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Kachooei A, Mirhoseinian M, Jalilvand S, Latifi T, Feizi M, Shahosseini Z, Arashkia A, Marashi SM, Shoja Z. Molecular characterization of human astrovirus infection in children under 5 years of age with acute gastroenteritis in Tehran, Iran, 2021-2022: co-infection with rotavirus. Virus Genes 2024; 60:357-369. [PMID: 38744749 DOI: 10.1007/s11262-024-02075-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/26/2024] [Indexed: 05/16/2024]
Abstract
Human astroviruses (HAstVs) are considered important causative pathogens of acute gastroenteritis (AGE) in children under 5 years of age worldwide, along with group A rotavirus (RVA), norovirus (NoV), and enteric adenovirus (EAdV). The present study was aimed to both detect HAstV and its co-infections and investigate genetic analysis of circulating HAstV and co-infected virus in hospitalized children under 5 years of age with AGE in Iran. Accordingly, a sum of 200 stool specimens were screened by PCR for HAstV during 2021-2022. The HAstV was found in 0.5% of 200 specimens (n = 1) while was co-infected with RVA. The genetic and phylogenetic analysis indicated HAstV1 genotype, which clustered with viruses from lineage 1b, which has not been previously reported in Iran. The detected RVA strain belonged to G1 lineage II/P[8]-lineage III, which has been reported previously in Iran as the most common strain. The further genetic analysis of RVA VP6 and NSP4 demonstrated an atypical genotype pattern G1P[8]-I1-E2, as a mono-reassortant of a Wa-like genogroup, which appeared to be reassorted with the NSP4 gene of E2 genotype of the G2P[4] DS-1 genogroup. Although the clinical outcomes of the AGE-causing viruses co-infection is not yet entirely clear, it seems that future studies will be helpful to merge clinical and epidemiological data of co-infecting viruses for a more accurate medical and clinical relevance in symptomatic children.
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Affiliation(s)
- Atefeh Kachooei
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mahtab Mirhoseinian
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Somayeh Jalilvand
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Tayebeh Latifi
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, USA
| | - Mahsa Feizi
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Arash Arashkia
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran
- Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Sayed Mahdi Marashi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Zabihollah Shoja
- Department of Virology, Pasteur Institute of Iran, Tehran, Iran.
- Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran.
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Xie Z, Khamrin P, Jampanil N, Yodmeeklin A, Ukarapol N, Maneekarn N, Kumthip K. Enterovirus genotype diversity with emergence of coxsackievirus A2 circulating in pediatric patients with acute gastroenteritis in Thailand, 2019-2022. Front Microbiol 2024; 15:1414698. [PMID: 38887714 PMCID: PMC11180827 DOI: 10.3389/fmicb.2024.1414698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 05/17/2024] [Indexed: 06/20/2024] Open
Abstract
Introduction Enteroviruses (EVs) are recognized as potential causative agents of acute gastroenteritis (AGE) in children worldwide. This study aimed to investigate the epidemiology and molecular characteristics of EV infection in children admitted to hospitals with AGE in Chiang Mai, Thailand from 2019 to 2022. Methods A total of 1,148 fecal samples collected from patients with AGE were screened for the presence of EV using RT-PCR. The prevalence, co-infection with common diarrheal viruses, and seasonal pattern of EV were examined. The genotypes of EV were identified based on the VP1 sequence and phylogenetic analysis. Results The overall prevalence of EV in AGE patients was 8.8% (101/1,148). After the COVID-19 outbreak in 2019, a significant decrease in the EV infection rate and genotype diversity was observed (p < 0.05). EV infection alone was observed in 68.3% (69/101) of cases while co-infection with other enteric viruses was 31.7% (32/101). The seasonal pattern of EV infection showed a peak prevalence during the rainy season. EV species A was the most prevalent (37.5%), followed by species B (32.3%), species C (29.2%), and species D (1.0%). Twenty-five genotypes of EV were identified with the most predominant of the coxsackievirus A2 (CV-A2) (13.5%), CV-B2 (7.3%) and CV-A24 (5.2%). Conclusion Our data demonstrate a significant decrease in the prevalence and diversity of EV circulating in AGE patients during the COVID-19 pandemic and highlight the emergence of CV-A2 during this study period. These findings contribute to a better understanding of the molecular epidemiology and diversity of EV in patients with AGE and provide useful information for further investigation into the potential association between specific EV genotypes and AGE in future studies.
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Affiliation(s)
- Zhenfeng Xie
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Guangxi Colleges and Universities Key Laboratory of Basic Research and Transformation of Cancer Immunity and Infectious Diseases, Youjiang Medical University for Nationalities, Baise, China
| | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-Emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Nutthawadee Jampanil
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Arpaporn Yodmeeklin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-Emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Nuthapong Ukarapol
- Center of Excellence in Emerging and Re-Emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
- Department of Pediatrics, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-Emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
| | - Kattareeya Kumthip
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Emerging and Re-Emerging Diarrheal Viruses, Chiang Mai University, Chiang Mai, Thailand
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Amoroso MG, Pucciarelli A, Serra F, Ianiro G, Iafusco M, Fiorito F, Polverino MG, Dimatteo M, Monini M, Ferrara D, Martemucci L, Di Bartolo I, De Carlo E, Fusco G. Ten different viral agents infecting and co-infecting children with acute gastroenteritis in Southern Italy: Role of known pathogens and emerging viruses during and after COVID-19 pandemic. J Med Virol 2024; 96:e29679. [PMID: 38767190 DOI: 10.1002/jmv.29679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/18/2024] [Accepted: 05/08/2024] [Indexed: 05/22/2024]
Abstract
Acute gastroenteritis (AGE) represents a world public health relevant problem especially in children. Enteric viruses are the pathogens mainly involved in the episodes of AGE, causing about 70.00% of the cases. Apart from well-known rotavirus (RVA), adenovirus (AdV) and norovirus (NoV), there are various emerging viral pathogens potentially associated with AGE episodes. In this study, the presence of ten different enteric viruses was investigated in 152 fecal samples collected from children hospitalized for gastroenteritis. Real time PCR results showed that 49.3% of them were positive for viral detection with the following prevalence: norovirus GII 19.7%, AdV 15.8%, RVA 10.5%, human parechovirus (HPeV) 5.3%, enterovirus (EV) 3.3%, sapovirus (SaV) 2.6%. Salivirus (SalV), norovirus GI and astrovirus (AstV) 1.3% each, aichivirus (AiV) found in only one patient. In 38.2% of feces only one virus was detected, while co-infections were identified in 11.8% of the cases. Among young patients, 105 were ≤5 years old and 56.0% tested positive for viral detection, while 47 were >5 years old with 40.0% of them infected. Results obtained confirm a complex plethora of viruses potentially implicated in gastroenteritis in children, with some of them previously known for other etiologies but detectable in fecal samples. Subsequent studies should investigate the role of these viruses in causing gastroenteritis and explore the possibility that other symptoms may be ascribed to multiple infections.
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Affiliation(s)
- Maria Grazia Amoroso
- Department of Animal Health, Unit of Virology, Experimental Zooprophylactic Institute of Southern Italy, Portici, Italy
| | - Alessia Pucciarelli
- Department of Animal Health, Unit of Virology, Experimental Zooprophylactic Institute of Southern Italy, Portici, Italy
| | - Francesco Serra
- Department of Animal Health, Unit of Virology, Experimental Zooprophylactic Institute of Southern Italy, Portici, Italy
| | - Giovanni Ianiro
- Istituto Superiore di Sanità Department of Food Safety, Nutrition and Veterinary Public Health, Rome, Italy
| | - Michele Iafusco
- Pediatrics Department, "Pediatria 2", National Specialty Hospital Santobono Pausilipon, Napoli, Italy
| | - Filomena Fiorito
- Department of Veterinary Science and Animal Production, University of Naples Federico II, Naples, Italy
| | - Maria Grazia Polverino
- Department of Animal Health, Unit of Virology, Experimental Zooprophylactic Institute of Southern Italy, Portici, Italy
| | - Maria Dimatteo
- Department of Animal Health, Unit of Virology, Experimental Zooprophylactic Institute of Southern Italy, Portici, Italy
| | - Marina Monini
- Istituto Superiore di Sanità Department of Food Safety, Nutrition and Veterinary Public Health, Rome, Italy
| | - Daniela Ferrara
- Pediatrics Department, "Pediatria 2", National Specialty Hospital Santobono Pausilipon, Napoli, Italy
| | - Luigi Martemucci
- Pediatrics Department, "Pediatria 2", National Specialty Hospital Santobono Pausilipon, Napoli, Italy
| | - Ilaria Di Bartolo
- Istituto Superiore di Sanità Department of Food Safety, Nutrition and Veterinary Public Health, Rome, Italy
| | - Esterina De Carlo
- Department of Animal Health, Unit of Virology, Experimental Zooprophylactic Institute of Southern Italy, Portici, Italy
| | - Giovanna Fusco
- Department of Animal Health, Unit of Virology, Experimental Zooprophylactic Institute of Southern Italy, Portici, Italy
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Jungbauer-Groznica M, Wiese K, Fischer I, Markus J, Chang TH, Gösler I, Kowalski H, Blaas D, Real-Hohn A. Aichivirus A1 replicates in human intestinal epithelium and bronchial tissue: Lung-gut axis? Virus Res 2024; 342:199338. [PMID: 38373599 PMCID: PMC10901855 DOI: 10.1016/j.virusres.2024.199338] [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: 12/28/2023] [Revised: 02/08/2024] [Accepted: 02/10/2024] [Indexed: 02/21/2024]
Abstract
The role of aichivirus A1 (AiV-A1) in acute gastroenteritis remains controversial and in vitro data illustrating its pathogenesis in suitable human models are scarce. Here, we demonstrate that AiV-A1 isolate A846/88 replicates in ApoA1- (absorptive) and Ki-67-positive (proliferative) enterocytes in stem cell-derived human small intestinal epithelium (HIE) as well as in patient biopsy samples, but not in any of the tested human cell lines. The infection did not result in tissue damage and did not trigger type I and type III interferon (IFN) signalling, whereas the control, human coxsackievirus B3 (strain Nancy), triggered both IFNs. To investigate the tissue tropism, we infected a human tracheal/bronchial epithelium model (HTBE) with AiV-A1 isolates A846/88 and kvgh99012632/2010 and, as a control, with rhinovirus A2 (RV-A2). AiV-A1 isolate kvgh99012632/2010, but not isolate A846/88, replicated in HTBE and induced type III IFN and ISGs signalling. By using various pharmacological inhibitors, we elaborated that cellular entry of AiV-A1 depends on clathrin, dynamin, and lipid rafts and is strongly reliant on endosome acidification. Viral particles co-localised with Rab5a-positive endosomes and promoted leakage of endosomal content. Our data shed light on the early events of AiV-A1 infection and reveal that different isolates exhibit distinct tissue tropism. This supports its clinical importance as a human pathogen with the potential to evolve toward broader tissue specificity.
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Affiliation(s)
- Martin Jungbauer-Groznica
- Center for Medical Biochemistry, Vienna Biocenter, Max Perutz Laboratories, Medical University of Vienna, Vienna, Austria; Virus and Immunity Unit, Institute Pasteur, Université Paris Cité, Paris, France
| | - Konstantin Wiese
- Center for Medical Biochemistry, Vienna Biocenter, Max Perutz Laboratories, Medical University of Vienna, Vienna, Austria
| | - Irmgard Fischer
- Histology Facility, Vienna Biocenter, Max Perutz Laboratories, Vienna, Austria
| | - Jan Markus
- MatTek In Vitro Life Science Laboratories, Bratislava, Slovakia
| | - Tsung-Hsien Chang
- National Defense Medical Center, Department of Microbiology and Immunology, Taipei, Taiwan
| | - Irene Gösler
- Center for Medical Biochemistry, Vienna Biocenter, Max Perutz Laboratories, Medical University of Vienna, Vienna, Austria
| | - Heinrich Kowalski
- Center for Medical Biochemistry, Vienna Biocenter, Max Perutz Laboratories, Medical University of Vienna, Vienna, Austria.
| | - Dieter Blaas
- Center for Medical Biochemistry, Vienna Biocenter, Max Perutz Laboratories, Medical University of Vienna, Vienna, Austria
| | - Antonio Real-Hohn
- Center for Medical Biochemistry, Vienna Biocenter, Max Perutz Laboratories, Medical University of Vienna, Vienna, Austria.
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5
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Flynn TG, Olortegui MP, Kosek MN. Viral gastroenteritis. Lancet 2024; 403:862-876. [PMID: 38340741 DOI: 10.1016/s0140-6736(23)02037-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/17/2023] [Accepted: 09/18/2023] [Indexed: 02/12/2024]
Abstract
Since the discovery of norovirus in 1972 as a cause of what was contemporarily known as acute infectious non-bacterial gastroenteritis, scientific understanding of the viral gastroenteritides has continued to evolve. It is now recognised that a small number of viruses are the predominant cause of acute gastroenteritis worldwide, in both high-income and low-income settings. Although treatment is still largely restricted to the replacement of fluid and electrolytes, improved diagnostics have allowed attribution of illness, enabling both targeted treatment of individual patients and prioritisation of interventions for populations worldwide. Questions remain regarding specific genetic and immunological factors underlying host susceptibility, and the optimal clinical management of patients who are susceptible to severe or prolonged manifestations of disease. Meanwhile, the worldwide implementation of rotavirus vaccines has led to substantial reductions in morbidity and mortality, and spurred interest in vaccine development to diminish the impact of the most prevalent viruses that are implicated in this syndrome.
