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Tang Y, Wang Z, Du D. Challenges and opportunities in research on BK virus infection after renal transplantation. Int Immunopharmacol 2024; 141:112793. [PMID: 39146777 DOI: 10.1016/j.intimp.2024.112793] [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: 04/15/2024] [Revised: 06/26/2024] [Accepted: 07/23/2024] [Indexed: 08/17/2024]
Abstract
Renal transplantation is one of the primary approaches for curing end-stage kidney disease. With advancements in immunosuppressive agents, the short-term and long-term survival rates of transplanted kidneys have significantly improved. However, infections associated with potent immunosuppression have remained a persistent challenge. Among them, BK virus (BKV) reactivation following renal transplantation leading to BK virus-associated nephropathy (BKVAN) is a major cause of graft dysfunction. However, we still face significant challenges in understanding the pathogenesis, prevention, diagnosis, and treatment of BKVAN. These challenges include: 1. The mechanism of BKV reactivation under immunosuppressive conditions has not been well elucidated, leading to difficulties in breakthroughs in clinical research on prevention, diagnosis, and treatment. 2. Lack of proper identification of high-risk individuals, and effective personalized clinical management strategies. 3.Lack of early and sensitive diagnostic markers. 4. Lack of direct and effective treatment options due to the absence of specific antiviral drugs. The purpose of this review is to summarize the current status and cutting-edge advancements in BKV-related research, providing new methods and perspectives to address future research challenges.
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Affiliation(s)
- Yukun Tang
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Key Laboratory of Organ Transplantation, Ministry of Education, NHC Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Zipei Wang
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Key Laboratory of Organ Transplantation, Ministry of Education, NHC Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Dunfeng Du
- Institute of Organ Transplantation, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Key Laboratory of Organ Transplantation, Ministry of Education, NHC Key Laboratory of Organ Transplantation, Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China.
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2
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Chokshi SM, Odegard EA, Meeds HL, Kleiboeker SB, Ziady A, Sabulski A, Jodele S, Seif AE, Davies SM, Laskin BL, Blackard JT. Uncommon BK polyomaviruses detected in allogeneic hematopoietic cell transplant recipients. Microbiol Resour Announc 2024; 13:e0000524. [PMID: 38647278 PMCID: PMC11237613 DOI: 10.1128/mra.00005-24] [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: 01/02/2024] [Accepted: 04/04/2024] [Indexed: 04/25/2024] Open
Abstract
The role of viral diversity in the pathogenesis of BK polyomavirus (BKPyV)-associated disease is poorly understood. Here, we report near full-length BKPyV genome sequences from two allogeneic hematopoietic cell transplant recipients infected with BKPyV genotype II, which is uncommon in the USA.
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Affiliation(s)
- Saagar M. Chokshi
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Elizabeth A. Odegard
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Heidi L. Meeds
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | | | - Assem Ziady
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Anthony Sabulski
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Sonata Jodele
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Alix E. Seif
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Stella M. Davies
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Benjamin L. Laskin
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Division of Nephrology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jason T. Blackard
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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3
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Smith MF, Maqsood R, Sullins RA, Driver EM, Halden RU, Lim ES. Seasonality of respiratory, enteric, and urinary viruses revealed by wastewater genomic surveillance. mSphere 2024; 9:e0010524. [PMID: 38712930 PMCID: PMC11237574 DOI: 10.1128/msphere.00105-24] [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: 02/08/2024] [Accepted: 04/05/2024] [Indexed: 05/08/2024] Open
Abstract
Wastewater surveillance can reveal population-level infectious disease burden and emergent public health threats can be reliably assessed through wastewater surveillance. While molecular methods for wastewater monitoring of microorganisms have traditionally relied on PCR-based approaches, next-generation sequencing (NGS) can provide deeper insights via genomic analyses of multiple diverse pathogens. We conducted a year-long sequencing surveillance of 1,408 composite wastewater samples collected from 12 neighborhood-level access points in the greater Tempe area, Arizona, USA, and show that variation in wastewater viruses is driven by seasonal time and location. The temporal dynamics of viruses in wastewater were influenced cyclically, with the most dissimilarity between samples 23 weeks apart (i.e., winter vs summer, spring vs fall). We identified diverse urinary and enteric viruses including polyomaviruses, astroviruses, and noroviruses, and showed that their genotypes/subtypes shifted across seasons. We show that while wastewater data of certain respiratory viruses like severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strongly correlate with clinical case rates, laboratory-reported case incidences were discordant with surges of high viral load in wastewater for other viruses like human coronavirus 229E. These results demonstrate the utility of wastewater sequencing for informing decision-making in public health.IMPORTANCEWastewater surveillance can provide insights into the spread of pathogens in communities. Advances in next-generation sequencing (NGS) methodologies allow for more precise detection of viruses in wastewater. Long-term wastewater surveillance of viruses is an important tool for public health preparedness. This system can act as a public health observatory that gives real-time early warning for infectious disease outbreaks and improved response times.
