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Jauhiainen MK, Mohanraj U, Perdomo MF, Hagström J, Haglund C, Mäkitie AA, Söderlund-Venermo M, Sinkkonen ST. Presence of herpesviruses, parvoviruses, and polyomaviruses in sinonasal lymphoma. Eur Arch Otorhinolaryngol 2024:10.1007/s00405-024-08702-0. [PMID: 38758242 DOI: 10.1007/s00405-024-08702-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024]
Abstract
PURPOSE Sinonasal lymphoma (SL) is a rare lymphatic neoplasm of the nasal cavities, paranasal sinuses and nasopharynx. Whereas some risk factors for SL subtypes have been identified, their aetiology is unknown. Along with other predisposing factors, the viral association of lymphomas, such as Epstein-Barr virus (EBV) and Burkitt and Hodgkin lymphomas, is well-established. Modern molecular biology techniques have enabled the discovery of novel human viruses, exemplified by the protoparvovirus cutavirus (CuV), associated with cutaneous T-cell lymphoma. These findings, and the anatomical location of the sinonasal tract with its rich microbiome and infectious agents, justify in-depth studies among SL. METHODS We analysed the presence of 20 viruses of Orthoherpesviridae, Parvoviridae, and Polyomaviridae by qPCR in 24 SL tumours. We performed RNAscope in situ hybridisation (RISH) to localize the viruses. Parvovirus-specific IgG was analysed by enzyme immunoassay and targeted next-generation sequencing (NGS) was applied to detect CuV in plasma. RESULTS We detected viral DNA in 15/24 (63%) tumours; nine of EBV, six of human herpesvirus (HHV) -7, four each of HHV-6B and parvovirus B19, two of cytomegalovirus, and one each of CuV and Merkel-cell polyomavirus. We found tumours with up to four viruses per tumour, and localized CuV and EBV DNAs by RISH. Two of the ten plasma samples exhibited CuV IgG, and one plasma sample demonstrated CuV viremia by NGS. CONCLUSION Viruses were frequent findings in SL. The EBV detection rate was high in diffuse large B-cell lymphoma, and co-detections with other viruses were prevalent.
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Affiliation(s)
- Maria K Jauhiainen
- Department of Otorhinolaryngology, Head and Neck Surgery, Head and Neck Center, Helsinki University Hospital and University of Helsinki, POB 263, 00029 HUS, Helsinki, Finland.
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- The Doctoral Programme in Clinical Research, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| | - Ushanandini Mohanraj
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Maria F Perdomo
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Jaana Hagström
- Department of Pathology, University Hospital of Helsinki, Helsinki, Finland
- Department of Oral Pathology and Radiology, University of Turku, Turku, Finland
- Translational Cancer Research Medicine, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Caj Haglund
- Translational Cancer Research Medicine, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Surgery, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | - Antti A Mäkitie
- Department of Otorhinolaryngology, Head and Neck Surgery, Head and Neck Center, Helsinki University Hospital and University of Helsinki, POB 263, 00029 HUS, Helsinki, Finland
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Division of Ear, Nose and Throat Diseases, Department of Clinical Sciences, Intervention and Technology, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
| | - Maria Söderlund-Venermo
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Saku T Sinkkonen
- Department of Otorhinolaryngology, Head and Neck Surgery, Head and Neck Center, Helsinki University Hospital and University of Helsinki, POB 263, 00029 HUS, Helsinki, Finland
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Ullah Khan N, Sadiq A, Khan J, Basharat N, Hassan ZU, Ali I, Shah TA, Bourhia M, Bin Jardan YA, Wondmie GF. Molecular characterization of plasma virome of hepatocellular carcinoma (HCC) patients. AMB Express 2024; 14:46. [PMID: 38664337 PMCID: PMC11045709 DOI: 10.1186/s13568-024-01696-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Hepatocellular carcinoma (HCC) stands as the most common cancer type, arising from various causes, and responsible for a substantial number of cancer-related fatalities. Recent advancements in viral metagenomics have empowered scientists to delve into the intricate diversity of the virosphere, viral evolution, interactions between viruses and their hosts, and the identification of viral causes behind disease outbreaks, the development of specific symptoms, and their potential role in altering the host's physiology. The present study had the objective of "Molecular Characterization of HBV, HCV, anelloviruses, CMV, SENV-D, SENV-H, HEV, and HPV viruses among individuals suffering from HCC." A total of 381 HCC patients contributed 10 cc of blood each for this study. The research encompassed the assessment of tumor markers, followed by molecular characterization of HBV, HCV, Anelloviruses (TTV, TTMV, and TTMDV), SENV-H and SENV-D viruses, HEV, CMV, and HPV, as well as histopathological examinations. The outcomes of this study revealed that majority of the HCC patients 72.4% (276/381) were male as compared to females. HCV infection, at 76.4% (291 out of 381), exhibited a significant association (p < 0.05) with HCC. Most patients displayed singular lesions in the liver, with Child Pugh Score Type B being the predominant finding in 45.2% of cases. Plasma virome analysis indicated the prevalence of TTMDV (75%), followed by TTMV (70%) and TTV (42.1%) among anelloviruses in HCC patients. Similarly, SENV-H (52%) was followed by SENV-D (20%), with co-infections at 15%. The presence of CMV and HEV among the HCC patients was recorded 5% each however 3.5% of the patients showed the presence of HPV. In conclusion, this study underscores that HCC patients serve as reservoirs for various pathogenic and non-pathogenic viruses, potentially contributing to the development, progression, and severity of the disease.
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Affiliation(s)
- Niamat Ullah Khan
- Molecular Virology Laboratory, Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Asma Sadiq
- Department of Microbiology, University of Jhang, Punjab, Pakistan
| | - Jadoon Khan
- Molecular Virology Laboratory, Department of Biosciences, COMSATS University, Islamabad, Pakistan.
- Department of Allied Health Sciences, Iqra University, Chak Shahzad Campus, Islamabad, Pakistan.
| | - Nosheen Basharat
- Department of Microbiology, University of Jhang, Punjab, Pakistan
| | - Zulfiqar Ul Hassan
- Department of Allied Health Sciences, Iqra University, Chak Shahzad Campus, Islamabad, Pakistan
| | - Ijaz Ali
- Molecular Virology Laboratory, Department of Biosciences, COMSATS University, Islamabad, Pakistan
- Center for Applied Mathematics and Bioinformatics (CAMB), Gulf University for Science and Technology, West Mishref, Kuwait
| | - Tawaf Ali Shah
- College of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, 255000, China
| | - Mohammed Bourhia
- Laboratory of Biotechnology and Natural Resources Valorization, Faculty of Sciences, Ibn Zohr University, Agadir, 80060, Morocco.
| | - Yousef A Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 11451, Riyadh, Saudi Arabia
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Zou H, Gao S, Liu X, Liu Y, Xiao Y, Li A, Jiang Y. Combination of metagenomic next-generation sequencing and conventional tests unraveled pathogen profiles in infected patients undergoing allogeneic hematopoietic stem cell transplantation in Jilin Province of China. Front Cell Infect Microbiol 2024; 14:1378112. [PMID: 38567023 PMCID: PMC10985322 DOI: 10.3389/fcimb.2024.1378112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024] Open
Abstract
Background Infection is the main cause of death for patients after allogeneic hematopoietic stem cell transplantation (HSCT). However, pathogen profiles still have not been reported in detail due to their heterogeneity caused by geographic region. Objective To evaluate the performance of metagenomic next-generation sequencing (mNGS) and summarize regional pathogen profiles of infected patients after HSCT. Methods From February 2021 to August 2022, 64 patients, admitted to the Department of Hematology of The First Hospital of Jilin University for HSCT and diagnosed as suspected infections, were retrospectively enrolled. Results A total of 38 patients were diagnosed as having infections, including bloodstream (n =17), pulmonary (n =16), central nervous system (CNS) (n =4), and chest (n =1) infections. Human betaherpesvirus 5 (CMV) was the most common pathogen in both bloodstream (n =10) and pulmonary (n =8) infections, while CNS (n =2) and chest (n =1) infections were mainly caused by Human gammaherpesvirus 4 (EBV). For bloodstream infection, Mycobacterium tuberculosis complex (n =3), Staphylococcus epidermidis (n =1), and Candida tropicalis (n =1) were also diagnosed as causative pathogens. Furthermore, mNGS combined with conventional tests can identify more causative pathogens with high sensitivity of 82.9% (95% CI 70.4-95.3%), and the total coincidence rate can reach up to 76.7% (95% CI 64.1-89.4%). Conclusions Our findings emphasized the importance of mNGS in diagnosing, managing, and ruling out infections, and an era of more rapid, independent, and impartial diagnosis of infections after HSCT can be expected.