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Affiliation(s)
- Thomas G Flynn
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | | | - Margaret N Kosek
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
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6
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Borkakoty B, Bali NK, Jakaria A, Hazarika R, Temsu T, Gohain M, Kaur H. Norovirus gastroenteritis in children under-five years hospitalized for diarrhea in two cities of northeast India: A retrospective study. Indian J Med Microbiol 2023; 45:100397. [PMID: 37573056 DOI: 10.1016/j.ijmmb.2023.100397] [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: 02/02/2023] [Revised: 04/25/2023] [Accepted: 05/27/2023] [Indexed: 08/14/2023]
Abstract
PURPOSE Norovirus gastroenteritis, known to cause 'winter vomiting disease' is increasingly being identified as a major cause of viral gastroenteritis worldwide. The impact and prevalence of this viral disease are lacking in many parts of India including northeast India. This study aimed to determine the prevalence and association of norovirus gastroenteritis among under-five-year-old hospitalized children in two cities in northeast India (Dibrugarh in Assam & Dimapur in Nagaland). MATERIALS AND METHODS A retrospective analysis of 407 randomly selected diarrheal stool samples was conducted using a commercial multiplex probed-based real-time RT-PCR assay capable of detecting six-viral gastroenteritis pathogens including Norovirus GI, Norovirus GII, Rotavirus, Human Adenovirus, Human Astrovirus, and Sapovirus. RESULTS Results showed that norovirus was detected in 18.4% of the samples (75/407; 95% CI: 14.8%-22.5%), with norovirus genogroup II being the predominant group in 97.3% of norovirus cases. A significant association of norovirus diarrhea was found with seasonality, with higher prevalence in colder months compared to warmer months (22.4% vs 9.1%, p-value:0.002). Additionally, 66.7% (50/75) of cases of norovirus gastroenteritis had reported vomiting as the major symptom and had a shorter duration of diarrhea (p-value 0.03). Co-infections with other viral pathogens were seen in 45.9% (187/407) of the cases. The detection of rotavirus was 67.1% (273/407), human adenovirus (45.9%; 187/407), sapovirus and astrovirus (5.9%, 24/407 each), and norovirus GI (0.5%, 2/407) among the cases. CONCLUSION This study reports the prevalence of norovirus gastroenteritis in northeast India and further highlights that norovirus gastroenteritis is responsible for substantial cases of hospitalization of under-five years children in the region.
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Affiliation(s)
- Biswajyoti Borkakoty
- Indian Council of Medical Research-Regional Medical Research Centre for NE Region, Bokel, Dibrugarh, 786010, Assam, India.
| | - Nargis K Bali
- Department of Clinical Microbiology, Sher-I Kashmir Institute of Medical Sciences, Soura, Srinagar, Jammu & Kashmir, India.
| | - Aniruddha Jakaria
- Indian Council of Medical Research-Regional Medical Research Centre for NE Region, Bokel, Dibrugarh, 786010, Assam, India.
| | - Rahul Hazarika
- Indian Council of Medical Research-Regional Medical Research Centre for NE Region, Bokel, Dibrugarh, 786010, Assam, India.
| | - T Temsu
- District Hospital Dimapur, 797112, Nagaland, India.
| | - Munmun Gohain
- NRSN Project, Department of Paediatrics, Assam Medical College & Hospital, Dibrugarh, 786005, Assam, India.
| | - Harpreet Kaur
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research-New Delhi-110029, India.
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Schmitz D, Zwagemaker F, van der Veer B, Vennema H, Laros JFJ, Koopmans MPG, De Graaf M, Kroneman A. Metagenomic Surveillance of Viral Gastroenteritis in a Public Health Setting. Microbiol Spectr 2023; 11:e0502222. [PMID: 37432120 PMCID: PMC10434279 DOI: 10.1128/spectrum.05022-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 06/06/2023] [Indexed: 07/12/2023] Open
Abstract
Norovirus is the primary cause of viral gastroenteritis (GE). To investigate norovirus epidemiology, there is a need for whole-genome sequencing and reference sets consisting of complete genomes. To investigate the potential of shotgun metagenomic sequencing on the Illumina platform for whole-genome sequencing, 71 reverse transcriptase quantitative PCR (RT-qPCR) norovirus positive-feces (threshold cycle [CT], <30) samples from norovirus surveillance within The Netherlands were subjected to metagenomic sequencing. Data were analyzed through an in-house next-generation sequencing (NGS) analysis workflow. Additionally, we assessed the potential of metagenomic sequencing for the surveillance of off-target viruses that are of importance for public health, e.g., sapovirus, rotavirus A, enterovirus, parechovirus, aichivirus, adenovirus, and bocaparvovirus. A total of 60 complete and 10 partial norovirus genomes were generated, representing 7 genogroup I capsid genotypes and 12 genogroup II capsid genotypes. In addition to the norovirus genomes, the metagenomic approach yielded partial or complete genomes of other viruses for 39% of samples from children and 6.7% of samples from adults, including adenovirus 41 (N = 1); aichivirus 1 (N = 1); coxsackievirus A2 (N = 2), A4 (N = 2), A5 (N = 1), and A16 (N = 1); bocaparvovirus 1 (N = 1) and 3 (N = 1); human parechovirus 1 (N = 2) and 3 (N = 1); Rotavirus A (N = 1); and a sapovirus GI.7 (N = 1). The sapovirus GI.7 was initially not detected through RT-qPCR and warranted an update of the primer and probe set. Metagenomic sequencing on the Illumina platform robustly determines complete norovirus genomes and may be used to broaden gastroenteritis surveillance by capturing off-target enteric viruses. IMPORTANCE Viral gastroenteritis results in significant morbidity and mortality in vulnerable individuals and is primarily caused by norovirus. To investigate norovirus epidemiology, there is a need for whole-genome sequencing and reference sets consisting of full genomes. Using surveillance samples sent to the Dutch National Institute for Public Health and the Environment (RIVM), we compared metagenomics against conventional techniques, such as RT-qPCR and Sanger-sequencing, with norovirus as the target pathogen. We determined that metagenomics is a robust method to generate complete norovirus genomes, in parallel to many off-target pathogenic enteric virus genomes, thereby broadening our surveillance efforts. Moreover, we detected a sapovirus that was not detected by our validated gastroenteritis RT-qPCR panel, which exemplifies the strength of metagenomics. Our study shows that metagenomics can be used for public health gastroenteritis surveillance, the generation of reference-sets for molecular epidemiology, and how it compares to current surveillance strategies.
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Affiliation(s)
- Dennis Schmitz
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
- Erasmus Medical Center, Viroscience, Rotterdam, The Netherlands
| | - Florian Zwagemaker
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
| | - Bas van der Veer
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
| | - Harry Vennema
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
| | - Jeroen F. J. Laros
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands
| | | | | | - Annelies Kroneman
- National Institute of Public Health and the Environment, Center for Infectious Disease Control, Bilthoven, The Netherlands
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8
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Stockdale SR, Blanchard AM, Nayak A, Husain A, Nashine R, Dudani H, McClure CP, Tarr AW, Nag A, Meena E, Sinha V, Shrivastava SK, Hill C, Singer AC, Gomes RL, Acheampong E, Chidambaram SB, Bhatnagar T, Vetrivel U, Arora S, Kashyap RS, Monaghan TM. RNA-Seq of untreated wastewater to assess COVID-19 and emerging and endemic viruses for public health surveillance. THE LANCET REGIONAL HEALTH. SOUTHEAST ASIA 2023; 14:100205. [PMID: 37193348 PMCID: PMC10150210 DOI: 10.1016/j.lansea.2023.100205] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 04/10/2023] [Accepted: 04/24/2023] [Indexed: 05/18/2023]
Abstract
Background The COVID-19 pandemic showcased the power of genomic sequencing to tackle the emergence and spread of infectious diseases. However, metagenomic sequencing of total microbial RNAs in wastewater has the potential to assess multiple infectious diseases simultaneously and has yet to be explored. Methods A retrospective RNA-Seq epidemiological survey of 140 untreated composite wastewater samples was performed across urban (n = 112) and rural (n = 28) areas of Nagpur, Central India. Composite wastewater samples were prepared by pooling 422 individual grab samples collected prospectively from sewer lines of urban municipality zones and open drains of rural areas from 3rd February to 3rd April 2021, during the second COVID-19 wave in India. Samples were pre-processed and total RNA was extracted prior to genomic sequencing. Findings This is the first study that has utilised culture and/or probe-independent unbiased RNA-Seq to examine Indian wastewater samples. Our findings reveal the detection of zoonotic viruses including chikungunya, Jingmen tick and rabies viruses, which have not previously been reported in wastewater. SARS-CoV-2 was detectable in 83 locations (59%), with stark abundance variations observed between sampling sites. Hepatitis C virus was the most frequently detected infectious virus, identified in 113 locations and co-occurring 77 times with SARS-CoV-2; and both were more abundantly detected in rural areas than urban zones. Concurrent identification of segmented virus genomic fragments of influenza A virus, norovirus, and rotavirus was observed. Geographical differences were also observed for astrovirus, saffold virus, husavirus, and aichi virus that were more prevalent in urban samples, while the zoonotic viruses chikungunya and rabies, were more abundant in rural environments. Interpretation RNA-Seq can effectively detect multiple infectious diseases simultaneously, facilitating geographical and epidemiological surveys of endemic viruses that could help direct healthcare interventions against emergent and pre-existent infectious diseases as well as cost-effectively and qualitatively characterising the health status of the population over time. Funding UK Research and Innovation (UKRI) Global Challenges Research Fund (GCRF) grant number H54810, as supported by Research England.
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Affiliation(s)
| | - Adam M. Blanchard
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - Amit Nayak
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Aliabbas Husain
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Rupam Nashine
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Hemanshi Dudani
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - C. Patrick McClure
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust, Nottingham, United Kingdom
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, United Kingdom
| | - Alexander W. Tarr
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust, Nottingham, United Kingdom
- Wolfson Centre for Global Virus Research, University of Nottingham, Nottingham, United Kingdom
- Queen's Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Aditi Nag
- Dr. B. Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Ekta Meena
- Dr. B. Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Vikky Sinha
- Dr. B. Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Sandeep K. Shrivastava
- Centre for Innovation, Research & Development, Dr. B. Lal Clinical Laboratory Pvt. Ltd., Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
| | - Andrew C. Singer
- UK Centre for Ecology and Hydrology, Wallingford, United Kingdom
| | - Rachel L. Gomes
- Food Water Waste Research Group, Faculty of Engineering, University of Nottingham, United Kingdom
| | - Edward Acheampong
- Food Water Waste Research Group, Faculty of Engineering, University of Nottingham, United Kingdom
- Department of Statistics and Actuarial Science, University of Ghana, P.O. Box, LG 115, Legon, Ghana
| | - Saravana B. Chidambaram
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru, 570015, KA, India
| | - Tarun Bhatnagar
- ICMR-National Institute of Epidemiology, Chennai, Tamil Nadu, India
| | - Umashankar Vetrivel
- National Institute of Traditional Medicine, Indian Council of Medical Research, Belagavi, 590010, India
- Virology and Biotechnology Division, ICMR-National Institute for Research in Tuberculosis, Chennai, 600031, India
| | - Sudipti Arora
- Dr. B. Lal Institute of Biotechnology, 6-E, Malviya Industrial Area, Malviya Nagar, Jaipur, India
| | - Rajpal Singh Kashyap
- Research Centre, Dr G.M. Taori Central India Institute of Medical Sciences (CIIMS), Nagpur, Maharashtra, India
| | - Tanya M. Monaghan
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Hospitals National Health Service Trust, Nottingham, United Kingdom
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
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9
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Chigor VN, Chidebelu PE, Digwo DC, Chigor CB, Nwagwu AU, Udeh OS, Oguonu CI, Dibua MEU, Farkas K. Assessment of the aetiology of acute gastroenteritis outbreaks in infants reveals rotavirus, noroviruses and adenovirus prevalence and viral coinfections in Nsukka, Nigeria. Virusdisease 2023; 34:297-306. [PMID: 37408547 PMCID: PMC10317937 DOI: 10.1007/s13337-023-00821-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/10/2023] [Indexed: 07/07/2023] Open
Abstract
A better understanding of the aetiology of acute gastroenteritis (AGE) outbreaks in Southeast Nigeria would help safeguarding public health. This study screened stool samples collected from infants (children < 5 years of age) attending selected hospitals in Nsukka for human enteric viruses and evaluated the seasonality of AGE based on three-year records available at selected hospitals. A total of 120 stool samples (109 from diarrhoeal-patients and 11 from non-diarrhoeal patients, as control) collected during the AGE outbreaks of January - March 2019 and January-February 2020. The samples were analysed using an immunochromatographic lateral flow assay for differential qualitative detection of rotavirus (RoV), adenovirus (AdV), and norovirus genogroups I and II (NoVI, NoVII). Three-year (2017-2019) retrospective data on the cases of AGE reported at the hospitals were also collected and analysed. The overall prevalence of acute gastroenteritis was high (75.83%), with 13.19%representing viral co-infections. Rotavirus detection rate (69.17%) was higher than that for other viral agents (15.83%). Both mono- and mixed infections were observed for RoV, AdV and NoVII, whereas NoVI was detected only in co-infection cases. Analysis of risk factors showed that acute gastroenteritis was detected more often in infants of age ˂1 year (73.53%) than in those 1 ≤ 2 years (22.55%) or > 2 years (3.92%) in age. Gender and age were not associated with the cases of co-infections (p˂0.05). The seasonality data indicated one peak of the infection occurring in January 2017 which has decreased consecutively in the subsequent two years. These results demonstrate the prevalence and co-occurrence of enteric viruses in cases of infantile diarrhoea in Nsukka. Further molecular characterization of enteric virus strains, especially noroviruses, in this region would contribute significantly to global epidemiological data. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-023-00821-2.
