 PMCID: PMC8006857 DOI: 10.1084/jem.20201044] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 12/19/2022] Open
Abstract
The diverse enteric viral communities that infect microbes and the animal host collectively constitute the gut virome. Although recent advances in sequencing and analysis of metaviromes have revealed the complexity of the virome and facilitated discovery of new viruses, our understanding of the enteric virome is still incomplete. Recent studies have uncovered how virome–host interactions can contribute to beneficial or detrimental outcomes for the host. Understanding the complex interactions between enteric viruses and the intestinal immune system is a prerequisite for elucidating their role in intestinal diseases. In this review, we provide an overview of the enteric virome composition and summarize recent findings about how enteric viruses are sensed by and, in turn, modulate host immune responses during homeostasis and disease.
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Affiliation(s)
- Yuhao Li
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO.,Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO
| | - Scott A Handley
- Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO.,Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO
| | - Megan T Baldridge
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, MO.,Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO
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16
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Rossouw E, Brauer M, Meyer P, du Plessis NM, Avenant T, Mans J. Virus Etiology, Diversity and Clinical Characteristics in South African Children Hospitalised with Gastroenteritis. Viruses 2021; 13:v13020215. [PMID: 33573340 PMCID: PMC7911269 DOI: 10.3390/v13020215] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Viral gastroenteritis remains a major cause of hospitalisation in young children. This study aimed to determine the distribution and diversity of enteric viruses in children ≤5 years, hospitalised with gastroenteritis at Kalafong Provincial Tertiary Hospital, Pretoria, South Africa, between July 2016 and December 2017. METHODS Stool specimens (n = 205) were screened for norovirus GI and GII, rotavirus, sapovirus, astrovirus and adenovirus by multiplex RT-PCR. HIV exposure and FUT2 secretor status were evaluated. Secretor status was determined by FUT2 genotyping. RESULTS At least one gastroenteritis virus was detected in 47% (96/205) of children. Rotavirus predominated (46/205), followed by norovirus (32/205), adenovirus (15/205), sapovirus (9/205) and astrovirus (3/205). Norovirus genotypes GI.3, GII.2, GII.3, GII.4, GII.7, GII.12, GII.21, and rotavirus strains G1P[8], G2P[4], G2P[6], G3P[4], G3P[8], G8P[4], G8P[6], G9P[6], G9P[8] and sapovirus genotypes GI.1, GI.2, GII.1, GII.4, GII.8 were detected; norovirus GII.4[P31] and rotavirus G3P[4] predominated. Asymptomatic norovirus infection (GI.3, GI.7, GII.4, GII.6, GII.13) was detected in 22% of 46 six-week follow up stools. HIV exposure (30%) was not associated with more frequent or severe viral gastroenteritis hospitalisations compared to unexposed children. Rotavirus preferentially infected secretor children (p = 0.143) and norovirus infected 78% secretors and 22% non-secretors. CONCLUSION Rotavirus was still the leading cause of gastroenteritis hospitalisations, but norovirus caused more severe symptoms.
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Affiliation(s)
- Esmari Rossouw
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa;
| | - Marieke Brauer
- Immunology Laboratory, Ampath, Pretoria 0001, South Africa;
| | - Pieter Meyer
- Department of Immunology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa or
- National Health Laboratory Service, Tshwane Academic Division, Pretoria 0001, South Africa
| | - Nicolette M. du Plessis
- Department of Paediatrics, Kalafong Provincial Tertiary Hospital, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa; (N.M.d.P.); (T.A.)
| | - Theunis Avenant
- Department of Paediatrics, Kalafong Provincial Tertiary Hospital, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa; (N.M.d.P.); (T.A.)
| | - Janet Mans
- Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa;
- Correspondence: ; Tel.: +27-12-319-2660
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17
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A Clinical Epidemiology and Molecular Attribution Evaluation of Adenoviruses in Pediatric Acute Gastroenteritis: a Case-Control Study. J Clin Microbiol 2020; 59:JCM.02287-20. [PMID: 33115841 DOI: 10.1128/jcm.02287-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 10/20/2020] [Indexed: 12/12/2022] Open
Abstract
The objective of this study was to characterize the etiological role of human adenovirus (HAdV) serotypes in pediatric gastroenteritis. Using a case-control design, we compared the frequencies of HAdV serotypes between children with ≥3 episodes of vomiting or diarrhea within 24 h and <7 days of symptoms (i.e., cases) and those with no infectious symptoms (i.e., controls). Stool samples and/or rectal swabs underwent molecular serotyping with cycle threshold (Ct) values provided by multiplex real-time reverse transcription-PCR testing. Cases without respiratory symptoms were analyzed to calculate the proportion of disease attributed to individual HAdV serotypes (i.e., attributable fraction). Between December 2014 and August 2018, adenoviruses were detected in 18.8% (629/3,347) of cases and 7.2% (97/1,355) of controls, a difference of 11.6% (95% confidence interval [CI], 9.6%, 13.5%). In 96% (95% CI, 92 to 98%) of HAdV F40/41 detections, the symptoms could be attributed to the identified serotype; when serotypes C1, C2, C5, and C6 were detected, they were responsible for symptoms in 52% (95% CI, 12 to 73%). Ct values were lower among cases than among controls (P < 0.001). HAdV F40/41, C2, and C1 accounted for 59.7% (279/467), 17.6% (82/467), and 12.0% (56/467) of all typed cases, respectively. Among cases, Ct values were lower for F40/41 serotypes than for non-F40/41 serotypes (P < 0.001). HAdV F40/41 serotypes account for the majority of HAdV-positive gastroenteritis cases, and when detected, disease is almost always attributed to infection with these pathogens. Non-F40/41 HAdV species have a higher frequency of asymptomatic infection and may not necessarily explain gastroenteritis symptoms. Real-time quantitative PCR may be useful in differentiating asymptomatic shedding from active infection.