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Affiliation(s)
- Matthew F Smith
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Rabia Maqsood
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Regan A Sullins
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Erin M Driver
- Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Rolf U Halden
- Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Efrem S Lim
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- National Centre for Infectious Diseases, Singapore, Singapore
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4
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Aubry A, Demey B, Castelain S, Helle F, Brochot E. The value and complexity of studying cellular immunity against BK Polyomavirus in kidney transplant recipients. J Clin Virol 2024; 171:105656. [PMID: 38412681 DOI: 10.1016/j.jcv.2024.105656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/09/2024] [Accepted: 02/16/2024] [Indexed: 02/29/2024]
Abstract
BK Polyomavirus is of particular concern for kidney transplant recipients, due to their immunosuppression. This problem is exacerbated by the high effectiveness of antirejection therapies, which also compromise the organism's ability to fight viral infections. The long-term risk is loss of graft function through BKPyV-associated nephropathy (BKPyVAN). The assessment of host immunity and its link to the control of viral infections is a major challenge. In terms of humoral immunity, researchers have highlighted the prognostic value of the pre-transplantation anti-BKPyV immunoglobulin G titer. However, humoral immunity alone does not guarantee viral clearance, and the correlation between the humoral response and the time course of the infection remains weak. In contrast, cellular immunity variables appear to be more closely associated with viral clearance, given that the cellular immune response to the kidney transplant is the main target of immunosuppressive treatments in recipients. However, the assessment of the cellular immune response to BK Polyomavirus is complex, and many details still need to be characterized. Here, we review the current state of knowledge about BKPyV cellular immunity, as well as the difficulties that may be encountered in studying it in kidney transplant recipient. This is an essential area of research for optimizing the management of transplant recipients and minimizing the risks associated with insidious BKPyV disease.
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Affiliation(s)
- Aurélien Aubry
- Department of Virology, Amiens University Medical Center, Amiens, France; Agents infectieux résistance et chimiothérapie Research Unit, UR4294, Jules Verne University of Picardie, Amiens, France
| | - Baptiste Demey
- Department of Virology, Amiens University Medical Center, Amiens, France; Agents infectieux résistance et chimiothérapie Research Unit, UR4294, Jules Verne University of Picardie, Amiens, France
| | - Sandrine Castelain
- Department of Virology, Amiens University Medical Center, Amiens, France; Agents infectieux résistance et chimiothérapie Research Unit, UR4294, Jules Verne University of Picardie, Amiens, France
| | - François Helle
- Agents infectieux résistance et chimiothérapie Research Unit, UR4294, Jules Verne University of Picardie, Amiens, France
| | - Etienne Brochot
- Department of Virology, Amiens University Medical Center, Amiens, France; Agents infectieux résistance et chimiothérapie Research Unit, UR4294, Jules Verne University of Picardie, Amiens, France.
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5
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Bezerra KC, Vieira CMAG, de Oliveira-Filho EF, Reis CRS, Oriá RB. Susceptibility of solid organ transplant recipients to viral pathogens with zoonotic potential: A mini-review. Braz J Infect Dis 2024; 28:103742. [PMID: 38670166 PMCID: PMC11078645 DOI: 10.1016/j.bjid.2024.103742] [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: 11/30/2023] [Revised: 02/28/2024] [Accepted: 04/14/2024] [Indexed: 04/28/2024] Open
Abstract
A substantial number of zoonotic diseases are caused by viral pathogens, representing a significant menace to public health, particularly to susceptible populations, such as pregnant women, the elderly, and immunocompromised individuals. Individuals who have undergone solid organ transplantation frequently experience immunosuppression, to prevent organ rejection, and, thus are more prone to opportunistic infections. Furthermore, the reactivation of dormant viruses can threaten transplant recipients and organ viability. This mini-review examines the up-to-date literature covering potential zoonotic and organ rejection-relevant viruses in solid organ transplant recipients. A comprehensive list of viruses with zoonotic potential is highlighted and the most important clinical outcomes in patients undergoing transplantation are described. Moreover, this mini-review calls attention to complex multifactorial events predisposing viral coinfections and the need for continuous health surveillance and research to understand better viral pathogens' transmission and pathophysiology dynamics in transplanted individuals.