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Affiliation(s)
- Hongyan Zou
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Sujun Gao
- Department of Hematology, The First Hospital of Jilin University, Changchun, China
| | - Xiaoliang Liu
- Department of Hematology, The First Hospital of Jilin University, Changchun, China
| | - Yong Liu
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Yunping Xiao
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Ao Li
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
| | - Yanfang Jiang
- Key Laboratory of Organ Regeneration & Transplantation of the Ministry of Education, Genetic Diagnosis Center, The First Hospital of Jilin University, Changchun, China
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Yuan H, Ma X, Xu J, Han P, Rao G, Chen G, Zhang K, Yang R, Han C, Jiang M. Application of metagenomic next-generation sequencing in the clinical diagnosis of infectious diseases after allo-HSCT: a single-center analysis. BMC Infect Dis 2024; 24:279. [PMID: 38438967 PMCID: PMC10910774 DOI: 10.1186/s12879-024-09153-y] [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: 05/11/2023] [Accepted: 02/19/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND We investigated the value of metagenomic next-generation sequencing (mNGS) in diagnosing infectious diseases in patients receiving allogeneic hematopoietic stem cell transplantation (allo-HSCT). METHODS Fifty-four patients who had fever following allo-HSCT from October 2019 to February 2022 were enrolled. Conventional microbiological tests (CMTs) and mNGS, along with imaging and clinical manifestations, were used to diagnose infection following allo-HSCT. The clinical diagnostic value of mNGS was evaluated. RESULTS A total of 61 mNGS tests were performed, resulting in the diagnosis of 46 cases of infectious diseases. Among these cases, there were 22 cases of viral infection, 13 cases of fungal infection, and 11 cases of bacterial infection. Moreover, 27 cases (58.7%) were classified as bloodstream infections, 15 (32.6%) as respiratory infections, 2 (4.3%) as digestive system infections, and 2 (4.3%) as central nervous system infections. Additionally, there were 8 cases with non-infectious diseases (8/54, 14.81%), including 2 cases of interstitial pneumonia, 2 cases of bronchiolitis obliterans, 2 cases of engraftment syndrome, and 2 cases of acute graft-versus-host disease. The positive detection rates of mNGS and CMT were 88.9% and 33.3%, respectively, with significant differences (P < 0.001). The sensitivity of mNGS was 97.82%, the specificity was 25%, the positive predictive value was 93.75%, and the negative predictive value was 50%. Following treatment, 51 patients showed improvement, and 3 cases succumbed to multidrug-resistant bacterial infections. CONCLUSIONS mNGS plays an important role in the early clinical diagnosis of infectious diseases after allo-HSCT, which is not affected by immunosuppression status, empiric antibiotic therapy, and multi-microbial mixed infection.
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Affiliation(s)
- Hailong Yuan
- Hematology Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Institute of Hematology, No.137 Liyushan South Road, Urumqi, 830054, China
| | - Xiaolu Ma
- Department of Hematology, Guangyuan Central Hospital, Guangyuan, Sichuan Province, China
| | - Jianli Xu
- Hematology Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Institute of Hematology, No.137 Liyushan South Road, Urumqi, 830054, China
| | - Peng Han
- Genskey Medical Technology Co., Ltd, Beijing, China
| | - Guanhua Rao
- Genskey Medical Technology Co., Ltd, Beijing, China
| | - Gang Chen
- Hematology Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Institute of Hematology, No.137 Liyushan South Road, Urumqi, 830054, China
| | - Kaile Zhang
- Hematology Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Institute of Hematology, No.137 Liyushan South Road, Urumqi, 830054, China
| | - Ruixue Yang
- Hematology Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Institute of Hematology, No.137 Liyushan South Road, Urumqi, 830054, China
| | - Chuixia Han
- Hematology Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Institute of Hematology, No.137 Liyushan South Road, Urumqi, 830054, China
| | - Ming Jiang
- Hematology Center, The First Affiliated Hospital of Xinjiang Medical University, Xinjiang Institute of Hematology, No.137 Liyushan South Road, Urumqi, 830054, China.
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Kilich G, Perelygina L, Sullivan KE. Rubella virus chronic inflammatory disease and other unusual viral phenotypes in inborn errors of immunity. Immunol Rev 2024; 322:113-137. [PMID: 38009321 DOI: 10.1111/imr.13290] [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] [Indexed: 11/28/2023]
Abstract
Infectious susceptibility is a component of many inborn errors of immunity. Nevertheless, antibiotic use is often used as a surrogate in history taking for infectious susceptibility, thereby disadvantaging patients who present with viral infections as their phenotype. Further complicating clinical evaluations are unusual manifestations of viral infections which may be less familiar that the typical respiratory viral infections. This review covers several unusual viral phenotypes arising in patients with inborn errors of immunity and other settings of immune compromise. In some cases, chronic infections lead to oncogenesis or tumor-like growths and the conditions and mechanisms of viral-induced oncogenesis will be described. This review covers enterovirus, rubella, measles, papillomavirus, and parvovirus B19. It does not cover EBV and hemophagocytic lymphohistiocytosis nor lymphomagenesis related to EBV. EBV susceptibility has been recently reviewed. Our goal is to increase awareness of the unusual manifestations of viral infections in patients with IEI and to describe treatment modalities utilized in this setting. Coincidentally, each of the discussed viral infections can have a cutaneous component and figures will serve as a reminder of the physical features of these viruses. Given the high morbidity and mortality, early recognition can only improve outcomes.
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Affiliation(s)
- Gonench Kilich
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ludmila Perelygina
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Pang F, Xu W, Zhao H, Chen S, Tian Y, Fu J, You Z, Song P, Xian Q, Zhao Q, Wang C, Jia X. Comprehensive evaluation of plasma microbial cell-free DNA sequencing for predicting bloodstream and local infections in clinical practice: a multicenter retrospective study. Front Cell Infect Microbiol 2024; 13:1256099. [PMID: 38362158 PMCID: PMC10868388 DOI: 10.3389/fcimb.2023.1256099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 12/12/2023] [Indexed: 02/17/2024] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) of plasma cell-free DNA (cfDNA) shows promising application for complicated infections that cannot be resolved by conventional microbiological tests (CMTs). The criteria for cfDNA sequencing are currently in need of agreement and standardization. Methods We performed a retrospective cohort observation of 653 patients who underwent plasma cfDNA mNGS, including 431 with suspected bloodstream infections (BSI) and 222 with other suspected systemic infections. Plasma mNGS and CMTs were performed simultaneously in clinical practice. The diagnostic efficacy of plasma mNGS and CMTs in the diagnosis of blood-borne and other systemic infections was evaluated using receiver operating characteristic (ROC) curves. The sensitivity and specificity of the two methods were analyzed based on the final clinical outcome as the gold standard. Results The mNGS test showed an overall positive rate of 72.3% (472/653) for detecting microorganisms in plasma cfDNA, with a range of 2 to 6 different microorganisms detected in 171 patient specimens. Patients with positive mNGS results were more immunocompromised and had a higher incidence of severe disease (P<0·05). The sensitivity of mNGS was higher for BSI (93·5%) and other systemic infections (83·6%) compared to CMTs (37·7% and 14·3%, respectively). The mNGS detected DNA from a total of 735 microorganisms, with the number of microbial DNA reads ranging from 3 to 57,969, and a higher number of reads being associated with clinical infections (P<0·05). Of the 472 patients with positive mNGS results, clinical management was positively affected in 203 (43%) cases. Negative mNGS results led to a modified clinical management regimen in 92 patients (14.1%). The study also developed a bacterial and fungal library for plasma mNGS and obtained comparisons of turnaround times and detailed processing procedures for rare pathogens. Conclusion Our study evaluates the clinical use and analytic approaches of mNGS in predicting bloodstream and local infections in clinical practice. Our results suggest that mNGS has higher positive predictive values (PPVs) for BSI and systemic infections compared to CMTs, and can positively affect clinical management in a significant number of patients. The standardized whole-process management procedure for plasma mNGS developed in this study will ensure improved pre-screening probabilities and yield clinically valuable data.
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Affiliation(s)
- Feng Pang
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Wenbin Xu
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Hui Zhao
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Shuai Chen
- Department of Clinical Laboratory, Liaocheng Thrid People’s Hospital, Liaocheng, Shandong, China
| | - Yaxian Tian
- Department of Center Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Juanjuan Fu
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Zhiqing You
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Pingping Song
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Qingjie Xian
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Qigang Zhao
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Chengtan Wang
- Department of Clinical Laboratory, Liaocheng People’s Hospital, Liaocheng, Shandong, China
| | - Xiuqin Jia
- The Key Laboratory of Molecular Pharmacology, Liaocheng People’s Hospital, Liaocheng, Shandong, China
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7
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Thiele Orberg E, Meedt E, Hiergeist A, Xue J, Heinrich P, Ru J, Ghimire S, Miltiadous O, Lindner S, Tiefgraber M, Göldel S, Eismann T, Schwarz A, Göttert S, Jarosch S, Steiger K, Schulz C, Gigl M, Fischer JC, Janssen KP, Quante M, Heidegger S, Herhaus P, Verbeek M, Ruland J, van den Brink MRM, Weber D, Edinger M, Wolff D, Busch DH, Kleigrewe K, Herr W, Bassermann F, Gessner A, Deng L, Holler E, Poeck H. Bacteria and bacteriophage consortia are associated with protective intestinal metabolites in patients receiving stem cell transplantation. NATURE CANCER 2024; 5:187-208. [PMID: 38172339 DOI: 10.1038/s43018-023-00669-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 10/13/2023] [Indexed: 01/05/2024]
Abstract
The microbiome is a predictor of clinical outcome in patients receiving allogeneic hematopoietic stem cell transplantation (allo-SCT). Microbiota-derived metabolites can modulate these outcomes. How bacteria, fungi and viruses contribute to the production of intestinal metabolites is still unclear. We combined amplicon sequencing, viral metagenomics and targeted metabolomics from stool samples of patients receiving allo-SCT (n = 78) and uncovered a microbiome signature of Lachnospiraceae and Oscillospiraceae and their associated bacteriophages, correlating with the production of immunomodulatory metabolites (IMMs). Moreover, we established the IMM risk index (IMM-RI), which was associated with improved survival and reduced relapse. A high abundance of short-chain fatty acid-biosynthesis pathways, specifically butyric acid via butyryl-coenzyme A (CoA):acetate CoA-transferase (BCoAT, which catalyzes EC 2.8.3.8) was detected in IMM-RI low-risk patients, and virome genome assembly identified two bacteriophages encoding BCoAT as an auxiliary metabolic gene. In conclusion, our study identifies a microbiome signature associated with protective IMMs and provides a rationale for considering metabolite-producing consortia and metabolite formulations as microbiome-based therapies.