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Affiliation(s)
- Vincent N. Chigor
- Water and Public Health Research Group (WPHRG), University of Nigeria, Nsukka, Enugu State Nigeria
| | - Paul E. Chidebelu
- Water and Public Health Research Group (WPHRG), University of Nigeria, Nsukka, Enugu State Nigeria
| | - Daniel C. Digwo
- Water and Public Health Research Group (WPHRG), University of Nigeria, Nsukka, Enugu State Nigeria
| | - Chinyere B. Chigor
- Water and Public Health Research Group (WPHRG), University of Nigeria, Nsukka, Enugu State Nigeria
| | - Aja U. Nwagwu
- Water and Public Health Research Group (WPHRG), University of Nigeria, Nsukka, Enugu State Nigeria
| | - Okwundu S. Udeh
- GOPD/Paediatrics, Faith Foundation Mission Hospital, Nsuk,Ka, Nsukka, Enugu State Nigeria
| | - Chukwunonso I. Oguonu
- GOPD/Paediatrics, Nsukka Medical Clinic, Ugwunkwo, Nsukka, Nsukka, Enugu State Nigeria
| | - Marie-Esther U. Dibua
- Water and Public Health Research Group (WPHRG), University of Nigeria, Nsukka, Enugu State Nigeria
| | - Kata Farkas
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey, UK
- School of Natural Sciences, Bangor University, Bangor, Gwynedd UK
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10
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Virus Association with Gastric Inflammation and Cancer: An Updated Overview. JOURNAL OF MEDICAL MICROBIOLOGY AND INFECTIOUS DISEASES 2022. [DOI: 10.52547/jommid.10.4.163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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11
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Hijazi G, Dakroub F, Khoueiry P, El-Kurdi A, Ezzeddine A, Alkalamouni H, Alansari K, Althani AA, Mathew S, AlKhatib HA, Yassine HM, Zaraket H. Viral metagenomics analysis of stool specimens from children with unresolved gastroenteritis in Qatar. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 105:105367. [PMID: 36115643 DOI: 10.1016/j.meegid.2022.105367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/26/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
Acute gastroenteritis (AGE) is associated with significant global morbidity and mortality, especially among children under five years of age. Viruses are well established as etiologic agents of gastroenteritis since they are the most common pathogens that contribute to the disease burden in developing countries. Despite the advances in molecular diagnosis, a substantial proportion of AGE etiology remain unresolved. We implemented a viral metagenomics pipeline to determine the potential viral etiology associated with AGE among children under the age of five years in Qatar with undiagnosed etiology. Following enriching for the viral genome, ∼1.3 billion sequences were generated from 89 stool specimens using the Illumina HiSeq platform, of which 7% were mapped to viral genomes. Human viruses were detected in 34 specimens (38.2%); 14 were adenovirus, nine coxsackievirus A16, five rotavirus (G9P[8] and G4P[8]), four norovirus (GII), one influenza A virus (H3), and one respiratory syncytial virus A (RSVA). In conclusion, the viral metagenomics approach is useful for determining AGE's etiology when routine molecular diagnostic assays fail.
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Affiliation(s)
- Ghina Hijazi
- Department of Experimental Pathology, Microbiology, and Immunology, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon; Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Fatima Dakroub
- Department of Experimental Pathology, Microbiology, and Immunology, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon; Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Pierre Khoueiry
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon; Pillar Genomics Institute, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Abdullah El-Kurdi
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon; Pillar Genomics Institute, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Amani Ezzeddine
- Department of Experimental Pathology, Microbiology, and Immunology, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon; Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Habib Alkalamouni
- Department of Experimental Pathology, Microbiology, and Immunology, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon; Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon
| | | | - Asmaa A Althani
- Biomedical Research Center, Qatar University, Doha 2713, Qatar
| | - Shilu Mathew
- Biomedical Research Center, Qatar University, Doha 2713, Qatar
| | | | - Hadi M Yassine
- Biomedical Research Center, Qatar University, Doha 2713, Qatar.
| | - Hassan Zaraket
- Department of Experimental Pathology, Microbiology, and Immunology, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon; Center for Infectious Diseases Research, Faculty of Medicine, American University of Beirut, Beirut 1107 2020, Lebanon.
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12
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Razizadeh MH, Pourrostami K, Kachooei A, Zarei M, Asghari M, Hamldar S, Khatami A. An annoying enteric virus: A systematic review and meta‐analysis of human astroviruses and gastrointestinal complications in children. Rev Med Virol 2022; 32:e2389. [DOI: 10.1002/rmv.2389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/22/2022] [Accepted: 07/21/2022] [Indexed: 11/11/2022]
Affiliation(s)
| | - Kumars Pourrostami
- Department of Pediatrics School of Medicine Alborz University of Medical Sciences Karaj Iran
- Dietary Supplements and Probiotic Research Center Alborz University of Medical Sciences Karaj Iran
| | - Atefeh Kachooei
- Department of Virology Faculty of Medicine Iran University of Medical Sciences Tehran Iran
| | - Mohammad Zarei
- Renal Division Harvard Medical School Brigham and Women's Hospital Boston Massachusetts USA
- Harvard T.H. Chan School of Public Health John B. Little Center for Radiation Sciences Boston Massachusetts USA
| | - Milad Asghari
- Department of Microbiology Faculty of Basic Science Tabriz Branch Islamic Azad University Tabriz Iran
| | - Shahrzad Hamldar
- Department of Virology Faculty of Medicine Iran University of Medical Sciences Tehran Iran
| | - Alireza Khatami
- Department of Virology Faculty of Medicine Iran University of Medical Sciences Tehran Iran
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13
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Kennedy EA, Holtz LR. Gut virome in early life: origins and implications. Curr Opin Virol 2022; 55:101233. [PMID: 35690009 PMCID: PMC9575407 DOI: 10.1016/j.coviro.2022.101233] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 12/15/2022]
Abstract
The human body is colonized by a multitude of bacteria, fungi, and viruses, which play important roles in health and disease. Microbial colonization during early life is thought to be a particularly important period with lasting consequences for health. Viral populations in the gut are particularly dynamic in early life before they stabilize in adulthood. The composition of the early-life virome is increasingly recognized as a determinant of disease later in life. Here, we review the development of the virome in healthy infants, as well as the role of the early-life virome in the development of disease states including diarrhea, malnutrition, and autoimmune diseases.
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Affiliation(s)
- Elizabeth A Kennedy
- Washington University School of Medicine, Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, St. Louis, MO 63110, USA
| | - Lori R Holtz
- Washington University School of Medicine, Department of Pediatrics, St. Louis, MO 63110, USA.
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14
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Microbiota succession throughout life from the cradle to the grave. Nat Rev Microbiol 2022; 20:707-720. [PMID: 35906422 DOI: 10.1038/s41579-022-00768-z] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2022] [Indexed: 11/08/2022]
Abstract
Associations between age and the human microbiota are robust and reproducible. The microbial composition at several body sites can predict human chronological age relatively accurately. Although it is largely unknown why specific microorganisms are more abundant at certain ages, human microbiota research has elucidated a series of microbial community transformations that occur between birth and death. In this Review, we explore microbial succession in the healthy human microbiota from the cradle to the grave. We discuss the stages from primary succession at birth, to disruptions by disease or antibiotic use, to microbial expansion at death. We address how these successions differ by body site and by domain (bacteria, fungi or viruses). We also review experimental tools that microbiota researchers use to conduct this work. Finally, we discuss future directions for studying the microbiota's relationship with age, including designing consistent, well-powered, longitudinal studies, performing robust statistical analyses and improving characterization of non-bacterial microorganisms.
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15
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Tiamani K, Luo S, Schulz S, Xue J, Costa R, Khan Mirzaei M, Deng L. The role of virome in the gastrointestinal tract and beyond. FEMS Microbiol Rev 2022; 46:6608358. [PMID: 35700129 PMCID: PMC9629487 DOI: 10.1093/femsre/fuac027] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 01/11/2023] Open
Abstract
The human gut virome is comprised of diverse commensal and pathogenic viruses. The colonization by these viruses begins right after birth through vaginal delivery, then continues through breastfeeding, and broader environmental exposure. Their constant interaction with their bacterial hosts in the body shapes not only our microbiomes but us. In addition, these viruses interact with the immune cells, trigger a broad range of immune responses, and influence different metabolic pathways. Besides its key role in regulating the human gut homeostasis, the intestinal virome contributes to disease development in distant organs, both directly and indirectly. In this review, we will describe the changes in the gut virome through life, health, and disease, followed by discussing the interactions between the virome, the microbiome, and the human host as well as providing an overview of their contribution to gut disease and disease of distant organs.
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Affiliation(s)
| | | | - Sarah Schulz
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany,Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Jinling Xue
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany,Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Rita Costa
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany,Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Mohammadali Khan Mirzaei
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany,Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Li Deng
- Corresponding author: Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany; Chair of Prevention of Microbial Diseases, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany. E-mail:
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16
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Cuevas-Ferrando E, Pérez-Cataluña A, Falcó I, Randazzo W, Sánchez G. Monitoring Human Viral Pathogens Reveals Potential Hazard for Treated Wastewater Discharge or Reuse. Front Microbiol 2022; 13:836193. [PMID: 35464930 PMCID: PMC9026171 DOI: 10.3389/fmicb.2022.836193] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/21/2022] [Indexed: 01/22/2023] Open
Abstract
Wastewater discharge to the environment or its reuse after sanitization poses a concern for public health given the risk of transmission of human viral diseases. However, estimating the viral infectivity along the wastewater cycle presents technical challenges and still remains underexplored. Recently, human-associated crAssphage has been investigated to serve as viral pathogen indicator to monitor fecal impacted water bodies, even though its assessment as biomarker for infectious enteric viruses has not been explored yet. To this end, the occurrence of potentially infectious norovirus genogroup I (GI), norovirus GII, hepatitis A virus (HAV), rotavirus A (RV), and human astrovirus (HAstV) along with crAssphage was investigated in influent and effluent water sampled in four wastewater treatment plants (WWTPs) over 1 year by a PMAxx-based capsid integrity RT-qPCR assay. Moreover, influent and effluent samples of a selected WWTP were additionally assayed by an in situ capture RT-qPCR assay (ISC-RT-qPCR) as estimate for viral infectivity in alternative to PMAxx-RT-qPCR. Overall, our results showed lower viral occurrence and concentration assessed by ISC-RT-qPCR than PMAxx-RT-qPCR. Occurrence of potentially infectious enteric virus was estimated by PMAxx-RT-qPCR as 88–94% in influent and 46–67% in effluent wastewaters with mean titers ranging from 4.77 to 5.89, and from 3.86 to 4.97 log10 GC/L, with the exception of HAV that was sporadically detected. All samples tested positive for crAssphage at concentration ranging from 7.41 to 9.99 log10 GC/L in influent and from 4.56 to 6.96 log10 GC/L in effluent wastewater, showing higher mean concentration than targeted enteric viruses. Data obtained by PMAxx-RT-qPCR showed that crAssphage strongly correlated with norovirus GII (ρ = 0.67, p < 0.05) and weakly with HAstV and RV (ρ = 0.25–0.30, p < 0.05) in influent samples. In effluent wastewater, weak (ρ = 0.27–0.38, p < 0.05) to moderate (ρ = 0.47–0.48, p < 0.05) correlations between crAssphage and targeted viruses were observed. Overall, these results corroborate crAssphage as an indicator for fecal contamination in wastewater but a poor marker for either viral occurrence and viral integrity/infectivity. Despite the viral load reductions detected in effluent compared to influent wastewaters, the estimates of viral infectivity based on viability molecular methods might pose a concern for (re)-using of treated water.