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Affiliation(s)
- Karine C Bezerra
- Universidade Federal do Ceará, Faculdade de Medicina, Laboratório da Biologia da Cicatrização, Ontogenia e Nutrição de Tecidos, Fortaleza, CE, Brazil
| | - Carlos Meton A G Vieira
- Universidade Federal do Ceará, Faculdade de Medicina, Laboratório da Biologia da Cicatrização, Ontogenia e Nutrição de Tecidos, Fortaleza, CE, Brazil
| | | | - Christian Robson S Reis
- Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Departamento de Microbiologia, Recife, PE, Brazil
| | - Reinaldo B Oriá
- Universidade Federal do Ceará, Faculdade de Medicina, Laboratório da Biologia da Cicatrização, Ontogenia e Nutrição de Tecidos, Fortaleza, CE, Brazil.
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Shokoofeh M, Malekshahi SS, Soltanghoraee H. The molecular footprints of BK virus in the product of conception over the second and third gestational trimesters. BMC Res Notes 2023; 16:367. [PMID: 38082354 PMCID: PMC10714513 DOI: 10.1186/s13104-023-06643-1] [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: 03/07/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
OBJECTIVE Prior studies have shown controversial results on the vertical transmission of BK virus (BKV). The present study aimed to assess the possibility of BKV vertical transmission from mother to fetus in the product of conception (embryo, fetuses, and/or placentas) over the three stages of pregnancy. RESULTS Of the 26 placental studied tissues, 6 were in the first trimester, and none of which were positive. Only one out of the 13 (7.7%) placental materials in the second trimester was positive. Only one out of 7 (14%) placental materials of the third trimester was positive. There were cases that no virus was detected in their placental but BKV was detected in their other tissues. Among 26 conceptuses, 17 (65%) were negative for BKV and 9 (34.6%) were positive, 7/13 (54%) were positive in the second, and 2/7 (29%) were positive in the third trimester fetuses. BKV was most frequently detected in the liver (eight cases), heart (three cases), and placenta (2 cases). There were cases that no virus was detected in their placental but BKV was detected in their other tissues.
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Affiliation(s)
- Mona Shokoofeh
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Haleh Soltanghoraee
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
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7
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Odegard EA, Meeds HL, Kleiboeker SB, Ziady A, Sabulski A, Jodele S, Seif AE, Davies SM, Laskin BL, Blackard JT. BK Polyomavirus Diversity After Hematopoietic Stem Cell Transplantation. J Infect Dis 2023; 228:1208-1218. [PMID: 37165301 PMCID: PMC10629712 DOI: 10.1093/infdis/jiad117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 04/21/2023] [Indexed: 05/12/2023] Open
Abstract
BK polyomavirus (BKPyV) infection is common after hematopoietic stem cell transplantation (HSCT) and is associated with the development of hemorrhagic cystitis (HC). The role that BKPyV plays in the pathogenesis of HC is not well characterized. We investigated the impact of BKPyV diversity on the development of HC using a previously established cohort of pediatric HSCT patients. There were 147 urine samples with quantifiable BKPyV at month 1 after HSCT; 137 (93.2%) were amplified using our in-house polymerase chain reaction approach and sent for next-generation sequencing. Subtype Ia was most frequent (61.3%), followed by subtype Ib1 (31.4%). The median viral load of subtype Ia samples was higher than for subtype Ib1 at month 1. Across the protein coding regions, APOBEC-induced mutations and signature patterns associated with HC were identified. This is the largest sequencing study of a single cohort of HSCT patients, providing a vast resource of sequence data for future analyses.
