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Riller Q, Schmutz M, Fourgeaud J, Fischer A, Neven B. Protective role of antibodies in enteric virus infections: Lessons from primary and secondary immune deficiencies. Immunol Rev 2024. [PMID: 39340232 DOI: 10.1111/imr.13402] [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] [Indexed: 09/30/2024]
Abstract
Enteric viruses are the main cause of acute gastroenteritis worldwide with a significant morbidity and mortality, especially among children and aged adults. Some enteric viruses also cause disseminated infections and severe neurological manifestations such as poliomyelitis. Protective immunity against these viruses is not well understood in humans, with most knowledge coming from animal models, although the development of poliovirus and rotavirus vaccines has extended our knowledge. In a classical view, innate immunity involves the recognition of foreign DNA or RNA by pathogen recognition receptors leading to the production of interferons and other inflammatory cytokines. Antigen uptake and presentation to T cells and B cells then activate adaptive immunity and, in the case of the mucosal immunity, induce the secretion of dimeric IgA, the more potent immunoglobulins in viral neutralization. The study of Inborn errors of immunity (IEIs) offers a natural opportunity to study nonredundant immunity toward pathogens. In the case of enteric viruses, patients with a defective production of antibodies are at risk of developing neurological complications. Moreover, a recent description of patients with low or absent antibody production with protracted enteric viral infections associated with hepatitis reinforces the prominent role of B cells and immunoglobulins in the control of enteric virus.
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Affiliation(s)
- Quentin Riller
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Imagine Institute, Université Paris Cité, INSERM UMR 1163, Paris, France
- IHU-Imagine, Paris, France
| | - Muriel Schmutz
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Imagine Institute, Université Paris Cité, INSERM UMR 1163, Paris, France
- IHU-Imagine, Paris, France
| | - Jacques Fourgeaud
- Université Paris Cité, FETUS, Paris, France
- Microbiology Department, AP-HP, Hôpital Necker, Paris, France
| | - Alain Fischer
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker-Children's Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- INSERM UMRS 1163, Institut Imagine, Paris, France
- Collège de France, Paris, France
| | - Bénédicte Neven
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Imagine Institute, Université Paris Cité, INSERM UMR 1163, Paris, France
- IHU-Imagine, Paris, France
- Pediatric Hematology-Immunology and Rheumatology Unit, Necker-Children's Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
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2
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Haga K, Tokui T, Miyamoto K, Takai-Todaka R, Kudo S, Ishikawa A, Ishiyama R, Kato A, Yokoyama M, Katayama K, Nakanishi A. Neonatal Fc receptor is a functional receptor for classical human astrovirus. Genes Cells 2024. [PMID: 39266307 DOI: 10.1111/gtc.13160] [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: 08/06/2024] [Accepted: 08/24/2024] [Indexed: 09/14/2024]
Abstract
Human astrovirus (HAstV) is a global cause of gastroenteritis in infants, the elderly, and the immunocompromised. However, the molecular mechanisms that control its susceptibility are not fully understood, as the functional receptor used by the virus has yet to be identified. Here, a genome-wide CRISPR-Cas9 library screen in Caco2 cells revealed that the neonatal Fc receptor (FcRn) can function as a receptor for classical HAstV (Mamastrovirus genotype 1). Deletion of FCGRT or B2M, which encode subunits of FcRn, rendered Caco2 cells and intestinal organoid cells resistant to HAstV infection. We also showed that human FcRn expression renders non-susceptible cells permissive to viral infection and that FcRn binds directly to the HAstV spike protein. Therefore, our findings provide insight into the entry mechanism of HAstV into susceptible cells. We anticipate that this information can be used to develop new therapies targeting human astroviruses, providing new strategies to treat this global health issue.
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Affiliation(s)
- Kei Haga
- Laboratory of Viral Infection Control, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Takashi Tokui
- Laboratory of Viral Infection Control, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Kana Miyamoto
- Laboratory of Viral Infection Control, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Reiko Takai-Todaka
- Laboratory of Viral Infection Control, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Shiori Kudo
- Laboratory of Viral Infection Control, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Azusa Ishikawa
- Laboratory of Viral Infection Control, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Ryoka Ishiyama
- Laboratory of Viral Infection Control, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Akiko Kato
- National Center for Geriatrics and Gerontology, Department of Aging Intervention, Laboratory of Gene Therapy, and Laboratory for Radiation safety, Aichi, Japan
| | - Masaru Yokoyama
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection Control, Department of Infection Control and Immunology, Ōmura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Akira Nakanishi
- National Center for Geriatrics and Gerontology, Department of Aging Intervention, Laboratory of Gene Therapy, and Laboratory for Radiation safety, Aichi, Japan
- Department of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
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Wilson P, Rosenstengle C, Spak C. Underrecognized cause diarrhea in solid organ transplant: a report of astroviridae enteritis in liver transplant. Transpl Infect Dis 2024; 26:e14257. [PMID: 38407512 DOI: 10.1111/tid.14257] [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: 01/02/2024] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/27/2024]
Abstract
We present a case of a 72-year-old liver transplant recipient 7 years prior who presents to our hospital with general malaise, fatigue, low-grade fevers, and watery diarrhea. He was found to have Astrovirus via PCR testing in a comprehensive stool panel. The patient's home mycophenolic acid was held upon admission, while cyclosporine was continued through his hospital stay. Generally, Astroviridae infection is a rarely identified cause of enteritis and even less so in the transplant population. Although reports have been published regarding devastating cases of encephalitis in immunocompromised patients, our patient did not exhibit these symptoms and draws into question the danger of this virus in other immunosuppressed populations. This case helps to better elucidate which patient populations should be approached with caution in the setting of Astroviridae infection.
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Affiliation(s)
- Parker Wilson
- Baylor University Medical Center, Dallas, Texas, USA
| | | | - Cedric Spak
- Baylor University Medical Center, Dallas, Texas, USA
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Cintron M, Jani K, Madhavappallil J, Kamboj M, Babady NE. Prevalence of astrovirus and sapovirus among adult oncology patients with acute gastroenteritis using a multiplexed gastrointestinal pathogen PCR panel. Eur J Clin Microbiol Infect Dis 2024; 43:525-531. [PMID: 38216845 DOI: 10.1007/s10096-024-04748-4] [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: 10/09/2023] [Accepted: 01/04/2024] [Indexed: 01/14/2024]
Abstract
BACKGROUND Multiplex syndromic gastrointestinal panels (GIPCR) have streamlined the diagnosis of infectious diarrhea. Additionally, they have expanded the number of pathogens that can be routinely evaluated, allowing further understanding of the prevalence of enteric pathogens in various patient populations. The goal of this study was to investigate the prevalence and clinical presentation of astrovirus and sapovirus gastroenteritis in adult oncology patients as detected by the FilmArray GIPCR. METHODS All GIPCR panel results from December 2017 to June 2021 were retrospectively reviewed to determine the prevalence of astrovirus and sapovirus in adult oncology patients. Medical records were also reviewed to obtain clinical information. Repeat GIPCR positivity and symptom duration were used to estimate prolonged viral shedding. RESULTS A total of 18,014 panels were performed on samples collected from 9303 adults. Overall, astrovirus and sapovirus were detected in 0.35% (33/9303) and 0.45% (42/9303) GIPCRs respectively. At least one viral target was detected in 424 (4.4%) patients. Astrovirus accounted for 7.8% (33/424) and sapovirus 9.9% (42/424) of patients. Diarrhea was the most common symptom documented. A subset of transplant patients had protracted viral detection with a median of ~27 days (range 23-43 days) for astrovirus and 97 days (range 11-495) for sapovirus. No clusters or outbreaks were identified during the study period. CONCLUSION In oncology patients with viral gastroenteritis, astrovirus and sapovirus were the causative agents in 18% of the cases. Both viruses were associated with mild disease. Prolonged diarrhea and viral shedding were observed in a few transplant patients.
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Affiliation(s)
- Melvili Cintron
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Krupa Jani
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Jerin Madhavappallil
- Infection Control Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mini Kamboj
- Infection Control Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - N Esther Babady
- Clinical Microbiology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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Ghosh A, Delgado-Cunningham K, López T, Green K, Arias CF, DuBois RM. Structure and antigenicity of the divergent human astrovirus VA1 capsid spike. PLoS Pathog 2024; 20:e1012028. [PMID: 38416796 PMCID: PMC10950212 DOI: 10.1371/journal.ppat.1012028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 03/19/2024] [Accepted: 02/05/2024] [Indexed: 03/01/2024] Open
Abstract
Human astrovirus (HAstV) is a known cause of viral gastroenteritis in children worldwide, but HAstV can cause also severe and systemic infections in immunocompromised patients. There are three clades of HAstV: classical, MLB, and VA/HMO. While all three clades are found in gastrointestinal samples, HAstV-VA/HMO is the main clade associated with meningitis and encephalitis in immunocompromised patients. To understand how the HAstV-VA/HMO can infect the central nervous system, we investigated its sequence-divergent capsid spike, which functions in cell attachment and may influence viral tropism. Here we report the high-resolution crystal structures of the HAstV-VA1 capsid spike from strains isolated from patients with gastrointestinal and neuronal disease. The HAstV-VA1 spike forms a dimer and shares a core beta-barrel structure with other astrovirus capsid spikes but is otherwise strikingly different, suggesting that HAstV-VA1 may utilize a different cell receptor, and an infection competition assay supports this hypothesis. Furthermore, by mapping the capsid protease cleavage site onto the structure, the maturation and assembly of the HAstV-VA1 capsid is revealed. Finally, comparison of gastrointestinal and neuronal HAstV-VA1 sequences, structures, and antigenicity suggests that neuronal HAstV-VA1 strains may have acquired immune escape mutations. Overall, our studies on the HAstV-VA1 capsid spike lay a foundation to further investigate the biology of HAstV-VA/HMO and to develop vaccines and therapeutics targeting it.
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Affiliation(s)
- Anisa Ghosh
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Kevin Delgado-Cunningham
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Tomás López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Kassidy Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Rebecca M. DuBois
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
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Jiang X, Yan J, Huang H, Ai L, Yu X, Zhong P, Chen Y, Liang Z, Qiu W, Huang H, Yan W, Liang Y, Chen P, Wang R. Development of novel parameters for pathogen identification in clinical metagenomic next-generation sequencing. Front Genet 2023; 14:1266990. [PMID: 38046047 PMCID: PMC10693447 DOI: 10.3389/fgene.2023.1266990] [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: 07/28/2023] [Accepted: 10/27/2023] [Indexed: 12/05/2023] Open
Abstract
Introduction: Metagenomic next-generation sequencing (mNGS) has emerged as a powerful tool for rapid pathogen identification in clinical practice. However, the parameters used to interpret mNGS data, such as read count, genus rank, and coverage, lack explicit performance evaluation. In this study, the developed indicators as well as novel parameters were assessed for their performance in bacterium detection. Methods: We developed several relevant parameters, including 10M normalized reads, double-discard reads, Genus Rank Ratio, King Genus Rank Ratio, Genus Rank Ratio*Genus Rank, and King Genus Rank Ratio*Genus Rank. These parameters, together with frequently used read indicators including raw reads, reads per million mapped reads (RPM), transcript per kilobase per million mapped reads (TPM), Genus Rank, and coverage were analyzed for their diagnostic efficiency in bronchoalveolar lavage fluid (BALF), a common source for detecting eight bacterium pathogens: Acinetobacter baumannii, Klebsiella pneumoniae, Streptococcus pneumoniae, Staphylococcus aureus, Hemophilus influenzae, Stenotrophomonas maltophilia, Pseudomonas aeruginosa, and Aspergillus fumigatus. Results: The results demonstrated that these indicators exhibited good diagnostic efficacy for the eight pathogens. The AUC values of all indicators were almost greater than 0.9, and the corresponding sensitivity and specificity values were almost greater than 0.8, excepted coverage. The negative predictive value of all indicators was greater than 0.9. The results showed that the use of double-discarded reads, Genus Rank Ratio*Genus Rank, and King Genus Rank Ratio*Genus Rank exhibited better diagnostic efficiency than that of raw reads, RPM, TPM, and in Genus Rank. These parameters can serve as a reference for interpreting mNGS data of BALF. Moreover, precision filters integrating our novel parameters were built to detect the eight bacterium pathogens in BALF samples through machine learning. Summary: In this study, we developed a set of novel parameters for pathogen identification in clinical mNGS based on reads and ranking. These parameters were found to be more effective in diagnosing pathogens than traditional approaches. The findings provide valuable insights for improving the interpretation of mNGS reports in clinical settings, specifically in BALF analysis.
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Affiliation(s)
- Xiwen Jiang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Jinghai Yan
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hao Huang
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lu Ai
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xuegao Yu
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Pengqiang Zhong
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yili Chen
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhikun Liang
- Guangzhou Darui Biotechnology Co., Ltd., Guangzhou, China
| | - Wancen Qiu
- Guangzhou Darui Biotechnology Co., Ltd., Guangzhou, China
| | - Huiying Huang
- Guangzhou Darui Biotechnology Co., Ltd., Guangzhou, China
| | - Wenyan Yan
- Guangzhou Darui Biotechnology Co., Ltd., Guangzhou, China
| | - Yan Liang
- Guangzhou Darui Biotechnology Co., Ltd., Guangzhou, China
| | - Peisong Chen
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ruizhi Wang
- Department of Laboratory Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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Kèbè O, Thiaw FD, Ndiaye N, Landoh DE, Cissé G, Faye O, Faye M. Near-complete genome sequence of human astrovirus recovered from a child with acute flaccid paralysis in Guinea, 2021. Microbiol Resour Announc 2023; 12:e0021423. [PMID: 37772851 PMCID: PMC10586129 DOI: 10.1128/mra.00214-23] [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: 03/23/2023] [Accepted: 08/11/2023] [Indexed: 09/30/2023] Open
Abstract
Astroviruses are common causes of gastroenteritis in humans and other animals. Herein, we reported a near-complete human astrovirus (HAstV) sequence detected in a child with acute flaccid paralysis. The sample was collected in Guinea in January 2021. Phylogenetic analyses indicated that this virus belonged to the HAstV-1 genotype.