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Affiliation(s)
- Erik Thiele Orberg
- Department of Internal Medicine III, School of Medicine, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany.
- German Cancer Consortium (DKTK), partner-site Munich, a partnership between DKFZ and Klinikum rechts der Isar, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.
| | - Elisabeth Meedt
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center, Regensburg, Germany
| | - Andreas Hiergeist
- Institute of Clinical Microbiology and Hygiene, University Medical Center, Regensburg, Germany
| | - Jinling Xue
- Institute of Virology, Helmholtz Zentrum Munich, Munich, Germany
- Chair of Prevention for Microbial Infectious Disease, Central Institute of Disease Prevention and School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Paul Heinrich
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center, Regensburg, Germany
- Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Jinlong Ru
- Institute of Virology, Helmholtz Zentrum Munich, Munich, Germany
- Chair of Prevention for Microbial Infectious Disease, Central Institute of Disease Prevention and School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Sakhila Ghimire
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center, Regensburg, Germany
| | - Oriana Miltiadous
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarah Lindner
- Department of Immunology, Sloan Kettering Institute, New York, NY, USA
| | - Melanie Tiefgraber
- Department of Internal Medicine III, School of Medicine, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
| | - Sophia Göldel
- Department of Internal Medicine III, School of Medicine, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
| | - Tina Eismann
- Department of Internal Medicine III, School of Medicine, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
| | - Alix Schwarz
- Department of Internal Medicine III, School of Medicine, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
| | - Sascha Göttert
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center, Regensburg, Germany
| | - Sebastian Jarosch
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich, Munich, Germany
| | - Katja Steiger
- German Cancer Consortium (DKTK), partner-site Munich, a partnership between DKFZ and Klinikum rechts der Isar, Munich, Germany
- Comparative Experimental Pathology, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Pathology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Christian Schulz
- Department of Internal Medicine II, University Hospital, Ludwig-Maximilians-Universität, Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Michael Gigl
- Bavarian Center for Biomolecular Mass Spectrometry, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Julius C Fischer
- Department of Radiation Oncology, School of Medicine, Technical University of Munich (TUM), Klinikum rechts der Isar TUM, Munich, Germany
| | - Klaus-Peter Janssen
- Department of Surgery, School of Medicine, Technical University of Munich (TUM), Klinikum rechts der Isar TUM, Munich, Germany
| | - Michael Quante
- Department of Internal Medicine II, University Medical Center, Freiburg, Germany
| | - Simon Heidegger
- Department of Internal Medicine III, School of Medicine, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Peter Herhaus
- Department of Internal Medicine III, School of Medicine, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
| | - Mareike Verbeek
- Department of Internal Medicine III, School of Medicine, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
| | - Jürgen Ruland
- German Cancer Consortium (DKTK), partner-site Munich, a partnership between DKFZ and Klinikum rechts der Isar, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
| | - Marcel R M van den Brink
- Department of Immunology, Sloan Kettering Institute, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Daniela Weber
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center, Regensburg, Germany
| | - Matthias Edinger
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center, Regensburg, Germany
- Leibniz Institute for Immunotherapy, Regensburg, Germany
| | - Daniel Wolff
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center, Regensburg, Germany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, School of Medicine, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Wolfgang Herr
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center, Regensburg, Germany
| | - Florian Bassermann
- Department of Internal Medicine III, School of Medicine, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
- German Cancer Consortium (DKTK), partner-site Munich, a partnership between DKFZ and Klinikum rechts der Isar, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
| | - André Gessner
- Institute of Clinical Microbiology and Hygiene, University Medical Center, Regensburg, Germany
| | - Li Deng
- Institute of Virology, Helmholtz Zentrum Munich, Munich, Germany
- Chair of Prevention for Microbial Infectious Disease, Central Institute of Disease Prevention and School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Ernst Holler
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center, Regensburg, Germany
| | - Hendrik Poeck
- Department of Internal Medicine III, Hematology and Medical Oncology, University Medical Center, Regensburg, Germany.
- Leibniz Institute for Immunotherapy, Regensburg, Germany.
- Bavarian Cancer Research Center (BZKF), Regensburg, Germany.
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8
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Li Y, Zheng L, He H, Xiong H, Chen J, Sun H, Chen C, Li Q, Fu J, Wu F, Gao Y, Xian J, Liang M, Xiao G, Chen Q. First detection of cutavirus DNA in stools of patients with rheumatic diseases in Guangzhou, China. Virol Sin 2023; 38:860-867. [PMID: 37839551 PMCID: PMC10786651 DOI: 10.1016/j.virs.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 10/08/2023] [Indexed: 10/17/2023] Open
Abstract
Cutavirus (CuV) is a novel protoparvovirus possibly associated with diarrhea and cutaneous T-cell lymphomas. Patients with rheumatic disease are immunosuppressed and may be more vulnerable to pathogenic viruses. A descriptive study was conducted among hospitalized patients with rheumatic diseases and individuals undergoing medical health check-ups between June 2019 and June 2022 in Guangzhou, China. Stool samples of subjects were tested for CuV DNA. Demographic and fecal examination data of patients were obtained from electronic medical records. A total of 505 patients with rheumatic diseases and 244 individuals who underwent medical health check-ups were included in the study. Of the patients with rheumatic disease, 5.74% [95% confidence interval (CI): 4.03%-8.12%] were positive for CuV DNA, while no individual in the medical health check-up group was positive, indicating a close correlation between CuV and rheumatic disease. Men and patients with rheumatoid arthritis or ankylosing spondylitis, according to the disease classification, were more susceptible to being infected with CuV (P < 0.01). After adjustments, being male remained the only significant factor, with an adjusted odd ratio (OR) of 4.4 (95% CI: 1.7-11.4, P = 0.002). Phylogenetic analysis of the CuV VP2 sequences showed three diverse clades, one of which was segregated to be a single branching independent of previously known sequences, which is possible a new genotype.
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Affiliation(s)
- Yongzhi Li
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Liting Zheng
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Huan He
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Husheng Xiong
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Jiaqi Chen
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Hengbiao Sun
- Clinical Laboratory of Third Affiliated Hospital of Southern Medical University, Guangzhou, 510500, China
| | - Caiyun Chen
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Qiushuang Li
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Jiaqi Fu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Fei Wu
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Yuhan Gao
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Juxian Xian
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Minyi Liang
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Gang Xiao
- Clinical Laboratory of Third Affiliated Hospital of Southern Medical University, Guangzhou, 510500, China.
| | - Qing Chen
- Guangdong Provincial Key Laboratory of Tropical Disease Research, Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
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9
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Pérez-Rodríguez FJ, Laubscher F, Chudzinski V, Kaiser L, Cordey S. Direct Dengue Virus Genome Sequencing from Antigen NS1 Rapid Diagnostic Tests: A Proof-of-Concept with the Standard Q Dengue Duo Assay. Viruses 2023; 15:2167. [PMID: 38005845 PMCID: PMC10674465 DOI: 10.3390/v15112167] [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: 09/26/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
With nearly half of the world's population being at risk of infection, dengue virus represents a major global health issue. The use of dengue antigen rapid diagnostic tests (Ag-RDTs) represents an alternative to PCR methods for the diagnosis of acute infections since they display excellent sensitivities and specificities and can be performed outside the laboratory. The high genetic diversity of the dengue virus genome represents a challenge for vaccine development, and the progressive expansion of this virus into previously nonendemic regions justifies the implementation of a genomic surveillance program. In this proof-of-concept study, we show the feasibility of sequencing dengue virus genomes directly from positive Ag-RDT (Standard Q Dengue Duo Test assay, n = 7) cassettes stored up to 31 days at room temperature after testing. For 5 of the 7 samples, a high number of reads were obtained allowing phylogenetic analyses to be carried out to determine not only the serotypes (dengue 1, 2, 3 and 4 were detected) but also the genotypes. Furthermore, in one sample, our unbiased metagenomic next-generation sequencing approach made it possible to detect epizootic hemorrhagic disease virus sequences, an arthropod-transmitted virus in ruminants. To conclude, as such an approach requires no cold storage or freezing of samples, dengue Ag-RDTs represent a very pragmatic and robust alternative for the genomic surveillance of dengue virus.
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Affiliation(s)
- Francisco-Javier Pérez-Rodríguez
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland; (F.-J.P.-R.); (F.L.); (V.C.); (L.K.)