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Younie S, Mitchell C, Bisson MJ, Crosby S, Kukona A, Laird K. Improving young children's handwashing behaviour and understanding of germs: The impact of A Germ's Journey educational resources in schools and public spaces. PLoS One 2020; 15:e0242134. [PMID: 33227004 PMCID: PMC7682880 DOI: 10.1371/journal.pone.0242134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 10/28/2020] [Indexed: 01/17/2023] Open
Abstract
CONTEXT Effective handwashing can prevent the spread of germs, including Covid-19. However, young children can lack a fundamental understanding of germ transfer. A Germ's Journey educational resources were designed to support young children in learning about germs and handwashing. These resources include a book, website, song, online games and glo-gel activities that are informed by a behaviour change model. RESEARCH GAP Prior research has not evaluated the impacts of these resources on behavioural outcomes. PURPOSE OF THE STUDY Two intervention studies evaluated the impacts of these resources on both knowledge and behavioural outcomes. METHOD In Study 1, children (n = 225) were recruited from four schools and randomly assigned by classrooms to participate in a multicomponent intervention (vs. control). In Study 2, children (n = 104) were recruited from a museum and randomly assigned to participate in a song intervention (vs. control). Trained observers recorded participants' engagement in six handwashing behaviours and their understanding of germs. These behavioural and knowledge outcomes were analysed using regression and related analyses. RESULTS In Study 1, significant improvements were observed between baseline and follow up in the intervention group for both behavioural scores (Est = 0.48, SE = 0.14, t = 3.30, p = 0.001) and knowledge scores (Est = 2.14, SE = 0.52, z = 4.11, p < 0.001), whereas these improvements were not observed in the control group (ts < 1). In Study 2, the intervention group had significantly higher behavioural scores compared to the control group (Est. = -0.71, SE = 0.34, t = -2.07, p = 0.04). CONCLUSION This research demonstrates that specifically designed hand hygiene educational resources can improve handwashing practice and understanding in young children, and could lead to the reduction of the transmission of disease within this group.
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Affiliation(s)
- Sarah Younie
- Institute for Research in Criminology, Community, Education and Social Justice, De Montfort University, Leicester, United Kingdom
| | - Chloe Mitchell
- Institute for Psychological Science, De Montfort University, Leicester, United Kingdom
- * E-mail:
| | - Marie-Josee Bisson
- Institute for Psychological Science, De Montfort University, Leicester, United Kingdom
| | - Sapphire Crosby
- Institute for Research in Criminology, Community, Education and Social Justice, De Montfort University, Leicester, United Kingdom
| | - Anuenue Kukona
- Institute for Psychological Science, De Montfort University, Leicester, United Kingdom
| | - Katie Laird
- Infectious Disease Research Group, Leicester Institute for Pharmaceutical Innovation, De Montfort University, Leicester, United Kingdom
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19
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Enteric Viral Co-Infections: Pathogenesis and Perspective. Viruses 2020; 12:v12080904. [PMID: 32824880 PMCID: PMC7472086 DOI: 10.3390/v12080904] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/10/2020] [Accepted: 08/14/2020] [Indexed: 02/06/2023] Open
Abstract
Enteric viral co-infections, infections involving more than one virus, have been reported for a diverse group of etiological agents, including rotavirus, norovirus, astrovirus, adenovirus, and enteroviruses. These pathogens are causative agents for acute gastroenteritis and diarrheal disease in immunocompetent and immunocompromised individuals of all ages globally. Despite virus–virus co-infection events in the intestine being increasingly detected, little is known about their impact on disease outcomes or human health. Here, we review what is currently known about the clinical prevalence of virus–virus co-infections and how co-infections may influence vaccine responses. While experimental investigations into enteric virus co-infections have been limited, we highlight in vivo and in vitro models with exciting potential to investigate viral co-infections. Many features of virus–virus co-infection mechanisms in the intestine remain unclear, and further research will be critical.
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20
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Brown JR, Roy S, Shah D, Williams CA, Williams R, Dunn H, Hartley J, Harris K, Breuer J. Norovirus Transmission Dynamics in a Pediatric Hospital Using Full Genome Sequences. Clin Infect Dis 2020; 68:222-228. [PMID: 29800111 PMCID: PMC6321856 DOI: 10.1093/cid/ciy438] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 05/23/2018] [Indexed: 12/12/2022] Open
Abstract
Background Norovirus is a leading cause of worldwide and nosocomial gastroenteritis. The study aim was to assess the utility of molecular epidemiology using full genome sequences compared to routine infection prevention and control (IPC) investigations. Methods Norovirus genomes were generated from new episodes of norovirus at a pediatric tertiary referral hospital over a 19-month period (n = 182). Phylogeny identified clusters of related sequences that were verified using epidemiological and clinical data. Results Twenty-four clusters of related norovirus sequences (“sequence clusters”) were observed, including 8 previously identified by IPC investigations (“IPC outbreaks”). Seventeen sequence clusters (involving 77/182 patients) were corroborated by epidemiological data (“epidemiologically supported clusters”), suggesting transmission between patients. Linked infections were identified among 44 patients who were missed by IPC investigations. Thirty-three percent of norovirus sequences were linked, suggesting nosocomial transmission; 24% of patients had nosocomial infections from an unknown source; and 43% were norovirus positive on admission. Conclusions We show there are frequent introductions of multiple norovirus strains with extensive onward nosocomial transmission of norovirus in a pediatric hospital with a high proportion of immunosuppressed patients nursed in isolation. Phylogenetic analysis using full genome sequences is more sensitive than classic IPC investigations for identifying linked cases and should be considered when investigating norovirus nosocomial transmission. Sampling of staff, visitors, and the environment may be required for complete understanding of infection sources and transmission routes in patients with nosocomial infections not linked to other patients and among patients with phylogenetically linked cases but no evidence of direct contact.
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Affiliation(s)
- Julianne R Brown
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital National Health Service Foundation Trust
| | - Sunando Roy
- Infection and Immunity, University College London, United Kingdom
| | - Divya Shah
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital National Health Service Foundation Trust
| | | | - Rachel Williams
- Infection and Immunity, University College London, United Kingdom
| | - Helen Dunn
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital National Health Service Foundation Trust
| | - John Hartley
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital National Health Service Foundation Trust
| | - Kathryn Harris
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital National Health Service Foundation Trust
| | - Judy Breuer
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital National Health Service Foundation Trust.,Infection and Immunity, University College London, United Kingdom
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21
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Redli PM, Wanzenried A, Huder JB, Berger C, Berlinger L, Capaul R, Böni J, Zbinden A. Evaluation of the RIDA®GENE RT-PCR assays for detection of sapovirus, astrovirus, adenovirus, and rotavirus in stool samples of adults in Switzerland. Diagn Microbiol Infect Dis 2019; 96:114924. [PMID: 31757559 DOI: 10.1016/j.diagmicrobio.2019.114924] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/05/2019] [Accepted: 10/29/2019] [Indexed: 12/15/2022]
Abstract
Sapovirus (SaV) and astrovirus (AstV) increasingly are recognized as cause of acute viral gastroenteritis (AGE). We evaluated the real-time RT-PCR assays RIDA®GENE SaV and viral stool panel II (RGN RT-PCR) for detection of SaV, AstV, adenovirus (AdV) F40/41 and rotavirus (RoV) in clinical stool samples (n = 69). Results were compared with reference singleplex RT-PCRs. The sensitivity for SaV, AstV and RoV are 100%, the specificity ranges from 98.1% to 100%. In 10 out of 11 AdV (all types) samples, the RGN RT-PCR for AdV F40/41 displayed negative results. Retrospectively, 196 stool specimens from adult patients previously tested negative for norovirus (NoV) were analyzed. In about 10% of NoV-negative stool samples, AdV (n = 9), RoV (n = 6), AstV (n = 3) or SaV (n = 3) were found. The RGN RT-PCR assays are useful for detection of enteric viruses other than NoV. This study emphasizes the need for further testing of NoV-negative stool samples in patients with AGE.