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Affiliation(s)
- Ousmane Kèbè
- Inter-country WHO reference laboratory for poliomyelitis, virology department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Fatou Diène Thiaw
- Inter-country WHO reference laboratory for poliomyelitis, virology department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Ndack Ndiaye
- Inter-country WHO reference laboratory for poliomyelitis, virology department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Gassim Cissé
- Ministry of Health and Public Hygiene, Conakry, Guinea
| | - Ousmane Faye
- Inter-country WHO reference laboratory for poliomyelitis, virology department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Martin Faye
- Inter-country WHO reference laboratory for poliomyelitis, virology department, Institut Pasteur de Dakar, Dakar, Senegal
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Fourgeaud J, Lecuit MM, Pérot P, Bruneau J, Regnault B, Da Rocha N, Bessaud M, Picard C, Jeziorski É, Fournier B, Levy R, Marçais A, Blanche S, Frange P, Fischer A, Cavazzana M, Ferroni A, Jamet A, Leruez-Ville M, Eloit M, Neven B. Chronic Aichi Virus Infection As a Cause of Long-Lasting Multiorgan Involvement in Patients With Primary Immune Deficiencies. Clin Infect Dis 2023; 77:620-628. [PMID: 37078608 DOI: 10.1093/cid/ciad237] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/08/2023] [Accepted: 04/14/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) was used to assess patients with primary or secondary immune deficiencies (PIDs and SIDs) who presented with immunopathological conditions related to immunodysregulation. METHODS Thirty patients with PIDs or SIDs who presented with symptoms related to immunodysregulation and 59 asymptomatic patients with similar PIDs or SIDs were enrolled. mNGS was performed on organ biopsy. Specific Aichi virus (AiV) reverse-transcription polymerase chain reaction (RT-PCR) was used to confirm AiV infection and screen the other patients. In situ hybridization (ISH) assay was done on AiV-infected organs to identify infected cells. Virus genotype was determined by phylogenetic analysis. RESULTS AiV sequences were detected using mNGS in tissue samples of 5 patients and by RT-PCR in peripheral samples of another patient, all of whom presented with PID and long-lasting multiorgan involvement, including hepatitis, splenomegaly, and nephritis in 4 patients. CD8+ T-cell infiltration was a hallmark of the disease. RT-PCR detected intermittent low viral loads in urine and plasma from infected patients but not from uninfected patients. Viral detection stopped after immune reconstitution obtained by hematopoietic stem cell transplantation. ISH demonstrated the presence of AiV RNA in hepatocytes (n = 1) and spleen tissue (n = 2). AiV belonged to genotype A (n = 2) or B (n = 3). CONCLUSIONS The similarity of the clinical presentation, the detection of AiV in a subgroup of patients suffering from immunodysregulation, the absence of AiV in asymptomatic patients, the detection of viral genome in infected organs by ISH, and the reversibility of symptoms after treatment argue for AiV causality.
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Affiliation(s)
- Jacques Fourgeaud
- Université Paris Cité, Fédération pour l'Étude et évaluation des Thérapeutiques intra-Utérines, Paris, France
- Microbiology Department, AP-HP, Hôpital Necker Paris, France
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, Paris, France
| | - Mathilde M Lecuit
- Pediatric Hematology Immunology and Rheumatology Unit, AP-HP, Hôpital Necker Paris, France
| | - Philippe Pérot
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, Paris, France
| | - Julie Bruneau
- Laboratory of Molecular Mechanisms of Hematologic Disorders and Therapeutic Implications, Université Paris Cité, Inserm, Institut Imagine Paris, France
- Department of Pathology, AP-HP, Hôpital Necker Paris, France
| | - Beatrice Regnault
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, Paris, France
| | - Nicolas Da Rocha
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, Paris, France
| | - Mael Bessaud
- Laboratoire signalisation antivirale, Institut Pasteur, Université Paris Cité, Paris, France
| | - Capucine Picard
- Laboratory of Lymphocyte Activation and Susceptibility to EBV Infection, Université Paris Cité, Inserm, Institut Imagine Paris, France
- Study Center for Primary Immunodeficiencies, Necker-Children's hospital, APHP Paris, France
| | - Éric Jeziorski
- Pediatric Hematology Immunology Unit, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Benjamin Fournier
- Pediatric Hematology Immunology and Rheumatology Unit, AP-HP, Hôpital Necker Paris, France
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Université Paris Cité, Inserm, Institut Imagine Paris, France
| | - Romain Levy
- Pediatric Hematology Immunology and Rheumatology Unit, AP-HP, Hôpital Necker Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Université Paris Cité, Inserm, Institut Imagine Paris, France
| | - Ambroise Marçais
- Laboratory of Molecular Mechanisms of Hematologic Disorders and Therapeutic Implications, Université Paris Cité, Inserm, Institut Imagine Paris, France
- Hepatology Unit, AP-HP, Hôpital Necker Paris, France
| | - Stéphane Blanche
- Pediatric Hematology Immunology and Rheumatology Unit, AP-HP, Hôpital Necker Paris, France
| | - Pierre Frange
- Université Paris Cité, Fédération pour l'Étude et évaluation des Thérapeutiques intra-Utérines, Paris, France
- Microbiology Department, AP-HP, Hôpital Necker Paris, France
| | - Alain Fischer
- Pediatric Hematology Immunology and Rheumatology Unit, AP-HP, Hôpital Necker Paris, France
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Université Paris Cité, Inserm, Institut Imagine Paris, France
- Médecine expérimentale, Collège de France, Paris, France
| | - Marina Cavazzana
- Laboratory of Human Lympho-Hematopoiesis, Université Paris Cité, Inserm, Institut Imagine Paris, France
- Department of Biotherapy, Hôpital Necker, AP-HP Paris, France
| | - Agnès Ferroni
- Microbiology Department, AP-HP, Hôpital Necker Paris, France
| | - Anne Jamet
- Microbiology Department, AP-HP, Hôpital Necker Paris, France
- Department of Pathogenesis of systemic infections, Université Paris Cité, CNRS, Inserm, Institut Necker-Enfants Malades, Paris, France
| | - Marianne Leruez-Ville
- Université Paris Cité, Fédération pour l'Étude et évaluation des Thérapeutiques intra-Utérines, Paris, France
- Microbiology Department, AP-HP, Hôpital Necker Paris, France
| | - Marc Eloit
- Pathogen Discovery Laboratory, Institut Pasteur, Université Paris Cité, Paris, France
- Département des Sciences biologiques et Pharmaceutiques, Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort, France
| | - Bénédicte Neven
- Pediatric Hematology Immunology and Rheumatology Unit, AP-HP, Hôpital Necker Paris, France
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Université Paris Cité, Inserm, Institut Imagine Paris, France
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9
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Maximova OA, Weller ML, Krogmann T, Sturdevant DE, Ricklefs S, Virtaneva K, Martens C, Wollenberg K, Minai M, Moore IN, Sauter CS, Barker JN, Lipkin WI, Seilhean D, Nath A, Cohen JI. Pathogenesis and outcome of VA1 astrovirus infection in the human brain are defined by disruption of neural functions and imbalanced host immune responses. PLoS Pathog 2023; 19:e1011544. [PMID: 37595007 PMCID: PMC10438012 DOI: 10.1371/journal.ppat.1011544] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/06/2023] [Indexed: 08/20/2023] Open
Abstract
Astroviruses (AstVs) can cause of severe infection of the central nervous system (CNS) in immunocompromised individuals. Here, we identified a human AstV of the VA1 genotype, HAstV-NIH, as the cause of fatal encephalitis in an immunocompromised adult. We investigated the cells targeted by AstV, neurophysiological changes, and host responses by analyzing gene expression, protein expression, and cellular morphology in brain tissue from three cases of AstV neurologic disease (AstV-ND). We demonstrate that neurons are the principal cells targeted by AstV in the brain and that the cerebellum and brainstem have the highest burden of infection. Detection of VA1 AstV in interconnected brain structures such as thalamus, deep cerebellar nuclei, Purkinje cells, and pontine nuclei indicates that AstV may spread between connected neurons transsynaptically. We found transcriptional dysregulation of neural functions and disruption of both excitatory and inhibitory synaptic innervation of infected neurons. Importantly, transcriptional dysregulation of neural functions occurred in fatal cases, but not in a patient that survived AstV-ND. We show that the innate, but not adaptive immune response was transcriptionally driving host defense in the brain of immunocompromised patients with AstV-ND. Both transcriptome and molecular pathology studies showed that most of the cellular changes were associated with CNS-intrinsic cells involved in phagocytosis and injury repair (microglia, perivascular/parenchymal border macrophages, and astrocytes), but not CNS-extrinsic cells (T and B cells), suggesting an imbalance of innate and adaptive immune responses to AstV infection in the brain as a result of the underlying immunodeficiencies. These results show that VA1 AstV infection of the brain in immunocompromised humans is associated with imbalanced host defense responses, disruption of neuronal somatodendritic compartments and synapses and increased phagocytic cellular activity. Improved understanding of the response to viral infections of the human CNS may provide clues for how to manipulate these processes to improve outcomes.
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Affiliation(s)
- Olga A. Maximova
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Melodie L. Weller
- Secretory Physiology Section, Molecular Physiology and Therapeutics Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tammy Krogmann
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Daniel E. Sturdevant
- Research Technologies Branch, Genomics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Stacy Ricklefs
- Research Technologies Branch, Genomics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Kimmo Virtaneva
- Research Technologies Branch, Genomics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Craig Martens
- Research Technologies Branch, Genomics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Kurt Wollenberg
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mahnaz Minai
- Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ian N. Moore
- Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Craig S. Sauter
- Department of Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Juliet N. Barker
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | | | - Avindra Nath
- Infections of the Nervous System Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jeffrey I. Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
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10
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Liu Q, Liu X, Hu B, Xu H, Sun R, Li P, Zhang Y, Yang H, Ma N, Sun X. Diagnostic performance and clinical impact of blood metagenomic next-generation sequencing in ICU patients suspected monomicrobial and polymicrobial bloodstream infections. Front Cell Infect Microbiol 2023; 13:1192931. [PMID: 37434786 PMCID: PMC10330723 DOI: 10.3389/fcimb.2023.1192931] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/09/2023] [Indexed: 07/13/2023] Open
Abstract
Introduction Early and effective application of antimicrobial medication has been evidenced to improve outcomes of patients with bloodstream infection (BSI). However, conventional microbiological tests (CMTs) have a number of limitations that hamper a rapid diagnosis. Methods We retrospectively collected 162 cases suspected BSI from intensive care unit with blood metagenomics next-generation sequencing (mNGS) results, to comparatively evaluate the diagnostic performance and the clinical impact on antibiotics usage of mNGS. Results and discussion Results showed that compared with blood culture, mNGS detected a greater number of pathogens, especially for Aspergillus spp, and yielded a significantly higher positive rate. With the final clinical diagnosis as the standard, the sensitivity of mNGS (excluding viruses) was 58.06%, significantly higher than that of blood culture (34.68%, P<0.001). Combing blood mNGS and culture results, the sensitivity improved to 72.58%. Forty-six patients had infected by mixed pathogens, among which Klebsiella pneumoniae and Acinetobacter baumannii contributed most. Compared to monomicrobial, cases with polymicrobial BSI exhibited dramatically higher level of SOFA, AST, hospitalized mortality and 90-day mortality (P<0.05). A total of 101 patients underwent antibiotics adjustment, among which 85 were adjusted according to microbiological results, including 45 cases based on the mNGS results (40 cases escalation and 5 cases de-escalation) and 32 cases on blood culture. Collectively, for patients suspected BSI in critical condition, mNGS results can provide valuable diagnostic information and contribute to the optimizing of antibiotic treatment. Combining conventional tests with mNGS may significantly improve the detection rate for pathogens and optimize antibiotic treatment in critically ill patients with BSI.
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Affiliation(s)
- Qilong Liu
- Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Xiaojing Liu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Bingxue Hu
- Department of Scientific Affairs, Vision Medicals for Infectious Diseases, Guangzhou, Guangdong Province, China
| | - Huan Xu
- Department of Scientific Affairs, Vision Medicals for Infectious Diseases, Guangzhou, Guangdong Province, China
| | - Rongqing Sun
- Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Pengfei Li
- Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Yunwei Zhang
- Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Hongfu Yang
- Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Ning Ma
- Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
| | - Xiaoge Sun
- Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan Province, China
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11
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Gauthier NPG, Chorlton SD, Krajden M, Manges AR. Agnostic Sequencing for Detection of Viral Pathogens. Clin Microbiol Rev 2023; 36:e0011922. [PMID: 36847515 PMCID: PMC10035330 DOI: 10.1128/cmr.00119-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
The advent of next-generation sequencing (NGS) technologies has expanded our ability to detect and analyze microbial genomes and has yielded novel molecular approaches for infectious disease diagnostics. While several targeted multiplex PCR and NGS-based assays have been widely used in public health settings in recent years, these targeted approaches are limited in that they still rely on a priori knowledge of a pathogen's genome, and an untargeted or unknown pathogen will not be detected. Recent public health crises have emphasized the need to prepare for a wide and rapid deployment of an agnostic diagnostic assay at the start of an outbreak to ensure an effective response to emerging viral pathogens. Metagenomic techniques can nonspecifically sequence all detectable nucleic acids in a sample and therefore do not rely on prior knowledge of a pathogen's genome. While this technology has been reviewed for bacterial diagnostics and adopted in research settings for the detection and characterization of viruses, viral metagenomics has yet to be widely deployed as a diagnostic tool in clinical laboratories. In this review, we highlight recent improvements to the performance of metagenomic viral sequencing, the current applications of metagenomic sequencing in clinical laboratories, as well as the challenges that impede the widespread adoption of this technology.