- Swiss Reference Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Florian Laubscher
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland; (F.-J.P.-R.); (F.L.); (V.C.); (L.K.)
| | - Valentin Chudzinski
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland; (F.-J.P.-R.); (F.L.); (V.C.); (L.K.)
| | - Laurent Kaiser
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland; (F.-J.P.-R.); (F.L.); (V.C.); (L.K.)
- Swiss Reference Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Samuel Cordey
- Laboratory of Virology, Department of Diagnostics, Geneva University Hospitals & Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland; (F.-J.P.-R.); (F.L.); (V.C.); (L.K.)
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10
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Mohanraj U, Konttinen T, Salava A, Väkevä L, Ranki A, Söderlund-Venermo M. Significant Association of Cutavirus With Parapsoriasis en Plaques: High Prevalence Both in Skin Swab and Biopsy Samples. Clin Infect Dis 2023; 77:987-990. [PMID: 37234048 PMCID: PMC10552579 DOI: 10.1093/cid/ciad320] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 05/24/2023] [Indexed: 05/27/2023] Open
Abstract
Cutavirus (CuV) is associated with cutaneous T-cell lymphoma (CTCL), of which parapsoriasis is a precursor. Our study reveals a significantly higher CuV-DNA prevalence in skin swabs of parapsoriasis patients (6/13; 46.2%) versus those of healthy adults (1/51; 1.96%). Eight patients (8/12; 66.7%) had CuV DNA in biopsied skin, and 4 developed CTCL.
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Affiliation(s)
| | - Tuomas Konttinen
- Department of Virology, University of Helsinki, Helsinki, Finland
- Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Alexander Salava
- Department of Dermatology, Allergology, and Venereology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Liisa Väkevä
- Department of Dermatology, Allergology, and Venereology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Annamari Ranki
- Department of Dermatology, Allergology, and Venereology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
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11
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Ma H, Bosma TJ, Khan AS. Long-Read High-Throughput Sequencing (HTS) Revealed That the Sf-Rhabdovirus X + Genome Contains a 3.7 kb Internal Duplication. Viruses 2023; 15:1998. [PMID: 37896775 PMCID: PMC10612052 DOI: 10.3390/v15101998] [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: 06/29/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
We previously reported a novel rhabdovirus produced from the Spodoptera frugiperda Sf9 cell line, designated as Sf-rhabdovirus X+ since it contained a unique accessory gene X. The Sf-rhabdovirus X+ genome sequence was generated using Sanger sequencing and short-read high-throughput sequencing (HTS). In this study, we have used long-read HTS technologies, PacBio's single-molecule real-time sequencing and Oxford's Nanopore RNA direct sequencing, to analyze the parent Sf9 cell line transcriptome and the virus RNA produced from an X+ cell clone, respectively. A unique 3.7 kb duplication was identified in the L gene between nucleotide position 8523 and 8524, preceded by a GA dinucleotide insertion. This duplication contained a partial G gene, the complete X gene, and a partial L gene, which extended from nucleotide positions 4767-8523 in the X+ virus. Thus, the X+ genome length is 17,361 nucleotides, and we have re-designated the virus as Sf-rhabdovirus X+3.7. The 3.7 kb duplication was found in all Sf9 cell clones producing the X+ variant virus. Furthermore, the Sf-rhabdovirus X+3.7 genome was stable at passage 30, which was the highest passage tested. These results highlight the importance of combining short-read and long-read technologies for accurately sequencing virus genomes using HTS.
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Affiliation(s)
| | | | - Arifa S. Khan
- Division of Viral Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA; (H.M.); (T.J.B.)
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12
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Huang J, Zhao Y, Jiang C, Han D, Pan Z, Zhang Z, Wang L, Chen W, Li S, Zhao Y, Hu X. Diagnostic efficiency of metagenomic next-generation sequencing for suspected infection in allogeneic hematopoietic stem cell transplantation recipients. Front Cell Infect Microbiol 2023; 13:1251509. [PMID: 37780852 PMCID: PMC10533937 DOI: 10.3389/fcimb.2023.1251509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 08/28/2023] [Indexed: 10/03/2023] Open
Abstract
Introduction Immunosuppression predisposes allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients to infection. Prompt and accurate identification of pathogens is crucial to optimize treatment strategies. This multi-center retrospective study aimed to assess the ability of metagenomic next-generation sequencing (mNGS) to detect causative pathogens in febrile allo-HSCT recipients and examined its concordance with conventional microbiological tests (CMT). Methods We performed mNGS and CMT on samples obtained from 153 patients with suspected infection during allo-HSCT. Patients were grouped based on their neutropenic status at the time of sampling. Results The mNGS test was more sensitive than CMT (81.1% vs. 53.6%, P<0.001) for diagnosing clinically suspected infection, especially in the non-neutropenia cohort. mNGS could detect fungi and viruses better than bacteria, with a higher sensitivity than CMT. Immune events were diagnosed in 57.4% (35/61) of the febrile events with negative mNGS results, and 33.5% (48/143) with negative CMT results (P=0.002). The treatment success rate of the targeted anti-infection strategy was significantly higher when based on mNGS than on empirical antibiotics (85% vs. 56.5%, P=0.004). Conclusion The mNGS test is superior to CMT for identifying clinically relevant pathogens, and provides valuable information for anti-infection strategies in allo-HSCT recipients. Additionally, attention should be paid to immune events in patients with negative mNGS results.
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Affiliation(s)
- Jiayu Huang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Collaborative Innovation Center of Hematology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yeqian Zhao
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Chuanhe Jiang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Collaborative Innovation Center of Hematology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dongsheng Han
- Centre of Clinical Laboratory, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Zengkai Pan
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Collaborative Innovation Center of Hematology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zilu Zhang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Collaborative Innovation Center of Hematology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Luxiang Wang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Collaborative Innovation Center of Hematology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Chen
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Su Li
- GoBroad Medical Institute of Hematology (Shanghai Center), Liquan Hospital, Shanghai, China
| | - Yanmin Zhao
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaoxia Hu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Shanghai Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Collaborative Innovation Center of Hematology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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13
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Zanella MC, Vu DL, Hosszu-Fellous K, Neofytos D, Van Delden C, Turin L, Poncet A, Simonetta F, Masouridi-Levrat S, Chalandon Y, Cordey S, Kaiser L. Longitudinal Detection of Twenty DNA and RNA Viruses in Allogeneic Hematopoietic Stem Cell Transplant Recipients Plasma. Viruses 2023; 15:v15040928. [PMID: 37112908 PMCID: PMC10142697 DOI: 10.3390/v15040928] [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: 02/12/2023] [Revised: 03/29/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Metagenomics revealed novel and routinely overlooked viruses, representing sources of unrecognized infections after allogeneic hematopoietic stem cell transplantation (allo-HSCT). We aim to describe DNA and RNA virus prevalence and kinetics in allo-HSCT recipients' plasma for one year post HSCT. We included 109 adult patients with first allo-HSCT from 1 March 2017 to 31 January 2019 in this observational cohort study. Seventeen DNA and three RNA viral species were screened with qualitative and/or quantitative r(RT)-PCR assays using plasma samples collected at 0, 1, 3, 6, and 12 months post HSCT. TTV infected 97% of patients, followed by HPgV-1 (prevalence: 26-36%). TTV (median 3.29 × 105 copies/mL) and HPgV-1 (median 1.18 × 106 copies/mL) viral loads peaked at month 3. At least one Polyomaviridae virus (BKPyV, JCPyV, MCPyV, HPyV6/7) was detected in >10% of patients. HPyV6 and HPyV7 prevalence reached 27% and 12% at month 3; CMV prevalence reached 27%. HSV, VZV, EBV, HHV-7, HAdV and B19V prevalence remained <5%. HPyV9, TSPyV, HBoV, EV and HPg-V2 were never detected. At month 3, 72% of patients had co-infections. TTV and HPgV-1 infections were highly prevalent. BKPyV, MCPyV and HPyV6/7 were frequently detected relative to classical culprits. Further investigation is needed into associations between these viral infections and immune reconstitution or clinical outcomes.
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Affiliation(s)
- Marie-Céline Zanella
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Diem-Lan Vu
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Krisztina Hosszu-Fellous
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, 1211 Geneva, Switzerland
| | - Dionysios Neofytos
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Chistian Van Delden
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Lara Turin
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Antoine Poncet
- Center for Clinical Research, Department of Health and Community Medicine, University of Geneva, 1206 Geneva, Switzerland
- Division of Clinical Epidemiology, Department of Health and Community Medicine, University Hospital of Geneva, 1211 Geneva, Switzerland
| | - Federico Simonetta
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Division of Hematology, Department of Oncology, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Stavroula Masouridi-Levrat
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Division of Hematology, Department of Oncology, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Yves Chalandon
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Division of Hematology, Department of Oncology, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Samuel Cordey
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Laurent Kaiser
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, 1211 Geneva, Switzerland
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14
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Evaluation of extraction and enrichment methods for recovery of respiratory RNA viruses in a metagenomics approach. J Virol Methods 2023; 314:114677. [PMID: 36657602 PMCID: PMC10009504 DOI: 10.1016/j.jviromet.2023.114677] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/09/2023] [Accepted: 01/14/2023] [Indexed: 01/18/2023]
Abstract
Viral metagenomics is increasingly applied in viral detection and virome characterization. Different extraction and enrichment techniques may be adopted, however, reports on their effective influence on viral recovery is often conflicting. Using a three step enrichment steps, the effect of three extraction kits and the influence of DNase treatment with or without rRNA removal for respiratory RNA virus recovery from nasopharyngeal swab samples was evaluated. The viral cocktail containing six different RNA viruses pooled in equal volume were subjected to the different extraction and enrichment methods, sequenced using the Illumina MiSeq, and analysed using Genome Detective. The PureLink® Viral RNA/DNA Mini Kit (PureLink) was highly efficient with better recovery of all the viral agents in the cocktail. The use of rRNA treatment resulted in increased viral recovery with PureLink and QIAamp® Viral RNA Mini kit, while having comparable recovery rate as DNase only with the QIAamp® MinElute Virus Spin Kit. The observed low reads and genome coverage of some of the viruses could be attributed to their low abundance. Depending on sample matrix, extraction choice and enrichment strategy may influence recovery of respiratory RNA virus in metagenomics studies, therefore individual evaluation and adoption may be necessary for a robust result.