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Affiliation(s)
- Patrick M Redli
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
| | - Adrian Wanzenried
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
| | - Jon B Huder
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
| | - Christoph Berger
- Division of Infectious Diseases and Hospital Epidemiology, University Children's Hospital Zurich, Zurich, Switzerland.
| | | | - Riccarda Capaul
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
| | - Andrea Zbinden
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland.
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22
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Crenshaw BJ, Jones LB, Bell CR, Kumar S, Matthews QL. Perspective on Adenoviruses: Epidemiology, Pathogenicity, and Gene Therapy. Biomedicines 2019; 7:E61. [PMID: 31430920 PMCID: PMC6784011 DOI: 10.3390/biomedicines7030061] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/03/2019] [Accepted: 08/14/2019] [Indexed: 02/06/2023] Open
Abstract
Human adenoviruses are large (150 MDa) doubled-stranded DNA viruses that cause respiratory infections. These viruses are particularly pathogenic in healthy and immune-compromised individuals, and currently, no adenovirus vaccine is available for the general public. The purpose of this review is to describe (i) the epidemiology and pathogenicity of human adenoviruses, (ii) the biological role of adenovirus vectors in gene therapy applications, and (iii) the potential role of exosomes in adenoviral infections.
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Affiliation(s)
- Brennetta J Crenshaw
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
| | - Leandra B Jones
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
| | - Courtnee' R Bell
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA
| | - Sanjay Kumar
- Departments of Pediatrics and Cell, Developmental and Integrative Biology, Division of Neonatology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Qiana L Matthews
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA.
- Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL 36104, USA.
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23
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Mann P, Pietsch C, Liebert UG. Genetic Diversity of Sapoviruses among Inpatients in Germany, 2008-2018. Viruses 2019; 11:v11080726. [PMID: 31394867 PMCID: PMC6723979 DOI: 10.3390/v11080726] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 07/28/2019] [Accepted: 08/07/2019] [Indexed: 12/13/2022] Open
Abstract
Sapovirus enteric disease affects people of all ages across the globe, in both sporadic cases and outbreak settings. Sapovirus is seldom assessed in Germany and its epidemiology in the country is essentially unknown. Thus, sapovirus occurrence and genetic diversity were studied by real-time reverse transcription polymerase chain reaction (RT-PCR) and partial sequencing of major viral structural protein (VP1) gene in two different sets of stool samples: (1) a selection of 342 diarrheal stools collected from inpatient children during 2008−2009, and (2) 5555 stool samples collected during 2010–2018 from inpatients of all age groups with gastrointestinal complaints. Results showed year-round circulation of sapoviruses, with peaks during cooler months. In total, 30 samples (8.8%) of the first and 112 samples of the second set of samples (2.0%) were sapovirus positive. Capsid gene sequencing was successful in 134/142 samples (94.4%) and showed circulation of all known human pathogenic genogroups. Genotype GI.1 predominated (31.8%), followed by GII.1 (16.7%), GII.3 (14.5%), GI.2 (13.8%) and GV.1 (12.3%). Additionally, minor circulation of GI.3, GI.6, GII.2, GII.4, GII.6 and GIV.1 was shown. Consequently, sapovirus diagnostics need broadly reactive RT-PCR protocols and should particularly be considered in infants and young children. Further studies from other sampling sites are essential to extend our knowledge on sapovirus epidemiology in Germany.
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Affiliation(s)
- Pia Mann
- Institute of Virology, Leipzig University, 04103 Leipzig, Germany
| | - Corinna Pietsch
- Institute of Virology, Leipzig University, 04103 Leipzig, Germany.
| | - Uwe G Liebert
- Institute of Virology, Leipzig University, 04103 Leipzig, Germany
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24
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Annamalai T, Lu Z, Jung K, Langel SN, Tuggle CK, Dekkers JCM, Waide EH, Kandasamy S, Saif LJ. Infectivity of GII.4 human norovirus does not differ between T-B-NK + severe combined immunodeficiency (SCID) and non-SCID gnotobiotic pigs, implicating the role of NK cells in mediation of human norovirus infection. Virus Res 2019; 267:21-25. [PMID: 31054932 DOI: 10.1016/j.virusres.2019.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/26/2019] [Accepted: 05/01/2019] [Indexed: 12/21/2022]
Abstract
Human noroviruses (HuNoVs) are a leading cause of acute gastroenteritis worldwide. It is unclear which arm of the immune system regulates resistance to HuNoV infection. Thus, we studied the pathogenesis of human norovirus (HuNoV) in T-B-NK+ Severe Combined Immunodeficiency (SCID) gnotobiotic pigs to investigate the role of innate (especially, natural killer (NK) cells) immunity in HuNoV infection. Forty SCID and non-SCID pigs were randomly grouped: 1) SCID+HuNoV (n = 12); 2) non-SCID+HuNoV (n = 14); 3) SCID mock-inoculated (n = 6); and 4) non-SCID mock-inoculated (n = 8). Pigs (8-14-day-old) were inoculated orally with GII.4 HuNoV strain HS292 (mean 9.1 log10 genomic equivalents/pig) or mock. Daily fecal consistency and fecal viral RNA shedding, and histopathology (at euthanasia) were evaluated. Frequencies of blood and ileal T, B, and NK cells were analyzed by flow cytometry, and a NK cell cytotoxicity assay was performed at post-inoculation day (PID) 8. Unlike the increased infectivity of HuNoV observed previously in T-B-NK- SCID pigs (Lei et al., 2016. Sci. Rep. 6, 25,222), there was no significant difference in frequency of pigs with diarrhea and diarrhea days between T-B-NK+ SCID+HuNoV and non-SCID+HuNoV groups. Cumulative fecal HuNoV RNA shedding at PIDs 1-8, PIDs 9-27, and PIDs 1-27 also did not differ statistically. These observations coincided with the presence of NK cells and NK cell cytotoxicity in the ileum and blood of the SCID pigs. Based on our observations, innate immunity, including NK cell activity, may be critical to mediate or reduce HuNoV infection in T-B-NK+ SCID pigs, and potentially in immunocompetent patients.