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Affiliation(s)
- Nick P. G. Gauthier
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Mel Krajden
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Amee R. Manges
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
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12
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Bami S, Hidinger J, Madni A, Hargest V, Schultz-Cherry S, Cortez V, Cross SJ, Ward DA, Hayden RT, Rubnitz J, Pui CH, Khan RB, Hijano DR. Human Astrovirus VA1 Encephalitis in Pediatric Patients With Cancer: Report of 2 Cases and Review of the Literature. J Pediatric Infect Dis Soc 2022; 11:408-412. [PMID: 35849135 DOI: 10.1093/jpids/piac045] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 05/25/2022] [Indexed: 11/14/2022]
Abstract
Novel human astroviruses (HAstVs) have recently been implicated as rare causes of fatal encephalitis in immunocompromised patients, for which there is no proven treatment. We report 2 cases from our institution in which HAstV-VA1 was detected in the cerebrospinal fluid by metagenomic next-generation sequencing after the initial evaluation revealed no etiology.
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Affiliation(s)
- Sakshi Bami
- Hospitalist Medicine Program, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jennifer Hidinger
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Arshia Madni
- Hospitalist Medicine Program, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Division of Quality of Life and Palliative Care, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Virginia Hargest
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Valerie Cortez
- Department of Molecular and Cell & Developmental Biology, University of California, Santa Cruz, California, USA
| | - Shane J Cross
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Deborah A Ward
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Randall T Hayden
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jeffrey Rubnitz
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Ching-Hon Pui
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Raja B Khan
- Division of Neurology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Diego R Hijano
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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13
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Potential zoonotic swine enteric viruses: The risk ignored for public health. Virus Res 2022; 315:198767. [PMID: 35421434 DOI: 10.1016/j.virusres.2022.198767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 03/30/2022] [Accepted: 04/03/2022] [Indexed: 12/28/2022]
Abstract
Swine could serve as a natural reservoir for a large variety of viruses, including potential zoonotic enteric viruses. The presence of viruses with high genetic similarity between porcine and human strains may result in the emergence of zoonotic or xenozoonotic infections. Furthermore, the globalization and intensification of swine industries exacerbate the transmission and evolution of zoonotic viruses among swine herds and individuals working in swine-related occupations. To effectively prevent the public health risks posed by zoonotic swine enteric viruses, designing, and implementing a comprehensive measure for early diagnosis, prevention, and mitigation, requires interdisciplinary a collaborative ''One Health" approach from veterinarians, environmental and public health professionals, and the swine industry. In this paper, we reviewed the current knowledge of selected potential zoonotic swine enteric viruses and explored swine intensive production and its associated public health risks.
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14
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Graff K, Dominguez SR, Messacar K. Metagenomic Next-Generation Sequencing for Diagnosis of Pediatric Meningitis and Encephalitis: A Review. J Pediatric Infect Dis Soc 2021; 10:S78-S87. [PMID: 34951470 PMCID: PMC8703254 DOI: 10.1093/jpids/piab067] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Metagenomic next-generation sequencing is a novel diagnostic test with the potential to revolutionize the diagnosis of pediatric meningitis and encephalitis through unbiased detection of bacteria, viruses, parasites, and fungi in cerebrospinal fluid. Current literature is mostly observational with variable indications, populations, and timing of testing with resulting variability in diagnostic yield and clinical impact. Diagnostic stewardship strategies are needed to direct testing toward high-impact pediatric populations, to optimize timing of testing, to ensure appropriate interpretation of results, and to guide prompt optimization of antimicrobials. This review highlights the high clinical potential of this test, though future studies are needed to gather clinical impact and cost-effectiveness data for specific indications in pediatric populations.
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Affiliation(s)
- Kelly Graff
- Section of Infectious Diseases, Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA,Corresponding Author: Kelly E. Graff, MD, Pediatric Infectious Diseases, Children’s Hospital Colorado, B055, 13123 E 16th Ave, Aurora, CO 80045, USA. E-mail:
| | - Samuel R Dominguez
- Section of Infectious Diseases, Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA,Department of Pathology and Laboratory Medicine, Children’s Hospital Colorado, Aurora, Colorado, USA
| | - Kevin Messacar
- Section of Infectious Diseases, Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA
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15
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Król L, Turkiewicz D, Nordborg K, Englund E, Stenberg L, Karlsson Lindsjö O, Lind Karlberg M, Pronk CJ. Astrovirus VA1/HMO encephalitis after allogeneic hematopoietic cell transplantation: Significant role of immune competence in virus control. Pediatr Blood Cancer 2021; 68:e29286. [PMID: 34411414 DOI: 10.1002/pbc.29286] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/07/2021] [Accepted: 07/21/2021] [Indexed: 11/08/2022]
Affiliation(s)
- Ladislav Król
- Childhood Cancer Centre, Skåne University Hospital, Lund, Sweden
| | | | - Karin Nordborg
- Department of Pediatric Neurology, Skåne University Hospital, Lund, Sweden
| | - Elisabet Englund
- Department of Genetics and Pathology, Skåne University Hospital, Lund, Sweden
| | - Lars Stenberg
- Department of Medical Imaging and Physiology, Skåne University Hospital, Lund, Sweden
| | | | | | - Cornelis Jan Pronk
- Childhood Cancer Centre, Skåne University Hospital, Lund, Sweden.,Division of Molecular Hematology, Lund University, Lund, Sweden.,Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
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16
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Casto AM, Fredricks DN, Hill JA. Diagnosis of infectious diseases in immunocompromised hosts using metagenomic next generation sequencing-based diagnostics. Blood Rev 2021; 53:100906. [PMID: 34802773 DOI: 10.1016/j.blre.2021.100906] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/28/2021] [Accepted: 11/01/2021] [Indexed: 02/07/2023]
Abstract
The diagnosis of infectious diseases in immunocompromised hosts presents unique challenges for the clinician. Metagenomic next generation sequencing (mNGS) based diagnostics that identify microbial nucleic acids in clinical samples (mNGS for pathogen identification or mNGSpi) may be a useful tool in addressing some of these challenges. Studies of mNGSpi in immunocompromised hosts have demonstrated that these diagnostics are capable of identifying causative organisms in a subset of patients for whom conventional testing has been negative. While these studies provide proof of concept for mNGSpi utility, they have a number of limitations, which make it difficult to confidently assess test performance and clinical impact based on current data. Future studies will likely feature larger cohort sizes and controlled interventional study designs that assess the impact of mNGSpi on clinical endpoints. They will also likely include assessments of the clinical value of data generated by mNGS beyond pathogen identification.
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Affiliation(s)
- Amanda M Casto
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, United States of America; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America.
| | - David N Fredricks
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, United States of America; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America.
| | - Joshua A Hill
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, United States of America; Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America.
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17
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Amirifar P, Yazdani R, Azizi G, Ranjouri MR, Durandy A, Plebani A, Lougaris V, Hammarstrom L, Aghamohammadi A, Abolhassani H. Known and potential molecules associated with altered B cell development leading to predominantly antibody deficiencies. Pediatr Allergy Immunol 2021; 32:1601-1615. [PMID: 34181780 DOI: 10.1111/pai.13589] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/12/2021] [Accepted: 06/24/2021] [Indexed: 12/14/2022]
Abstract
Predominantly antibody deficiencies (PADs) encompass a heterogeneous group of disorders characterized by low immunoglobulin serum levels in the presence or absence of peripheral B cells. Clinical presentation of affected patients may include recurrent respiratory and gastrointestinal infections, invasive infections, autoimmune manifestations, allergic reactions, lymphoproliferation, and increased susceptibility to malignant transformation. In the last decades, several genetic alterations affecting B-cell development/maturation have been identified as causative of several forms of PADs, adding important information on the genetic background of PADs, which in turn should lead to a better understanding of these disorders and precise clinical management of affected patients. This review aimed to present a comprehensive overview of the known and potentially involved molecules in the etiology of PADs to elucidate the pathogenesis of these disorders and eventually offer a better prognosis for affected patients.
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Affiliation(s)
- Parisa Amirifar
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Yazdani
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Primary Immunodeficiency Diseases Network (PIDNet), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Gholamreza Azizi
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Mohammad Reza Ranjouri
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Anne Durandy
- Human Lymphohematopoiesis Laboratory, Institut Imagine, Inserm U1163, Paris Descartes Sorbonne, Paris Cite University, Paris, France
| | - Alessandro Plebani
- Pediatrics Clinic and "A. Nocivelli" Institute for Molecular Medicine, Department of Clinical and Experimental Sciences, University of Brescia, ASST Spedali Civili of Brescia, Brescia, Italy
| | - Vassilios Lougaris
- Pediatrics Clinic and "A. Nocivelli" Institute for Molecular Medicine, Department of Clinical and Experimental Sciences, University of Brescia, ASST Spedali Civili of Brescia, Brescia, Italy
| | - Lennart Hammarstrom
- Division of Clinical Immunology, Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden.,Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Asghar Aghamohammadi
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Hassan Abolhassani
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Division of Clinical Immunology, Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden.,Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute at Karolinska University Hospital Huddinge, Stockholm, Sweden
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18
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Janowski AB, Owen MC, Dudley H, López T, Espinosa R, Elvin-Lewis M, Colichon A, Arias CF, Burbelo PD, Wang D. High Seropositivity Rate of Neutralizing Antibodies to Astrovirus VA1 in Human Populations. mSphere 2021; 6:e0048421. [PMID: 34468168 PMCID: PMC8550256 DOI: 10.1128/msphere.00484-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/17/2021] [Indexed: 02/04/2023] Open
Abstract
Astroviruses are common pathogens of the human gastrointestinal tract, but they have been recently identified from cases of fatal meningoencephalitis. Astrovirus VA1 is the most frequently detected astrovirus genotype from cases of human encephalitis, but the prevalence of neutralizing antibodies to VA1 in human sera is unknown. We developed a focus reduction neutralization assay (FRNT) for VA1 and measured the seroprevalence of neutralizing antibodies from two cohorts of adult and pediatric serum samples: (i) an age-stratified cohort from St. Louis, MO, collected from 2007 to 2008 and (ii) a cohort from the Peruvian Amazonian River Basin collected in the late 1990s. In the St. Louis cohort, the lowest seropositivity rate was in children 1 year of age (6.9%), rising to 63.3% by ages 9 to 12, and 76.3% of adults ≥20 years were positive. The Peruvian Amazon cohort showed similar seropositivity rates across all ages, with individuals under age 20 having a rate of 75%, while 78.2% of adults ≥20 years were seropositive. In addition, we also identified the presence neutralizing antibodies to VA1 from commercial lots of intravenous immunoglobulin (IVIG). Our results demonstrate that a majority of humans are exposed to VA1 by adulthood, with the majority of infections occurring between 2 and 9 years of age. In addition, our results indicate that VA1 has been circulating in two geographically and socioeconomically divergent study cohorts over the past 20 years. Nonetheless, a significant proportion of the human population lacks neutralizing immunity and remains at risk for acute infection. IMPORTANCE Astroviruses are human pathogens with emerging disease associations, including the recent recognition of their capacity to cause meningoencephalitis. Astrovirus VA1 is the most commonly identified astrovirus genotype from cases of human encephalitis, but it is unknown what percentage of the human population has neutralizing antibodies to VA1. We found that 76.3 to 78.2% of adult humans ≥20 years of age in two geographically and socioeconomically distinct cohorts are seropositive for VA1, with the majority of infections occurring between 2 and 9 years of age. These results demonstrate that VA1 has been circulating in human populations over the past 2 decades and that most humans develop neutralizing antibodies against this virus by adulthood. However, a subset of humans lack evidence of neutralizing antibodies and are at risk for diseases caused by VA1, including encephalitis.
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Affiliation(s)
- Andrew B. Janowski
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Macee C. Owen
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Holly Dudley
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Tomás López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Rafaela Espinosa
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | | | - Alejandro Colichon
- Department of Immunology, Peruvian University Cayetano Heredia, Lima, Peru
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Peter D. Burbelo
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
| | - David Wang
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
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19
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Ferreyra FM, Arruda PEH, Bradner LK, Harmon KM, Zhang M, Giménez-Lirola L, Arruda BL. Experimental porcine astrovirus type 3-associated polioencephalomyelitis in swine. Vet Pathol 2021; 58:1064-1074. [PMID: 34657543 DOI: 10.1177/03009858211025794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Porcine astrovirus type 3 (PoAstV3) is an emerging virus in the family Astroviridae that has been recently associated with polioencephalomyelitis/encephalitis. Herein, we describe the experimental oral and intravenous inoculation of an infectious central nervous system (CNS) tissue homogenate containing PoAstV3 to cesarean-derived, colostrum-deprived pigs, and the subsequent development of clinical signs, histologic lesions, specific humoral immune response, and detection of viral particles by electron microscopy (EM) and viral RNA by RT-qPCR (reverse transcriptase quantitative polymerase chain reaction) and in situ hybridization (ISH). IgG against a portion of the PoAstV3 ORF2 capsid was first detected at 7 days post-inoculation (DPI) in 2 of 4 inoculated animals and in all inoculated animals by 14 DPI. At 21 and 28 DPI, 2 of 4 inoculated animals developed ataxia, tetraparesis, and/or lateral recumbency. All inoculated animals had histologic lesions in the CNS including perivascular lymphoplasmacytic cuffs, multifocal areas of gliosis with neuronal necrosis, satellitosis, and radiculoneuritis, and PoAstV3 RNA as detected by RT-qPCR within multiple anatomic regions of the CNS. Consistent viral structures were within the soma of a spinal cord neuron in the single pig examined by EM. Of note, PoAstV3 was not only detected by ISH in neurons of the cerebrum and spinal cord but also neurons of the dorsal root ganglion and nerve roots consistent with viral dissemination via axonal transport. This is the first study reproducing CNS disease with a porcine astrovirus strain consistent with natural infection, suggesting that pigs may serve as an animal model to study the pathogenesis of neurotropic astroviruses.