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Affiliation(s)
- Elizabeth A Odegard
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Ohio
| | - Heidi L Meeds
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Ohio
| | | | - Assem Ziady
- Department of Pediatrics, University of Cincinnati College of Medicine, Ohio
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Ohio
| | - Anthony Sabulski
- Department of Pediatrics, University of Cincinnati College of Medicine, Ohio
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Ohio
| | - Sonata Jodele
- Department of Pediatrics, University of Cincinnati College of Medicine, Ohio
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Ohio
| | - Alix E Seif
- Perelman School of Medicine, University of Pennsylvania, Pennsylvania
- Division of Oncology, The Children's Hospital of Philadelphia, Pennsylvania
| | - Stella M Davies
- Department of Pediatrics, University of Cincinnati College of Medicine, Ohio
- Division of Bone Marrow Transplantation and Immune Deficiency, Cincinnati Children's Hospital Medical Center, Ohio
| | - Benjamin L Laskin
- Perelman School of Medicine, University of Pennsylvania, Pennsylvania
- Division of Nephrology, The Children's Hospital of Philadelphia, Pennsylvania
| | - Jason T Blackard
- Division of Digestive Diseases, University of Cincinnati College of Medicine, Ohio
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Zhou X, Zhu C, Li H. BK polyomavirus: latency, reactivation, diseases and tumorigenesis. Front Cell Infect Microbiol 2023; 13:1263983. [PMID: 37771695 PMCID: PMC10525381 DOI: 10.3389/fcimb.2023.1263983] [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: 07/20/2023] [Accepted: 08/29/2023] [Indexed: 09/30/2023] Open
Abstract
The identification of the first human polyomavirus BK (BKV) has been over half century, The previous epidemiological and phylogenetic studies suggest that BKV prevailed and co-evolved with humans, leading to high seroprevalence all over the world. In general, BKV stays latent and symptomless reactivation in healthy individuals. BKV has been mainly interlinked with BKV-associated nephropathy (BKVAN) in kidney-transplant recipients and hemorrhagic cystitis (HC) in hematopoietic stem cell transplant recipients (HSCTRs). However, the mechanisms underlying BKV latency and reactivation are not fully understood and lack of extensive debate. As Merkel cell polyomavirus (MCV) was identified as a pathogenic agent of malignant cutaneous cancer Merkel cell carcinoma (MCC) since 2008, linking BKV to tumorigenesis of urologic tumors raised concerns in the scientific community. In this review, we mainly focus on advances of mechanisms of BKV latency and reactivation, and BKV-associated diseases or tumorigenesis with systematical review of formerly published papers following the PRISMA guidelines. The potential tumorigenesis of BKV in two major types of cancers, head and neck cancer and urologic cancer, was systematically updated and discussed in depth. Besides, BKV may also play an infectious role contributing to HIV-associated salivary gland disease (HIVSGD) presentation. As more evidence indicates the key role of BKV in potential tumorigenesis, it is important to pay more attention on its etiology and pathogenicity in vitro and in vivo.
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Affiliation(s)
- Xianfeng Zhou
- Cancer Research Center, Jiangxi University of Chinese Medicine, Nanchang, China
- Jiangxi Engineering Research Center for Translational Cancer Technology, Nanchang, China
- Jiangxi Provincial Health Commission Key Laboratory of Pathogenic Diagnosis and Genomics of Emerging Infectious Diseases, Nanchang Center for Disease Control and Prevention, Nanchang, China
| | - Chunlong Zhu
- Clinical Laboratory, Third Hospital of Nanchang, Nanchang, China
| | - Hui Li
- Jiangxi Provincial Health Commission Key Laboratory of Pathogenic Diagnosis and Genomics of Emerging Infectious Diseases, Nanchang Center for Disease Control and Prevention, Nanchang, China
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Rogers A, Pryce TM, Chakera A, Boan P. BK virus subtype correlation with viral loads in Western Australia. Pathology 2022; 54:968-971. [PMID: 35570026 DOI: 10.1016/j.pathol.2022.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 01/13/2022] [Accepted: 01/30/2022] [Indexed: 12/14/2022]
Affiliation(s)
- Alan Rogers
- Microbiology Department, Fiona Stanley Hospital, PathWest Laboratory Medicine WA, Murdoch, WA, Australia
| | - Todd M Pryce
- Microbiology Department, Fiona Stanley Hospital, PathWest Laboratory Medicine WA, Murdoch, WA, Australia
| | - Aron Chakera
- Department of Nephrology, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | - Peter Boan
- Microbiology Department, Fiona Stanley Hospital, PathWest Laboratory Medicine WA, Murdoch, WA, Australia; Department of Infectious Diseases, Fiona Stanley Hospital, Murdoch, WA, Australia.
