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Bhagchandani T, Nikita, Verma A, Tandon R. Exploring the Human Virome: Composition, Dynamics, and Implications for Health and Disease. Curr Microbiol 2023; 81:16. [PMID: 38006423 DOI: 10.1007/s00284-023-03537-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/24/2023] [Indexed: 11/27/2023]
Abstract
Humans are colonized by large number of microorganisms-bacteria, fungi, and viruses. The overall genome of entire viruses that either lives on or inside the human body makes up the human virome and is indeed an essential fraction of the human metagenome. Humans are constantly exposed to viruses as they are ubiquitously present on earth. The human virobiota encompasses eukaryotic viruses, bacteriophages, retroviruses, and even giant viruses. With the advent of Next-generation sequencing (NGS) and ongoing development of numerous bioinformatic softwares, identification and taxonomic characterization of viruses have become easier. The viruses are abundantly present in humans; these can be pathogenic or commensal. The viral communities occupy various niches in the human body. The viruses start colonizing the infant gut soon after birth in a stepwise fashion and the viral composition diversify according to their feeding habits. Various factors such as diet, age, medications, etc. influence and shape the human virome. The viruses interact with the host immune system and these interactions have beneficial or detrimental effects on their host. The virome composition and abundance change during the course of disease and these alterations impact the immune system. Hence, the virome population in healthy and disease conditions influences the human host in numerous ways. This review presents an overview of assembly and composition of the human virome in healthy asymptomatic individuals, changes in the virome profiles, and host-virome interactions in various disease states.
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Affiliation(s)
- Tannu Bhagchandani
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Nikita
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Anjali Verma
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ravi Tandon
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
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Moreno-Sánchez E, Castillo-Viera E, Vélez-Moreno E, Gago-Valiente FJ. Facts and Challenges about Asthma and COVID-19 among the Paediatric Population: A Systematic Literature Review. MEDICINA (KAUNAS, LITHUANIA) 2021; 57:medicina57121306. [PMID: 34946251 PMCID: PMC8706787 DOI: 10.3390/medicina57121306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/26/2021] [Accepted: 11/28/2021] [Indexed: 01/02/2023]
Abstract
A systematic review of the literature was conducted to analyse the factors that affect the probability of the paediatric asthma population suffering from COVID-19 or SARS-CoV-2, such as asthma phenotypes, inhaled corticosteroids, and the effects of lockdown. This systematic review was based on PRISMA guidelines. A bibliographic search was conducted using BNE, BVS (LILAC), CSIC (IME, ISOC), IBECS, Scielo, Scopus, Medline, and PubMed, using the following search profile: (COVID-19 or 2019-NCOV or SARS-CoV-2 or COV-19) AND asthma AND (children or adolescents or youths or children or teenagers). The results were limited to those articles published between December 2019 and December 2020, selecting only articles published in Spanish, English and French that included the study population (children aged 0–18 years). Among the 1066 results of the bibliographic search and seven articles selected from a manual search, only 19 articles were found to fit our eligibility criteria. Most of the articles highlight the effects of lockdown on the paediatric asthma population, increased therapeutic compliance, and the role of inhaled corticosteroids and intrinsic factors such as ACE2 receptors as causes of the decreased prevalence of COVID-19 among the paediatric asthma population. This population has unique characteristics that serve as protective factors against COVID-19. The safety measures implemented during the lockdown period along with inhaled corticosteroid treatment also contributed to this protection.
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Affiliation(s)
- Emilia Moreno-Sánchez
- Department of Pedagogy, Faculty of Education, Psychology and Sports Sciences, University of Huelva, 21071 Huelva, Spain;
| | - Estefanía Castillo-Viera
- Faculty of Education, Psychology and Sports Sciences, University of Huelva, 21071 Huelva, Spain
- Correspondence: ; Tel.: +34-959219272
| | - Emilia Vélez-Moreno
- Medicine Department, Faculty of Medicine, University of Malaga, 29071 Malaga, Spain;
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Dodi G, Attanasi M, Di Filippo P, Di Pillo S, Chiarelli F. Virome in the Lungs: The Role of Anelloviruses in Childhood Respiratory Diseases. Microorganisms 2021; 9:microorganisms9071357. [PMID: 34201449 PMCID: PMC8307813 DOI: 10.3390/microorganisms9071357] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 12/24/2022] Open
Abstract
More recently, increasing attention has been directed to exploring the function of the global virome in health and disease. Currently, by new molecular techniques, such as metagenomic DNA sequencing, the virome has been better unveiled. By investigating the human lung virome, we could provide novel insights into respiratory diseases. The virome, as a part of the microbiome, is characterized by a constant change in composition related to the type of diet, environment, and our genetic code, and other incalculable factors. The virome plays a substantial role in modulating human immune defenses and contributing to the inflammatory processes. Anelloviruses (AVs) are new components of the virome. AVs are already present during early life and reproduce without apparently causing harm to the host. The role of AVs is still unknown, but several reports have shown that AVs could activate the inflammasomes, intracellular multiprotein oligomers of the innate immune system, which show a crucial role in the host defense to several pathogens. In this narrative revision, we summarize the epidemiological data related to the possible link between microbial alterations and chronic respiratory diseases in children. Briefly, we also describe the characteristics of the most frequent viral family present in the lung virome, Anelloviridae. Furthermore, we discuss how AVs could modulate the immune system in children, affecting the development of chronic respiratory diseases, particularly asthma, the most common chronic inflammatory disease in childhood.