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Affiliation(s)
- Thavamathi Annamalai
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, Ohio, USA
| | - Zhongyan Lu
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, Ohio, USA
| | - Kwonil Jung
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, Ohio, USA.
| | - Stephanie N Langel
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, Ohio, USA
| | | | | | - Emily H Waide
- Department of Animal Science, Iowa Stte University, Ames, IA
| | - Sukumar Kandasamy
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, Ohio, USA
| | - Linda J Saif
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, The Ohio State University, Wooster, Ohio, USA.
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25
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Pietsch C, Liebert UG. Intrahost viral evolution during chronic sapovirus infections. J Clin Virol 2019; 113:1-7. [DOI: 10.1016/j.jcv.2019.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/22/2018] [Accepted: 02/04/2019] [Indexed: 12/27/2022]
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26
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Human Sapovirus among Outpatients with Acute Gastroenteritis in Spain: A One-Year Study. Viruses 2019; 11:v11020144. [PMID: 30744057 PMCID: PMC6409837 DOI: 10.3390/v11020144] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/06/2019] [Accepted: 02/07/2019] [Indexed: 02/06/2023] Open
Abstract
Viral agents of human gastroenteritis affect people of all ages across the globe. As a mainly self-limiting disease, it is difficult to evaluate the real prevalence of etiological agents circulating in each region. Many of the analyzed outbreaks are caused by viruses of the family Caliciviridae, especially the genus Norovirus (NoV). Most studies have focused on other enteric viruses, leaving sapovirus (SaV) underestimated as an important emerging human threat. This one-year study analyzed clinical samples from hospital outpatients with acute gastroenteritis in Spain, with the aim of revealing the importance of human SaV as an emerging viral pathogen. A total of 2667 stools were tested using reverse transcription (RT)-qPCR to detect and quantify SaV. Sapovirus was detected in all age groups, especially in infants, children, and the elderly. The prevalence was 15.64% (417/2667), and was slightly higher in 0–2- and 3–5-year-olds (19.53% and 17.95%, respectively) and much lower in 13–18-year-olds (9.86%). Positive samples were detected throughout the year, with peaks of detection during autumn and the late winter to early spring months. The mean value for the quantified samples was 6.5 × 105 genome copies per gram of stool (GC/g) (range 2.4 × 103–6.6 × 1011 GC/g). RT-nested PCR and sequencing were used for further genotyping. Genetic characterization showed a predominance of genogroup I (GI), followed by GII and GIV. The detection of multiple genotypes suggests the circulation of different strains without any clear tendency. The results obtained suggest SaV as the second major gastroenteritis agent after NoV in the region.
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Guerrero-Latorre L, Romero B, Bonifaz E, Timoneda N, Rusiñol M, Girones R, Rios-Touma B. Quito's virome: Metagenomic analysis of viral diversity in urban streams of Ecuador's capital city. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 645:1334-1343. [PMID: 30248857 DOI: 10.1016/j.scitotenv.2018.07.213] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/16/2018] [Accepted: 07/16/2018] [Indexed: 06/08/2023]
Abstract
In Quito, the microbiological contamination of surface water represents a public health problem, mainly due to the lack of sewage treatment from urban wastewater. Contaminated water contributes to the transmission of many enteric pathogens through direct consumption, agricultural and recreational use. Among the different pathogens present in urban discharges, viruses play an important role on disease, being causes of gastroenteritis, hepatitis, meningitis, respiratory infections, among others. This study analyzes the presence of viruses in highly impacted surface waters of urban rivers using next-generation sequencing techniques. Three representative locations of urban rivers, receiving the main discharges from Quito sewerage system, were selected. Water samples of 500 mL were concentrated by skimmed-milk flocculation method and the viral nucleic acid was extracted and processed for high throughput sequencing using Illumina MiSeq. The results yielded very relevant data of circulating viruses in the capital of Ecuador. A total of 29 viral families were obtained, of which 26 species were associated with infections in humans. Among the 26 species identified, several were related to gastroenteritis: Human Mastadenovirus F, Bufavirus, Sapporovirus, Norwalk virus and Mamastrovirus 1. Also detected were: Gammapapillomavirus associated with skin infections, Polyomavirus 1 related to cases of kidney damage, Parechovirus A described as cause of neonatal sepsis with neurological affectations and Hepatovirus A, the etiologic agent of Hepatitis A. Other emergent viruses identified, of which its pathogenicity remains to be fully clarified, were: Bocavirus, Circovirus, Aichi Virus and Cosavirus. The wide diversity of species detected through metagenomics gives us key information about the public health risks present in the urban rivers of Quito. In addition, this study describes for the first time the presence of important infectious agents not previously reported in Ecuador and with very little reports in Latin America.
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Affiliation(s)
- Laura Guerrero-Latorre
- Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Ingeniería en Biotecnología, Universidad de las Américas, Quito, Ecuador.
| | - Brigette Romero
- Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Ingeniería en Biotecnología, Universidad de las Américas, Quito, Ecuador.
| | - Edison Bonifaz
- Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Ingeniería en Biotecnología, Universidad de las Américas, Quito, Ecuador.
| | - Natalia Timoneda
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain
| | - Marta Rusiñol
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain.
| | - Rosina Girones
- Laboratory of Virus Contaminants of Water and Food, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Catalonia, Spain.
| | - Blanca Rios-Touma
- Grupo de investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Aplicadas (FICA), Ingeniería Ambiental, Universidad de las Américas, Quito, Ecuador.
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Daniel-Wayman S, Fahle G, Palmore T, Green KY, Prevots DR. Norovirus, astrovirus, and sapovirus among immunocompromised patients at a tertiary care research hospital. Diagn Microbiol Infect Dis 2018; 92:143-146. [PMID: 29934072 PMCID: PMC11036324 DOI: 10.1016/j.diagmicrobio.2018.05.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/15/2018] [Accepted: 05/23/2018] [Indexed: 02/07/2023]
Abstract
We estimated the prevalence of astrovirus, sapovirus, and norovirus among patients enrolled in research protocols and receiving medical care at the Clinical Center of the National Institutes of Health, Bethesda, MD, a clinical research hospital with a large immunocompromised patient population. We identified patients whose fecal specimens were submitted to the Clinical Center for testing on the Biofire FilmArray Gastrointestinal Panel from September 15, 2015 through November 30, 2016. Among 442 patients with fecal specimens submitted for multiplex testing, 11% had norovirus identified, 2% had astrovirus, and 2% had sapovirus. Like norovirus, astrovirus was detected in multiple sequential samples from a single patient, consistent with chronic infection or the occurrence of multiple reinfections. Coinfection with non-viral gastrointestinal pathogens was detected in 31% of patients with positive results for norovirus, astrovirus, or sapovirus. Norovirus remains common in this immunocompromised patient population, and both sapovirus and astrovirus are present.