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10
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Fan Y, Guo D, Zhao S, Wei Q, Li Y, Lin T. Human genes with relative synonymous codon usage analogous to that of polyomaviruses are involved in the mechanism of polyomavirus nephropathy. Front Cell Infect Microbiol 2022; 12:992201. [PMID: 36159639 PMCID: PMC9492876 DOI: 10.3389/fcimb.2022.992201] [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: 07/12/2022] [Accepted: 08/12/2022] [Indexed: 11/28/2022] Open
Abstract
Human polyomaviruses (HPyVs) can cause serious and deleterious infections in human. Yet, the molecular mechanism underlying these infections, particularly in polyomavirus nephropathy (PVAN), is not well-defined. In the present study, we aimed to identify human genes with codon usage bias (CUB) similar to that of HPyV genes and explore their potential involvement in the pathogenesis of PVAN. The relative synonymous codon usage (RSCU) values of genes of HPyVs and those of human genes were computed and used for Pearson correlation analysis. The involvement of the identified correlation genes in PVAN was analyzed by validating their differential expression in publicly available transcriptomics data. Functional enrichment was performed to uncover the role of sets of genes. The RSCU analysis indicated that the A- and T-ending codons are preferentially used in HPyV genes. In total, 5400 human genes were correlated to the HPyV genes. The protein-protein interaction (PPI) network indicated strong interactions between these proteins. Gene expression analysis indicated that 229 of these genes were consistently and differentially expressed between normal kidney tissues and kidney tissues from PVAN patients. Functional enrichment analysis indicated that these genes were involved in biological processes related to transcription and in pathways related to protein ubiquitination pathway, apoptosis, cellular response to stress, inflammation and immune system. The identified genes may serve as diagnostic biomarkers and potential therapeutic targets for HPyV associated diseases, especially PVAN.
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Affiliation(s)
- Yu Fan
- Department of Urology, National Clinical Research Center for Geriatrics and Organ Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
| | - Duan Guo
- Department of Palliative Medicine, West China School of Public Health and West China fourth Hospital, Sichuan University, Chengdu, China
- Palliative Medicine Research Center, West China−Peking Union Medical College, Chen Zhiqian (PUMC C.C). Chen Institute of Health, Sichuan University, Chengdu, China
| | - Shangping Zhao
- Department of Urology, West China School of Nursing and Organ Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
| | - Qiang Wei
- Department of Urology, National Clinical Research Center for Geriatrics and Organ Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
| | - Yi Li
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Tao Lin, ; ; Yi Li,
| | - Tao Lin
- Department of Urology, National Clinical Research Center for Geriatrics and Organ Transplantation Center, West China Hospital of Sichuan University, Chengdu, China
- *Correspondence: Tao Lin, ; ; Yi Li,
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11
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Yuan H, Chen G, Xu J, Yang R, Muhashi M, Aizezi G, Jiang M. Incidence of late-onset hemorrhagic cystitis and its effect on PFS in acute leukemia patients after haplo-PBSCT: The 5-year single-center data. Front Oncol 2022; 12:913802. [PMID: 35912244 PMCID: PMC9334683 DOI: 10.3389/fonc.2022.913802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/28/2022] [Indexed: 12/02/2022] Open
Abstract
We conducted a single-center 5-year retrospective study on the occurrence of hemorrhagic cystitis (HC) and its effect on survival after haploid high-dose peripheral blood stem cell transplantation (haplo-PBSCT) in patients with acute leukemia. We retrospectively analyzed 153 patients with acute leukemia who were treated with non-in vitro T-cell depleted haplo-PBSCT and myeloablative conditioning regimen. All patients were followed up for more than 180 days after transplantation. HC occurrence and its effect on long-term progression free survival (PFS) were retrospectively analyzed. Totally, 64 out of 153 patients had late onset HC (LOHC). No early onset HC occurred. The median onset time was 38.5 (17-163) days after transplantation. The cumulative incidence of LOHC was 41.8%. The cumulative incidence of LOHC in patients under 27 years old (50.0%) and in ALL patients (54.1%) was significantly higher than that in patients over 27 years old (34.5%) and in AML patients (36.9%), respectively. The cumulative incidence of mild LOHC was 44.2% and that of severe LOHC was 28.6%. However, urine copies of BK virus were not related to LOHC duration. There was no significant difference in 3-year expected PFS between AML and ALL patients with and without LOHC, or between LOHC duration more than and less than 38.5 days (P>0.05). Conclusively, LOHC incidence is higher in patients under 27 years old and in ALL patients. LOHC occurrence is related to urine BK virus copy, but not blood BK virus load. LOHC duration and severity has no significant effect on PFS.