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15
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Lučiūnaitė A, Dalgėdienė I, Vasiliūnaitė E, Norkienė M, Kučinskaitė-Kodzė I, Žvirblienė A, Gedvilaitė A. Immunogenic Properties and Antigenic Similarity of Virus-like Particles Derived from Human Polyomaviruses. Int J Mol Sci 2023; 24:ijms24054907. [PMID: 36902338 PMCID: PMC10003412 DOI: 10.3390/ijms24054907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Polyomaviruses (PyVs) are highly prevalent in humans and animals. PyVs cause mild illness, however, they can also elicit severe diseases. Some PyVs are potentially zoonotic, such as simian virus 40 (SV40). However, data are still lacking about their biology, infectivity, and host interaction with different PyVs. We investigated the immunogenic properties of virus-like particles (VLPs) derived from viral protein 1 (VP1) of human PyVs. We immunised mice with recombinant HPyV VP1 VLPs mimicking the structure of viruses and compared their immunogenicity and cross-reactivity of antisera using a broad spectrum of VP1 VLPs derived from the PyVs of humans and animals. We demonstrated a strong immunogenicity of studied VLPs and a high degree of antigenic similarity between VP1 VLPs of different PyVs. PyV-specific monoclonal antibodies were generated and applied for investigation of VLPs phagocytosis. This study demonstrated that HPyV VLPs are highly immunogenic and interact with phagocytes. Data on the cross-reactivity of VP1 VLP-specific antisera revealed antigenic similarities among VP1 VLPs of particular human and animal PyVs and suggested possible cross-immunity. As the VP1 capsid protein is the major viral antigen involved in virus-host interaction, an approach based on the use of recombinant VLPs is relevant for studying PyV biology regarding PyV interaction with the host immune system.
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Luciola Zanette D, Andrade Coelho KBC, de Carvalho E, Aoki MN, Nardin JM, Araújo Lalli L, dos Santos Bezerra R, Giovanetti M, Simionatto Zucherato V, Montenegro de Campos G, de Souza Todão Bernardino J, Louis Viala V, Ciccozzi M, Junior Alcantara LC, Coccuzzo Sampaio S, Elias MC, Kashima S, Tadeu Covas D, Nanev Slavov S. Metagenomic insights into the plasma virome of Brazilian patients with prostate cancer. Mol Cell Oncol 2023; 10:2188858. [PMID: 36950183 PMCID: PMC10026895 DOI: 10.1080/23723556.2023.2188858] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Growing evidence suggests that metavirome changes could be associated increased risk for malignant cell transformation. Considering Viruses have been proposed as factors for prostate cancer induction. The objective of this study was to examine the composition of the plasma metavirome of patients with prostate cancer. Blood samples were obtained from 49 male patients with primary prostate adenocarcinoma. Thirty blood donors were included as a control group. The obtained next-generation sequencing data were analyzed using a bioinformatic pipeline for virus metagenomics. Viral reads with higher abundance were assembled in contigs and analyzed taxonomically. Viral agents of interest were also confirmed by qPCR. Anelloviruses and the Human Pegivirus-1 (HPgV-1) were the most abundant component of plasma metavirome. Clinically important viruses like hepatitis C virus (HCV), cytomegalovirus and human adenovirus type C were also identified. In comparison, the blood donor virome was exclusively composed of torque teno virus types (TTV) types. The performed HPgV-1 and HCV phylogeny revealed that these viruses belong to commonly detected in Brazil genotypes. Our study sheds light on the plasma viral abundance in patients with prostatic cancer. The obtained viral diversity allowed us to separate the patients and controls, probably suggesting that malignant processes may influence virome composition. More complex and multiple approach investigations are necessary to examine the likely causal relationship between metavirome and its nvolvement in prostate cancer.
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Affiliation(s)
- Dalila Luciola Zanette
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (FIOCRUZ), Professor Algacyr Munhoz Mader, Curitiba, Parana, Brazil
| | | | | | - Mateus Nobrega Aoki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (FIOCRUZ), Professor Algacyr Munhoz Mader, Curitiba, Parana, Brazil
| | | | - Larissa Araújo Lalli
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (FIOCRUZ), Professor Algacyr Munhoz Mader, Curitiba, Parana, Brazil
| | - Rafael dos Santos Bezerra
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Marta Giovanetti
- Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy
- Laboratory of Flaviviruses, Oswaldo Cruz Foundation, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Victória Simionatto Zucherato
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Gabriel Montenegro de Campos
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | | | | | - Massimo Ciccozzi
- Epidemiology and Statistic Unit, University of Campus Bio-Medico di Roma, Rome, Italy
| | | | | | | | - Simone Kashima
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Dimas Tadeu Covas
- Butantan Institute, São Paulo, São Paulo, Brazil
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Svetoslav Nanev Slavov
- Butantan Institute, São Paulo, São Paulo, Brazil
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
- CONTACT Svetoslav Nanev Slavov Laboratory of Bioinformatics, Department of Biotechnology (NuCeL), Butantan Institute in Ribeirao Preto, 2501 Tenente Catao Roxo Street, Ribeirao Preto, Sao Paulo14051-140, Brazil
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Cadar D, Simonin Y. Human Usutu Virus Infections in Europe: A New Risk on Horizon? Viruses 2022; 15:77. [PMID: 36680117 PMCID: PMC9866956 DOI: 10.3390/v15010077] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
The Usutu virus (USUV), a neurotropic mosquito-borne flavivirus discovered in 1959 in South Africa, has spread over the last twenty years across the European continent. This virus follows an enzootic cycle involving mosquitoes and birds. This caused epizootics with significant bird mortality in Europe in 2016 and 2018. It can also occasionally infect humans and other mammals, including horses and bats, which act as incidental or dead-end hosts. The zoonotic risk associated with this succession of avian epizootics in Europe deserves attention, even if, to date, human cases remain exceptional. Human infection is most often asymptomatic or responsible for mild clinical symptoms. However, human Usutu infections have also been associated with neurological disorders, such as encephalitis and meningoencephalitis. One of the major complexities of the study of USUV pathogenesis is the presence of a great diversity of lineages which could co-circulate spatiotemporally. In this review we discuss several aspects of the circulation of Usutu virus in humans in Europe, the neurological disorders associated, involved viral lineages, and the issues and questions raised by their circulation.
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Affiliation(s)
- Dániel Cadar
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, 20359 Hamburg, Germany
| | - Yannick Simonin
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, 34000 Montpellier, France
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Zhang M, Lu W, Xie D, Wang J, Xiao X, Pu Y, Meng J, Lyu H, Zhao M. Metagenomic Next-Generation Sequencing for Diagnostically Challenging Mucormycosis in Patients with Hematological Malignancies. Infect Drug Resist 2022; 15:7509-7517. [PMID: 36570711 PMCID: PMC9784388 DOI: 10.2147/idr.s393201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/26/2022] [Indexed: 12/23/2022] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) is a fast, sensitive and accurate diagnostic method for pathogens detection. However, reports on the application of mNGS in mucormycosis remain scarce. Methods From January 2019 to December 2021, we recruited 13 patients with hematological malignancies who were suspected of mucormycosis and completed mNGS in D20. Then we retrospectively analyze the clinical data, diagnosis, therapeutic process, and outcomes. In order to evaluate the diagnostic value of mNGS in hematological malignancies patients with suspected mucormycosis. Results All patients had high risk factors of Invasive Fungal Disease, including hematopoietic stem cell transplantation, immunosuppression, glucocorticoids, etc. The clinical presentations were pulmonary (n=9), rhino-orbito-cerebral (n=4). But the manifestations were nonspecific. All enrolled patients completed mNGS. And most (8/13, 61.54%) of the samples were from blood. Fungi can be detected in all specimens, including Rhizopus (n=7), Rhizomucor (n=4) and Mucor (n=2). In addition, 7/13 (53.85%) specimens were detected bacteria at the same time and virus were detected in 5/13 (38.46%). Histopathological examination was completed in 5 patients, 3 of which were completely consistent with the results of mNGS. After treatment, 6 patients were cured, while the other 7 patients died. Conclusion mNGS may be a complementary method for early diagnosis, especially for patients who are not suitable for histopathology examination or unable to obtain culture specimen. mNGS can also help detect bacteria and viruses simultaneously, allowing for appropriate and timely antibiotic administration and thus improving patient outcomes.