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Affiliation(s)
- Shelby Daniel-Wayman
- Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 8 West Drive, MSC 2665, Bethesda, MD 20892, USA.
| | - Gary Fahle
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA.
| | - Tara Palmore
- Hospital Epidemiology Service, Clinical Center, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA.
| | - Kim Y Green
- Calicivirus Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bldg 50 Rm 6318 MSC 8026, 50 South Dr, Bethesda, MD 20892, USA.
| | - D Rebecca Prevots
- Epidemiology Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 8 West Drive, MSC 2665, Bethesda, MD 20892, USA.
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Houldcroft CJ, Beale MA, Sayeed MA, Qadri F, Dougan G, Mutreja A. Identification of novel adenovirus genotype 90 in children from Bangladesh. Microb Genom 2018; 4. [PMID: 30248001 PMCID: PMC6249435 DOI: 10.1099/mgen.0.000221] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Novel adenovirus genotypes are associated with outbreaks of disease, such as acute gastroenteritis, renal disease, upper respiratory tract infection and keratoconjunctivitis. Here, we identify novel and variant adenovirus genotypes in children coinfected with enterotoxigenic Escherichia coli, in Bangladesh. Metagenomic sequencing of stool was performed and whole adenovirus genomes were extracted. A novel species D virus, designated genotype 90 (P33H27F67) was identified, and the partial genome of a putative recombinant species B virus was recovered. Furthermore, the enteric types HAdV-A61 and HAdV-A40 were found in stool specimens. Knowledge of the diversity of adenovirus genomes circulating worldwide, especially in low-income countries where the burden of disease is high, will be required to ensure that future vaccination strategies cover the diversity of adenovirus strains associated with disease.
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Affiliation(s)
| | - Mathew A Beale
- 2Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Md Abu Sayeed
- 3International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Firdausi Qadri
- 3International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Gordon Dougan
- 1Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ankur Mutreja
- 1Department of Medicine, University of Cambridge, Cambridge, UK
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Houldcroft CJ, Roy S, Morfopoulou S, Margetts BK, Depledge DP, Cudini J, Shah D, Brown JR, Romero EY, Williams R, Cloutman-Green E, Rao K, Standing JF, Hartley JC, Breuer J. Use of Whole-Genome Sequencing of Adenovirus in Immunocompromised Pediatric Patients to Identify Nosocomial Transmission and Mixed-Genotype Infection. J Infect Dis 2018; 218:1261-1271. [PMID: 29917114 DOI: 10.1093/infdis/jiy323] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/26/2018] [Indexed: 01/26/2023] Open
Abstract
Background Adenoviruses are significant pathogens for the immunocompromised, arising from primary infection or reinfection. Serotyping is insufficient to support nosocomial transmission investigations. We investigate whether whole-genome sequencing (WGS) provides clinically relevant information on transmission among patients in a pediatric tertiary hospital. Methods We developed a target-enriched adenovirus WGS technique for clinical samples and retrospectively sequenced 107 adenovirus-positive residual diagnostic samples, including viremias (>5 × 104 copies/mL), from 37 patients collected January 2011-March 2016. Whole-genome sequencing was used to determine genotype and for phylogenetic analysis. Results Adenovirus sequences were recovered from 105 of 107 samples. Full genome sequences were recovered from all 20 nonspecies C samples and from 36 of 85 species C viruses, with partial genome sequences recovered from the rest. Whole-genome phylogenetic analysis suggested linkage of 3 genotype A31 cases and uncovered an unsuspected epidemiological link to an A31 infection first detected on the same ward 4 years earlier. In 9 samples from 1 patient who died, we identified a mixed genotype adenovirus infection. Conclusions Adenovirus WGS from clinical samples is possible and useful for genotyping and molecular epidemiology. Whole-genome sequencing identified likely nosocomial transmission with greater resolution than conventional genotyping and distinguished between adenovirus disease due to single or multiple genotypes.
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Affiliation(s)
- Charlotte J Houldcroft
- Infection, Immunity and Inflammation Section, UCL Great Ormond Street Institute of Child Health, University College London, United Kingdom.,Division of Infection and Immunity, University College London, United Kingdom
| | - Sunando Roy
- Division of Infection and Immunity, University College London, United Kingdom
| | - Sofia Morfopoulou
- Division of Infection and Immunity, University College London, United Kingdom
| | - Ben K Margetts
- Infection, Immunity and Inflammation Section, UCL Great Ormond Street Institute of Child Health, University College London, United Kingdom.,Centre for Computation, Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, United Kingdom.,Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Daniel P Depledge
- Infection, Immunity and Inflammation Section, UCL Great Ormond Street Institute of Child Health, University College London, United Kingdom
| | - Juliana Cudini
- Division of Infection and Immunity, University College London, United Kingdom
| | - Divya Shah
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Julianne R Brown
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Erika Yara Romero
- Division of Infection and Immunity, University College London, United Kingdom
| | - Rachel Williams
- Division of Infection and Immunity, University College London, United Kingdom
| | - Elaine Cloutman-Green
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Kanchan Rao
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Joseph F Standing
- Infection, Immunity and Inflammation Section, UCL Great Ormond Street Institute of Child Health, University College London, United Kingdom.,Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - John C Hartley
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Judith Breuer
- Infection, Immunity and Inflammation Section, UCL Great Ormond Street Institute of Child Health, University College London, United Kingdom.,Division of Infection and Immunity, University College London, United Kingdom.,Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
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Xie J, Nettel-Aguirre A, Lee BE, Chui L, Pang XL, Zhuo R, Parsons B, Vanderkooi OG, Tarr PI, Ali S, Dickinson JA, Hagen E, Svenson LW, MacDonald SE, Drews SJ, Tellier R, Graham T, Lavoie M, MacDonald J, Freedman SB. Relationship between enteric pathogens and acute gastroenteritis disease severity: a prospective cohort study. Clin Microbiol Infect 2018; 25:454-461. [PMID: 29964235 DOI: 10.1016/j.cmi.2018.06.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/28/2018] [Accepted: 06/09/2018] [Indexed: 12/18/2022]
Abstract
OBJECTIVES To evaluate the relationship between individual bacterial and viral pathogens and disease severity. METHODS Children <18 years with three or more episodes of vomiting and/or diarrhoea were enrolled in two Canadian paediatric emergency departments between December 2014 and August 2016. Specimens were analysed employing molecular panels, and outcome data were collected 14 days after enrolment. The primary outcome was severe disease over the entire illness (symptom onset until 14-day follow-up), quantified employing the Modified Vesikari Scale (MVS) score. The score was additionally analysed in two other time periods: index (symptom onset until enrolment) and follow-up (enrolment until 14-day follow-up). RESULTS Median participant age was 20.7 (IQR: 11.3, 44.2) months; 47.4% (518/1093) and 73.4% (802/1093) of participants had index and total MVS scores ≥11, respectively. The most commonly identified pathogens were rotavirus (289/1093; 26.4%) and norovirus (258/1093; 23.6%). In multivariable analysis, severe disease over the entire illness was associated with rotavirus (OR = 9.60; 95%CI: 5.69, 16.19), Salmonella (OR = 6.61; 95%CI: 1.50, 29.17), adenovirus (OR = 2.53; 95%CI: 1.62, 3.97), and norovirus (OR = 1.43; 95%CI: 1.01, 2.01). Pathogens associated with severe disease at the index visit were: rotavirus only (OR = 6.13; 95%CI: 4.29, 8.75), Salmonella (OR = 4.59; 95%CI: 1.71, 12.29), adenovirus only (OR = 2.06; 95%CI: 1.41, 3.00), rotavirus plus adenovirus (OR = 3.15; 95%CI: 1.35, 7.37), and norovirus (OR = 0.68; 95%CI: 0.49, 0.94). During the follow-up period, rotavirus (OR = 2.21; 95%CI: 1.50, 3.25) and adenovirus (OR = 2.10; 95%CI: 1.39, 3.18) were associated with severe disease. CONCLUSIONS In children presenting for emergency department care with acute gastroenteritis, pathogens identified were predominantly viruses, and several of which were associated with severe disease. Salmonella was the sole bacterium independently associated with severe disease.