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12
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Kamminga S, Sidorov IA, Tadesse M, van der Meijden E, de Brouwer C, Zaaijer HL, Feltkamp MC, Gorbalenya AE. Translating genomic exploration of the family Polyomaviridae into confident human polyomavirus detection. iScience 2022; 25:103613. [PMID: 35036862 PMCID: PMC8749223 DOI: 10.1016/j.isci.2021.103613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/27/2021] [Accepted: 12/09/2021] [Indexed: 12/26/2022] Open
Abstract
The Polyomaviridae is a family of ubiquitous dsDNA viruses that establish persistent infection early in life. Screening for human polyomaviruses (HPyVs), which comprise 14 diverse species, relies upon species-specific qPCRs whose validity may be challenged by accelerating genomic exploration of the virosphere. Using this reasoning, we tested 64 published HPyV qPCR assays in silico against the 1781 PyV genome sequences that were divided in targets and nontargets, based on anticipated species specificity of each qPCR. We identified several cases of problematic qPCR performance that were confirmed in vitro and corrected through using degenerate oligos. Furthermore, our study ranked 8 out of 52 tested BKPyV qPCRs as remaining of consistently high quality in the wake of recent PyV discoveries and showed how sensitivity of most other qPCRs could be rescued by annealing temperature adjustment. This study establishes an efficient framework for ensuring confidence in available HPyV qPCRs in the genomic era.
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Affiliation(s)
- Sergio Kamminga
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Department of Blood-borne Infections, Sanquin Research, 1066 CX Amsterdam, the Netherlands
| | - Igor A. Sidorov
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Michaël Tadesse
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Els van der Meijden
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Caroline de Brouwer
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Hans L. Zaaijer
- Department of Blood-borne Infections, Sanquin Research, 1066 CX Amsterdam, the Netherlands
| | - Mariet C.W. Feltkamp
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Alexander E. Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
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BK Polyomavirus Subtypes II and IV in Hematopoietic Cell Transplant Recipients. Microbiol Resour Announc 2022; 11:e0105321. [PMID: 34989611 PMCID: PMC8759406 DOI: 10.1128/mra.01053-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Symptomatic BK polyomavirus (BKPyV) infections are common and relevant in immunocompromised patients. Here, we present full-length BKPyV genomes from samples from patients who received hematopoietic cell transplants in the United States. These individuals had non-subtype I BKPyV, as determined by amplification, next-generation sequencing, and phylogenetic analysis.
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Myint TM, Chong CHY, Wyld M, Nankivell B, Kable K, Wong G. Polyoma BK Virus in Kidney Transplant Recipients: Screening, Monitoring, and Management. Transplantation 2022; 106:e76-e89. [PMID: 33908382 DOI: 10.1097/tp.0000000000003801] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Polyomavirus BK virus (BKPyV) infection is an important complication of kidney transplantation and allograft failure. The prevalence of viremia is 10%-15%, compared with BK-associated nephropathy (BKPyVAN) at 3%-5%. Given that there are no effective antiviral prophylaxis or treatment strategies for BKPyVAN, active screening to detect BKPyV viremia is recommended, particularly during the early posttransplant period. Immunosuppression reduction to allow viral clearance may avoid progression to severe and irreversible allograft damage. The frequency and duration of screening are highly variable between transplant centers because the evidence is reliant largely on observational data. While the primary treatment goals center on achieving viral clearance through immunosuppression reduction, prevention of subsequent acute rejection, premature graft loss, and return to dialysis remain as major challenges. Treatment strategies for BKPyV infection should be individualized to the recipient's underlying immunological risk and severity of the allograft infection. Efficacy data for adjuvant therapies including intravenous immunoglobulin and cidofovir are sparse. Future well-powered and high-quality randomized controlled trials are needed to inform evidence-based clinical practice for the management of BKPy infection.