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17
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Bruijnesteijn van Coppenraet LES, Flipse J, Wallinga JA, Vermeer M, van der Reijden WA, Weel JFL, van der Zanden AGM, Schuurs TA, Ruijs GJHM. From a case-control survey to a diagnostic viral gastroenteritis panel for testing of general practitioners' patients. PLoS One 2021; 16:e0258680. [PMID: 34731182 PMCID: PMC8565752 DOI: 10.1371/journal.pone.0258680] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 10/01/2021] [Indexed: 01/31/2023] Open
Abstract
OBJECTIVE To evaluate the pathogenicity of a broad range of 11 possible gastroenteritis viruses, by means of statistical relationships with cases vs. controls, or Ct-values, in order to establish the most appropriate diagnostic panel for our general practitioner (GP) patients in the Netherlands (2010-2012). METHODS Archived stool samples from 1340 cases and 1100 controls were retested using internally controlled multiplex real-time PCRs for putative pathogenic gastroenteritis viruses: adenovirus, astrovirus, bocavirus, enterovirus, norovirus GI and GII, human parechovirus, rotavirus, salivirus, sapovirus, and torovirus. RESULTS The prevalence of any virus in symptomatic cases and asymptomatic controls was 16.6% (223/1340) and 10.2% (112/1100), respectively. Prevalence of astrovirus (adjusted odds ratio (aOR) 10.37; 95% confidence interval (CI) 1.34-80.06) and norovirus GII (aOR 3.10; CI 1.62-5.92) was significantly higher in cases versus controls. Rotavirus was encountered only in cases. We did not find torovirus and there was no statistically significant relationship with cases for salivirus (aOR 1,67; (CI) 0.43-6.54)), adenovirus non-group F (aOR 1.20; CI 0.75-1.91), bocavirus (aOR 0.85; CI 0.05-13.64), enterovirus (aOR 0.83; CI 0.50-1.37), human parechovirus (aOR 1.61; CI 0.54-4.77) and sapovirus (aOR 1.15; CI 0.67-1.98). Though adenovirus group F (aOR 6.37; CI 0.80-50.92) and norovirus GI (aOR 2.22, CI: 0.79-6.23) are known enteropathogenic viruses and were more prevalent in cases than in controls, this did not reach significance in this study. The Ct value did not discriminate between carriage and disease in PCR-positive subjects. CONCLUSIONS In our population, diagnostic gastroenteritis tests should screen for adenovirus group F, astrovirus, noroviruses GI and GII, and rotavirus. Case-control studies as ours are lacking and should also be carried out in populations from other epidemiological backgrounds.
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Affiliation(s)
| | - Jacky Flipse
- Laboratory of Medical Microbiology and Infectious Diseases, Isala, Zwolle, The Netherlands
| | - Janny A. Wallinga
- Laboratory of Medical Microbiology and Infectious Diseases, Isala, Zwolle, The Netherlands
| | - Marloes Vermeer
- ZGT Academy, Ziekenhuisgroep Twente, Almelo, The Netherlands
| | - Wil A. van der Reijden
- Regional Laboratory for Medical Microbiology and Public Health Kennemerland, Haarlem, The Netherlands
| | - Jan F. L. Weel
- Izore, Center for Infectious Diseases Friesland, Leeuwarden, The Netherlands
| | | | - Theo A. Schuurs
- Izore, Center for Infectious Diseases Friesland, Leeuwarden, The Netherlands
| | - Gijs J. H. M. Ruijs
- Laboratory of Medical Microbiology and Infectious Diseases, Isala, Zwolle, The Netherlands
- * E-mail:
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18
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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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19
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Huang D, Wang Z, Zhang G, Sai L. Molecular and epidemiological characterization of human adenoviruses infection among children with acute diarrhea in Shandong Province, China. Virol J 2021; 18:195. [PMID: 34579757 PMCID: PMC8474830 DOI: 10.1186/s12985-021-01666-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/20/2021] [Indexed: 12/30/2022] Open
Abstract
Background Human adenovirus (HAdV) had been recognized as one of the most common enteric viruses associated with acute diarrhea in children. The present study was carried out to demonstrate the molecular and epidemiological characterization of HAdV Infections among children in Shandong province in China between July 2017 and June 2018. Methods Fecal specimens were collected from children under 5 years old with acute diarrhea. DNA was extracted from the stool specimens and adenovirus DNA was detected by PCR amplification with specific primers. The amplification products were subjected to electrophoresis and visualized on a UV transilluminator. All positive RT-PCR amplification products were sequenced and the obtained sequences analyzed by MEGA (version 7.0). Demographic information and clinical manifestation data were also analyzed. Results In total, 656 fecal specimens were collected and the overall positive rate of HAdV was 7.47%. HAdV infections were detected in all age groups, in which children aged 13–24 months presented the highest positive rate. Seasonal pattern could be observed with a peak in December, January and February. Diarrhea, vomiting, dehydration and fever were the main clinical manifestations, in which vomiting was the most common accompanied symptom. By phylogenetic analysis, four species (A, B, C, and F) were detected and seven different serotypes were identified. HAdV-41 (48.98%, 24/49) was the most common serotype followed by HAdV-3 (18.37%, 9/49), HAdV-31 (14.29%, 7/49), HAdV-7 (8.16%, 4/49), HAdV-40 (4.08%, 2/49), HAdV-1 (4.08%, 2/49) and HAdV-2 (2.04%, 1/49). Conclusion This study indicated that HAdV infection was an important cause of acute diarrhea among children under 5 years old in Shandong province. The results will contribute to (a) increase understanding of the role of HAdV in diarrheal children and enhance identification of the predominant diarrhea pathogen for diagnosis; (b) avoid abuse of antibiotics; (c) monitor the change of prevalent HAdV serotypes and promote vaccine development and vaccination.
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Affiliation(s)
- Deyu Huang
- Department of Infectious Diseases, Affiliated Hospital of Qingdao University, Jiangsu Road 16, Qingdao, 266000, Shandong, China
| | - Zheng Wang
- Department of Infectious Diseases, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Wenhua Xi Road 107, Jinan, 250012, Shandong, China
| | - Guanyou Zhang
- Department of Infectious Diseases, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Wenhua Xi Road 107, Jinan, 250012, Shandong, China
| | - Lintao Sai
- Department of Infectious Diseases, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Wenhua Xi Road 107, Jinan, 250012, Shandong, China.
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20
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Merk VM, Brunner T. Immunosuppressive glucocorticoids at epithelial barriers in the regulation of anti-viral immune response. VITAMINS AND HORMONES 2021; 117:77-100. [PMID: 34420586 DOI: 10.1016/bs.vh.2021.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The anti-inflammatory action of adrenal-derived glucocorticoids has been recognized since several decades. This knowledge has found broad application in the clinics and today synthetic glucocorticoids are widely used in the treatment of various inflammatory diseases. However, the use of synthetic glucocorticoids in the treatment of diseases associated with viral infections of epithelial surfaces, like the lung or the intestine, is still under debate and seems not as efficient as desired. Basic research on the anti-viral immune responses and on regulatory mechanisms in the prevention of immunopathological disorders, however, has led us back again to focus on endogenous glucocorticoid synthesis. It has become established that this synthesis is not restricted to the adrenal glands alone, but that numerous tissues also produce glucocorticoids in situ. Extra-adrenal derived glucocorticoids have the capacity to locally control and maintain immune homeostasis under steady-state and inflammatory conditions. Here, we discuss the current knowledge of extra-adrenal glucocorticoid synthesis in the lung and the intestine, and its role in the regulation of anti-viral immune responses.
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Affiliation(s)
- V M Merk
- Chair of Biochemical Pharmacology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - T Brunner
- Chair of Biochemical Pharmacology, Department of Biology, University of Konstanz, Konstanz, Germany.
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Ali DA, Tesema TS, Belachew YD. RETRACTED ARTICLE: Molecular detection of pathogenic Escherichia coli strains and their antibiogram associated with risk factors from diarrheic calves in Jimma Ethiopia. Sci Rep 2021; 11:14356. [PMID: 34257358 PMCID: PMC8277816 DOI: 10.1038/s41598-021-93688-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 06/22/2021] [Indexed: 02/06/2023] Open
Abstract
Diarrheagenic Escherichia coli are a number of pathogenic E. coli strains that cause diarrheal infection both in animal and human hosts due to their virulence factors. A cross sectional study was conducted between November, 2016 and April, 2017 to isolate and molecularly detect pathogenic E. coli from diarrheic calves to determine the pathogenic strains, antibiogram and associated risk factors in Jimma town. Purposive sampling technique was used to collect 112 fecal samples from diarrheic calves. Conventional culture and biochemical methods were conducted to isolate E. coli isolates. Molecular method was followed to identify virulence factors of pathogenic E. coli strains. Antimicrobial sensitivity patterns of the isolates were tested using the Kirby-Bauer disk diffusion method. A structured questionnaire was also used to collect information from dairy farms and socio-demographic data. The overall isolation rate of E. coli in calves was 51.8% (58/112) (95% CI 42.0-61.0). The occurrence of the bacterium differed significantly by age, colostrum feeding time, amount of milk given per time and navel treatment (P < 0.05). Multivariable analysis revealed that the odds of being infected was significantly highest in calves which fed 1-1.5 L amount of milk per a time (OR 5.38, 95% CI 1.66-17.45, P = 0.005). The overall virulence genes detection rate was 53.5% (95% CI 40.0-67.0). Eleven (19.6%) of eaeA, 6 (10.7%) of Stx1 and 13 (23.2%) of Stx2 genes were detected from calves isolates. Except ciprofloxacillin, all isolates were resistant to at least one drug. Multi drug resistance was recorded in 68.0% (38/56) of calves isolates. Neomycin, 83.3% (25/30), followed by amoxicillin, 53.3% (16/30) were the highest resisted virulence genes. The study demonstrated considerable isolation rate, multiple antimicrobial resistant isolates and high resistant virulent genes in diarrheic calves. It also indicated that the potential importance of calves as source of pathogenic E. coli strains and resistant genes for human diarrhea infection. Improving the hygienic practice of farms and wise use of antimicrobials could help to reduce the occurrence of pathogenic E. coli in farms. Hence, further studies are needed to describe all virulent factors and serotypes associated with the emergence of drug resistant pathogenic E. coli strains in calves.
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Affiliation(s)
- Destaw Asfaw Ali
- College of Veterinary Medicine and Animal Sciences, University of Gondar, Gondar, Ethiopia.
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22
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Bonura F, Mascarella C, Filizzolo C, Bonura C, Ferraro D, Di Bernardo F, Collura A, Martella V, Giammanco GM, De Grazia S. Evaluation of the diagnostic performances of two commercially available assays for the detection of enteric adenovirus antigens. Diagn Microbiol Infect Dis 2021; 101:115459. [PMID: 34280672 DOI: 10.1016/j.diagmicrobio.2021.115459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/01/2021] [Accepted: 06/15/2021] [Indexed: 12/21/2022]
Abstract
The performance of 2 antigenic commercial assays for enteric adenovirus (AdV) infection, bioNexia Rota-Adeno ImmunoChromatographic Tests (ICT) and LIAISON® Adenovirus ChemiLuminescence Immuno Assays (CLIA), was evaluated on 321 stools from children hospitalized for acute gastroenteritis in Palermo, Italy, using a Real time-PCR (Rt-PCR) as reference method. The CLIA showed higher sensitivity (77% vs 60%), accuracy (94.4 vs 90.9) and concordance (k: 0.81 vs 0.67) with respect to ICT, despite equivalent specificity (98.8%). Using the Ct values of the Rt-PCR as a proxy of the fecal viral load, similar Ct values (mean 9.32 vs 9.89) were observed among the true positive samples, whilst a significant difference (P < 0.05) was observed in false negative samples of CLIA (mean Ct 25.68) and ICT (mean Ct 19.87). Cross-reactivity with other enteric viruses was not observed. These results indicate that both the assays tested are suitable for diagnosis of AdV gastroenteritis.
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Affiliation(s)
- Floriana Bonura
- Dipartimento di Scienze per la Promozione della Salute e Materno Infantile "G. D'Alessandro", Palermo, Italy
| | - Chiara Mascarella
- Dipartimento di Scienze per la Promozione della Salute e Materno Infantile "G. D'Alessandro", Palermo, Italy
| | - Chiara Filizzolo
- Dipartimento di Scienze per la Promozione della Salute e Materno Infantile "G. D'Alessandro", Palermo, Italy
| | - Celestino Bonura
- Dipartimento di Scienze per la Promozione della Salute e Materno Infantile "G. D'Alessandro", Palermo, Italy
| | - Donatella Ferraro
- Dipartimento di Scienze per la Promozione della Salute e Materno Infantile "G. D'Alessandro", Palermo, Italy
| | - Francesca Di Bernardo
- Unità Operativa di Microbiologia e Virologia, Ospedale Civico e Di Cristina, ARNAS, Palermo, Italy
| | - Antonella Collura
- Unità Operativa di Microbiologia e Virologia, Ospedale Civico e Di Cristina, ARNAS, Palermo, Italy
| | - Vito Martella
- Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Valenzano, Italy
| | - Giovanni M Giammanco
- Dipartimento di Scienze per la Promozione della Salute e Materno Infantile "G. D'Alessandro", Palermo, Italy
| | - Simona De Grazia
- Dipartimento di Scienze per la Promozione della Salute e Materno Infantile "G. D'Alessandro", Palermo, Italy.
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23
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Levi ME. Identification and Management of Traveler's Diarrhea. J Midwifery Womens Health 2021; 66:380-384. [PMID: 34101972 DOI: 10.1111/jmwh.13256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Traveler's diarrhea (TD) is a common occurrence when people travel to foreign countries and can affect individuals of all ages, including those who are pregnant. This clinical syndrome is caused by a variety of intestinal pathogens, and treatment is based on the acuity of the patient's symptoms. This case report describes the clinical presentation and management of a pregnant woman with a history of TD who requests an antibiotic prescription for the potential need of empiric self-treatment of TD for an upcoming business trip outside of the United States. The clinical presentation of TD, differential diagnoses, treatment plan options, prevention recommendations, and empiric self-treatment are reviewed. Current evidence-based guidelines are discussed, and high-risk conditions such as pregnancy are considered.