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Affiliation(s)
| | - Paulo E H Arruda
- 1177Iowa State University, Ames, IA, USA.,Veterinary Resources Inc, Cambridge, IA, USA
| | | | | | - Min Zhang
- 1177Iowa State University, Ames, IA, USA
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20
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Grammatikos A, Donati M, Johnston SL, Gompels MM. Peripheral B Cell Deficiency and Predisposition to Viral Infections: The Paradigm of Immune Deficiencies. Front Immunol 2021; 12:731643. [PMID: 34527001 PMCID: PMC8435594 DOI: 10.3389/fimmu.2021.731643] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 08/09/2021] [Indexed: 12/11/2022] Open
Abstract
In the era of COVID-19, understanding how our immune system responds to viral infections is more pertinent than ever. Immunodeficiencies with very low or absent B cells offer a valuable model to study the role of humoral immunity against these types of infection. This review looks at the available evidence on viral infections in patients with B cell alymphocytosis, in particular those with X-linked agammaglobulinemia (XLA), Good’s syndrome, post monoclonal-antibody therapy and certain patients with Common Variable Immune Deficiency (CVID). Viral infections are not as infrequent as previously thought in these conditions and individuals with very low circulating B cells seem to be predisposed to an adverse outcome. Particularly in the case of SARS-CoV2 infection, mounting evidence suggests that peripheral B cell alymphocytosis is linked to a poor prognosis.
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Affiliation(s)
- Alexandros Grammatikos
- Department of Immunology, Southmead Hospital, North Bristol National Health Service (NHS) Trust, Bristol, United Kingdom
| | - Matthew Donati
- Severn Infection Sciences and Public Health England National Infection Service South West, Department of Virology, Southmead Hospital, North Bristol NHS Trust, Bristol, United Kingdom
| | - Sarah L Johnston
- Department of Immunology, Southmead Hospital, North Bristol National Health Service (NHS) Trust, Bristol, United Kingdom
| | - Mark M Gompels
- Department of Immunology, Southmead Hospital, North Bristol National Health Service (NHS) Trust, Bristol, United Kingdom
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21
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d'Humières C, Salmona M, Dellière S, Leo S, Rodriguez C, Angebault C, Alanio A, Fourati S, Lazarevic V, Woerther PL, Schrenzel J, Ruppé E. The Potential Role of Clinical Metagenomics in Infectious Diseases: Therapeutic Perspectives. Drugs 2021; 81:1453-1466. [PMID: 34328626 PMCID: PMC8323086 DOI: 10.1007/s40265-021-01572-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2021] [Indexed: 12/24/2022]
Abstract
Clinical metagenomics (CMg) is the process of sequencing nucleic acid of clinical samples to obtain clinically relevant information such as the identification of microorganisms and their susceptibility to antimicrobials. Over the last decades, sequencing and bioinformatic solutions supporting CMg have much evolved and an increasing number of case reports and series covering various infectious diseases have been published. Metagenomics is a new approach to infectious disease diagnosis that is currently being developed and is certainly one of the most promising for the coming years. However, most CMg studies are retrospective, and few address the potential impact CMg could have on patient management, including initiation, adaptation, or cessation of antimicrobials. In this narrative review, we have discussed the potential role of CMg in bacteriology, virology, mycology, and parasitology. Several reports and case-series confirm that CMg is an innovative tool with which one can (i) identify more microorganisms than with conventional methods in a single test, (ii) obtain results within hours, and (iii) tailor the antimicrobial regimen of patients. However, the cost-efficiency of CMg and its real impact on patient management are still to be determined.
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Affiliation(s)
- Camille d'Humières
- Université de Paris, IAME, INSERM, 75018, Paris, France.,AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, 46 rue Henri Huchard, 75018, Paris, France
| | - Maud Salmona
- Unité de Paris, INSERM U976, Insight Team, 75010, Paris, France.,AP-HP, Hôpital Saint-Louis, Laboratoire de Virologie, 75010, Paris, France
| | - Sarah Dellière
- AP-HP, Hôpital Saint-Louis, Laboratoire de Parasitologie-Mycologie, 75010, Paris, France.,Molecular Mycology Unit, Institut Pasteur, CNRS UMR2000, 75015, Paris, France
| | - Stefano Leo
- Faculty of Medicine, CMU, University of Geneva, Geneva, Switzerland.,Service of Infectious Diseases, Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Christophe Rodriguez
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,INSERM U955, Université Paris-Est, 94000, Créteil, France
| | - Cécile Angebault
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,Université Paris Est Créteil, Ecole Nationale Vétérinaire d'Alfort, USC ANSES, EA7380 Dynamic, 94000, Créteil, France
| | - Alexandre Alanio
- AP-HP, Hôpital Saint-Louis, Laboratoire de Parasitologie-Mycologie, 75010, Paris, France.,Molecular Mycology Unit, Institut Pasteur, CNRS UMR2000, 75015, Paris, France
| | - Slim Fourati
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,INSERM U955, Université Paris-Est, 94000, Créteil, France
| | - Vladimir Lazarevic
- Faculty of Medicine, CMU, University of Geneva, Geneva, Switzerland.,Service of Infectious Diseases, Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Paul-Louis Woerther
- Département de Microbiologie, AP-HP, Hôpital Henri Mondor, 94000, Créteil, France.,Université Paris Est Créteil, Ecole Nationale Vétérinaire d'Alfort, USC ANSES, EA7380 Dynamic, 94000, Créteil, France
| | - Jacques Schrenzel
- Faculty of Medicine, CMU, University of Geneva, Geneva, Switzerland.,Service of Infectious Diseases, Genomic Research Laboratory, Geneva University Hospitals, Geneva, Switzerland
| | - Etienne Ruppé
- Université de Paris, IAME, INSERM, 75018, Paris, France. .,AP-HP, Hôpital Bichat, Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, 46 rue Henri Huchard, 75018, Paris, France.
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22
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Thannesberger J, Rascovan N, Eisenmann A, Klymiuk I, Zittra C, Fuehrer HP, Scantlebury-Manning T, Gittens-St Hilaire M, Austin S, Landis RC, Steininger C. Viral metagenomics reveals the presence of novel Zika virus variants in Aedes mosquitoes from Barbados. Parasit Vectors 2021; 14:343. [PMID: 34187544 PMCID: PMC8244189 DOI: 10.1186/s13071-021-04840-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/11/2021] [Indexed: 01/08/2023] Open
Abstract
Background The Zika virus (ZIKV) epidemic of 2015/2016 spread throughout numerous countries. It emerged in mainland Latin America and spread to neighboring islands, including the Caribbean island of Barbados. Recent studies have indicated that the virus must have already been circulating in local mosquito populations in Brazil for almost 2 years before it was identified by the World Health Organization in 2015. Metagenomic detection assays have the potential to detect emerging pathogens without prior knowledge of their genomic nucleic acid sequence. Yet their applicability as vector surveillance tools has been widely limited by the complexity of DNA populations from field-collected mosquito preparations. The aim of this study was to investigate local vector biology and characterize metagenomic arbovirus diversity in Aedes mosquitoes during the ongoing 2015/2016 ZIKV epidemic. Methods We performed a short-term vector screening study on the island of Barbados during the ongoing 2015/2016 ZIKV epidemic, where we sampled local Aedes mosquitoes. We reanalyzed mosquito viral microbiome data derived from standard Illumina MiSeq sequencing to detect arbovirus sequences. Additionally, we employed deep sequencing techniques (Illumina HiSeq) and designed a novel bait capture enrichment assay to increase sequencing efficiency for arbovirus sequences from complex DNA samples. Results We found that Aedes aegypti seemed to be the most likely vector of ZIKV, although it prevailed at a low density during the observed time period. The number of detected viruses increased with sequencing depth. Arbovirus sequence enrichment of metagenomic DNA preparations allowed the detection of arbovirus sequences of two different ZIKV genotypes, including a novel one. To our knowledge, this is the first report of the S3116W mutation in the NS5 gene region of ZIKV polyprotein. Conclusions The metagenomic arbovirus detection approach presented here may serve as a useful tool for the identification of epidemic-causing arboviruses with the additional benefit of enabling the collection of phylogenetic information on the source. Apart from detecting more than 88 viruses using this approach, we also found evidence of novel ZIKV variants circulating in the local mosquito population during the observed time period. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-04840-0.
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Affiliation(s)
- J Thannesberger
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
| | - N Rascovan
- Department of Genomes & Genetics, Institut Pasteur, Paris, France
| | - A Eisenmann
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
| | - I Klymiuk
- Department of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - C Zittra
- Institute of Parasitology, University of Veterinary Medicine, Vienna, Austria
| | - H P Fuehrer
- Institute of Parasitology, University of Veterinary Medicine, Vienna, Austria
| | - T Scantlebury-Manning
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, Barbados
| | | | - S Austin
- Department of Biological and Chemical Sciences, University of the West Indies, Cave Hill Campus, Cave Hill, Barbados
| | - R C Landis
- Edmund Cohen Laboratory for Vascular Research, George Alleyne Chronic Disease Research Centre, The University of the West Indies, Bridgetown, Barbados
| | - C Steininger
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria.
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23
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Bucciol G, Tousseyn T, Jansen K, Casteels I, Tangye SG, Breuer J, Brown JR, Wollants E, Van Ranst M, Moens L, Mekahli D, Meyts I. Hematopoietic Stem Cell Transplantation Cures Chronic Aichi Virus Infection in a Patient with X-linked Agammaglobulinemia. J Clin Immunol 2021; 41:1403-1405. [PMID: 33948812 DOI: 10.1007/s10875-021-01056-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/27/2021] [Indexed: 01/08/2023]
Affiliation(s)
- Giorgia Bucciol
- Department of Pediatrics, University Hospital Leuven, Herestraat 49, 3000, Leuven, Belgium.,Laboratory of Inborn Errors of Immunity, Department of Immunology, Microbiology and Transplantation, KU Leuven, Leuven, Belgium
| | - Thomas Tousseyn
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Katrien Jansen
- Department of Pediatrics, University Hospital Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Ingele Casteels
- Department of Ophthalmology, University Hospital Leuven, Leuven, Belgium
| | - Stuart G Tangye
- Immunity & Inflammation Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia.,Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, Australia
| | - Judy Breuer
- Department of Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, UK
| | - Julianne R Brown
- Department of Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, UK
| | - Elke Wollants
- Laboratory of Clinical and Epidemiological Virology (Rega Institute), KU Leuven, Leuven, Belgium
| | - Marc Van Ranst
- Laboratory of Clinical and Epidemiological Virology (Rega Institute), KU Leuven, Leuven, Belgium.,Department of Immunology, Microbiology and Transplantation, KU Leuven, Leuven, Belgium
| | - Leen Moens
- Laboratory of Inborn Errors of Immunity, Department of Immunology, Microbiology and Transplantation, KU Leuven, Leuven, Belgium
| | - Djalila Mekahli
- Department of Pediatric Nephrology, University Hospital Leuven, Leuven, Belgium.,PKD Research Group, Pediatric Laboratory, Department of Development and Regeneration, GPURE, KU Leuven, Leuven, Belgium
| | - Isabelle Meyts
- Department of Pediatrics, University Hospital Leuven, Herestraat 49, 3000, Leuven, Belgium. .,Laboratory of Inborn Errors of Immunity, Department of Immunology, Microbiology and Transplantation, KU Leuven, Leuven, Belgium.
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24
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Beyond the Gastrointestinal Tract: The Emerging and Diverse Tissue Tropisms of Astroviruses. Viruses 2021; 13:v13050732. [PMID: 33922259 PMCID: PMC8145421 DOI: 10.3390/v13050732] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 12/19/2022] Open
Abstract
Astroviruses are single stranded, positive-sense RNA viruses that have been historically associated with diseases of the gastrointestinal tract of vertebrates, including humans. However, there is now a multitude of evidence demonstrating the capacity of these viruses to cause extraintestinal diseases. The most striking causal relationship is neurological diseases in humans, cattle, pigs, and other mammals, caused by astrovirus infection. Astroviruses have also been associated with disseminated infections, localized disease of the liver or kidneys, and there is increasing evidence suggesting a potential tropism to the respiratory tract. This review will discuss the current understanding of the tissue tropisms for astroviruses and their emerging capacity to cause disease in multiple organ systems.