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Affiliation(s)
- Thida Maung Myint
- Sydney School of Public Health, University of Sydney, Sydney, NSW, Australia
- Newcastle Transplant Unit, John Hunter Hospital, Newcastle, NSW, Australia
| | - Chanel H Y Chong
- Sydney School of Public Health, University of Sydney, Sydney, NSW, Australia
| | - Melanie Wyld
- Department of Renal Medicine, Centre for Transplant and Renal Research, Westmead Hospital, Westmead, NSW, Australia
| | - Brian Nankivell
- Department of Renal Medicine, Centre for Transplant and Renal Research, Westmead Hospital, Westmead, NSW, Australia
| | - Kathy Kable
- Department of Renal Medicine, Centre for Transplant and Renal Research, Westmead Hospital, Westmead, NSW, Australia
| | - Germaine Wong
- Sydney School of Public Health, University of Sydney, Sydney, NSW, Australia
- Department of Renal Medicine, Centre for Transplant and Renal Research, Westmead Hospital, Westmead, NSW, Australia
- Centre for Kidney Research, The Children's Hospital at Westmead, Westmead, NSW, Australia
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15
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Optimized amplification of BK polyomavirus in urine. J Virol Methods 2021; 299:114319. [PMID: 34627948 DOI: 10.1016/j.jviromet.2021.114319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 11/20/2022]
Abstract
BK polyomavirus (BKPyV) is a ubiquitous pathogen that typically results in asymptomatic infection. However, in immunocompromised individuals, BKPyV viral shedding in the urine can reach 109 copies per mL. These high viral levels within urine provide ideal samples for next-generation sequencing to accurately determine BKPyV genotype and identify mutations associated with pathogenesis. Sequencing data obtained can be further analyzed to better understand and characterize the genetic diversity present in BKPyV. Here, methods are described for the successful extraction of viral DNA from urine and the subsequent amplification methods to prepare a sample for next-generation sequencing.
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Louise Benelli J, Basso RP, Rodrigues MDL, Poester VR, Munhoz LS, Aquino VR, Stevens DA, Xavier MO. Coinfection of disseminated cryptococcosis and BK Virus, a casualty of missed diagnosis during the COVID-19 Pandemic: A case report and review of the literature. Curr Med Mycol 2021; 7:44-49. [PMID: 35528625 PMCID: PMC9006733 DOI: 10.18502/cmm.7.2.7802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/14/2021] [Accepted: 10/17/2021] [Indexed: 11/16/2022] Open
Abstract
Background and Purpose The COVID-19 pandemic resulted in an overload of health services and healthcare professionals. The result is a setback in health promotion and prevention, delays in diagnosis, and deaths from other diseases that are currently receiving inadequate attention. This article illustrates the risk of this negligence. Case report This study aimed to report a case of coinfection of disseminated cryptococcosis and BK virus in a patient without a previous diagnosis of human immunodeficiency virus infection and COVID-19 negative in the context of the COVID-19 pandemic. Despite receiving antifungal therapy, the patient died. Conclusion This fatal case is a warning regarding delay of diagnosis and neglect of other serious illnesses owing to the current pandemic, including fungal diseases and neglected diagnoses.