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Affiliation(s)
- Miriam E Levi
- Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota
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24
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Comparative Analysis of Public RNA-Sequencing Data from Human Intestinal Enteroid (HIEs) Infected with Enteric RNA Viruses Identifies Universal and Virus-Specific Epithelial Responses. Viruses 2021; 13:v13061059. [PMID: 34205050 PMCID: PMC8227290 DOI: 10.3390/v13061059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/18/2021] [Accepted: 05/28/2021] [Indexed: 01/18/2023] Open
Abstract
Acute gastroenteritis (AGE) has a significant disease burden on society. Noroviruses, rotaviruses, and astroviruses are important viral causes of AGE but are relatively understudied enteric pathogens. Recent developments in novel biomimetic human models of enteric disease are opening new possibilities for studying human-specific host-microbe interactions. Human intestinal enteroids (HIE), which are epithelium-only intestinal organoids derived from stem cells isolated from human intestinal biopsy tissues, have been successfully used to culture representative norovirus, rotavirus, and astrovirus strains. Previous studies investigated host-virus interactions at the intestinal epithelial interface by individually profiling the epithelial transcriptional response to a member of each virus family by RNA sequencing (RNA-seq). Despite differences in the tissue origin, enteric virus used, and hours post infection at which RNA was collected in each data set, the uniform analysis of publicly available datasets identified a conserved epithelial response to virus infection focused around "type I interferon production" and interferon-stimulated genes. Additionally, transcriptional changes specific to only one or two of the enteric viruses were also identified. This study can guide future explorations into common and unique aspects of the host response to virus infections in the human intestinal epithelium and demonstrates the promise of comparative RNA-seq analysis, even if performed under different experimental conditions, to discover universal and virus-specific genes and pathways responsible for antiviral host defense.
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25
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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:e20201044. [PMID: 33760921 PMCID: PMC8006857 DOI: 10.1084/jem.20201044] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [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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26
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Hrdy J, Vasickova P, Nesvadbova M, Novotny J, Mati T, Kralik P. MOL-PCR and xMAP Technology: A Multiplex System for Fast Detection of Food- and Waterborne Viruses. J Mol Diagn 2021; 23:765-776. [PMID: 33864939 DOI: 10.1016/j.jmoldx.2021.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/26/2021] [Accepted: 03/30/2021] [Indexed: 11/30/2022] Open
Abstract
Viruses are common causes of food- and waterborne diseases worldwide. Conventional identification of these agents is based on cultivation, antigen detection, electron microscopy, or real-time PCR. Because recent technological advancements in detection methods are focused on fast and robust analysis, a rapid multiplexing technology, which can detect a broad spectrum of pathogenic viruses connected to food or water contamination, was utilized. A new semiquantitative magnetic bead-based multiplex system has been designed for simultaneous detection of several targets in one reaction. The system includes adenoviruses 40/41 (AdV), rotavirus A (RVA), norovirus (NoV), hepatitis E virus (HEV), hepatitis A virus (HAV), and a target for external control of the system. To evaluate the detection system, interlaboratory ring tests were performed in four independent laboratories. Analytical specificity of the tool was tested on a cohort of pathogenic agents and biological samples with quantitative PCR as a reference method. Limit of detection (analytical sensitivity) of 5 × 100 (AdV, HEV, and RVA) and 5 × 101 (HAV and NoV) genome equivalents per reaction was reached. This robust, senstivie, and rapid multiplexing technology may be used to routinely monitor and manage viruses in food and water to prevent food and waterborne diseases.
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Affiliation(s)
- Jakub Hrdy
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Brno, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Petra Vasickova
- Department of Microbiology and Antimicrobial Resistance, Veterinary Research Institute, Brno, Czech Republic
| | - Michaela Nesvadbova
- Department of Animal Origin Food and Gastronomic Sciences, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | - Jiri Novotny
- Military Health Institute, Military Medical Agency, Prague, Czech Republic
| | - Tomas Mati
- Military Veterinary Institute, Hlucin, Czech Republic
| | - Petr Kralik
- Department of Animal Origin Food and Gastronomic Sciences, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
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27
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IFN-λ4 is associated with increased risk and earlier occurrence of several common infections in African children. Genes Immun 2021; 22:44-55. [PMID: 33850301 PMCID: PMC8042471 DOI: 10.1038/s41435-021-00127-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 03/23/2021] [Accepted: 03/29/2021] [Indexed: 02/01/2023]
Abstract
Genetic polymorphisms within the IFNL3/IFNL4 genomic region, which encodes type III interferons, have been strongly associated with clearance of hepatitis C virus. We hypothesized that type III interferons might be important for the immune response to other pathogens as well. In a cohort of 914 Malian children, we genotyped functional variants IFNL4-rs368234815, IFNL4-rs117648444, and IFNL3-rs4803217 and analyzed episodes of malaria, gastrointestinal, and respiratory infections recorded at 30,626 clinic visits from birth up to 5 years of age. Compared to children with the rs368234815-TT/TT genotype (IFN-λ4-Null), rs368234815-dG allele was most strongly associated with an earlier time-to-first episode of gastrointestinal infections (p = 0.003). The risk of experiencing an infection episode during the follow-up was also significantly increased with rs368234815-dG allele, with OR = 1.53, 95%CI (1.13-2.07), p = 0.005 for gastrointestinal infections and OR = 1.30, 95%CI (1.02-1.65), p = 0.033 for malaria. All the associations for the moderately linked rs4803217 (r2 = 0.78 in this set) were weaker and lost significance after adjusting for rs368234815. We also analyzed all outcomes in relation to IFN-λ4-P70S groups. Our results implicate IFN-λ4 and not IFN-λ3 as the primary functional cause of genetic associations with increased overall risk and younger age at first clinical episodes but not with recurrence or intensity of several common pediatric infections.
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28
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Abstract
The human body hosts vast microbial communities, termed the microbiome. Less well known is the fact that the human body also hosts vast numbers of different viruses, collectively termed the 'virome'. Viruses are believed to be the most abundant and diverse biological entities on our planet, with an estimated 1031 particles on Earth. The human virome is similarly vast and complex, consisting of approximately 1013 particles per human individual, with great heterogeneity. In recent years, studies of the human virome using metagenomic sequencing and other methods have clarified aspects of human virome diversity at different body sites, the relationships to disease states and mechanisms of establishment of the human virome during early life. Despite increasing focus, it remains the case that the majority of sequence data in a typical virome study remain unidentified, highlighting the extent of unexplored viral 'dark matter'. Nevertheless, it is now clear that viral community states can be associated with adverse outcomes for the human host, whereas other states are characteristic of health. In this Review, we provide an overview of research on the human virome and highlight outstanding recent studies that explore the assembly, composition and dynamics of the human virome as well as host-virome interactions in health and disease.
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29
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Understanding Pediatric Norovirus Epidemiology: A Decade of Study among Ghanaian Children. Viruses 2020; 12:v12111321. [PMID: 33217894 PMCID: PMC7698731 DOI: 10.3390/v12111321] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 02/05/2023] Open
Abstract
Understanding the epidemiology of human norovirus infection in children within Ghana and the entire sub-Saharan African region, where future norovirus vaccines would have the greatest impact, is essential. We analyzed 1337 diarrheic stool samples collected from children <5 years from January 2008 to December 2017 and found 485 (36.2%) shedding the virus. GII.4 (54.1%), GII.3 (7.7%), GII.6 (5.3%), GII.17 (4.7%), and GII.5 (4.7%) were the most common norovirus genotypes. Although norovirus GII.4 remained the predominant capsid genotype throughout the study period, an increase in GII.6 and GII.3 capsid genotypes was observed in 2013 and 2014, respectively. The severity of clinical illness in children infected with GII.4 norovirus strains was similar to illness caused by non-GII.4 strains. Since the epidemiology of norovirus changes rapidly, establishment of systematic surveillance within sentinel sites across the country would enhance the monitoring of circulating norovirus strains and allow continuous understanding of norovirus infection in Ghana.
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30
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Wan Q, Song D, Li H, He ML. Stress proteins: the biological functions in virus infection, present and challenges for target-based antiviral drug development. Signal Transduct Target Ther 2020; 5:125. [PMID: 32661235 PMCID: PMC7356129 DOI: 10.1038/s41392-020-00233-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/26/2020] [Accepted: 06/13/2020] [Indexed: 02/06/2023] Open
Abstract
Stress proteins (SPs) including heat-shock proteins (HSPs), RNA chaperones, and ER associated stress proteins are molecular chaperones essential for cellular homeostasis. The major functions of HSPs include chaperoning misfolded or unfolded polypeptides, protecting cells from toxic stress, and presenting immune and inflammatory cytokines. Regarded as a double-edged sword, HSPs also cooperate with numerous viruses and cancer cells to promote their survival. RNA chaperones are a group of heterogeneous nuclear ribonucleoproteins (hnRNPs), which are essential factors for manipulating both the functions and metabolisms of pre-mRNAs/hnRNAs transcribed by RNA polymerase II. hnRNPs involve in a large number of cellular processes, including chromatin remodelling, transcription regulation, RNP assembly and stabilization, RNA export, virus replication, histone-like nucleoid structuring, and even intracellular immunity. Dysregulation of stress proteins is associated with many human diseases including human cancer, cardiovascular diseases, neurodegenerative diseases (e.g., Parkinson’s diseases, Alzheimer disease), stroke and infectious diseases. In this review, we summarized the biologic function of stress proteins, and current progress on their mechanisms related to virus reproduction and diseases caused by virus infections. As SPs also attract a great interest as potential antiviral targets (e.g., COVID-19), we also discuss the present progress and challenges in this area of HSP-based drug development, as well as with compounds already under clinical evaluation.
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Affiliation(s)
- Qianya Wan
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Dan Song
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Huangcan Li
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Ming-Liang He
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, China. .,CityU Shenzhen Research Institute, Shenzhen, China.
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31
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Strubbia S, Schaeffer J, Besnard A, Wacrenier C, Le Mennec C, Garry P, Desdouits M, Le Guyader FS. Metagenomic to evaluate norovirus genomic diversity in oysters: Impact on hexamer selection and targeted capture-based enrichment. Int J Food Microbiol 2020; 323:108588. [PMID: 32200157 DOI: 10.1016/j.ijfoodmicro.2020.108588] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 02/08/2023]
Abstract
Human virus transmission through food consumption has been identified since many years and the international trade increases the risk of dissemination of viral pathogens. The development of metagenomic approach holds many promises for the surveillance of viruses in food and water. This work aimed to analyze norovirus diversity and to evaluate strain-dependent accumulation patterns in three oyster types by using a metagenomic approach. Different hexamer sets to prime cDNA were evaluated before capture-based approach to enhance virus reads recovery during deep sequencing. The study includes the use of technical replicates of artificially contaminated oysters and the analysis of multiple negatives controls. Results showed a clear impact of the hexamer set used for cDNA synthesis. A set of In-house designed (I-HD) hexamers, selected to lower mollusk amplification, gave promising results in terms of viral reads abundancy. However, the best correlation between CT values, thus concentrations, and number of reads was observed using random hexamers. Random hexamers also provided the highest numbers of reads and allowed the identification of sequence of different human enteric viruses. Regarding human norovirus, different genogroups and genotypes were identified among contigs longer than 500 bp. Two full genomes and six sequences longer than 3600 bases were obtained allowing a precise strain identification. The use of technical triplicates was found valuable to increase the chances to sequence viral strains present at low concentrations. Analyzing viral contamination in shellfish samples is quite challenging, however this work demonstrates that the recovery of full genome or long contigs, allowing clear identification of viral strains is possible.
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Affiliation(s)
| | | | - Alban Besnard
- Ifremer, Laboratoire de Microbiologie LSEM-SG2M, France
| | | | | | - Pascal Garry
- Ifremer, Laboratoire de Microbiologie LSEM-SG2M, France
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32
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De Grazia S, Bonura F, Bonura C, Mangiaracina L, Filizzolo C, Martella V, Giammanco GM. Assessing the burden of viral co-infections in acute gastroenteritis in children: An eleven-year-long investigation. J Clin Virol 2020; 129:104513. [PMID: 32575023 DOI: 10.1016/j.jcv.2020.104513] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/05/2020] [Accepted: 06/14/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Acute gastroenteritis is an important cause of childhood morbidity and mortality worldwide. A number of pathogens are responsible for human acute gastroenteritis. The recent introduction of syndromic assays for the diagnosis of enteric infections, including a wide panel of enteric pathogens, has unveiled the frequency of mixed infections. This study was carried out to assess the burden of viral co-infections and the genetic diversity of the viruses detected in children hospitalized with acute gastroenteritis in Italy. METHODS A total of 4161 stool samples collected from diarrheic children over 11 years, from January 2008 to December 2018, were investigated for the presence of four enteric viruses, i.e. group A rotavirus, norovirus, astrovirus and adenovirus. The samples were initially screened by either molecular or immunochromatographic assays and subsequently confirmed by Real-time PCR and sequence analyses. RESULTS At least one viral agent was detected in 48.6 %of specimens. Rotavirus was the most prevalent virus (24.7 %) followed by norovirus (19.6 %), adenovirus (5.3 %) and astrovirus (3%). Co-infections were detected in 8.3 % of virus-positive patients, with common viral combination being rotavirus with norovirus (70.6 % of co-infections) or with astrovirus (9.6 %). A variety of viral genotypes was detected in co-infections and in single infections. Using Real-time PCR cycle thresholds as a proxy measure of fecal viral load, rotavirus was generally detected at higher levels in co-infected patients. CONCLUSIONS Combining and deciphering measurable indicators of viral load and epidemiological information could be useful for an accurate interpretation of viral co-infections.