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Affiliation(s)
- Meng Zhang
- First Center Clinic College of Tianjin Medical University, Tianjin, 300192, People’s Republic of China
| | - Wenyi Lu
- Department of Hematology, Tianjin First Central Hospital, Tianjin, 300192, People’s Republic of China
| | - Danni Xie
- First Center Clinic College of Tianjin Medical University, Tianjin, 300192, People’s Republic of China
| | - Jiaxi Wang
- First Center Clinic College of Tianjin Medical University, Tianjin, 300192, People’s Republic of China
| | - Xia Xiao
- Department of Hematology, Tianjin First Central Hospital, Tianjin, 300192, People’s Republic of China
| | - Yedi Pu
- Department of Hematology, Tianjin First Central Hospital, Tianjin, 300192, People’s Republic of China
| | - Juanxia Meng
- Department of Hematology, Tianjin First Central Hospital, Tianjin, 300192, People’s Republic of China
| | - Hairong Lyu
- Department of Hematology, Tianjin First Central Hospital, Tianjin, 300192, People’s Republic of China
| | - Mingfeng Zhao
- Department of Hematology, Tianjin First Central Hospital, Tianjin, 300192, People’s Republic of China,Correspondence: Mingfeng Zhao; Hairong Lyu, Department of Hematology, Tianjin First Central Hospital, Tianjin, 300192, People’s Republic of China, Email ;
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Delgado-Cunningham K, López T, Khatib F, Arias CF, DuBois RM. Structure of the divergent human astrovirus MLB capsid spike. Structure 2022; 30:1573-1581.e3. [PMID: 36417907 PMCID: PMC9722636 DOI: 10.1016/j.str.2022.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/30/2022] [Accepted: 10/27/2022] [Indexed: 11/23/2022]
Abstract
Despite their worldwide prevalence and association with human disease, the molecular bases of human astrovirus (HAstV) infection and evolution remain poorly characterized. Here, we report the structure of the capsid protein spike of the divergent HAstV MLB clade (HAstV MLB). While the structure shares a similar folding topology with that of classical-clade HAstV spikes, it is otherwise strikingly different. We find no evidence of a conserved receptor-binding site between the MLB and classical HAstV spikes, suggesting that MLB and classical HAstVs utilize different receptors for host-cell attachment. We provide evidence for this hypothesis using a novel HAstV infection competition assay. Comparisons of the HAstV MLB spike structure with structures predicted from its sequence reveal poor matches, but template-based predictions were surprisingly accurate relative to machine-learning-based predictions. Our data provide a foundation for understanding the mechanisms of infection by diverse HAstVs and can support structure determination in similarly unstudied systems.
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Affiliation(s)
- Kevin Delgado-Cunningham
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Tomás López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, Mexico
| | - Firas Khatib
- Department of Computer and Information Science, University of Massachusetts Dartmouth, Dartmouth, MA 02747, USA
| | - Carlos F Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, Mexico
| | - Rebecca M DuBois
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
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20
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Sun T, Liu Y, Cai Y, Zhai T, Zhou Y, Yang B, Wu X, Zhan Q. A Paired Comparison of Plasma and Bronchoalveolar Lavage Fluid for Metagenomic Next-Generation Sequencing in Critically Ill Patients with Suspected Severe Pneumonia. Infect Drug Resist 2022; 15:4369-4379. [PMID: 35971554 PMCID: PMC9375561 DOI: 10.2147/idr.s374906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/03/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Plasma metagenomic next-generation sequencing (mNGS) has emerged as an attractive and minimally invasive technique for pathogen detection. However, few studies have demonstrated the need for simultaneous plasma and bronchoalveolar lavage fluid (BALF) mNGS in patients with severe pneumonia. Patients and Methods This study retrospectively performed a paired comparison of BALF and plasma mNGS in critically ill patients with suspected severe pneumonia from April 2019 to December 2020. The diagnostic performance of BALF and plasma mNGS was compared using the clinical composite diagnosis as the reference standard. Results In total, 57 patients were included in this study. Patients with positive plasma mNGS had shorter hospital stay days at the time of specimen acquisition (4.5 vs 11, P = 0.028) and a higher positivity rate of BALF culture (50% vs 22.9%, P = 0.033) than patients with negative plasma mNGS. Fifty-three patients (93%) were finally diagnosed with severe pneumonia. Significant differences were observed in the sensitivity of BALF and plasma mNGS (100% vs 42%, P < 0.001), and the diagnostic accuracy was 96% and 46%, respectively. The proportion of virus in positive plasma mNGS results was higher than that in BALF mNGS (23% vs 11%, P = 0.173) without significant difference. Although plasma mNGS detected additional microorganisms in 11/53 patients, the beneficial effect was observed in only 5/53 (9%) patients. Conclusion In this study, the clinical effect of simultaneously conducting mNGS of BALF and plasma samples was found to be limited. For patients with the suspected virus infection, plasma mNGS may be a supplementary test. Further studies are needed to identify the optimal indications for plasma mNGS.
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Affiliation(s)
- Ting Sun
- Capital Medical University China-Japan Friendship School of Clinical Medicine, Beijing, People's Republic of China
| | - Yijie Liu
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Ying Cai
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, People's Republic of China
| | - Tianshu Zhai
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, People's Republic of China
| | - Yun Zhou
- Laboratory Medicine, China-Japan Friendship Hospital, Beijing, People's Republic of China
| | - Bin Yang
- Vision Medicals Center for Infection Diseases, Guangzhou, People's Republic of China
| | - Xiaojing Wu
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, People's Republic of China
| | - Qingyuan Zhan
- Capital Medical University China-Japan Friendship School of Clinical Medicine, Beijing, People's Republic of China.,Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, People's Republic of China
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Fan S, Si M, Xu N, Yan M, Pang M, Liu G, Gong J, Wang H. Metagenomic next-generation sequencing-guided antimicrobial treatment versus conventional antimicrobial treatment in early severe community-acquired pneumonia among immunocompromised patients (MATESHIP): A study protocol. Front Microbiol 2022; 13:927842. [PMID: 35983331 PMCID: PMC9379097 DOI: 10.3389/fmicb.2022.927842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundSevere community-acquired pneumonia (SCAP) is the main cause of mortality in immunocompromised patients. Compared with conventional microbiological tests (CMT), metagenomic next-generation sequencing (mNGS) can quickly and simultaneously detect a wide array of bacteria, viruses, and fungi in an unbiased manner. It is increasingly used for severe respiratory infectious diseases, especially for immunocompromised patients. However, the effects of mNGS-based antimicrobial treatment procedures on clinical outcomes in immunocompromised patients with SCAP have not been evaluated.Methods/DesignThe MATESHIP study is a prospective, multicenter, parallel-group, open-label, randomized controlled trial from 20 ICUs in university hospitals and academic teaching hospitals across Shandong Province, China. We will enroll 342 immunocompromised patients with early onset SCAP who are admitted to an intensive care unit (ICU). Participants will be randomly allocated to an mNGS-guided treatment group or a conventional treatment group (guided by CMT), according to centrally computer-based block randomization stratified by participating centers. Participants will undergo CMT tests using appropriate lower respiratory tract (LRT) and other necessary specimens, with or without mNGS tests using LRT specimens. The primary outcomes will be: (1) The relative change in Sequential Organ Failure Assessment (SOFA) score from randomization to day 5, day 7, day 10, or the day of ICU discharge/death; and (2) the consumption of antimicrobial agents during ICU stay (expressed as defined daily doses). The secondary outcome measures will be: days from randomization to initiation of definitive antimicrobial treatment; overall antimicrobial agent use and cost; total cost of hospitalization; length of ICU stay; 28- and 90-day mortality; and clinical cure rate. This study hypothesizes that mNGS-guided treatment will decrease the degree of organ dysfunction/failure, the consumption of antimicrobial agents, and mortality, while the cure rate will be increased, and the time to initiation of appropriate therapy will be advanced.DiscussionThe MATESHIP study will evaluate for the first time whether mNGS-guided antimicrobial therapy improves the outcomes of SCAP in an immunocompromised population, and provide high-level evidence on the application of mNGS in the management of this population.Clinical Trial Registration[ClinicalTrials.gov], identifier [NCT05290454].