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25
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Paccoud O, Mahlaoui N, Moshous D, Aguilar C, Neven B, Lanternier F, Suarez F, Picard C, Fischer A, Blanche S, Lecuit M, Hermine O, Lortholary O. Current Spectrum of Infections in Patients with X-Linked Agammaglobulinemia. J Clin Immunol 2021; 41:1266-1271. [PMID: 33880703 DOI: 10.1007/s10875-021-01043-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 04/12/2021] [Indexed: 10/21/2022]
Abstract
Outcome of patients with X-linked agammaglobulinemia (XLA) has improved with the widespread use of immunoglobulin replacement therapy (IgRT). There are few data on the spectrum of infections experienced by patients undergoing IgRT. We carried out a retrospective cross-sectional analysis of the records of XLA patients seen at Necker-Enfants Malades Hospital, Paris. For each infection, we evaluated infection site, microbial etiology, antibiotic prophylaxis, immunosuppressive treatment, IgRT route, and last known IgG trough level. Sixty patients were included, who cumulated a follow-up of 1470 patient-years. We recorded 188 infections, including 97 after initiation of IgRT. The rate of infection was highest before IgRT (0.66 vs. 0.06 per person-year (ppy), p < 0.001) and was higher after the age of 16 compared to before (0.14 vs. 0.05 ppy, p = 0.048). It was similar for patients receiving intravenous or subcutaneous Ig (0.09 vs 0.05 ppy, p = 0.54). The lungs and gastrointestinal tract accounted for 71% of infection sites. Forty-six (47%) infections occurred in patients receiving antibiotic prophylaxis. Sixteen (16.5%) infections occurred in patients receiving immunosuppressive therapy, which more frequently occurred after age 16 (35% vs. 2.4%, p < 0.001). The median IgG trough level prior to all infections was 8.4 g/L. Almost half (44.3%) of infections occurred with prior IgG trough levels > 8 g/L, and 16/97 (16.7%) in patients with trough levels > 10 g/L. Infection remains a significant issue in patients with XLA undergoing IgRT despite adequate IgG trough levels. Chronic inflammatory manifestations of X-linked agammaglobulinemia and immunosuppressive therapies may be significant drivers of infection during adulthood.
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Affiliation(s)
- Olivier Paccoud
- Necker-Pasteur Center for Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique des Hôpitaux de Paris (AP-HP), Université de Paris, 149 Rue de Sèvres, 75015, Paris, France.
| | - Nizar Mahlaoui
- Pediatric Immuno-Hematology and Rheumatology Unit, Necker-Enfants Malades University Hospital, AP-HP, Université de Paris, Paris, France.,Imagine Institute, INSERM UMR1163, Université de Paris, Paris, France.,French National Reference Center for Primary Immune Deficiencies (CEREDIH), Necker-Enfants Malades University Hospital, AP-HP, Paris, France
| | - Despina Moshous
- Pediatric Immuno-Hematology and Rheumatology Unit, Necker-Enfants Malades University Hospital, AP-HP, Université de Paris, Paris, France.,Imagine Institute, INSERM UMR1163, Université de Paris, Paris, France.,French National Reference Center for Primary Immune Deficiencies (CEREDIH), Necker-Enfants Malades University Hospital, AP-HP, Paris, France
| | - Claire Aguilar
- Necker-Pasteur Center for Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique des Hôpitaux de Paris (AP-HP), Université de Paris, 149 Rue de Sèvres, 75015, Paris, France.,Imagine Institute, INSERM UMR1163, Université de Paris, Paris, France
| | - Bénédicte Neven
- Pediatric Immuno-Hematology and Rheumatology Unit, Necker-Enfants Malades University Hospital, AP-HP, Université de Paris, Paris, France.,Imagine Institute, INSERM UMR1163, Université de Paris, Paris, France.,French National Reference Center for Primary Immune Deficiencies (CEREDIH), Necker-Enfants Malades University Hospital, AP-HP, Paris, France
| | - Fanny Lanternier
- Necker-Pasteur Center for Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique des Hôpitaux de Paris (AP-HP), Université de Paris, 149 Rue de Sèvres, 75015, Paris, France
| | - Felipe Suarez
- Imagine Institute, INSERM UMR1163, Université de Paris, Paris, France.,French National Reference Center for Primary Immune Deficiencies (CEREDIH), Necker-Enfants Malades University Hospital, AP-HP, Paris, France.,Department of Hematology, Necker-Enfants Malades University Hospital, AP-HP, Université de Paris, Paris, France
| | - Capucine Picard
- Imagine Institute, INSERM UMR1163, Université de Paris, Paris, France.,French National Reference Center for Primary Immune Deficiencies (CEREDIH), Necker-Enfants Malades University Hospital, AP-HP, Paris, France.,Study Center for Primary Immunodeficiencies (CEDI), Necker-Enfants Malades University Hospital, AP-HP, Paris, France
| | - Alain Fischer
- Pediatric Immuno-Hematology and Rheumatology Unit, Necker-Enfants Malades University Hospital, AP-HP, Université de Paris, Paris, France.,Imagine Institute, INSERM UMR1163, Université de Paris, Paris, France.,French National Reference Center for Primary Immune Deficiencies (CEREDIH), Necker-Enfants Malades University Hospital, AP-HP, Paris, France
| | - Stéphane Blanche
- Pediatric Immuno-Hematology and Rheumatology Unit, Necker-Enfants Malades University Hospital, AP-HP, Université de Paris, Paris, France.,Imagine Institute, INSERM UMR1163, Université de Paris, Paris, France.,French National Reference Center for Primary Immune Deficiencies (CEREDIH), Necker-Enfants Malades University Hospital, AP-HP, Paris, France
| | - Marc Lecuit
- Necker-Pasteur Center for Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique des Hôpitaux de Paris (AP-HP), Université de Paris, 149 Rue de Sèvres, 75015, Paris, France.,Imagine Institute, INSERM UMR1163, Université de Paris, Paris, France.,Biology of Infection Unit, Inserm U1117, Pasteur Institute, Paris, France
| | - Olivier Hermine
- Imagine Institute, INSERM UMR1163, Université de Paris, Paris, France.,French National Reference Center for Primary Immune Deficiencies (CEREDIH), Necker-Enfants Malades University Hospital, AP-HP, Paris, France.,Department of Hematology, Necker-Enfants Malades University Hospital, AP-HP, Université de Paris, Paris, France
| | - Olivier Lortholary
- Necker-Pasteur Center for Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Assistance Publique des Hôpitaux de Paris (AP-HP), Université de Paris, 149 Rue de Sèvres, 75015, Paris, France.,Imagine Institute, INSERM UMR1163, Université de Paris, Paris, France
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26
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Huang D, Wang Z, Zhang F, Wang T, Zhang G, Sai L. Molecular and clinical epidemiological features of human astrovirus infections in children with acute gastroenteritis in Shandong province, China. J Med Virol 2021; 93:4883-4890. [PMID: 33811682 DOI: 10.1002/jmv.26995] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/19/2021] [Accepted: 03/30/2021] [Indexed: 11/10/2022]
Abstract
Human astrovirus (HAstV) is one of the most common causative agents of acute gastroenteritis in children with an infection rate estimated to range from 2% to 9% worldwide. This study was aimed at investigating the molecular and clinical epidemiological features of human astrovirus infections in children under 5 years old with acute gastroenteritis in Shandong province, China from July 2017 to June 2018. In total, 376 fecal samples and the corresponding clinical information were collected and analyzed. HAstV infections were detected in all age groups with an overall positive rate of 8.51%. In addition to acute diarrhea, the main clinical manifestations were fever, abdominal pain, vomiting, and dehydration, in which fever was the most common complication. Infections could be seen throughout the year with a peak in the colder season. Four genotypes were detected in which HAstV-1 was the most prevalent genotype with a prevalence of 78.12%, followed by HAstV-5 (9.38%), MLB-1 (9.38%), and MLB-2 (3.12%). HAstV-1 strains were classified as lineage 1a, 1b, and 1d, in which lineage 1a strains were the most prevalent followed by lineage 1b and lineage 1d strains. All HAstV-5 strains were classified as lineage 5b and no other lineages were detected. The results showed that HAstV infection was an important cause of acute gastroenteritis among children under 5 years old in Shandong province. Given that their disease spectrum had been broadened, HAstVs should be paid more attention, not only as a causative agent of acute gastroenteritis but also as a potential pathogen of unexpected diseases.
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Affiliation(s)
- Deyu Huang
- Department of Infectious Diseases, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zheng Wang
- Department of Infectious Diseases, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, China
| | - Fengjuan Zhang
- Department of Infectious Diseases, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ting Wang
- Department of Infectious Diseases, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Guanyou Zhang
- Department of Infectious Diseases, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, China
| | - Lintao Sai
- Department of Infectious Diseases, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Ji'nan, China
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27
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Human Astroviruses: A Tale of Two Strains. Viruses 2021; 13:v13030376. [PMID: 33673521 PMCID: PMC7997325 DOI: 10.3390/v13030376] [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: 02/04/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 12/13/2022] Open
Abstract
Since the 1970s, eight closely related serotypes of classical human astroviruses (HAstV) have been associated with gastrointestinal illness worldwide. In the late 2000s, three genetically unique human astrovirus clades, VA1-VA3, VA2-VA4, and MLB, were described. While the exact disease associated with these clades remains to be defined, VA1 has been associated with central nervous system infections. The discovery that VA1 could be grown in cell culture, supports exciting new studies aimed at understanding viral pathogenesis. Given the association of VA1 with often lethal CNS infections, we tested its susceptibility to the antimicrobial drug, nitazoxanide (NTZ), which we showed could inhibit classical HAstV infections. Our studies demonstrate that NTZ inhibited VA1 replication in Caco2 cells even when added at 12 h post-infection, which is later than in HAstV-1 infection. These data led us to further probe VA1 replication kinetics and cellular responses to infection in Caco-2 cells in comparison to the well-studied HAstV-1 strain. Overall, our studies highlight that VA1 replicates more slowly than HAstV-1 and elicits significantly different cellular responses, including the inability to disrupt cellular junctions and barrier permeability.
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28
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Li ZY, Dang D, Wu H. Next-generation Sequencing of Cerebrospinal Fluid for the Diagnosis of Unexplained Central Nervous System Infections. Pediatr Neurol 2021; 115:10-20. [PMID: 33310532 DOI: 10.1016/j.pediatrneurol.2020.10.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Central nervous system infections cause substantial morbidity and mortality in pediatric patients. However, in approximately half of the clinical cases, the etiology is unidentified. As an unbiased molecular diagnostic technology, next-generation sequencing is gradually being applied to investigate central nervous system infections. This review summarizes and critiques the literature on this new technology for etiologic identification of unexplained central nervous system infections in pediatric patients and discusses the future prospects for development of this technology in pediatrics. METHODS A comprehensive PubMed search was conducted of articles published from January 1, 2008, to June 26, 2020 in order to retrieve all available studies on this topic. Other relevant articles were identified from recent reviews and the bibliographies of the retrieved full-text articles. RESULTS Among the 441 studies retrieved, 26 pediatric studies, comprising 15 case reports and 11 case series, used next-generation sequencing as a diagnostic tool. In these 26 studies, next-generation sequencing was performed on cerebrospinal fluid samples from 529 pediatric patients, and potential causal pathogens were identified in 22.1% of the cases. CONCLUSION There is increasing evidence that next-generation sequencing can play a role in identifying the causes of unexplained encephalitis, meningoencephalitis, and meningitis in pediatric patients, although the diagnostic value of next-generation sequencing is difficult to quantify. There is an increasing need for close collaboration between laboratory scientists and clinicians. We believe that further clinical studies should be performed to evaluate the performance of next-generation sequencing for individual targets and in high-risk populations.
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Affiliation(s)
- Zhen Yu Li
- Department of Pediatrics, The First Hospital of Jilin University, Changchun, Jilin, PR China
| | - Dan Dang
- Department of Pediatrics, The First Hospital of Jilin University, Changchun, Jilin, PR China
| | - Hui Wu
- Department of Pediatrics, The First Hospital of Jilin University, Changchun, Jilin, PR China.
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29
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Wu L, Teng Z, Lin Q, Liu J, Wu H, Kuang X, Cui X, Wang W, Cui X, Yuan ZA, Zhang X, Xie Y. Epidemiology and Genetic Characterization of Classical Human Astrovirus Infection in Shanghai, 2015-2016. Front Microbiol 2020; 11:570541. [PMID: 33101242 PMCID: PMC7546348 DOI: 10.3389/fmicb.2020.570541] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/26/2020] [Indexed: 11/13/2022] Open
Abstract
Objective Human astroviruses (HAstVs) are single-stranded RNA viruses of the Astroviridae family. Infection of classic HAstVs is one of the most common causes of acute viral gastroenteritis (infectious viral diarrhea). There is a lack of data on the prevalence and genetic characterization of classic HAstVs in acute viral gastroenteritis in the whole population. This study aimed to investigate the epidemiological trend, genotypes, viral co-infections, and viral loads of classic HAstVs in Shanghai, China, from January 2015 to December 2016. Methods A total of 6,051 non-redundant stool samples were collected in outpatients with acute diarrhea in Shanghai from January 2015 to December 2016. One-step real-time RT-PCR was used for screening viral diarrhea, including rotavirus A, rotavirus B, rotavirus C, norovirus genotype I and II, classic human astroviruses, and sapovirus. Real-time PCR was used for screening human enteric adenoviruses. Conventional RT-PCR was used for the amplification of viral fragments for genotyping. PCR products were sequenced and used for the construction of phylogenetic trees. Results The detection rate of classic HAstVs was 1.55% (94/6,051). The prevalence of HAstV infection displayed a typical winter/spring (December to March) seasonality and was highest in the 5–14 age group. Eighty-six samples were genotyped, which revealed HAstV-1 as the most prevalent genotype, followed by HAstV-5, HAstV-4, HAstV- 2, HAstV-8, and HAstV-3. There was a dramatic rise in the prevalence of HAstV-4 from December 2015 to March 2016, and the viral loads of HAstV-4 were significantly higher than those of other genotypes. Among the mixed infection samples, noroviruses were found to be the most frequently co-infected enteric viruses with HAstV. Conclusion Multiple genotypes of classic HAstVs circulated in Shanghai from January 2015 to December 2016. For the first time, HAstV-3\4\5\8 were detected in Shanghai.