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Affiliation(s)
- J Xie
- Section of Pediatric Emergency Medicine, Alberta Children's Hospital, University of Calgary, Calgary, Alberta, Canada
| | - A Nettel-Aguirre
- Departments of Pediatrics and of Community Health Sciences, Cumming School of Medicine, Faculty of Kinesiology, Alberta Children's Hospital Research Institute, O'Brien Population Health Institute, University of Calgary, Calgary, Alberta, Canada
| | - B E Lee
- Department of Pediatrics, Faculty of Medicine and Dentistry, Women and Children's Health Research Institute, University of Alberta, Edmonton, Alberta, Canada
| | - L Chui
- Provincial Laboratory for Public Health, Alberta, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - X L Pang
- Provincial Laboratory for Public Health, Alberta, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - R Zhuo
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - B Parsons
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - O G Vanderkooi
- Departments of Pediatrics, Microbiology, Immunology and Infectious Diseases, Pathology and Laboratory Medicine and Community Health Sciences and the Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - P I Tarr
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
| | - S Ali
- Department of Pediatrics, Faculty of Medicine and Dentistry, Women and Children's Health Research Institute, University of Alberta, Edmonton, Alberta, Canada
| | - J A Dickinson
- Department of Family Medicine, University of Calgary, Calgary, Alberta, Canada; Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada
| | - E Hagen
- Section of Pediatric Emergency Medicine, Alberta Children's Hospital, University of Calgary, Calgary, Alberta, Canada
| | - L W Svenson
- Analytics and Performance Reporting, Alberta Health Division of Preventive Medicine, School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - S E MacDonald
- Faculty of Nursing, University of Alberta, Edmonton, Canada; School of Public Health, University of Alberta, Edmonton, Canada; Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada
| | - S J Drews
- Provincial Laboratory for Public Health, Alberta, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - R Tellier
- Provincial Laboratory for Public Health, Alberta, Canada; Departments of Pathology and Laboratory Medicine and Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - T Graham
- Alberta Health Services, Edmonton Zone, Alberta, Canada; Department of Emergency Medicine, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - M Lavoie
- Population and Public Health, Fraser Health, Surrey, British Columbia, Canada
| | - J MacDonald
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - S B Freedman
- Sections of Pediatric Emergency Medicine and Gastroenterology, Alberta Children's Hospital, Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.
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McHugh MP, Guerendiain D, Hardie A, Kenicer J, MacKenzie L, Templeton KE. Detection of Norovirus by BD MAX™, Xpert ® Norovirus, and xTAG ® Gastrointestinal Pathogen Panel in stool and vomit samples. J Clin Virol 2018; 105:72-76. [PMID: 29908520 DOI: 10.1016/j.jcv.2018.06.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/09/2018] [Accepted: 06/07/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND Norovirus is a leading cause of infectious gastroenteritis, characterized by outbreaks of diarrhoea and vomiting in closed settings. Nucleic acid amplification tests allow rapid and sensitive laboratory diagnosis of norovirus, with a number of commercial platforms now available. OBJECTIVES Evaluate the performance of the Becton Dickinson BD-MAX™System, Cepheid Xpert® Norovirus Assay, and Luminex xTAG® Gastrointestinal Pathogen Panel (GPP) for norovirus detection in stool. Assess the performance of the Xpert® Norovirus Assay and BD-MAX™ in vomit samples. STUDY DESIGN 163 diarrhoeal stool samples were tested on four diagnostic systems (laboratory-defined real time RT-PCR (assigned as gold standard), BD MAX™, Xpert® Norovirus Assay, and xTAG® GPP). A further 70 vomit samples were tested on the Xpert and BD MAX platforms. RESULTS In stool, sensitivity and specificity of the BD-MAX™ was 96.8% and 100%, for Xpert® Norovirus Assay was 91.9% and 100%, and for xTAG® GPP was 79.0% and 87.1%. In vomit samples positive and negative percent agreement was 95.6% and 92.0%, between the BD-MAX™ and Xpert® Norovirus. CONCLUSIONS The BD-MAX™ System with user defined settings and the Xpert® Norovirus Assay showed acceptable sensitivity and specificity for detection of norovirus from stool and vomit. The xTAG GPP assay was less reliable for norovirus detection but can detect a number of other clinically useful enteropathogens. Clinical laboratories must consider skill mix, budget, and sample throughput to determine the best fit for their service.
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Affiliation(s)
- Martin P McHugh
- Department of Molecular Microbiology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Daniel Guerendiain
- Department of Molecular Microbiology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Alison Hardie
- Department of Molecular Microbiology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Juliet Kenicer
- Department of Molecular Microbiology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Laura MacKenzie
- Department of Molecular Microbiology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Kate E Templeton
- Department of Molecular Microbiology, Royal Infirmary of Edinburgh, Edinburgh, UK.