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Affiliation(s)
- Shaohua Fan
- Department of Critical Care Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Min Si
- Department of Critical Care Medicine, Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Nana Xu
- Department of Cardiac Surgery, Cardiac Surgery Care Unit, Qilu Hospital of Shandong University, Jinan, China
| | - Meichen Yan
- Department of Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Mingmin Pang
- Department of Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Guangfeng Liu
- Department of Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Jibin Gong
- Department of Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Hao Wang
- Department of Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, China
- *Correspondence: Hao Wang,
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Plasma Virome Reveals Blooms and Transmission of Anellovirus in Intravenous Drug Users with HIV-1, HCV, and/or HBV Infections. Microbiol Spectr 2022; 10:e0144722. [PMID: 35758682 PMCID: PMC9431549 DOI: 10.1128/spectrum.01447-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intravenous drug users (IDUs) are a high-risk group for HIV-1, hepatitis C virus (HCV), and hepatitis B virus (HBV) infections, which are the leading causes of death in IDUs. However, the plasma virome of IDUs and how it is influenced by above viral infections remain unclear. Using viral metagenomics, we determined the plasma virome of IDUs and its association with HIV-1, HCV, and/or HBV infections. Compared with healthy individuals, IDUs especially those with major viral infections had higher viral abundance and diversity. Anelloviridae dominated plasma virome. Coinfections of multiple anelloviruses were common, and anelloviruses from the same genus tended to coexist together. In this study, 4,487 anellovirus ORF1 sequences were identified, including 1,620 (36.1%) with less than 69% identity to any known sequences, which tripled the current number. Compared with healthy controls (HC), more anellovirus sequences were observed in neg-IDUs, and HIV-1, HCV, and/or HBV infections further expanded the sequence number in IDUs, which was characterized by the emergence of novel divergent taxons and blooms of resident anelloviruses. Pegivirus was mainly identified in infected IDUs. Five main pegivirus transmission clusters (TCs) were identified by phylogenetic analysis, suggesting a transmission link. Similar anellovirus profiles were observed in IDUs within the same TC, suggesting transmission of anellome among IDUs. Our data suggested that IDUs suffered higher plasma viral burden especially anelloviruses, which was associated with HIV-1, HCV, and/or HBV infections. Blooms in abundance and unprecedented diversity of anellovirus highlighted active evolution and replication of this virus in blood circulation, and an uncharacterized role it may engage with the host. IMPORTANCE Virome is associated with immune status and determines or influences disease progression through both pathogenic and resident viruses. Increased viral burden in IDUs especially those with major viral infections indicated the suboptimal immune status and high infection risks of these population. Blooms in abundance and unprecedented diversity of anellovirus highlighted its active evolution and replication in the blood circulation, and sensitive response to other viral infections. In addition, transmission cluster analysis revealed the transmission link of pegivirus among IDUs, and the individuals with transmission links shared similar anellome profiles. In-depth monitoring of the plasma virome in high-risk populations is not only needed for surveillance for emerging viruses and transmission networks of major and neglected bloodborne viruses, but also important for a better understanding of commensal viruses and their role it may engage with immune system.
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23
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Chen MH, Abernathy E, Icenogle JP, Perelygina LM. Improved diagnostic and multiplex RT-qPCR for detecting rubella viral RNA. J Virol Methods 2022; 306:114555. [PMID: 35654258 DOI: 10.1016/j.jviromet.2022.114555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/19/2022] [Accepted: 05/27/2022] [Indexed: 11/18/2022]
Abstract
An examination of the nucleic acid sequence alignment of 48 full-length rubella virus genomes revealed that the 5' terminus of the genome is more conserved than the commonly used detection windows for rubella virus RNA located in the E1 protein coding region, suggesting that the 5' terminus could be a target for improving detection of all rubella virus genotypes. Two candidate primer sets were tested and the window between nucleotides (nts) 98 and 251 was found to have the greatest analytical sensitivity for detection of different genotypes. The new method had a limit of detection of four copies of rubella RNA per reaction with high specificity. The average coefficient variation of Ct was 2.2%. Concordance between the new method and currently used method, based on testing 251 clinical specimens collected from a rubella outbreak, was 99.4%. The assay was further improved upon by the incorporation of detection of both rubella virus RNA and mRNA from a cellular reference gene in a multiplex format. The multiplex format did not reduce the sensitivity or the reproducibility of rubella RNA detection and, of 60 specimens tested, the concordance between the single target and multiplex assays was 85.0%. To assess the utility of the multiplex assay for molecular surveillance, 62 rubella IgM positive serum samples from a rubella outbreak were tested, and eleven tested positive using the multiplex method while none were positive using the method targeting E1. These results show that the assay based on the new detection window near the 5' terminus of the genome can improve the detection of rubella virus for the purpose of molecular surveillance and case confirmation, with the added benefit of improved efficiency due to multiplexing.
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Affiliation(s)
- Min-Hsin Chen
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
| | - Emily Abernathy
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Joseph P Icenogle
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Ludmila M Perelygina
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
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Ludowyke N, Phumiphanjarphak W, Apiwattanakul N, Manopwisedjaroen S, Pakakasama S, Sensorn I, Pasomsub E, Chantratita W, Hongeng S, Aiewsakun P, Thitithanyanont A. Target Enrichment Metagenomics Reveals Human Pegivirus-1 in Pediatric Hematopoietic Stem Cell Transplantation Recipients. Viruses 2022; 14:v14040796. [PMID: 35458526 PMCID: PMC9025367 DOI: 10.3390/v14040796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 11/17/2022] Open
Abstract
Human pegivirus-1 (HPgV-1) is a lymphotropic human virus, typically considered nonpathogenic, but its infection can sometimes cause persistent viremia both in immunocompetent and immunosuppressed individuals. In a viral discovery research program in hematopoietic stem cell transplant (HSCT) pediatric patients, HPgV-1 was detected in 3 out of 14 patients (21.4%) using a target enrichment next-generation sequencing method, and the presence of the viruses was confirmed by agent-specific qRT-PCR assays. For the first time in this patient cohort, complete genomes of HPgV-1 were acquired and characterized. Phylogenetic analyses indicated that two patients had HPgV-1 genotype 2 and one had HPgV-1 genotype 3. Intra-host genomic variations were described and discussed. Our results highlight the necessity to screen HSCT patients and blood and stem cell donors to reduce the potential risk of HPgV-1 transmission.
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Affiliation(s)
- Natali Ludowyke
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (N.L.); (W.P.); (S.M.)
| | - Worakorn Phumiphanjarphak
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (N.L.); (W.P.); (S.M.)
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Nopporn Apiwattanakul
- Department of Pediatrics, Division of Hematology and Oncology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.A.); (S.P.); (S.H.)
| | - Suwimon Manopwisedjaroen
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (N.L.); (W.P.); (S.M.)
| | - Samart Pakakasama
- Department of Pediatrics, Division of Hematology and Oncology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.A.); (S.P.); (S.H.)
| | - Insee Sensorn
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (I.S.); (W.C.)
| | - Ekawat Pasomsub
- Virology and Molecular Microbiology Unit, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (I.S.); (W.C.)
| | - Suradej Hongeng
- Department of Pediatrics, Division of Hematology and Oncology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.A.); (S.P.); (S.H.)
| | - Pakorn Aiewsakun
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (N.L.); (W.P.); (S.M.)
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Correspondence: (P.A.); (A.T.); Tel.: +66-22015676 (P.A.); +66-22015528 (A.T.)
| | - Arunee Thitithanyanont
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (N.L.); (W.P.); (S.M.)
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Correspondence: (P.A.); (A.T.); Tel.: +66-22015676 (P.A.); +66-22015528 (A.T.)
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Pradier A, Cordey S, Zanella MC, Melotti A, Wang S, Mamez AC, Chalandon Y, Masouridi-Levrat S, Kaiser L, Simonetta F, Vu DL. Human pegivirus-1 replication influences NK cell reconstitution after allogeneic haematopoietic stem cell transplantation. Front Immunol 2022; 13:1060886. [PMID: 36713419 PMCID: PMC9876574 DOI: 10.3389/fimmu.2022.1060886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/15/2022] [Indexed: 01/12/2023] Open
Abstract
Introduction Human pegivirus-1 (HPgV-1) is a so-called commensal virus for which no known associated organ disease has been found to date. Yet, it affects immune-reconstitution as previously studied in the HIV population, in whom active co-infection with HPgV-1 can modulate T and NK cell activation and differentiation leading to a protective effect against the evolution of the disease. Little is known on the effect of HPgV-1 on immune-reconstitution in allogeneic hematopoietic stem cell transplant (allo-HSCT) recipients, a patient population in which we and others have previously reported high prevalence of HPgV-1 replication. The aim of this study was to compare the immune reconstitution after allo-HSCT among HPgV-1-viremic and HPgV-1-non-viremic patients. Methods Within a cohort study of 40 allo-HSCT patients, 20 allo-HSCT recipients positive in plasma sample for HPgV-1 by rRT-PCR during the first year (1, 3, 6, 12 months) after transplantation were matched with 20 allo-HSCT recipients negative for HPgV-1. T and NK cell reconstitution was monitored by flow cytometry in peripheral blood samples from allo-HSCT recipients at the same time points. Results We observed no significant difference in the absolute number and subsets proportions of CD4 and CD8 T cells between patient groups at any analysed timepoint. We observed a significantly higher absolute number of NK cells at 3 months among HPgV-1-viremic patients. Immunophenotypic analysis showed a significantly higher proportion of CD56bright NK cells mirrored by a reduced percentage of CD56dim NK cells in HPgV-1-positive patients during the first 6 months after allo-HSCT. At 6 months post-allo-HSCT, NK cell phenotype significantly differed depending on HPgV-1, HPgV-1-viremic patients displaying NK cells with lower CD16 and CD57 expression compared with HPgV-1-negative patients. In accordance with their less differentiated phenotype, we detected a significantly reduced expression of granzyme B in NK cells in HPgV-1-viremic patients at 6 months. Discussion Our study shows that HPgV-1-viremic allo-HSCT recipients displayed an impaired NK cell, but not T cell, immune-reconstitution compared with HPgV-1-non-viremic patients, revealing for the first time a potential association between replication of the non-pathogenic HPgV-1 virus and immunomodulation after allo-HSCT.