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Affiliation(s)
- Limeng Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China.,Shanghai Institute of Preventive Medicine, Shanghai, China
| | - Zheng Teng
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Qingneng Lin
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Jing Liu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Huanyu Wu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Xiaozhou Kuang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Xiaoqing Cui
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Wei Wang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Xiaoxian Cui
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Zheng-An Yuan
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Xi Zhang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Youhua Xie
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
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Rawal G, Ferreyra FM, Macedo NR, Bradner LK, Harmon KM, Allison G, Linhares DCL, Arruda BL. Ecology of Porcine Astrovirus Type 3 in a Herd with Associated Neurologic Disease. Viruses 2020; 12:E992. [PMID: 32906600 PMCID: PMC7552043 DOI: 10.3390/v12090992] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/28/2020] [Accepted: 08/31/2020] [Indexed: 12/16/2022] Open
Abstract
Astroviruses (AstVs) cause disease in a wide variety of species. Porcine AstVs are highly genetically diverse and conventionally assigned to five genetic lineages (PoAstV1-5). Due to the increasing evidence that porcine astrovirus type 3 (PoAstV3) is a cause of encephalomyelitis in swine and to elucidate important ecologic characteristics, the infection dynamics and environmental distribution of PoAstV3 were investigated in a herd with PoAstV3-associated neurologic disease. Over a 22 week period, the frequency of PoAstV3 fecal shedding varied by pig and age. The peak detection by RT-qPCR of PoAstV3 on fecal swabs (95%; 61 of 64) occurred at 3 weeks of age. The lowest frequency of detection was at 21 weeks of age (4%; 2 of 47); however, the frequency increased to 41% (19 of 46) at the final sampling time point (25 weeks of age). Viremia was rare (0.9%: 4 of 433). Detection in oral fluid was consistent with 75% to 100% of samples positive at each time point. Pens and feeders also had a high rate of detection with a majority of samples positive at a majority of sampling time points. Based on the data presented, PoAstV3 can be consistently detected in the environment with a majority of pigs being infected and a subset intermittently shedding the virus in feces out to 25 weeks of age. These findings suggest the importance of as-yet unidentified risk factors associated with the development of PoAstV3-associated polioencephalomyelitis.
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Affiliation(s)
- Gaurav Rawal
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (F.M.F.); (N.R.M.); (L.K.B.); (K.M.H.); (D.C.L.L.)
| | - Franco Matias Ferreyra
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (F.M.F.); (N.R.M.); (L.K.B.); (K.M.H.); (D.C.L.L.)
| | - Nubia R. Macedo
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (F.M.F.); (N.R.M.); (L.K.B.); (K.M.H.); (D.C.L.L.)
| | - Laura K. Bradner
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (F.M.F.); (N.R.M.); (L.K.B.); (K.M.H.); (D.C.L.L.)
| | - Karen M. Harmon
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (F.M.F.); (N.R.M.); (L.K.B.); (K.M.H.); (D.C.L.L.)
| | - Grant Allison
- Walcott Veterinary Clinic, Durant St, Walcott, IA 52773, USA;
| | - Daniel C. L. Linhares
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (F.M.F.); (N.R.M.); (L.K.B.); (K.M.H.); (D.C.L.L.)
| | - Bailey L. Arruda
- Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA; (G.R.); (F.M.F.); (N.R.M.); (L.K.B.); (K.M.H.); (D.C.L.L.)
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Carbo EC, Buddingh EP, Karelioti E, Sidorov IA, Feltkamp MC, Borne PAVD, Verschuuren JJ, Kroes AC, Claas EC, de Vries JJ. Improved diagnosis of viral encephalitis in adult and pediatric hematological patients using viral metagenomics. J Clin Virol 2020; 130:104566. [DOI: 10.1016/j.jcv.2020.104566] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 07/23/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023]
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Yu JM, Wang ZH, Liu N, Zhang Q, Dong YJ, Duan ZJ. Complete genome of a novel recombinant human astrovirus and its quasispecies in patients following hematopoietic stem cell transplantation. Virus Res 2020; 288:198138. [PMID: 32827625 DOI: 10.1016/j.virusres.2020.198138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/01/2020] [Accepted: 08/17/2020] [Indexed: 12/30/2022]
Abstract
Human astroviruses (HAstVs) were first identified in 1975 and can be classified into three clades: classic HAstVs (HAstV 1-8), MLB (MLB1-3) and VA (VA1-5), with MLB and VA were newly identified. Recombination and a high mutation rate make HAstV as one of the rapidly evolving infectious agents. This study reported a novel identified recombinant human astrovirus (Y/1-CHN) and its long existence in two immunocompromised patients with diarrhea following allogeneic hematopoietic stem cell transplantation (allo-HSCT). The identified Yu/1-CHN genome contains 6801 base pairs encoding three open reading frames, with ORF1a best hit to the HAstV1 (Pune strain, 97 % nucleotide identity), while ORF1b and ORF2 best hit to HAstV-5 (DL30 strain, 99 % nucleotide identity). Possible recombination breakpoint was predicted to be located in the boundary of ORF1a and ORF1b. Different quasispecies were found in the host, and the dN/dS ratios of the S and P domains were determined to be 1.189 and 1.444, respectively, suggesting a positive selection existed. Fecal samples collected in different clinical phases from the two patients were all positive for Yu/1-CHN, suggesting a long existence of the virus in the host. It was indicated that immunocompromised patients may a reservoir for astrovirus, their excreta should be monitored even after discharge from hospital.
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Affiliation(s)
- Jie-Mei Yu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing 100044, China; National Institute for Viral Disease Control and Prevention, China CDC, Beijing 100052, China
| | - Zhen-Hua Wang
- Department of Hematology, Peking University First Hospital, Beijing 100034, China; Department of Hematology, Qingdao Municipal Hospital (Group), Qingdao, 266071, China
| | - Na Liu
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing 100052, China
| | - Qing Zhang
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing 100052, China
| | - Yu-Jun Dong
- Department of Hematology, Peking University First Hospital, Beijing 100034, China.
| | - Zhao-Jun Duan
- National Institute for Viral Disease Control and Prevention, China CDC, Beijing 100052, China.
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Detection of Astrovirus in a Cow with Neurological Signs by Nanopore Technology, Italy. Viruses 2020; 12:v12050530. [PMID: 32403368 PMCID: PMC7290991 DOI: 10.3390/v12050530] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/07/2020] [Accepted: 05/09/2020] [Indexed: 01/16/2023] Open
Abstract
In this study, starting from nucleic acids purified from the brain tissue, Nanopore technology was used to identify the etiological agent of severe neurological signs observed in a cow which was immediately slaughtered. Histological examination revealed acute non-suppurative encephalomyelitis affecting the brainstem, cerebrum, cerebellum, and medulla oblongata, while by using PCR-based assays, the nucleic acids of major agents for neurological signs were not detected. By using Nanopore technology, 151 sequence reads were assigned to Bovine Astrovirus (BoAstV). Real-time RT-PCR and in situ hybridization (ISH) confirmed the presence of viral RNA in the brain. Moreover, using the combination of fluorescent ISH and immunofluorescence (IF) techniques, it was possible to detect BoAstV RNA and antigens in the same cells, suggesting the active replication of the virus in infected neurons. The nearly whole genome of the occurring strain (BoAstV PE3373/2019/Italy), obtained by Illumina NextSeq 500, showed the highest nucleotide sequence identity (94.11%) with BoAstV CH13/NeuroS1 26,730 strain, an encephalitis-associated bovine astrovirus. Here, we provide further evidence of the role of AstV as a neurotropic agent. Considering that in a high proportion of non-suppurative encephalitis cases, which are mostly indicative of a viral infection, the etiologic agent remains unknown, our result underscores the value and versatility of Nanopore technology for a rapid diagnosis when the PCR-based algorithm gives negative results.
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Vu DL, Sabrià A, Aregall N, Michl K, Sabrià J, Rodriguez Garrido V, Goterris L, Bosch A, Pintó RM, Guix S. A Spanish case-control study in <5 year-old children reveals the lack of association between MLB and VA astrovirus and diarrhea. Sci Rep 2020; 10:1760. [PMID: 32020041 PMCID: PMC7000717 DOI: 10.1038/s41598-020-58691-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 01/13/2020] [Indexed: 01/01/2023] Open
Abstract
Novel human astroviruses (HAstV) were discovered 10 years ago and have been associated with fatal cases of central nervous system infections. Their role in gastroenteritis is controversial, as they have been identified in symptomatic and asymptomatic subjects. The aim of the study was to investigate novel HAstV in a gastroenteritis case-control study including a pediatric population in Spain over a one-year period. We included stool samples from patients with gastroenteritis and negative results for viruses screened by routine diagnostics, and stool samples of control subjects who sought for a routine medical consultation. All samples were screened by real-time RT-PCR assays for novel HAstV. An additional screening for rotavirus, norovirus GI, GII, sapovirus, classic HAstV and adenovirus was also performed for the control group. Overall, 23/363 stool samples from case patients (6.3%) and 8/199 stool samples from control patients (4%) were positive for ≥1 novel HAstV. MLB1 was predominant (64.5% of positives). Seasonality was observed for the case group (p = 0.015), but not the control group (p = 0.95). No difference was observed in the prevalence of novel HAstV between the case and control groups (OR 1.78, 95% CI 0.68–5.45; p = 0.30). Nevertheless, MLB genome copy numbers/ml of fecal suspension was significantly higher in the control group than in the case group (p = 0.008). In our study, we identified a lack of association between novel HAstV and gastroenteritis in the studied population, which could indicate a potential role of reservoir for children, especially given the higher viral load observed in the asymptomatic group for some of them.
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Affiliation(s)
- Diem-Lan Vu
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain. .,Nutrition and Food Safety Research Institute (INSA·UB), University of Barcelona, Barcelona, Spain. .,Department of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland.
| | - Aurora Sabrià
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain.,Nutrition and Food Safety Research Institute (INSA·UB), University of Barcelona, Barcelona, Spain
| | - Nuria Aregall
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Kristina Michl
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain
| | - Jaume Sabrià
- Primary Health Care Center El Serral, Generalitat de Catalunya, Sant Vicenç dels Horts, Spain
| | | | - Lidia Goterris
- Microbiology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain.,Nutrition and Food Safety Research Institute (INSA·UB), University of Barcelona, Barcelona, Spain
| | - Rosa Maria Pintó
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain.,Nutrition and Food Safety Research Institute (INSA·UB), University of Barcelona, Barcelona, Spain
| | - Susana Guix
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, University of Barcelona, Barcelona, Spain. .,Nutrition and Food Safety Research Institute (INSA·UB), University of Barcelona, Barcelona, Spain.
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Fulton BD, Proudman DG, Sample HA, Gelfand JM, Chiu CY, DeRisi JL, Wilson MR. Exploratory analysis of the potential for advanced diagnostic testing to reduce healthcare expenditures of patients hospitalized with meningitis or encephalitis. PLoS One 2020; 15:e0226895. [PMID: 31940319 PMCID: PMC6961903 DOI: 10.1371/journal.pone.0226895] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 12/08/2019] [Indexed: 11/19/2022] Open
Abstract
Objective To estimate healthcare expenditures that could be impacted by advanced diagnostic testing for patients hospitalized with meningitis or encephalitis Methods Patients hospitalized with meningitis (N = 23,933) or encephalitis (N = 7,858) in the U.S. were identified in the 2010–2014 Truven Health MarketScan Commercial Claims and Encounters Database using ICD-9-CM diagnostic codes. The database included an average of 40.8 million commercially insured enrollees under age 65 per year. Clinical, demographic and healthcare utilization criteria were used to identify patient subgroups early in their episode who were at risk to have high inpatient expenditures. Healthcare expenditures of patients within each subgroup were bifurcated: those expenditures that remained five days after the patient could be classified into the subgroup versus those that had occurred previously. Results The hospitalization episode rate per 100,000 enrollee-years for meningitis was 13.0 (95% CI: 12.9–13.2) and for encephalitis was 4.3 (95% CI: 4.2–4.4), with mean inpatient expenditures of $36,891 (SD = $92,636) and $60,181 (SD = $130,276), respectively. If advanced diagnostic testing had been administered on the day that a patient could be classified into a subgroup, then a test with a five-day turnaround time could impact the following mean inpatient expenditures that remained by subgroup for patients with meningitis or encephalitis, respectively: had a neurosurgical procedure ($83,337 and $56,020), had an ICU stay ($34,221 and $46,051), had HIV-1 infection or a previous organ transplant ($37,702 and $62,222), were age <1 year ($35,371 and $52,812), or had a hospital length of stay >2 days ($18,325 and $30,244). Discussion Inpatient expenditures for patients hospitalized with meningitis or encephalitis were substantial and varied widely. Patient subgroups who had high healthcare expenditures could be identified early in their stay, raising the potential for advanced diagnostic testing to lower these expenditures.