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Affiliation(s)
- Simona De Grazia
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy.
| | - Floriana Bonura
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy
| | - Celestino Bonura
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy
| | - Leonardo Mangiaracina
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy
| | - Chiara Filizzolo
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy
| | - Vito Martella
- Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Valenzano, Italy
| | - Giovanni M Giammanco
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy
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33
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Liang G, Zhao C, Zhang H, Mattei L, Sherrill-Mix S, Bittinger K, Kessler LR, Wu GD, Baldassano RN, DeRusso P, Ford E, Elovitz MA, Kelly MS, Patel MZ, Mazhani T, Gerber JS, Kelly A, Zemel BS, Bushman FD. The stepwise assembly of the neonatal virome is modulated by breastfeeding. Nature 2020; 581:470-474. [PMID: 32461640 PMCID: PMC7263352 DOI: 10.1038/s41586-020-2192-1] [Citation(s) in RCA: 152] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 02/14/2020] [Indexed: 01/01/2023]
Abstract
The gut of healthy human neonates is usually devoid of viruses at birth, but quickly becomes colonized, in some cases leading to gastrointestinal disorders1–4. Here we report that viral community assembly in neonates takes place in distinct steps. Fluorescent staining of virus-like particles purified from infant meconium/early stool samples show few or no particles, but by one month of life particle numbers achieve 109 per gram, and these numbers appear to persist through life5–7. We investigated the origin of these viral populations using shotgun metagenomic sequencing of viral-enriched preparations and whole microbial communities, and followed up with targeted microbiological analyses. Results indicate that, early after birth, pioneer bacteria colonize the infant gut, and by one month prophage induced from these bacteria provide the predominant population of virus-like particles. By four months of life, identifiable viruses that replicate in human cells become more prominent. Multiple human viruses were more abundant in stool samples from babies exclusively fed formula versus those fed partially or fully on breast milk, paralleling reports that breast milk can be protective against viral infections8–10. Phage populations also differed associated with breastfeeding. Evidently colonization of the infant gut is stepwise, first mainly by temperate bacteriophages induced from pioneer bacteria, and later by viruses that replicate in human cells, with the second phase modulated by breastfeeding.
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Affiliation(s)
- Guanxiang Liang
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Chunyu Zhao
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Huanjia Zhang
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lisa Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Scott Sherrill-Mix
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lyanna R Kessler
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gary D Wu
- Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert N Baldassano
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Patricia DeRusso
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Eileen Ford
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michal A Elovitz
- Maternal and Child Health Research Center, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Matthew S Kelly
- Division of Pediatric Infectious Diseases, Duke University, Durham, NC, USA
| | - Mohamed Z Patel
- Department of Paediatric and Adolescent Health, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Tiny Mazhani
- Department of Paediatric and Adolescent Health, Faculty of Medicine, University of Botswana, Gaborone, Botswana
| | - Jeffrey S Gerber
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Andrea Kelly
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Babette S Zemel
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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UV Inactivation of Rotavirus and Tulane Virus Targets Different Components of the Virions. Appl Environ Microbiol 2020; 86:AEM.02436-19. [PMID: 31811032 DOI: 10.1128/aem.02436-19] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 11/25/2019] [Indexed: 12/19/2022] Open
Abstract
Enteric viruses are shed in fecal material by humans and other animals and are common contaminants in wastewater and surface water. Wastewater treatment plants often disinfect this effluent with low-pressure and medium-pressure UV lamps, which emit 254-nm and 220- to 280-nm irradiation, respectively. It is not known whether this treatment is efficacious against enteric viruses or how such treatments may inactivate these enteric viruses. This study examined UV disinfection for two enteric viruses: rotavirus (RV) (strain OSU with double-stranded RNA and a three-layer capsid) and Tulane virus (TV) (a cultivable surrogate for human norovirus with single-stranded RNA and a single-layer capsid). Viruses were treated with UV irradiation at 220 or 254 nm under conditions relevant to wastewater stabilization ponds, whose water is often used for irrigation. TV was susceptible to 220- or 254-nm UV at similar levels. It appears that UV irradiation inactivated TV by mutagenizing both its genome and capsid binding proteins. RV was more susceptible to UV at 220 nm than to UV at 254 nm. UV irradiation of RV at either 220 or 254 nm resulted in a virus that retained its ability to bind to its host cell receptor. After 220-nm treatment, the VP7 segment of the RV genome could not be amplified by PCR, suggesting that this treatment mutagenized the viral genome. However, this correlation was not observed when UV at 254 nm was used. Thus, RV and TV, with different genome and capsid contents, are targeted by UV irradiation in different ways.IMPORTANCE UV irradiation is becoming common for disinfection in water treatment plants, but little is known about the effectiveness of this treatment for enteric RNA viruses. Here, we observed that 220-nm UV irradiation was efficacious against rotavirus (RV) and Tulane virus (TV). UV irradiation at 254 nm inactivated TV to a greater extent than RV. Additional assays showed that UV irradiation compromised different portions of the RV and TV life cycles. UV irradiation decreased the binding of TV to its host receptor and mutagenized the TV genome. UV irradiation at 220 nm appeared to allow RV-host receptor interaction but halted RV genome replication. These findings provide knowledge about the disinfection of waterborne viruses, information that is important for the safe reuse or release of treated wastewater.
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Mohammad HA, Madi NM, Al-Nakib W. Analysis of viral diversity in stool samples from infants and children with acute gastroenteritis in Kuwait using Metagenomics approach. Virol J 2020; 17:10. [PMID: 32000795 PMCID: PMC6993487 DOI: 10.1186/s12985-020-1287-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 01/20/2020] [Indexed: 12/27/2022] Open
Abstract
Background Current molecular target-dependent methods are used to detect only known viruses. However, metagenomics based on next-generation sequencing (NGS) technique is a target-independent assay that enables simultaneous detection and genomic characterisation of all microorganisms present in a sample. In this study, we aimed to develop a metagenomics approach using NGS to identify and characterise viruses in stool samples from infants and children with Acute Gastroenteritis (AGE) in Kuwait. Methods We have investigated 84 stool samples from infants and children aged one month to ten years old with signs and symptoms of gastroenteritis who attended Mubarak Al-Kabeer and Al-Amiri hospitals in Kuwait from January to December 2017. A metagenomics approach using NGS to characterise viruses in clinical samples was used. Also, the commercial Real-Time PCR assay was used to detect viruses causing gastroenteritis. Results Metagenomics analysis revealed an average of 280,768 reads in which 5% of the reads were derived from viruses. The analysis of viral sequences verified that single infection of human adenovirus was the leading cause of gastroenteritis among infants and children, which was detected in 23.2% of the patients, followed by a mixed infection of human adenovirus and other viruses, which was detected in 20.9% of patients. Also, the newly discovered viruses known to cause gastroenteritis were detected, such as astrovirus MLB2, primate bocaparvovirus-1, Aichivirus A, cardiovirus, parechovirus A, astrovirus VA4, cosavirus-F, and bufavirus-3. Our results showed 71% agreement (k = 0.445, P = 0.000) between multiplex Real-Time PCR, which is used as a routine diagnostic test and metagenomics approach in the detection of viruses causing gastroenteritis in clinical samples. Conclusion Despite the difficulties in sample preparation and analysis process, we showed that metagenomics approach is a powerful and promising tool for the detection and characterisation of different viruses in clinical samples.
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Affiliation(s)
- Hawraa Adel Mohammad
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, P.O.Box 24923, 13110, Safat, Kuwait
| | - Nada Mohammed Madi
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, P.O.Box 24923, 13110, Safat, Kuwait.
| | - Widad Al-Nakib
- Virology Unit, Department of Microbiology, Faculty of Medicine, Kuwait University, P.O.Box 24923, 13110, Safat, Kuwait
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Mousavi Nasab SD, Zali F, Kaghazian H, Aghasadeghi MR, Mardani R, Gachkar L, Ahmadi Vasmehjani A, Ahmadi N, Ghasemzadeh A. Prevalence of astrovirus, adenovirus, and sapovirus infections among Iranian children with acute gastroenteritis. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2020; 13:S122-S127. [PMID: 33585013 PMCID: PMC7881414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
AIM This study aimed to determine the prevalence of Human Astroviruses (HAstVs), enteric Adenoviruses (HAdVs), and Sapoviruses (SaVs) in acute diarrhea patients, as well as their relation to age, sex, and season. BACKGROUND Acute gastroenteritis is one of the most common diseases affecting children <5 years old and viral agents with approximately >75% are the major causative agent of acute infectious diarrhea. After Rotavirus and Norovirus, the greater viral agents of acute gastroenteritis include HAstVs, HAdVs, and SaVs. To the best of our knowledge, there are sparse studies in Iran detecting at least three enteric viruses as causative agents of diarrhea simultaneously. METHODS The sample was collected from children referring to pediatric medical centers in Tehran, Iran; they were tested for Astrovirus, enteric Adenovirus, and Sapovirus by conventional PCR method. The association of incidence of viral enteric agents was evaluated with age, sex and seasonal pattern in children <5 years old. RESULTS The positive case number among acute gastroenteritis patients was 17/120 (14.1%). Patients ranged in age within 1-60 months, but 52.9% were aged ≤ 12 months. Males comprised the majority (70.6), and the male: female ratio was 2.4. HAstV was the most frequently detected virus (6.7%), while SaVs were detected only in 2.5% of cases. Mixed infections were not detected in these samples. The highest rate of HAstV was identified in winter (66.7%), HAdV in fall (66.7%), and SaV in winter (33.3%). CONCLUSION These findings underscore the importance of monitoring the epidemiology of HAstV, HAdV, and SaV as causative agents of viral diarrhea infections.
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Affiliation(s)
- Seyed Dawood Mousavi Nasab
- Department of Research and Development, Production and Research Complex, Pasteur Institute of Iran ,Viral vaccine research center, Pasteur Institute of Iran, Iran
| | - Fatemeh Zali
- Department of Clinical Biochemistry, Faculty of Medicine, Tehran University of Medical Science, Tehran, Iran
| | - Hooman Kaghazian
- Department of Research and Development, Production and Research Complex, Pasteur Institute of Iran ,Viral vaccine research center, Pasteur Institute of Iran, Iran
| | - Mohammad Reza Aghasadeghi
- Department of Research and Development, Production and Research Complex, Pasteur Institute of Iran ,Department of Hepatitis, AIDS and Blood-borne diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Rajab Mardani
- Department of Viral vaccines, Pasteur Institute of Iran, Tehran
| | - Latif Gachkar
- Infectious Diseases and Tropical Medicine Research Center, Infectious Diseases Department, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Ahmadi Vasmehjani
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Nayebali Ahmadi
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Ghasemzadeh
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Kawata K, Hikita T, Takanashi S, Hikita H, Ogita K, Okitsu S, Hoque SA, Phan TG, Ushijima H. Diagnosis of Acute Gastroenteritis with Immunochromatography and Effectiveness of Rotavirus Vaccine in a Japanese Clinic. Access Microbiol 2019; 2:acmi000085. [PMID: 32974566 PMCID: PMC7470309 DOI: 10.1099/acmi.0.000085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 01/13/2023] Open
Abstract
Despite the well known effectiveness of two licensed live attenuated oral rotavirus (RV)-vaccines, Rotarix and RotaTeq, constant monitoring of vaccine effectiveness (VE) is essential considering the evolving power and reassortment capability of RVs. In this study, we detected RV, norovirus (NV) and adenovirus (AV) infections using immunochromatography (IC)-based kits in children with acute gastroenteritis (AGE) who attended a pediatric clinic in Kiryu city, Gunma, Japan during June, 2014-September, 2018. VEs were determined using a test-negative study design. Among 1658 AGE-children, RV, NV and AV were detected in 96 (5.8 %), 146 (8.8 %) and 46 (2.8 %) children, respectively. Interestingly, the distributions of infections were found to be associated with age and sex. Namely, RV infections were significantly higher in female (P=0.02) and in the 19-30 month age group children, while NV and AV infections predominated in the 13-24 month and 7-18 month age groups, respectively. The disease severity for RV and NV infections remained similar and significantly higher than that of AV infections. The VE of RV-vaccines was 49.8 % (95 % CI: 22.7 to 67.3 %) against all RV infections, which was increased up to 67.2 % (95 % CI: 35.3 to 83.4 %) against severe RV infections. RV-vaccinated children experienced less severe symptoms in RV-infections while non-RV AGE remained less serious for both RV-vaccinated and unvaccinated children. Finally, the prevalence of RV infection remained minimized (≤5.4 %) in this population since 2015. Thus, this study provided important information on distribution of major AGEs in young children and exhibited the effective role of RV vaccines in post-vaccine era.