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Fonseca W, Lukacs NW, Elesela S, Malinczak CA. Role of ILC2 in Viral-Induced Lung Pathogenesis. Front Immunol 2021; 12:675169. [PMID: 33953732 PMCID: PMC8092393 DOI: 10.3389/fimmu.2021.675169] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 03/31/2021] [Indexed: 12/16/2022] Open
Abstract
Innate lymphoid type-2 cells (ILC2) are a population of innate cells of lymphoid origin that are known to drive strong Type 2 immunity. ILC2 play a key role in lung homeostasis, repair/remodeling of lung structures following injury, and initiation of inflammation as well as more complex roles during the immune response, including the transition from innate to adaptive immunity. Remarkably, dysregulation of this single population has been linked with chronic lung pathologies, including asthma, chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrotic diseases (IPF). Furthermore, ILC2 have been shown to increase following early-life respiratory viral infections, such as respiratory syncytial virus (RSV) and rhinovirus (RV), that may lead to long-term alterations of the lung environment. The detrimental roles of increased ILC2 following these infections may include pathogenic chronic inflammation and/or alterations of the structural, repair, and even developmental processes of the lung. Respiratory viral infections in older adults and patients with established chronic pulmonary diseases often lead to exacerbated responses, likely due to previous exposures that leave the lung in a dysregulated functional and structural state. This review will focus on the role of ILC2 during respiratory viral exposures and their effects on the induction and regulation of lung pathogenesis. We aim to provide insight into ILC2-driven mechanisms that may enhance lung-associated diseases throughout life. Understanding these mechanisms will help identify better treatment options to limit not only viral infection severity but also protect against the development and/or exacerbation of other lung pathologies linked to severe respiratory viral infections.
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Affiliation(s)
- Wendy Fonseca
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Nicholas W Lukacs
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States.,Mary H. Weiser Food Allergy Center, University of Michigan, Ann Arbor, MI, United States
| | - Srikanth Elesela
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States.,Mary H. Weiser Food Allergy Center, University of Michigan, Ann Arbor, MI, United States
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Alamri A. Diversity of Microbial Signatures in Asthmatic Airways. Int J Gen Med 2021; 14:1367-1378. [PMID: 33889017 PMCID: PMC8057789 DOI: 10.2147/ijgm.s304339] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
Asthma is a chronic inflammatory disease affecting the respiratory system. The global incidence of asthma is rising. Clinical and experimental models of asthma clearly indicate that the disease is multifactorial in nature with a wide array of factors contributing to progression and exacerbation, including interactions between immunological markers and the microbial community populating the respiratory tract. In particular, strict hygiene compliance during the early years of life and early exposure to antibiotics are linked to alterations in the biological environment within the airways and to changes in immunological markers, leading to allergies, such as asthma. With the gap in current research knowledge on the various non-bacterial microbial communities in the asthmatic airways, this review summarizes current methods used to assess microbial diversity as well as evidence for the link between microbial alterations and asthma, including changes in the bacterial microbiome, often characterized by the outgrowth of certain bacterial phyla such as proteobacteria and Firmicutes, in addition to disrupted mycobiome, virome, and parasitome. The current review emphasizes the dynamic, context-dependent changes in the microbiome in asthma and the importance of broad-scope analyses, covering a wide range of taxa. In conclusion, the interaction between the resident microbiota and the immune system is essential and significant in modulating the inflammatory responses; however, further investigations are needed to improve our understanding of the risk factors that disrupt the diversity of the microbiome in the different body systems.