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Affiliation(s)
- Amandine Pradier
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Haematology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine and Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Samuel Cordey
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Laboratory of virology, Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Marie-Céline Zanella
- Laboratory of virology, Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
- Division of Infectious diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Astrid Melotti
- Translational Research Center for Oncohematology, Department of Medicine and Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Sisi Wang
- Translational Research Center for Oncohematology, Department of Medicine and Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Anne-Claire Mamez
- Division of Haematology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
| | - Yves Chalandon
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Haematology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine and Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Laurent Kaiser
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Laboratory of virology, Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
- Division of Infectious diseases, Geneva University Hospitals, Geneva, Switzerland
- Center for emerging viruses, Geneva University Hospitals, Geneva, Switzerland
| | - Federico Simonetta
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Haematology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine and Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Diem-Lan Vu
- Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Laboratory of virology, Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
- Division of Infectious diseases, Geneva University Hospitals, Geneva, Switzerland
- *Correspondence: Diem-Lan Vu, ;
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Zhang B, Zhou J, Gui R, Li Z, Zu Y, Wang J, Yu F, Zhang Y, Zhao H, Ji Z, Song Y. Metagenomic Next Generation Sequencing in the Detection of Pathogens in Cerebrospinal Fluid of Patients After Alternative Donor Transplantation: A Feasibility Analysis. Front Cell Infect Microbiol 2021; 11:720132. [PMID: 34595132 PMCID: PMC8476959 DOI: 10.3389/fcimb.2021.720132] [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: 06/03/2021] [Accepted: 08/20/2021] [Indexed: 11/19/2022] Open
Abstract
Central nervous system (CNS) complications can occur in 9%–15% of patients after allogeneic hematopoietic stem cell transplantation (allo-HSCT). The clinical manifestations of the CNS complications are non-specific, with most of them being disturbances of consciousness, convulsions, headaches, fever, and epilepsy, making it difficult to infer the cause of the complications based on clinical manifestations. We retrospectively analyzed the sensitivity and feasibility of metagenomic next generation sequencing (mNGS) in the diagnosis of CNS infections after allo-HSCT. Lumbar punctures were performed on 20 patients with CNS symptoms after receiving alternative donor HSCT(AD-HSCT) at the Affiliated Cancer Hospital of Zhengzhou University from February 2019 to December 2020, and their cerebrospinal fluid (CSF) was collected. The mNGS technique was used to detect pathogens in the CSF. Routine CSF testing, biochemical analyses, G experiments, GM experiments, ink staining, acid-fast staining, and bacterial cultures were carried out, and quantitative PCR (qPCR) tests were used to detect cytomegalovirus (CMV), Epstein-Barr virus (EBV), BK polyomavirus (BKPyV), and human alphaherpesvirus (HHV). A total of 29 tests were performed with 21 of them being positive. Of the five negative patients, three were diagnosed with a posterior reversible encephalopathy syndrome, one as having transplantation-associated thrombotic microangiopathy, and one with transient seizure caused by hypertension. Fifteen patients tested positive, of which four had single infections and eleven had mixed infections. Five cases of fungal infections, six cases of bacterial infections, and 13 cases of viral infections were detected. Among the 13 cases of viral infections, ten cases were CMV(HHV-5); three were BKPyV; two were Torque teno virus (TTV); Two were HHV-1,two were EBV(HHV4), and one each of HpyV5 and HHV-6B. Thirteen patients tested positive for virus while the qPCR detection method of 6 identical specimens were below the minimum detection limit(<1×103 U/ml). The mNGS technique is highly sensitive, and it can be used to diagnose CNS infections after allo-HSCT.
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Affiliation(s)
- Binglei Zhang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China.,Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China.,Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jian Zhou
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Ruirui Gui
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Zhen Li
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Yingling Zu
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Juan Wang
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Fengkuan Yu
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Yanli Zhang
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Huifang Zhao
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Zhenyu Ji
- Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yongping Song
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
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Investigation of Bufavirus and Parvovirus 4 in Patients with Gastro-Enteritis from the South-East of France. Pathogens 2021; 10:pathogens10091151. [PMID: 34578183 PMCID: PMC8472301 DOI: 10.3390/pathogens10091151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/30/2021] [Accepted: 09/04/2021] [Indexed: 11/30/2022] Open
Abstract
Bufavirus (BuV) and human parvovirus 4 (PARV4) belong to the Parvoviridae family. We assessed BuV and PARV4 DNA presence by real-time PCR analysis in stool, blood and respiratory samples collected in patients from Marseille and Nice, two large cities in the South-East of France. Bu-V DNA was detected in diarrheic stool samples from 92 patients (3.6% of 2583 patients), particularly men and adults, and patients from the nephrology and the infectious disease departments. Among the patients with a BuV-positive stool sample and for whom at least one blood sample was available (n = 30 patients), BuV DNA was detected also in 3 blood samples. In contrast, BuV DNA was not detected in any of the respiratory samples from 23 patients with BuV-positive stool. BuV detection rate was comparable in stool samples from patients with and without diarrhea. We did not detect PARV4 DNA in any of the stool specimens (n = 2583 patients). Our results suggest that PARV4 fecal–oral transmission is rare or non-existent in the South-East of France while BuV circulates with a relatively high rate in this area.
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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: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [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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Mohanraj U, Jokinen M, Thapa RR, Paloniemi M, Vesikari T, Lappalainen M, Tarkka E, Nora-Krūkle Z, Vilmane A, Vettenranta K, Mangani C, Oikarinen S, Fan YM, Ashorn P, Väisänen E, Söderlund-Venermo M. Human Protoparvovirus DNA and IgG in Children and Adults with and without Respiratory or Gastrointestinal Infections. Viruses 2021; 13:v13030483. [PMID: 33804173 PMCID: PMC7999311 DOI: 10.3390/v13030483] [Citation(s) in RCA: 9] [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: 02/22/2021] [Revised: 03/05/2021] [Accepted: 03/12/2021] [Indexed: 01/14/2023] Open
Abstract
Three human protoparvoviruses, bufavirus (BuV), tusavirus (TuV) and cutavirus (CuV), have recently been discovered in diarrheal stool. BuV has been associated with diarrhea and CuV with cutaneous T-cell lymphoma, but there are hardly any data for TuV or CuV in stool or respiratory samples. Hence, using qPCR and IgG enzyme immunoassays, we analyzed 1072 stool, 316 respiratory and 445 serum or plasma samples from 1098 patients with and without gastroenteritis (GE) or respiratory-tract infections (RTI) from Finland, Latvia and Malawi. The overall CuV-DNA prevalences in stool samples ranged between 0-6.1% among our six patient cohorts. In Finland, CuV DNA was significantly more prevalent in GE patients above rather than below 60 years of age (5.1% vs 0.2%). CuV DNA was more prevalent in stools among Latvian and Malawian children compared with Finnish children. In 10/11 CuV DNA-positive adults and 4/6 CuV DNA-positive children with GE, no known causal pathogens were detected. Interestingly, for the first time, CuV DNA was observed in two nasopharyngeal aspirates from children with RTI and the rare TuV in diarrheal stools of two adults. Our results provide new insights on the occurrence of human protoparvoviruses in GE and RTI in different countries.
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Affiliation(s)
- Ushanandini Mohanraj
- Department of Virology, University of Helsinki, 00290 Helsinki, Finland; (M.J.); (R.R.T.); (E.V.); (M.S.-V.)
- Correspondence: ; Tel.: +358-469505437
| | - Maija Jokinen
- Department of Virology, University of Helsinki, 00290 Helsinki, Finland; (M.J.); (R.R.T.); (E.V.); (M.S.-V.)
| | - Rajita Rayamajhi Thapa
- Department of Virology, University of Helsinki, 00290 Helsinki, Finland; (M.J.); (R.R.T.); (E.V.); (M.S.-V.)
| | - Minna Paloniemi
- Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland; (M.P.); (S.O.); (Y.-M.F.); (P.A.)
| | | | - Maija Lappalainen
- Helsinki University Hospital Laboratory (HUSLAB), 00290 Helsinki, Finland; (M.L.); (E.T.)
| | - Eveliina Tarkka
- Helsinki University Hospital Laboratory (HUSLAB), 00290 Helsinki, Finland; (M.L.); (E.T.)
| | - Zaiga Nora-Krūkle
- Institute of Microbiology and Virology, Rīga Stradiņš University, 1067 Riga, Latvia; (Z.N.-K.); (A.V.)
| | - Anda Vilmane
- Institute of Microbiology and Virology, Rīga Stradiņš University, 1067 Riga, Latvia; (Z.N.-K.); (A.V.)
| | | | - Charles Mangani
- College of Medicine, University of Malawi, Blantyre 3, Malawi;
| | - Sami Oikarinen
- Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland; (M.P.); (S.O.); (Y.-M.F.); (P.A.)
| | - Yue-Mei Fan
- Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland; (M.P.); (S.O.); (Y.-M.F.); (P.A.)
| | - Per Ashorn
- Faculty of Medicine and Health Technology, Tampere University, 33100 Tampere, Finland; (M.P.); (S.O.); (Y.-M.F.); (P.A.)
| | - Elina Väisänen
- Department of Virology, University of Helsinki, 00290 Helsinki, Finland; (M.J.); (R.R.T.); (E.V.); (M.S.-V.)
| | - Maria Söderlund-Venermo
- Department of Virology, University of Helsinki, 00290 Helsinki, Finland; (M.J.); (R.R.T.); (E.V.); (M.S.-V.)
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