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Affiliation(s)
- Jéssica Louise Benelli
- Laboratory of Mycology, Faculty of Medicine, Federal University of Rio Grande, Rio Grande (FURG), Brazil
- Postgraduate Program in Health Science, Federal University of Rio Grande (PPGCS-FURG), Rio Grande, Brazil
- Clinical Analysis Laboratory, Dr. Miguel Riet Correa University Hospital, Rio Grande (HU-FURG/EBSERH), Brazil
| | - Rossana Patrícia Basso
- Postgraduate Program in Health Science, Federal University of Rio Grande (PPGCS-FURG), Rio Grande, Brazil
- Specialized Care Service in Infectious Diseases, Dr. Miguel Riet Correa University Hospital, Rio Grande, Brazil
| | - Márcia de Lima Rodrigues
- Specialized Care Service in Infectious Diseases, Dr. Miguel Riet Correa University Hospital, Rio Grande, Brazil
| | - Vanice Rodrigues Poester
- Laboratory of Mycology, Faculty of Medicine, Federal University of Rio Grande, Rio Grande (FURG), Brazil
- Postgraduate Program in Health Science, Federal University of Rio Grande (PPGCS-FURG), Rio Grande, Brazil
| | - Lívia Silveira Munhoz
- Postgraduate Program in Health Science, Federal University of Rio Grande (PPGCS-FURG), Rio Grande, Brazil
| | - Valerio Rodrigues Aquino
- Laboratory Diagnostic Service, Microbiology Unit, Hospital de Clinicas de Porto Alegre, Porto Alegre, Brazil
| | - David A Stevens
- California Institute for Medical Research, San Jose, and Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Melissa Orzechowski Xavier
- Laboratory of Mycology, Faculty of Medicine, Federal University of Rio Grande, Rio Grande (FURG), Brazil
- Postgraduate Program in Health Science, Federal University of Rio Grande (PPGCS-FURG), Rio Grande, Brazil
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Jandial A, Mishra K, Sandal R, Kant Sahu K. Management of BK virus-associated haemorrhagic cystitis in allogeneic stem cell transplant recipients. Ther Adv Infect Dis 2021; 8:2049936121991377. [PMID: 33614030 PMCID: PMC7871057 DOI: 10.1177/2049936121991377] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 01/04/2021] [Indexed: 12/18/2022] Open
Abstract
BK virus (BKV)-related haemorrhagic cystitis (HC) is an important cause of morbidity following allogeneic haematopoietic stem cell transplantation (HSCT). The various risk factors include high-level BKV viruria and/or viremia, myeloablative conditioning, acute graft versus host disease (GVHD), cytomegalovirus viremia, and unrelated or HLA-mismatched donor. The presence of high plasma BK viral load and cytopenias have been implicated as important predictors for protracted disease course. These patients frequently require hospitalisation which may extend for several weeks. Supportive measures in the form of analgesics, intravenous hydration, bladder irrigation, and transfusion support remain the mainstay of management. Various drugs have been used with limited success in this setting. These include antiviral drugs, fluoroquinolones, leflunomide, growth factors, clotting factors, estrogens, and prostaglandins. The role of adoptive cellular immunotherapy has also been explored but lacks clinical validation. The strategies aimed at expediting urothelial repair like hyperbaric oxygen therapy (HBOT), intravesical fibrin glue and platelet-rich plasma (PRP) are emerging. Some patients with severe disease do require surgical intervention to relieve urinary obstruction. The frequent co-occurrence of acute GVHD and CMV disease further complicates the management in such patients. There is an unmet need for effective and evidence-based options for the prevention and management of this disease. Due to lack of robust data supported by randomised trials, the acceptability of the available guidelines to simplify the treatment is expected to be low. Despite the availability of various treatment options, the management of BKV-related HC in day-to-day practice continues to be a challenge. The aim of this article is to put forward an up-to-date review of the preventive and therapeutic strategies for BKV-related HC.
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Affiliation(s)
- Aditya Jandial
- Department of Internal Medicine (Adult Clinical Hematology Division), Postgraduate Institute of Medical Education and Research, Chandigarh (Union Territory), India
| | - Kundan Mishra
- Department of Clinical Hematology and Stem Cell Transplant, Army Hospital (Research & Referral) New Delhi, India
| | - Rajeev Sandal
- Department of Radiotherapy and Oncology, Indira Gandhi Medical College Shimla, Himachal Pradesh, India
| | - Kamal Kant Sahu
- Department of Internal Medicine, Saint Vincent Hospital, Worcester, MA 01608, USA
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BK Polyomavirus Genotypes in Two Patients after Hematopoietic Cell Transplant. Microbiol Resour Announc 2021; 10:10/2/e01122-20. [PMID: 33446585 PMCID: PMC7849698 DOI: 10.1128/mra.01122-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
BK polyomavirus (BKPyV) infection can lead to nephropathy and hemorrhagic cystitis (HC). We evaluated BKPyV genotypes in two individuals after hematopoietic cell transplant (HCT). The first case developed HC and was infected with genotype Ib-2, while the second did not develop HC and was infected with genotype Ia. BK polyomavirus (BKPyV) infection can lead to nephropathy and hemorrhagic cystitis (HC). We evaluated BKPyV genotypes in two individuals after hematopoietic cell transplant (HCT). The first case developed HC and was infected with genotype Ib-2, while the second did not develop HC and was infected with genotype Ia.
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