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Affiliation(s)
- Kimiko Kawata
- Division on Nursing Sciences, Midwifery, Department of Health Sciences, Faculty of Medical Sciences, Kyushu University Faculty of Medical Sciences, 3-1-1, Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Toshiyuki Hikita
- Hikita Pediatric Clinic, 2-7-20 Nakamchi, Kiryu city, Gunma, 376-0035, Japan
| | - Sayaka Takanashi
- Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Hiroyuki Hikita
- Hikita Pediatric Clinic, 2-7-20 Nakamchi, Kiryu city, Gunma, 376-0035, Japan
| | - Kaori Ogita
- Hikita Pediatric Clinic, 2-7-20 Nakamchi, Kiryu city, Gunma, 376-0035, Japan
| | - Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiolgy, Nihon University School of Medicine, 30-1, Oyaguchikamicho, Itabashi-ku, Tokyo, Japan
| | - Sheikh Ariful Hoque
- Cell and Tissue Culture Laboratory, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka-1000, Bangladesh
| | - Tung Gia Phan
- Division of Clinical Microbiology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiolgy, Nihon University School of Medicine, 30-1, Oyaguchikamicho, Itabashi-ku, Tokyo, Japan
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Leli C, Di Matteo L, Gotta F, Vay D, Cavallo V, Mazzeo R, Busso S, Carrabba L, Rocchetti A. Evaluation of a multiplex gastrointestinal PCR panel for the aetiological diagnosis of infectious diarrhoea. Infect Dis (Lond) 2019; 52:114-120. [DOI: 10.1080/23744235.2019.1688861] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Christian Leli
- Microbiology Laboratory, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
| | - Luigi Di Matteo
- Microbiology Laboratory, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
| | - Franca Gotta
- Microbiology Laboratory, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
| | - Daria Vay
- Pathology Unit, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
| | - Valeria Cavallo
- Microbiology Laboratory, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
| | - Roberta Mazzeo
- Microbiology Laboratory, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
| | - Simone Busso
- Microbiology Laboratory, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
| | - Laura Carrabba
- Microbiology Laboratory, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
| | - Andrea Rocchetti
- Microbiology Laboratory, SS. Antonio e Biagio e C. Arrigo Hospital, Alessandria, Italy
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Human polyomaviruses 10 and 11 in faecal samples from Brazilian children. Braz J Microbiol 2019; 51:585-591. [PMID: 31667802 DOI: 10.1007/s42770-019-00166-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 09/26/2019] [Indexed: 12/22/2022] Open
Abstract
The human polyomaviruses (HPyVs) 10 and 11 have been detected in faecal material and are tentatively associated with diarrhoeal disease. However, to date, there are insufficient data to confirm or rule out this association, or even to provide basic information about these viruses, such as how they are distributed in the population, the persistence sites and their pathogenesis. In this study, we analysed stool specimens from Brazilian children with and without acute diarrhoea to investigate the excretion of HPyV10 and HPyV11 as well as their possible associations with diarrhoea. A total of 460 stool specimens were obtained from children with acute diarrhoea of unknown aetiology, and 106 stool specimens were obtained from healthy asymptomatic children under 10 years old. Samples were collected during the periods of 1999-2006, 2010-2012 and 2016-2017, and found previously to be negative for other enteric viruses and bacteria. The specimens were screened for HPyV10 and HPyV11 DNA by the polymerase chain reaction (PCR). Randomly selected positive samples were sequenced to confirm the presence of HPyV10 and HPyV11. The sequenced strains showed a percent of nucleotide identity of 93.4-99.6% and 85.5-98.9% with the reference HPyV10 and HPyV11 strains, respectively, confirming the PCR results. HPyV10 and HPyV11 were detected in 7.2% and 4.7% of the stool specimens from children with and without diarrhoea, respectively. The prevalence of both viruses was the same among children with diarrhoea and healthy children. There was also no difference between boys and girls or the degree of disease (severe, moderate or mild) among groups. Phylogenetic analysis showed that all of the genotypes described so far for HPyV10 and HPyV11 circulate in Rio de Janeiro. Our results do not support an association between HPyV10 and HPyV11 in stool samples and paediatric gastroenteritis. Nevertheless, the excretion of HPyV10 and HPyV11 in faeces indicates that faecal-oral transmission is possible.
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Sciandra I, Piccioni L, Coltella L, Ranno S, Giannelli G, Falasca F, Antonelli G, Concato C, Turriziani O. Comparative analysis of 2 commercial molecular tests for the detection of gastroenteric viruses on stool samples. Diagn Microbiol Infect Dis 2019; 96:114893. [PMID: 31677959 DOI: 10.1016/j.diagmicrobio.2019.114893] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/14/2019] [Accepted: 08/30/2019] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Our purpose was to compare the performance of 2 recently introduced molecular tests for the identification of gastrointestinal viral infections. METHODS One hundred fecal samples from pediatric patients were analyzed using 2 workflows, each including nucleic acids extraction and multiplex Real-Time PCR: Allplex™ GI-Virus Assay and FTD Viral gastroenteritis. The agreement was evaluated calculating Cohen's kappa and applying McNemar's test. RESULTS AND CONCLUSION Allplex and FTD assays showed 100% overall agreement for Norovirus GI/GII and Sapovirus (κ: 1.00), and 99% for Astrovirus (κ: 0.66). A lower agreement was detected for Adenovirus (89%; κ: 0.72) and Rotavirus (91%, k: 0.53), owing to samples resulted positive only with FTD test. The discrepancies were attributed to a different efficiency of extraction/amplification and to the different Adenovirus serotype specificity of the tests since Allplex detects only AdVF40 and AdVF41. FTD test should be used when non enteric adenovirus could have a clinical significance.
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Affiliation(s)
- I Sciandra
- National Institute of Gastroenterology "S. de Bellis", Research Hospital, Castellana Grotte, Italy
| | - L Piccioni
- Virology Unit, Bambino Gesù Children's Hospital, Rome, Italy
| | - L Coltella
- Virology Unit, Bambino Gesù Children's Hospital, Rome, Italy
| | - S Ranno
- Virology Unit, Bambino Gesù Children's Hospital, Rome, Italy
| | - G Giannelli
- National Institute of Gastroenterology "S. de Bellis", Research Hospital, Castellana Grotte, Italy
| | - F Falasca
- Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - G Antonelli
- Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - C Concato
- Virology Unit, Bambino Gesù Children's Hospital, Rome, Italy
| | - O Turriziani
- Department of Molecular Medicine, Sapienza University, Rome, Italy.
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Performance evaluation of gastrointestinal viral ELIte panel multiplex RT-PCR assay for the diagnosis of rotavirus, adenovirus and astrovirus infection. J Virol Methods 2019; 268:48-52. [DOI: 10.1016/j.jviromet.2019.03.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/22/2019] [Accepted: 03/19/2019] [Indexed: 01/25/2023]
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de Moraes MTB, Olivares AIO, Fialho AM, Malta FC, da Silva E Mouta Junior S, de Souza Bispo R, Velloso AJ, Alves Leitão GA, Cantelli CP, Nordgren J, Svenson L, Miagostovich MP, Leite JPG. Phenotyping of Lewis and secretor HBGA from saliva and detection of new FUT2 gene SNPs from young children from the Amazon presenting acute gastroenteritis and respiratory infection. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2019; 70:61-66. [PMID: 30790699 DOI: 10.1016/j.meegid.2019.02.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/16/2019] [Accepted: 02/13/2019] [Indexed: 11/17/2022]
Abstract
The Histo-blood group antigens (HBGA) are host genetic factors associated with susceptibility to rotavirus (RV) and human norovirus (HuNoV), the major etiological agents of viral acute gastroenteritis (AGE) worldwide. The FUT2 gene expressing the alpha-1, 2-L- fucosyltransferase enzyme is important for gut HBGA expression, and also provides a composition of the phenotypic profile achieved through mutations occurring in populations with different evolutionary histories; as such, it can be considered a genetic population marker. In this study, Lewis and secretor HBGA phenotyping was performed using 352 saliva samples collected from children between three months and five years old born in the Amazon (Brazil, Venezuela and English Guyana) presenting AGE or acute respiratory infection (ARI), the latter considered as control samples. The total of children phenotyped as secretors was 323, corresponding to 91.80%. From these, 207 (58.80%) had a Le (a + b+) profile. The HBGA profiles were equally found in children with AGE as well as with ARI. The rs1047781 of the FUT2 gene was not detected in DNA from saliva cells with a Le (a+b+) profile. However, mutations not yet described in the FUT2 gene were observed: missense 325A>T, 501C>T, 585C>T, 855A>T and missense substitutions 327C>T [S (Ser) > C (Cys)], 446 T>C [L(Leu) > P(Pro)], 723C>A [N(Asn) > K(Lys)], 724A>T [I(Ile) > F(Phe)], 736C>A [H(His) > N(Asn)]. The SNP distribution in the FUT2 gene of the analyzed samples was very similar to that described in Asian populations, including indigenous tribes.
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Affiliation(s)
- Marcia Terezinha Baroni de Moraes
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Avenida Brasil, 4365-Manguinhos, Rio de Janeiro, RJ, Brazil.
| | - Alberto Ignácio Olivares Olivares
- Federal University of Roraima, Research Center Roraima Health Observatory (ObservaRR), Avenida Capitão Ene Garcês, 2413-Aeroporto, Boa Vista, RR, Brazil; Post-Graduate Program in Parasite Biology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Avenida Brasil, 4365-Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Alexandre Madi Fialho
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Avenida Brasil, 4365-Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Fábio Correia Malta
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Avenida Brasil, 4365-Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Sergio da Silva E Mouta Junior
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Avenida Brasil, 4365-Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Romanul de Souza Bispo
- Federal University of Roraima, Research Center Roraima Health Observatory (ObservaRR), Avenida Capitão Ene Garcês, 2413-Aeroporto, Boa Vista, RR, Brazil
| | - Alvaro Jorge Velloso
- Department of Viral Vaccines and Department of Quality Control, Immunobiological Technology Institute (BioManguinhos) - Oswaldo Cruz Foundation (FIOCRUZ), Avenida Brasil, 4365-Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Gabriel Azevedo Alves Leitão
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Avenida Brasil, 4365-Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Carina Pacheco Cantelli
- Post-Graduate Program in Parasite Biology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Avenida Brasil, 4365-Manguinhos, Rio de Janeiro, RJ, Brazil; Department of Viral Vaccines and Department of Quality Control, Immunobiological Technology Institute (BioManguinhos) - Oswaldo Cruz Foundation (FIOCRUZ), Avenida Brasil, 4365-Manguinhos, Rio de Janeiro, RJ, Brazil
| | - Johan Nordgren
- Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, 581 85 Linköping, Sweden
| | - Lennart Svenson
- Division of Molecular Virology, Department of Clinical and Experimental Medicine, Linköping University, 581 85 Linköping, Sweden
| | - Marize Pereira Miagostovich
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Avenida Brasil, 4365-Manguinhos, Rio de Janeiro, RJ, Brazil
| | - José Paulo Gagliardi Leite
- Laboratory of Comparative and Environmental Virology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Avenida Brasil, 4365-Manguinhos, Rio de Janeiro, RJ, Brazil
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Vilcu AM, Blanchon T, Sabatte L, Souty C, Maravic M, Hanslik T, Steichen O. Cross-validation of an algorithm detecting acute gastroenteritis episodes from prescribed drug dispensing data in France: comparison with clinical data reported in a primary care surveillance system, winter seasons 2014/15 to 2016/17. BMC Med Res Methodol 2019; 19:110. [PMID: 31151387 PMCID: PMC6545010 DOI: 10.1186/s12874-019-0745-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 04/29/2019] [Indexed: 12/15/2022] Open
Abstract
Background This study compares an algorithm to detect acute gastroenteritis (AG) episodes from drug dispensing data to the validated data reported in a primary care surveillance system in France. Methods We used drug dispensing data collected in a drugstore database and data collected by primary care physicians involved in a French surveillance network, from season 2014/15 to 2016/17. We used an adapted version of an AG discrimination algorithm to identify AG episodes from the drugstore database. We used Pearson’s correlation coefficient to evaluate the agreement between weekly AG signals obtained from the two data sources during winter months, in the overall population, by specific age-groups and by regions. Results Correlations between AG signals for all ages were 0.84 [95%CI 0.69; 0.92] for season 2014/15, 0.87 [95%CI 0.75; 0.93] for season 2015/16 and 0.94 [95%CI 0.88; 0.97] for season 2016/17. The association between AG signals estimated from two data sources varied significantly across age groups in season 2016/17 (p-value < 0.01), and across regions in all three seasons studied (p-value < 0.01). Conclusions There is a strong agreement between the dynamic of AG activity estimated from drug dispensing data and from validated primary care surveillance data collected during winter months in the overall population but the agreement is poorer in several age groups and in several regions. Once automated, the reuse of drug dispensing data, already collected for reimbursement purposes, could be a cost-efficient method to monitor AG activity at the national level. Electronic supplementary material The online version of this article (10.1186/s12874-019-0745-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana-Maria Vilcu
- Sorbonne Université, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F-75012, Paris, France.