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Affiliation(s)
- Aisha Alamri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences Imam Abdulrahman Bin Faisal University, Dammam, Kingdom of Saudi Arabia
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You C, Ran G, Wu X, Wang Y, Tian H, Fan J, Yao Z, Wang F. High immunoglobulin E level is associated with increased readmission in children with bronchopneumonia. Ther Adv Respir Dis 2020; 13:1753466619879832. [PMID: 31588854 PMCID: PMC6783659 DOI: 10.1177/1753466619879832] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Background: Increased immunoglobulin E (IgE) is associated with lower respiratory tract
infections. The study aimed to evaluate the association between IgE and the
rate of bronchopneumonia-related readmission within 12 months in
children. Methods: A total of 1099 children aged over 1 year with bronchopneumonia, from 1
January 2015 to 31 December 2016, were enrolled. Unplanned readmissions
within 12 months after discharge were observed. Multivariate regression
analysis was used to identify independent risk factors for
rehospitalization. Results: The rate of rehospitalization was 11.4% (125/1099). Compared to the
nonreadmission children, IgE levels, the proportion of children with asthma
and hospitalization duration were significantly higher in the readmission
children (p < 0.05). Compared to the children with
normal IgE (≤ 165 IU/ml) levels, the risk of rehospitalization was
significantly higher in children with abnormal IgE [odds ratio (OR) 1.781,
95% confidence interval (CI) 1.209–2.624, p = 0.004].
Children with IgE level more than three times the upper limit had even
higher risks of readmission (OR 2.037, 95%CI 1.172–3.540, p
= 0.012). Meanwhile, the risk of readmission in children with abnormal IgE
combined with or without bronchial asthma was significantly higher (OR 2.548
and 1.918, 95% CI 1.490–4.358 and 1.218–3.020, p = 0.001
and 0.005, respectively). Conclusions: Children aged over 1 year with bronchopneumonia who had higher IgE levels are
at increased risk for rehospitalization within the first 12 months of the
index hospitalization and IgE level may be used as a predictor of
rehospitalization in children with bronchopneumonia.
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Affiliation(s)
- Cun You
- Department of Pediatrics, Minhang Branch, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Guo Ran
- Department of Anesthesiology, Eye, Ear, Nose, and Throat Hospital, Fudan University, Shanghai, China
| | - Xiao Wu
- Emergency Department, Jiading District Central Hospital Affiliated Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Yu Wang
- Jiuting Town Community Healthcare Center of Songjiang District, Shanghai, China
| | - Hua Tian
- Jiuting Town Community Healthcare Center of Songjiang District, Shanghai, China
| | - Jiabao Fan
- Department of Clinical Laboratory, Minhang Branch, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zezhong Yao
- Department of pediatrics, Minhang Branch, Zhongshan Hospital, Fudan University, No.170, Xinsong Rd, Minhang, Shanghai 201199, China
| | - Fei Wang
- Emergency Department, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, No.1, Chengbei Rd, Jiading, Shanghai 201800, China
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Adeli M, El-Shareif T, Hendaus MA. Asthma exacerbation related to viral infections: An up to date summary. J Family Med Prim Care 2019; 8:2753-2759. [PMID: 31681638 PMCID: PMC6820381 DOI: 10.4103/jfmpc.jfmpc_86_19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/01/2019] [Accepted: 08/27/2019] [Indexed: 12/21/2022] Open
Abstract
Asthma exacerbation can be a major life threatening event. Viruses have been pinned as the cause behind the vast majority of these exacerbations. The purpose of this short review is to explore the mechanisms behind these exacerbations, focusing mostly on viral infections as triggers. We will also be discussing the phenotypes prone to asthma exacerbation, the pathophysiology of viral induced asthma and ventilation patterns of asthmatic lungs. This manuscript will assist primary care physicians in delineating the proper pathophysiology of the disease as well as the management.
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Affiliation(s)
- Mehdi Adeli
- Department of Pediatrics, Section of Academic General Pediatrics, Sidra Medicine, Doha, Qatar.,Department of Pediatrics, Hamad General Corporation, Doha, Qatar.,Department of Clinical Pediatrics, Weill- Cornell Medicine, Doha, Qatar
| | | | - Mohamed A Hendaus
- Department of Pediatrics, Section of Academic General Pediatrics, Sidra Medicine, Doha, Qatar.,Department of Pediatrics, Hamad General Corporation, Doha, Qatar.,Department of Clinical Pediatrics, Weill- Cornell Medicine, Doha, Qatar
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