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Abstract
Norovirus is a leading cause of childhood vomiting and diarrhea in the United States and globally. Although most illnesses caused by norovirus are self-resolving, severe outcomes may occur from dehydration, including hospitalization and death. A vast majority of deaths from norovirus occur in developing countries. Immunocompromised children are at risk for more severe outcomes. Treatment of norovirus illness is focused on early correction of dehydration and maintenance of fluid status and nutrition. Hand hygiene, exclusion of ill individuals, and environmental cleaning are important for norovirus outbreak prevention and control, and vaccines to prevent norovirus illness are currently under development.
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Affiliation(s)
- Minesh P Shah
- Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road Northeast, Atlanta, GA 30329, USA.
| | - Aron J Hall
- Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road Northeast, Atlanta, GA 30329, USA
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34
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Verstraeten T, Cattaert T, Harris J, Lopman B, Tam CC, Ferreira G. Estimating the Burden of Medically Attended Norovirus Gastroenteritis: Modeling Linked Primary Care and Hospitalization Datasets. J Infect Dis 2017; 216:957-965. [PMID: 28961927 PMCID: PMC5853278 DOI: 10.1093/infdis/jix410] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/17/2017] [Indexed: 12/11/2022] Open
Abstract
Background Norovirus is the leading cause of community-acquired and nosocomial acute gastroenteritis. Routine testing for norovirus is seldom undertaken, and diagnosis is mainly based on presenting symptoms. This makes understanding the burden of medically attended norovirus-attributable gastroenteritis (MA-NGE) and targeting care and prevention strategies challenging. Methods We used linked population-based healthcare datasets (Clinical Practice Research Datalink General Practice OnLine Database linked with Hospital Episode Statistics Admitted Patient Care) to model the incidence of MA-NGE associated with primary care consultations or hospitalizations according to age groups in England in the period July 2007–June 2013. Results Mean annual incidence rates of MA-NGE were 4.9/1000 person-years and 0.7/1000 person-years for episodes involving primary care or hospitalizations, respectively. Incidence rates were highest in children aged <5 years: 34.0 consultations/1000 person-years and 3.3 hospitalizations/1000 person-years. Medically attended norovirus-attributable gastroenteritis hospitalization rates were second highest in adults aged >65 years (1.7/1000 person-years). Conclusions In this particular study, the burden of MA-NGE estimated from healthcare datasets was higher than previously estimated in small cohort studies in England. Routinely collected primary care and hospitalization datasets are useful resources to estimate and monitor the burden of MA-NGE in a population over time.
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Affiliation(s)
- Thomas Verstraeten
- P95 Pharmacovigilance and Epidemiology, Heverlee, Belgium
- Correspondence: T. Verstraeten Koning Leopold III Laan 1, 3001 Heverlee, Belgium ()
| | - Tom Cattaert
- P95 Pharmacovigilance and Epidemiology, Heverlee, Belgium
| | - John Harris
- National Institute for Health Research Health Protection Research Unit in Gastrointestinal Infections, University of Liverpool
| | - Ben Lopman
- Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Clarence C Tam
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, United Kingdom
- Saw Swee Hock School of Public Health, National University of Singapore
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Biswas S, Jackson P, Shannon R, Dulwich K, Sukla S, Dixon RA. Molecular screening of blue mussels indicated high mid-summer prevalence of human genogroup II Noroviruses, including the pandemic "GII.4 2012" variants in UK coastal waters during 2013. Braz J Microbiol 2017; 49:279-284. [PMID: 29097140 PMCID: PMC5914202 DOI: 10.1016/j.bjm.2017.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/05/2017] [Accepted: 06/22/2017] [Indexed: 11/19/2022] Open
Abstract
This molecular study is the first report, to the best of our knowledge, on identification of norovirus, NoV GII.4 Sydney 2012 variants, from blue mussels collected from UK coastal waters. Blue mussels (three pooled samples from twelve mussels) collected during the 2013 summer months from UK coastal sites were screened by RT-PCR assays. PCR products of RdRP gene for noroviruses were purified, sequenced and subjected to phylogenetic analysis. All the samples tested positive for NoVs. Sequencing revealed that the NoV partial RdRP gene sequences from two pooled samples clustered with the pandemic "GII.4 Sydney variants" whilst the other pooled sample clustered with the NoV GII.2 variants. This molecular study indicated mussel contamination with pathogenic NoVs even during mid-summer in UK coastal waters which posed potential risk of NoV outbreaks irrespective of season. As the detection of Sydney 2012 NoV from our preliminary study of natural coastal mussels interestingly corroborated with NoV outbreaks in nearby areas during the same period, it emphasizes the importance of environmental surveillance work for forecast of high risk zones of NoV outbreaks.
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Affiliation(s)
- Subhajit Biswas
- University of Lincoln, School of Life Sciences, Brayford Pool, Lincoln, Lincolnshire, United Kingdom.
| | - Philippa Jackson
- University of Lincoln, School of Life Sciences, Brayford Pool, Lincoln, Lincolnshire, United Kingdom
| | - Rebecca Shannon
- University of Lincoln, School of Life Sciences, Brayford Pool, Lincoln, Lincolnshire, United Kingdom
| | - Katherine Dulwich
- University of Lincoln, School of Life Sciences, Brayford Pool, Lincoln, Lincolnshire, United Kingdom
| | - Soumi Sukla
- University of Lincoln, School of Life Sciences, Brayford Pool, Lincoln, Lincolnshire, United Kingdom
| | - Ronald A Dixon
- University of Lincoln, School of Life Sciences, Brayford Pool, Lincoln, Lincolnshire, United Kingdom
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Brown JR, Roy S, Tutill H, Williams R, Breuer J. Super-infections and relapses occur in chronic norovirus infections. J Clin Virol 2017; 96:44-48. [PMID: 28950185 DOI: 10.1016/j.jcv.2017.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/12/2017] [Accepted: 09/18/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND Norovirus causes chronic infections in immunocompromised patients with considerable associated morbidity. It is not known whether chronic infections involve super- or re-infections or relapses. OBJECTIVES To retrospectively investigate whether longitudinal sampling in chronically infected patients demonstrates persistent infection with the same virus, or super- or re-infection. STUDY DESIGN Norovirus full genomes were generated from 86 longitudinal samples from 25 paediatric patients. Consensus sequences were used for phylogenetic analysis and genotyping. RESULTS Super-infections occurred in 17% of chronically infected patients who were continuously PCR positive; including two with mixed norovirus infections. The median duration of infection was 107days longer in those with super-infections; however this was not statistically significant. A third of patients with interrupted norovirus shedding continued to be infected with the same virus despite up to 2 months of PCR negative stools, classified as a relapse. The majority (67%) of patients with interrupted shedding were re-infected with a different genotype. CONCLUSIONS Chronically infected patients who are continuously PCR positive are most likely to remain infected with the same virus; however super-infections do occur leading to mixed infection. Patients with interrupted shedding are likely to represent re-infection with a different genotype, however relapsing infections also occur. Our findings have implications for infection control as immunosuppressed patients remain susceptible to new norovirus infections despite current or recent infection and may continue to be infectious after norovirus is undetectable in stool. The relevance to children without co-morbidities remains to be determined.