| | - Thierry Blanchon
- Sorbonne Université, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F-75012, Paris, France
| | - Laure Sabatte
- Sorbonne Université, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F-75012, Paris, France
| | - Cécile Souty
- Sorbonne Université, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F-75012, Paris, France
| | - Milka Maravic
- Real World Insight, IQVIA, F-92099, La Défense Cedex, France.,Assistance Publique - Hôpitaux de Paris (APHP), hôpital Lariboisière, Service de Rhumatologie, F-75010, Paris, France
| | - Thomas Hanslik
- Sorbonne Université, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F-75012, Paris, France.,Université de Versailles Saint-Quentin-en-Yvelines, UVSQ, UFR de Médecine, F-78000, Versailles, France.,Assistance Publique - Hôpitaux de Paris (APHP), hôpital Ambroise Paré, Service de Médecine Interne, F-92100, Boulogne Billancourt, France
| | - Olivier Steichen
- Sorbonne Université, Inserm, université Paris 13, Laboratoire d'informatique médicale et d'ingénierie des connaissances en e-santé, LIMICS, F-75006, Paris, France.,Assistance Publique - Hôpitaux de Paris (APHP), hôpital Tenon, Service de Médecine Interne, F-75020, Paris, France
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44
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Hoque SA, Thongprachum A, Takanashi S, Mostafa SM, Saito H, Anwar KS, Nomura A, Hoque SA, Begum R, Sultana UN, Hossain T, Khamrin P, Okitsu S, Hayakawa S, Ushijima H. Alarming Situation of Spreading Enteric Viruses Through Sewage Water in Dhaka City: Molecular Epidemiological Evidences. FOOD AND ENVIRONMENTAL VIROLOGY 2019; 11:65-75. [PMID: 30607905 DOI: 10.1007/s12560-018-09363-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/13/2018] [Indexed: 06/09/2023]
Abstract
Global burden of acute viral gastroenteritis remains high, particularly in developing countries including Bangladesh. Sewage water (SW) is an important node to monitor enteric pathogens both in the environment and among the population. Analysis of SW in Dhaka city deems crucially important because a large number of urban-city dwellers live in Dhaka city, the capital of Bangladesh, under a constant threat of precarious sewerage system. In this study, we collected raw SW from five locations of Dhaka city every month from June 2016 to May 2017. It was concentrated with polyethylene glycol (PEG) and investigated for three major enteric viruses, rotavirus A (RVA), norovirus GII (NoV GII) and adenovirus (AdV) using polymerase chain reaction (PCR). Most of these SW samples collected from both hospitals and non-hospital areas yielded enteric viruses: 76% samples were positive for AdV, followed by 53% NoV GII and 38% RVA. Viral load was determined as much as 1 × 107 copies/ml for RVA and 3.5 × 103 copies/ml for NoV GII. Importantly, NoV GII and AdV that can affect people of all ages were predominated during monsoon also when SW overflows and spreads over a wide and crowded area. Genotypes G1, G2, G3, G8, and G9 for RVA, GII.4 for NoV, and type 41 for AdV were detected representing the current profile of circulating genotypes in the population. This study provides the first evidence of distribution of major diarrheal viruses in SW in Dhaka city which is alarming showing grave risk of impending outbreaks through exposure.
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Affiliation(s)
- Sheikh Ariful Hoque
- Cell and Tissue Culture Laboratory, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh.
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan.
| | - Aksara Thongprachum
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
- Faculty of Public Health, Chiang Mai University, Chiang Mai, Thailand
| | - Sayaka Takanashi
- Department of Developmental Medical Sciences, School of International Health, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Salwa Mohd Mostafa
- Cell and Tissue Culture Laboratory, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh
| | - Hiroyuki Saito
- Akita Prefectural Research Center for Public Health and Environment, Akita, Japan
| | - Kazi Selim Anwar
- Department of Infectious Diseases, International University of Health and Welfare (IUHW), Narita Campus, Narita, Chiba, Japan
| | - Akiko Nomura
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Sk Azimul Hoque
- National Institute Neuroscience and Hospital, Agargaon, Dhaka, Bangladesh
| | - Rokeya Begum
- Genetic Engineering and Biotechnology Research Laboratory, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh
| | - Ummay Nasrin Sultana
- Cell and Tissue Culture Laboratory, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh
| | - Tania Hossain
- Cell and Tissue Culture Laboratory, Centre for Advanced Research in Sciences (CARS), University of Dhaka, Dhaka, Bangladesh
| | - Pattara Khamrin
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Shoko Okitsu
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
- Faculty of Public Health, Chiang Mai University, Chiang Mai, Thailand
| | - Satoshi Hayakawa
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
- Faculty of Public Health, Chiang Mai University, Chiang Mai, Thailand
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45
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Thakur N, Changotra H, Grover N, Vashistt J. Elucidation of bacterial species during childhood diarrhea through 16S rRNA Illumina Miseq approach. Meta Gene 2018. [DOI: 10.1016/j.mgene.2018.03.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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46
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Lizasoain A, Tort L, García M, Gillman L, Alberti A, Leite J, Miagostovich M, Pou S, Cagiao A, Razsap A, Huertas J, Berois M, Victoria M, Colina R. Human enteric viruses in a wastewater treatment plant: evaluation of activated sludge combined with UV disinfection process reveals different removal performances for viruses with different features. Lett Appl Microbiol 2018; 66:215-221. [DOI: 10.1111/lam.12839] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 12/13/2017] [Accepted: 12/18/2017] [Indexed: 12/15/2022]
Affiliation(s)
- A. Lizasoain
- Laboratorio de Virología Molecular; CENUR Litoral Norte; Sede Salto Uruguay
- Universidad de la República; Salto Uruguay
| | - L.F.L. Tort
- Laboratorio de Virología Molecular; CENUR Litoral Norte; Sede Salto Uruguay
- Universidad de la República; Salto Uruguay
| | - M. García
- Laboratorio de Virología Molecular; CENUR Litoral Norte; Sede Salto Uruguay
- Universidad de la República; Salto Uruguay
| | - L. Gillman
- Sección Virología; Facultad de Ciencias; Universidad de la República; Montevideo Uruguay
| | - A. Alberti
- Sección Virología; Facultad de Ciencias; Universidad de la República; Montevideo Uruguay
| | - J.P.G. Leite
- Laboratório de Virologia Comparada e Ambiental; Instituto Oswaldo Cruz; Fundação Oswaldo Cruz Rio de Janeiro Brasil
| | - M.P. Miagostovich
- Laboratório de Virologia Comparada e Ambiental; Instituto Oswaldo Cruz; Fundação Oswaldo Cruz Rio de Janeiro Brasil
| | - S.A. Pou
- Instituto de Investigaciones en Ciencias de la Salud; Facultad de Ciencias Médicas; CONICET; Universidad Nacional de Córdoba; Córdoba Argentina
| | - A. Cagiao
- Obras Sanitarias del Estado; Montevideo Uruguay
| | - A. Razsap
- Obras Sanitarias del Estado; Montevideo Uruguay
| | - J. Huertas
- Obras Sanitarias del Estado; Montevideo Uruguay
| | - M. Berois
- Sección Virología; Facultad de Ciencias; Universidad de la República; Montevideo Uruguay
| | - M. Victoria
- Laboratorio de Virología Molecular; CENUR Litoral Norte; Sede Salto Uruguay
- Universidad de la República; Salto Uruguay
| | - R. Colina
- Laboratorio de Virología Molecular; CENUR Litoral Norte; Sede Salto Uruguay
- Universidad de la República; Salto Uruguay
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47
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Kowada K, Takeuchi K, Hirano E, Toho M, Sada K. Development of a multiplex real-time PCR assay for detection of human enteric viruses other than norovirus using samples collected from gastroenteritis patients in Fukui Prefecture, Japan. J Med Virol 2017; 90:67-75. [PMID: 28845896 DOI: 10.1002/jmv.24926] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 07/27/2017] [Indexed: 11/09/2022]
Abstract
There are many varieties of gastroenteritis viruses, of which norovirus (NoV) accounts for over 90% of the viral food poisoning incidents in Japan. However, protocols for rapidly identifying other gastroenteritis viruses need to be established to investigate NoV-negative cases intensively. In this study, a multiplex real-time PCR assay targeting rotavirus A, rotavirus C, sapovirus, astrovirus, adenovirus, and enterovirus was developed using stool samples collected from gastroenteritis patients between 2010 and 2013 in Fukui Prefecture, Japan. Of the 126 samples collected sporadically from pediatric patients with suspected infectious gastroenteritis, 51 were positive for non-NoV target viruses, whereas 27 were positive for NoV, showing a high prevalence of non-NoV viruses in pediatric patients. In contrast, testing in 382 samples of 58 gastroenteritis outbreaks showed that non-NoV viruses were detected in 13 samples, with NoV in 267. Of the 267 NoV-positive patients, only two were co-infected with non-NoV target viruses, suggesting that testing for non-NoV gastroenteritis viruses in NoV-positive samples was mostly unnecessary in outbreak investigations. Given these results, multiplex real-time PCR testing for non-NoV gastroenteritis viruses, conducted separately from NoV testing, may be helpful to deal with two types of epidemiological investigations, regular surveillance of infectious gastroenteritis and urgent testing when gastroenteritis outbreaks occur.
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Affiliation(s)
- Kazuaki Kowada
- Fukui Prefectural Institute of Public Health and Environmental Science, Fukui, Japan.,University of Fukui, Fukui, Japan
| | | | - Eiko Hirano
- Fukui Prefectural Institute of Public Health and Environmental Science, Fukui, Japan
| | - Miho Toho
- Fukui Prefectural Institute of Public Health and Environmental Science, Fukui, Japan
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48
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Li P, Yang L, Guo J, Zou W, Xu X, Yang X, Du X, Qiu S, Song H. Circulation of HAdV-41 with diverse genome types and recombination in acute gastroenteritis among children in Shanghai. Sci Rep 2017; 7:3548. [PMID: 28615624 PMCID: PMC5471248 DOI: 10.1038/s41598-017-01293-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/22/2017] [Indexed: 12/17/2022] Open
Abstract
Human adenovirus F (HAdV-F) is one of the major causative species detected in acute gastroenteritis in children worldwide. HAdV-F is composed of serotypes 40 and 41. Most studies have reported the prevalence of HAdV-41 and focused on its epidemiologic characteristics. In this study, seventeen samples were identified as HAdV-41 out of 273 fecal specimens from children with acute diarrhea in Shanghai. Five isolates were isolated and subjected to whole genome sequencing and analysis to characterize the genetic variation and evolution. Full genome analysis revealed low genetic variation (99.07-99.92% identity) among the isolates, and InDels are observed in the E2A gene and the hexon gene compared to the reference strain NIVD103. Phylogenetic analysis showed that all isolates mainly formed two genome-type clusters but with incongruence in the trees of whole genomes and individual genes. The recombination breakpoints of the five isolates were inferred by the Recombination Detection Program (RDP) and varied in the number and location of the recombination events, indicating different evolution origins. Overall, our study highlights the genetic diversity of HAdV-41 isolates circulating in Shanghai, which may have evolved from inter-strain recombination.
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Affiliation(s)
- Peng Li
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Lang Yang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Jiayin Guo
- Shanghai Changning District Center for Disease Control and Prevention, Shanghai, 200051, China
| | - Wenwei Zou
- Shanghai Pudong New Area Center for Disease Control and Prevention, Shanghai, 200136, China
| | - Xuebin Xu
- Shanghai Center for Disease Control and Prevention, Shanghai, 200236, China
| | - Xiaoxia Yang
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Xinying Du
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Shaofu Qiu
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, 100071, China.
| | - Hongbin Song
- Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, 100071, China.
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49
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Balsalobre-Arenas L, Alarcón-Cavero T. Rapid diagnosis of gastrointestinal tract infections due to parasites, viruses, and bacteria. Enferm Infecc Microbiol Clin 2017; 35:367-376. [PMID: 28238506 PMCID: PMC7103346 DOI: 10.1016/j.eimc.2017.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 01/14/2017] [Indexed: 12/31/2022]
Abstract
Rapid diagnostic techniques are valuable tools in the diagnosis of gastrointestinal infections, especially for the detection of some microorganisms and in certain groups of patients. While antigen detection techniques are widely used in Clinical Microbiology laboratories, for the diagnosis of viruses, some parasites and some bacteria, molecular techniques are routinely used only for some pathogens (such as Clostridium difficile). However, molecular techniques are constantly evolving, and they allow a rapid diagnosis for an increasing number of pathogens, with high sensitivity and specificity. In addition, they are also able to detect virulence factors or resistance mechanisms. Syndromic surveillance systems, which detect different pathogens simultaneously, are very promising because they enable the most frequent pathogens to be diagnosed in a few hours and they can be very useful in certain patients. For the diagnosis of Helicobacter pylori infection, molecular techniques are able to detect bacteria and its resistance to clarithromycin and levofloxacin, allowing the most appropriate treatment to be selected for each patient when bacterial culture is not possible.
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Affiliation(s)
- Luz Balsalobre-Arenas
- Servicio de Microbiología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa, Madrid, España
| | - Teresa Alarcón-Cavero
- Servicio de Microbiología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa, Madrid, España; Departamento de Medicina Preventiva, Salud Publica y Microbiologia, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, España.
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50
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Balsalobre-Arenas L, Alarcón-Cavero T. Rapid diagnosis of gastrointestinal tract infections due to parasites, viruses, and bacteria. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2017. [PMCID: PMC7172322 DOI: 10.1016/j.eimce.2017.01.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Rapid diagnostic techniques are valuable tools in the diagnosis of gastrointestinal infections, especially for the detection of some microorganisms and in certain groups of patients. While antigen detection techniques are widely used in Clinical Microbiology laboratories, for the diagnosis of viruses, some parasites and some bacteria, molecular techniques are routinely used only for some pathogens (such as Clostridium difficile). However, molecular techniques are constantly evolving, and they allow a rapid diagnosis for an increasing number of pathogens, with high sensitivity and specificity. In addition, they are also able to detect virulence factors or resistance mechanisms. Syndromic surveillance systems, which detect different pathogens simultaneously, are very promising because they enable the most frequent pathogens to be diagnosed in a few hours and they can be very useful in certain patients. For the diagnosis of Helicobacter pylori infection, molecular techniques are able to detect bacteria and its resistance to clarithromycin and levofloxacin, allowing the most appropriate treatment to be selected for each patient when bacterial culture is not possible.
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