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Affiliation(s)
- Brent D. Fulton
- School of Public Health, University of California, Berkeley, Berkeley, California, United States of America
- * E-mail:
| | - David G. Proudman
- School of Public Health, University of California, Berkeley, Berkeley, California, United States of America
| | - Hannah A. Sample
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America
| | - Jeffrey M. Gelfand
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Charles Y. Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California, United States of America
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States of America
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California, United States of America
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - Michael R. Wilson
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, California, United States of America
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Kasahara Y, Imamura M, Shin C, Shimizu H, Utsumi J, Hosokai R, Iwabuchi H, Takachi T, Kakita A, Kanegane H, Saitoh A, Imai C. Fatal Progressive Meningoencephalitis Diagnosed in Two Members of a Family With X-Linked Agammaglobulinemia. Front Pediatr 2020; 8:579. [PMID: 33042921 PMCID: PMC7530192 DOI: 10.3389/fped.2020.00579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/06/2020] [Indexed: 01/03/2023] Open
Abstract
Chronic enteroviral meningoencephalitis is a well-known complication in patients with X-linked agammaglobulinemia (XLA). However, progressive neurodegenerative disorders or chronic neuroinflammatory diseases with no causative microorganisms have been recognized as rare central nervous system (CNS) complications in XLA. We herein report a family in which two of three members with XLA had developed progressive meningoencephalitis with an unknown etiology. A 15-month-old male infant presented with left-sided ptosis. Initially, the family denied any family history of inherited diseases, but later disclosed a family history of agammaglobulinemia previously diagnosed in two family members. In the early 1980s, one of the elder brothers of the index patient's mother who had been treated with intramuscular immunoglobulin [or later intravenous immunoglobulin (IVIG)] for agammaglobulinemia deceased at 10 years of age after showing progressive neurological deterioration during the last several years of his life. The index patient was diagnosed with XLA caused by Bruton tyrosine kinase deficiency (654delG; Val219Leufs*9), and chronic meningoencephalitis with an unknown infectious etiology. Magnetic resonance imaging of the brain demonstrated inflammatory changes in the basal ganglia, hypothalamus, midbrain, and pons, with multiple nodular lesions with ring enhancement, which showed impressive amelioration after the initiation of IVIG replacement therapy. Pleocytosis, which was characterized by an increase in CD4-positive and CD8-positive T cells expressing an activation marker and an elevation in inflammatory cytokines in the cerebrospinal fluid, was identified. No microorganism was identified as a cause of CNS complications. He thereafter developed brain infarction at 19 months of age and fatal status epilepticus at 5 years of age, despite regular IVIG with high trough levels and regular intraventricular immunoglobulin administration. The etiology of this rare CNS complication in XLA is currently unknown. Previous studies have suggested a possible association of IVIG, which was clearly denied in our index case because of the demonstration of his neurological disorder at presentation. In the future, extensive and unbiased molecular methods to detect causative microorganisms, as well as to investigate the possible role of autoimmunity are needed to clarify the etiology of CNS complications.
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Affiliation(s)
- Yasushi Kasahara
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Masaru Imamura
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Chansu Shin
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hiroshi Shimizu
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Jirou Utsumi
- Department of Pediatrics, Niigata Cancer Center Hospital, Niigata, Japan
| | - Ryosuke Hosokai
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Haruko Iwabuchi
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Takayuki Takachi
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Hirokazu Kanegane
- Department of Pediatrics, Graduate School of Medicine, University of Toyama, Toyama, Japan.,Department of Child Health and Development, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Akihiko Saitoh
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Chihaya Imai
- Department of Pediatrics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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Antiviral activity of ribavirin and favipiravir against human astroviruses. J Clin Virol 2019; 123:104247. [PMID: 31864069 DOI: 10.1016/j.jcv.2019.104247] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/09/2019] [Accepted: 12/16/2019] [Indexed: 01/22/2023]
Abstract
BACKGROUND Recent recognition of invasive astrovirus infections, including encephalitis and viremia in humans, have highlighted the need for effective anti-astrovirus therapeutics. However, there is a paucity of data regarding the in vitro activity of broad-spectrum RNA antivirals against astroviruses, including ribavirin and favipiravir. OBJECTIVES We quantified the EC50 values for ribavirin and favipiravir against two human astrovirus strains, astrovirus VA1 (VA1) and human astrovirus 4 (HAstV4). STUDY DESIGN Caco-2 cells were infected with VA1 or HAstV4 in the presence of ribavirin or favipiravir (dose range 0.1-1000 μM), and the cells were maintained in media containing the drugs for 72 h. Viral RNA was extracted and quantified by qRT-PCR. As a surrogate for cytotoxicity, cellular adenosine triphosphate (ATP) from each drug treatment was also measured. RESULTS VA1 replication was inhibited 10-100-fold by both ribavirin (EC50 = 154 μM) and favipiravir (EC50 = 246 μM). In contrast, ribavirin inhibited HAstV4 replication (EC50 = 268 μM) but favipiravir only reduced replication by 44% at the highest dose. Mild reductions in ATP (17-31%) was only observed at the highest concentration of ribavirin (1000 μM) and no significant decrease in ATP was detected for any concentration of favipiravir. CONCLUSIONS Ribavirin inhibited both human astrovirus species and favipiravir was only active against VA1. In the future, the in vivo efficacy of these drugs could be tested with development of an animal model of human astrovirus infection.
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Abstract
PURPOSE OF REVIEW This article describes the clinical presentation, diagnostic approach (including the use of novel diagnostic platforms), and treatment of select infectious and noninfectious etiologies of chronic meningitis. RECENT FINDINGS Identification of the etiology of chronic meningitis remains challenging, with no cause identified in at least one-third of cases. Often, several serologic, CSF, and neuroimaging studies are indicated, although novel diagnostic platforms including metagenomic deep sequencing may hold promise for identifying organisms. Infectious etiologies are more common in those at risk for disseminated disease, specifically those who are immunocompromised because of human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (AIDS), transplantation, or immunosuppressant medications. An important step in identifying the etiology of chronic meningitis is assembling a multidisciplinary team of individuals, including those with specialized expertise in ophthalmology, dermatology, rheumatology, and infectious diseases, to provide guidance regarding diagnostic procedures. SUMMARY Chronic meningitis is defined as inflammation involving the meninges that lasts at least 4 weeks and is associated with a CSF pleocytosis. Chronic meningitis has numerous possible infectious and noninfectious etiologies, making it challenging to definitively diagnose patients. Therefore, a multifaceted approach that combines history, physical examination, neuroimaging, and laboratory analysis, including novel diagnostic platforms, is needed. This article focuses on key aspects of the evaluation of and approach to patients with chronic meningitis. Specific infectious etiologies and differential diagnoses of subacute and chronic meningitis, including noninfectious etiologies, are addressed.
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Detection of Murine Astrovirus and Myocoptes musculinus in individually ventilated caging systems: Investigations to expose suitable detection methods for routine hygienic monitoring. PLoS One 2019; 14:e0221118. [PMID: 31408494 PMCID: PMC6692027 DOI: 10.1371/journal.pone.0221118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/30/2019] [Indexed: 12/26/2022] Open
Abstract
Murine Astrovirus is one of the most prevalent viral agents in laboratory rodent facilities worldwide, but its influence on biomedical research results is poorly examined. Due to possible influence on research results and high seroprevalence rates in mice, it appears useful to include this virus into routine health monitoring programs. In order to establish exhaust air particle PCR as a reliable detection method for Murine Astrovirus infections in mice kept in individually ventilated cages (IVC) and compare the method to sentinel mice monitoring regarding reproducibility and detection limit, we conducted a study with defined Murine Astrovirus cage prevalence. In parallel, the efficacy of both detection strategies (soiled-bedding sentinel (SBS) and exhaust air dust (EAD) analysis) was tested for Myocoptes musculinus. The fur mite was used as a reference organism during the whole study period to ensure the validity of this method. Because some publications already demonstrated successful detection of several pathogens, including murine fur mite species, via EAP-PCR. Detection of Murine Astrovirus infections at low prevalence is possible with both methods tested. Detection by exhaust air particles (EAP) is faster, more sensitive and more reliable compared to soiled bedding sentinels (SBS). Exhaust air particle PCR also detected the reference organism Myocoptes musculinus, which was not detected at all by sentinel mice, not even by high sensitivity fur swab qPCR. In conclusion, Murine Astrovirus can be detected by both exhaust air particle PCR and soiled bedding sentinels. We recommend exhaust air particle PCR as the better detection technique for Murine Astrovirus, because it is more reliable. Environmental samples are the method of choice for detection of Myocoptes musculinus because relying on soiled bedding sentinels harbors a big risk of missing existing infestations.
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Abstract
Patients with central nervous system (CNS) infection experience very high levels of morbidity and mortality, in part because of the many challenges inherent to the diagnosis of CNS infection and identification of a causative pathogen. The clinical presentation of CNS infection is nonspecific, so clinicians must often order and interpret many diagnostic tests in parallel. This can be a daunting task given the large number of potential pathogens and the availability of different testing modalities. Here, we review traditional diagnostic techniques including Gram stain and culture, serology, and polymerase chain reaction (PCR). We highlight which of these are recommended for the pathogens most commonly tested among U.S. patients with suspected CNS infection. Finally, we describe the newer broad-range diagnostic approaches, multiplex PCR and metagenomic sequencing, which are increasingly used in clinical practice.
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Affiliation(s)
- Sanjat Kanjilal
- Division of Infectious Diseases, Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.,Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts
| | - Tracey A Cho
- Department of Neurology, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - Anne Piantadosi
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts
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Abstract
Encephalitis remains a diagnostic conundrum in humans as over 50% of cases are managed without the identification of an etiology. Astroviruses have been detected from the central nervous system of mammals in association with disease, suggesting that this family of RNA viruses could be responsible for cases of some neurological diseases that are currently without an ascribed etiology. However, there are significant barriers to understanding astrovirus infection as the capacity of these viruses to replicate in nervous system cells in vitro has not been determined. We describe primary and immortalized cultured cells of the nervous system that support infection by astroviruses. These results further corroborate the role of astroviruses in causing neurological diseases and will serve as an essential model to interrogate the neuropathogenesis of astrovirus infection. Recent advances in unbiased pathogen discovery have implicated astroviruses as pathogens of the central nervous system (CNS) of mammals, including humans. However, the capacity of astroviruses to be cultured in CNS-derived cells in vitro has not been reported to date. Both astrovirus VA1/HMO-C (VA1; mamastrovirus 9) and classic human astrovirus 4 (HAstV4; mamastrovirus 1) have been previously detected from cases of human encephalitis. We tested the ability of primary human neurons, primary human astrocytes, and other immortalized human nervous system cell lines (SK-N-SH, U87 MG, and SW-1088) to support infection and replication of these two astrovirus genotypes. Primary astrocytes and SK-N-SH cells supported the full viral life cycle of VA1 with a >100-fold increase in viral RNA levels during a multistep growth curve, detection of viral capsid, and a >100-fold increase in viral titer. Primary astrocytes were permissive with respect to HAstV4 infection and replication but did not yield infectious virus, suggesting abortive infection. Similarly, abortive infection of VA1 was observed in SW-1088 and U87 MG cells. Elevated expression of the chemokine CXCL10 was detected in VA1-infected primary astrocytes and SK-N-SH cells, suggesting that VA1 infection can induce a proinflammatory host response. These findings establish an in vitro cell culture model that is essential for investigation of the basic biology of astroviruses and their neuropathogenic potential.
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Novel Human Astroviruses: Prevalence and Association with Common Enteric Viruses in Undiagnosed Gastroenteritis Cases in Spain. Viruses 2019; 11:v11070585. [PMID: 31252663 PMCID: PMC6669616 DOI: 10.3390/v11070585] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 12/14/2022] Open
Abstract
A remarkable percentage of acute gastroenteritis cases remain etiologically undiagnosed. The aim of the study was to determine the prevalence of common and emerging enteric viruses, such as novel human astroviruses, among undiagnosed samples from children with acute gastroenteritis. Epidemiological studies for novel human astroviruses are still scarce. Stool samples collected over two consecutive winter seasons (2016–2017) from children with gastroenteritis in Spain, which were negative for bacteria, rotavirus, and adenovirus by routine diagnostics were screened by real-time RT-PCR assays for the presence of classical and novel astrovirus, rotavirus, norovirus GI and GII, sapovirus, and adenovirus. Overall, 220/384 stool samples (57.3%) were positive for at least one virus. Co-infections were identified in 21% of cases. Among a total of 315 viruses identified, adenovirus was the most prevalent (n = 103), followed by rotavirus (n = 51), sapovirus (n = 50), classical astrovirus (n = 43), novel astroviruses (n = 42), and norovirus (n = 26). Novel astroviruses were present in 13.3% of virus-positive cases. Most novel astroviruses were found in children <2-year-old (30/39 children, 77%, p = 0.01) and were found in co-infection (66%). Only classical astroviruses demonstrated significant differences in the Cq values during mono-infections compared to co-infections. In conclusion, common enteric viruses may be frequently found in children with undiagnosed gastroenteritis, indicating the need to implement more sensitive diagnostic methods. Novel astroviruses circulate in the community and could be the cause of gastroenteritis among young children.
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Human Astrovirus MLB Replication In Vitro: Persistence in Extraintestinal Cell Lines. J Virol 2019; 93:JVI.00557-19. [PMID: 31019055 DOI: 10.1128/jvi.00557-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 04/12/2019] [Indexed: 02/06/2023] Open
Abstract
MLB astroviruses were identified 10 years ago in feces from children with gastroenteritis of unknown etiology and have been unexpectedly detected in severe cases of meningitis/encephalitis, febrile illness of unknown etiology, and respiratory syndromes. The aim of this study was to establish a cell culture system supporting MLB astrovirus replication. We used two clinical strains to infect several cell lines, an MLB1 strain from a gastroenteritis case, and an MLB2 strain associated with a neurologic infection. Efforts to propagate the viruses in the Caco-2 cell line were unsuccessful. In contrast, we identified two human nonintestinal cell lines, Huh-7 and A549, permissive for both genotypes. After serial passages in the Huh-7.5 cell line, the adapted strains were able to establish persistent infections in the Huh-7.5, Huh-7AI, and A549 cell lines, with high viral loads (up to 10 log10 genome copies/ml) detected by quantitative reverse transcription-PCR (RT-qPCR) in the culture supernatant. Immunofluorescence assays demonstrated infection in about 10% of cells in persistently infected cultures. Electron microscopy revealed particles of 32 to 33 nm in diameter after negative staining of cell supernatants and capsid arrays in ultrathin sections with a particularly high production in Huh-7.5 cells. Interferon (IFN) expression by infected cells and effect of exogenous IFN varied depending on the type of infection and the cell line. The availability of a cell culture system to propagate MLB astroviruses represents a key step to better understand their replicative cycle, as well as a source of viruses to conduct a wide variety of basic virologic studies.IMPORTANCE MLB astroviruses are emerging viruses infecting humans. More studies are required to determine their exact epidemiology, but several reports have already identified them as the cause of unexpected clinical diseases, including severe neurologic diseases. Our study provides the first description of a cell culture system for the propagation of MLB astroviruses, enabling the study of their replicative cycle. Moreover, we demonstrated the unknown capacity of MLB astrovirus to establish persistent infections in cell culture. Whether these persistent infections are also established in vivo remains unknown, but the clinical consequences would be of high interest if persistence was confirmed in vivo Finally, our analysis of IFN expression provides some trails to understand the mechanism by which MLB astroviruses can cause persistent infections in the assayed cultures.