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Affiliation(s)
- Julianne R Brown
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children NHS Foundation Trust, UK.
| | - Sunando Roy
- Infection and Immunity, University College London, UK
| | - Helena Tutill
- Infection and Immunity, University College London, UK
| | | | - Judith Breuer
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children NHS Foundation Trust, UK; Infection and Immunity, University College London, UK
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Yandle Z, Coughlan S, Drew RJ, O’Flaherty N, O’Gorman J, De Gascun C. Circulating rotavirus genotypes in the Irish paediatric population prior to the introduction of the vaccination programme. Ir J Med Sci 2017; 186:1003-1007. [DOI: 10.1007/s11845-017-1604-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/24/2017] [Indexed: 02/07/2023]
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Genotype analysis of noroviruses associated with gastroenteritis outbreaks in childcare centres, Victoria, Australia, 2012-2015. Epidemiol Infect 2017; 145:1933-1941. [PMID: 28397614 DOI: 10.1017/s0950268817000681] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The characteristics of norovirus outbreaks in children (0-5 years) in childcare centres in Victoria, Australia (2012-2015) were examined. The three most common open reading frame (ORF) 2 genotypes in childcare centre outbreaks were GII.4 (42%), GII.6 (21%) and GII.3 (14%); the remaining genotypes (GI.2, GI.3, GI.4, GI.8, GI.13, GII.1, GII.2, GII.7 and GII.13) each made up <10%. The GII.4 genotype was the only norovirus genotype seen in all 4 years of the study and was the most common genotype in 2012-2014 but in 2015 the most common genotype was GII.2. The GII.4 genotype was more common in children 0-2 years, whereas GII.2 and GII.7 were more common in children 4-5 years. ORF 1/ORF 2 recombinant forms identified were GII.P4_NewOrleans_2009/GII.4_Sydney_2012, GII.P12/GII.3, GII.Pb (GII.21)/GII.3, GII.Pe/GII.2, GII.Pe/GII.4_Sydney_2012 and GII.Pg/GII.1. The findings indicate that norovirus genotype prevalence patterns in children were influenced by the age of the children and the year in which the analysis was carried out. The majority of norovirus infections (84%) occurred after the first year of life so that vaccination before the age of one would appear to be the most efficacious.
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Abstract
Accurate diagnosis of viral infections enhances the ability of the clinician to make decisions on appropriate treatment of patients, evaluate disease progression and prevent misuse of antibiotics. Knowledge of the pathogen involved also allow implementation of infection control and monitoring of success of antiviral treatments that may affect the prognosis of patients. Epidemiological data collected through accurate diagnostics play an important role in public health through identification and control of outbreaks, implementation of appropriate diagnostic tests, vaccination programs and treatment but also to recognize common and emerging pathogens in a community. It is key that the clinician have an understanding of appropriate specimens to send to the laboratory and the value of specific nucleic acid and serological testing for different viral pathogens. Molecular techniques have revolutionized viral diagnoses over the past decade and enhanced both the sensitivity and specificity of tests and the speed by which a diagnosis can be made and new tests be developed. The continued use of serology for viruses with a short viremia, or for chronic infections should however complement these tests. This chapter aims to provide an overview of the available tests, the principles of testing and appropriate tests to select for different viruses and syndromes. Also provided is a glimpse of new developments in diagnostics that may further enhance the capacity to make a conclusive diagnosis in the near future.
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Affiliation(s)
- Robin J. Green
- Department of Paediatrics and Child Health, University of Pretoria, School of Medicine, Pretoria, ZA, South Africa
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40
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Brown JR, Roy S, Ruis C, Yara Romero E, Shah D, Williams R, Breuer J. Norovirus Whole-Genome Sequencing by SureSelect Target Enrichment: a Robust and Sensitive Method. J Clin Microbiol 2016; 54:2530-7. [PMID: 27487952 PMCID: PMC5035417 DOI: 10.1128/jcm.01052-16] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/21/2016] [Indexed: 01/11/2023] Open
Abstract
Norovirus full-genome sequencing is challenging due to sequence heterogeneity among genomes. Previous methods have relied on PCR amplification, which is problematic due to primer design, and transcriptome sequencing (RNA-Seq), which nonspecifically sequences all RNA, including host and bacterial RNA, in stool specimens. Target enrichment uses a panel of custom-designed 120-mer RNA baits that are complementary to all publicly available norovirus sequences, with multiple baits targeting each position of the genome, which overcomes the challenge of primer design. Norovirus genomes are enriched from stool RNA extracts to minimize the sequencing of nontarget RNA. SureSelect target enrichment and Illumina sequencing were used to sequence full genomes from 507 norovirus-positive stool samples with reverse transcription-real-time PCR cycle threshold (CT) values of 10 to 43. Sequencing on an Illumina MiSeq system in batches of 48 generated, on average, 81% on-target reads per sample and 100% genome coverage with >12,000-fold read depth. Samples included genotypes GI.1, GI.2, GI.3, GI.6, GI.7, GII.1, GII.2, GII.3, GII.4, GII.5, GII.6, GII.7, GII.13, GII.14, and GII.17. When outliers were accounted for, we generated >80% genome coverage for all positive samples, regardless of CT values. A total of 164 samples were tested in parallel with conventional PCR genotyping of the capsid shell domain; 164/164 samples were successfully sequenced, compared to 158/164 samples that were amplified by PCR. Four of the samples that failed capsid PCR analysis had low titers, which suggests that target enrichment is more sensitive than gel-based PCR. Two samples failed PCR due to primer mismatches; target enrichment uses multiple baits targeting each position, thus accommodating sequence heterogeneity among norovirus genomes.
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Affiliation(s)
- Julianne R Brown
- Microbiology, Virology, and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom NIHR Biomedical Research Centre at Great Ormond Street Hospital for Children NHS Foundation Trust and University College London, London, United Kingdom
| | - Sunando Roy
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Christopher Ruis
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Erika Yara Romero
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Divya Shah
- Microbiology, Virology, and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom NIHR Biomedical Research Centre at Great Ormond Street Hospital for Children NHS Foundation Trust and University College London, London, United Kingdom
| | - Rachel Williams
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Judy Breuer
- Microbiology, Virology, and Infection Control, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom Division of Infection and Immunity, University College London, London, United Kingdom
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