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Haston JC, Rostad CA, Jerris RC, Milla SS, McCracken C, Pratt C, Wiley M, Prieto K, Palacios G, Shane AL, McElroy AK. Prospective Cohort Study of Next-Generation Sequencing as a Diagnostic Modality for Unexplained Encephalitis in Children. J Pediatric Infect Dis Soc 2019; 9:326-333. [PMID: 31107955 PMCID: PMC7457329 DOI: 10.1093/jpids/piz032] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 04/25/2019] [Indexed: 11/12/2022]
Abstract
BACKGROUND Encephalitis is an inflammatory condition of the brain associated with long-term neurologic sequelae and even death in children. Although viruses are often implicated, an etiology is not identified in the majority of cases. Metagenomics-based next-generation sequencing (mNGS) is a high-throughput sequencing technique that can enhance the detection of novel or low-frequency pathogens. METHODS Hospitalized immunocompetent children aged 6 months to 18 years with encephalitis of unidentified etiology were eligible for enrollment. Demographic, historical, and clinical information was obtained, and residual blood and cerebrospinal fluid (CSF) samples were subjected to mNGS. Pathogens were identified by querying the sequence data against the NCBI GenBank database. RESULTS Twenty children were enrolled prospectively between 2013 and 2017. mNGS of CSF identified 7 nonhuman nucleic acid sequences of significant frequency in 6 patients, including that of Mycoplasma bovis, parvovirus B19, Neisseria meningitidis, and Balamuthia mandrillaris. mNGS also detected Cladophialophora species, tobacco mosaic virus, and human bocavirus, which were presumed to be contaminants or nonpathogenic organisms. One patient was found to have positive serology results for California encephalitis virus, but mNGS did not detect it. Patients for whom mNGS identified a diagnosis had a significantly higher CSF white blood cell count, a higher CSF protein concentration, and a lower CSF glucose level than patients for whom mNGS did not identify a diagnosis. CONCLUSION We describe here the results of a prospective cohort analysis to evaluate mNGS as a diagnostic tool for children with unexplained encephalitis. Although mNGS detected multiple nonpathogenic organisms, it also identified multiple pathogens successfully and was most useful in patients with a CSF abnormality.
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Affiliation(s)
- Julia C Haston
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia,Children’s Healthcare of Atlanta, Georgia
| | - Christina A Rostad
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia,Children’s Healthcare of Atlanta, Georgia
| | | | - Sarah S Milla
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia,Children’s Healthcare of Atlanta, Georgia
| | - Courtney McCracken
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia,Children’s Healthcare of Atlanta, Georgia
| | - Catherine Pratt
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, Maryland,College of Public Health, University of Nebraska Medical Center, Omaha
| | - Michael Wiley
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, Maryland,College of Public Health, University of Nebraska Medical Center, Omaha
| | - Karla Prieto
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, Maryland,College of Public Health, University of Nebraska Medical Center, Omaha
| | - Gustavo Palacios
- US Army Medical Research Institute of Infectious Diseases (USAMRIID), Frederick, Maryland
| | - Andi L Shane
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia,Children’s Healthcare of Atlanta, Georgia
| | - Anita K McElroy
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia,Children’s Healthcare of Atlanta, Georgia,Department of Pediatrics, University of Pittsburgh, Pennsylvania,Correspondence: A. K. McElroy, MD, PhD, University of Pittsburgh, Department of Pediatrics, 3501 Fifth Ave, Pittsburgh, PA 15261 ()
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46
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Miller S, Naccache SN, Samayoa E, Messacar K, Arevalo S, Federman S, Stryke D, Pham E, Fung B, Bolosky WJ, Ingebrigtsen D, Lorizio W, Paff SM, Leake JA, Pesano R, DeBiasi R, Dominguez S, Chiu CY. Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid. Genome Res 2019; 29:831-842. [PMID: 30992304 PMCID: PMC6499319 DOI: 10.1101/gr.238170.118] [Citation(s) in RCA: 335] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 02/25/2019] [Indexed: 02/06/2023]
Abstract
Metagenomic next-generation sequencing (mNGS) for pan-pathogen detection has been successfully tested in proof-of-concept case studies in patients with acute illness of unknown etiology but to date has been largely confined to research settings. Here, we developed and validated a clinical mNGS assay for diagnosis of infectious causes of meningitis and encephalitis from cerebrospinal fluid (CSF) in a licensed microbiology laboratory. A customized bioinformatics pipeline, SURPI+, was developed to rapidly analyze mNGS data, generate an automated summary of detected pathogens, and provide a graphical user interface for evaluating and interpreting results. We established quality metrics, threshold values, and limits of detection of 0.2-313 genomic copies or colony forming units per milliliter for each representative organism type. Gross hemolysis and excess host nucleic acid reduced assay sensitivity; however, spiked phages used as internal controls were reliable indicators of sensitivity loss. Diagnostic test accuracy was evaluated by blinded mNGS testing of 95 patient samples, revealing 73% sensitivity and 99% specificity compared to original clinical test results, and 81% positive percent agreement and 99% negative percent agreement after discrepancy analysis. Subsequent mNGS challenge testing of 20 positive CSF samples prospectively collected from a cohort of pediatric patients hospitalized with meningitis, encephalitis, and/or myelitis showed 92% sensitivity and 96% specificity relative to conventional microbiological testing of CSF in identifying the causative pathogen. These results demonstrate the analytic performance of a laboratory-validated mNGS assay for pan-pathogen detection, to be used clinically for diagnosis of neurological infections from CSF.
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Affiliation(s)
- Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94143, USA
| | - Samia N Naccache
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94143, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California 90027, USA
| | - Erik Samayoa
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - Kevin Messacar
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Shaun Arevalo
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94143, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94143, USA
| | - Doug Stryke
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94143, USA
| | - Elizabeth Pham
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - Becky Fung
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | | | - Danielle Ingebrigtsen
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - Walter Lorizio
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - Sandra M Paff
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
| | - John A Leake
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California 92675, USA
| | - Rick Pesano
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California 92675, USA
| | - Roberta DeBiasi
- Department of Pediatrics, Division of Pediatric Infectious Diseases, Children's National Health System, Washington, DC 20010, USA
- Department of Pediatrics, Microbiology, Immunology, and Tropical Medicine, The George Washington University School of Medicine, Washington, DC 20037, USA
| | - Samuel Dominguez
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, California 94143, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, California 94143, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, California 94143, USA
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47
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Jones TPW, Buckland M, Breuer J, Lowe DM. Viral infection in primary antibody deficiency syndromes. Rev Med Virol 2019; 29:e2049. [PMID: 31016825 DOI: 10.1002/rmv.2049] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 03/24/2019] [Accepted: 03/25/2019] [Indexed: 12/22/2022]
Abstract
Patients with primary antibody deficiency syndromes such as X-linked agammaglobulinemia (XLA) and common variable immunodeficiency (CVID) are at increased risk of severe and invasive infection. Viral infection in these populations has been of increasing interest as evidence mounts that viruses contribute significant morbidity and mortality: this is mediated both directly and via aberrant immune responses. We explain the importance of the humoral immune system in defence against viral pathogens before highlighting several significant viral syndromes in patients with antibody deficiency. We explore historical cases of hepatitis C via contaminated immunoglobulin products, the predisposition to invasive enteroviral infections, prolonged excretion of vaccine-derived poliovirus, the morbidity of chronic norovirus infection, and recent literature revealing the importance of respiratory viral infections. We discuss evidence that herpesviruses may play a role in driving the inflammatory disease seen in a subset of patients. We explore the phenomenon of within-host evolution during chronic viral infection and the potential emergence of new pathogenic strains. We highlight novel and emerging viruses identified via deep sequencing techniques. We describe the treatment strategies that have been attempted in all these scenarios and the urgent outstanding questions for research.
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Affiliation(s)
- Timothy P W Jones
- Department of Infectious Disease and Microbiology, Royal Free Hospital, London, UK
| | - Matthew Buckland
- Institute of Immunity and Transplantation, Royal Free Campus, University College, London, UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
| | - David M Lowe
- Institute of Immunity and Transplantation, Royal Free Campus, University College, London, UK
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48
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Wang J, Xu H, Li Z, Li F, Yang Y, Yu X, Jiang D, Xing L, Sun H, Shao M. Pathogens in patients with granulomatous lobular mastitis. Int J Infect Dis 2019; 81:123-127. [DOI: 10.1016/j.ijid.2019.01.034] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/14/2019] [Accepted: 01/19/2019] [Indexed: 10/27/2022] Open
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49
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Huang B, Jennison A, Whiley D, McMahon J, Hewitson G, Graham R, De Jong A, Warrilow D. Illumina sequencing of clinical samples for virus detection in a public health laboratory. Sci Rep 2019; 9:5409. [PMID: 30931974 PMCID: PMC6443674 DOI: 10.1038/s41598-019-41830-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 01/31/2019] [Indexed: 11/29/2022] Open
Abstract
High-throughput sequencing (HTS) provides the opportunity, once a diagnostic result is obtained, to extract additional information from a virus-containing sample. Hence, it offers advantages over established quantitative amplification technology, such as quantitative PCR, particularly in a public health environment. At this early stage of its clinical application, there have been limited studies comparing HTS performance to that of the more established quantitative PCR technology for direct detection of viruses. In this pilot-scale study, we tested HTS with a range of viruses and sample types routinely encountered in a public health virology laboratory. In comparison with quantitative PCR, our HTS method was able to sensitively (92%) detect all viruses in any sample type with the exception of certain tissues. Moreover, sufficient nucleotide sequence information was obtained to enable genotyping of strains detected, thus providing additional useful epidemiological information. While HTS sensitivity may not yet match that of PCR, the added value through enhanced epidemiological data has considerable potential to enable real-time surveillance of circulating strains so as to facilitate rapid and appropriate response to outbreaks and virus zoonotic spillover events.
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Affiliation(s)
- Bixing Huang
- Public Health Virology Laboratory, Queensland Health Forensic and Scientific Services, PO Box 594, Archerfield, Queensland, 4108, Australia
| | - Amy Jennison
- Public Health Microbiology Laboratory, Queensland Health Forensic and Scientific Services, PO Box 594, Archerfield, Queensland, 4108, Australia
| | - David Whiley
- Microbiology Division, Pathology Queensland Central Laboratory, Brisbane, Queensland, 4029, Australia.,Faculty of Medicine, University of Queensland Centre for Clinical Research, The University of Queensland, Brisbane, Queensland, 4029, Australia
| | - Jamie McMahon
- Public Health Virology Laboratory, Queensland Health Forensic and Scientific Services, PO Box 594, Archerfield, Queensland, 4108, Australia
| | - Glen Hewitson
- Public Health Virology Laboratory, Queensland Health Forensic and Scientific Services, PO Box 594, Archerfield, Queensland, 4108, Australia
| | - Rikki Graham
- Public Health Microbiology Laboratory, Queensland Health Forensic and Scientific Services, PO Box 594, Archerfield, Queensland, 4108, Australia
| | - Amanda De Jong
- Public Health Virology Laboratory, Queensland Health Forensic and Scientific Services, PO Box 594, Archerfield, Queensland, 4108, Australia
| | - David Warrilow
- Public Health Virology Laboratory, Queensland Health Forensic and Scientific Services, PO Box 594, Archerfield, Queensland, 4108, Australia.
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50
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Bassetto M, Van Dycke J, Neyts J, Brancale A, Rocha-Pereira J. Targeting the Viral Polymerase of Diarrhea-Causing Viruses as a Strategy to Develop a Single Broad-Spectrum Antiviral Therapy. Viruses 2019; 11:v11020173. [PMID: 30791582 PMCID: PMC6409847 DOI: 10.3390/v11020173] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 02/15/2019] [Accepted: 02/15/2019] [Indexed: 01/01/2023] Open
Abstract
Viral gastroenteritis is an important cause of morbidity and mortality worldwide, being particularly severe for children under the age of five. The most common viral agents of gastroenteritis are noroviruses, rotaviruses, sapoviruses, astroviruses and adenoviruses, however, no specific antiviral treatment exists today against any of these pathogens. We here discuss the feasibility of developing a broad-spectrum antiviral treatment against these diarrhea-causing viruses. This review focuses on the viral polymerase as an antiviral target, as this is the most conserved viral protein among the diverse viral families to which these viruses belong to. We describe the functional and structural similarities of the different viral polymerases, the antiviral effect of reported polymerase inhibitors and highlight common features that might be exploited in an attempt of designing such pan-polymerase inhibitor.
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Affiliation(s)
- Marcella Bassetto
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, CF10 3NB Cardiff, UK.
| | - Jana Van Dycke
- KU Leuven-Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Leuven 3000, Belgium.
| | - Johan Neyts
- KU Leuven-Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Leuven 3000, Belgium.
| | - Andrea Brancale
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, CF10 3NB Cardiff, UK.
| | - Joana Rocha-Pereira
- KU Leuven-Laboratory of Virology and Chemotherapy, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Leuven 3000, Belgium.
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