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Zheng S, Verjans GMGM, Evers A, van den Wittenboer E, Tjhie JHT, Snoeck R, Wiertz EJHJ, Andrei G, van Kampen JJA, Lebbink RJ. CRISPR/Cas9-mediated genome editing of the thymidine kinase gene in a clinical HSV-1 isolate identifies F289S as novel acyclovir-resistant mutation. Antiviral Res 2024:105950. [PMID: 38944159 DOI: 10.1016/j.antiviral.2024.105950] [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: 02/02/2023] [Revised: 06/21/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Herpes simplex virus type 1 (HSV-1) is a neurotropic alphaherpesvirus that establishes a lifelong infection in sensory neurons of infected individuals, accompanied with intermittent reactivation of latent virus causing (a)symptomatic virus shedding. Whereas acyclovir (ACV) is a safe and highly effective antiviral to treat HSV-1 infections, long-term usage can lead to emergence of ACV resistant (ACVR) HSV-1 and subsequently ACV refractory disease. Here, we isolated an HSV-1 strain from a patient with reactivated herpetic eye disease that did not respond to ACV treatment. The isolate carried a novel non-synonymous F289S mutation in the viral UL23 gene encoding the thymidine kinase (TK) protein. Because ACV needs conversion by viral TK and subsequently cellular kinases to inhibit HSV-1 replication, the UL23 gene is commonly mutated in ACVR HSV-1 strains. The potential role of the F289S mutation causing ACVR was investigated using CRISPR/Cas9-mediated HSV-1 genome editing. Reverting the F289S mutation in the original clinical isolate to the wild-type sequence S289F resulted in an ACV-sensitive (ACVS) phenotype, and introduction of the F289S substitution in an ACVS HSV-1 reference strain led to an ACVR phenotype. In summary, we identified a new HSV-1 TK mutation in the eye of a patient with ACV refractory herpetic eye disease, which was identified as the causative ACVR mutation with the aid of CRISPR/Cas9-mediated genome engineering technology. Direct editing of clinical HSV-1 isolates by CRISPR/Cas9 is a powerful strategy to assess whether single residue substitutions are causative to a clinical ACVR phenotype.
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Affiliation(s)
- Shuxuan Zheng
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Anouk Evers
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Jeroen H T Tjhie
- Department of Medical Microbiology and Immunology, Microvida, Tilburg, The Netherlands
| | - Robert Snoeck
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Emmanuel J H J Wiertz
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Graciela Andrei
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | | | - Robert Jan Lebbink
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.
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Alsanea MS, Al-Qahtani AA, Almaghrabi RS, AlAbdulkareem MA, Alahideb BM, Obeid D, Alsuwairi FA, Alhamlan FS. Diagnosis of Human Cytomegalovirus Drug Resistance Mutations in Solid Organ Transplant Recipients-A Review. Diagnostics (Basel) 2024; 14:203. [PMID: 38248079 PMCID: PMC10814084 DOI: 10.3390/diagnostics14020203] [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: 05/02/2023] [Revised: 06/11/2023] [Accepted: 06/21/2023] [Indexed: 01/23/2024] Open
Abstract
Human cytomegalovirus (HCMV) infection may be asymptomatic in healthy individuals but can cause severe complications in immunocompromised patients, including transplant recipients. Breakthrough and drug-resistant HCMV infections in such patients are major concerns. Clinicians are first challenged to accurately diagnose HCMV infection and then to identify the most effective antiviral drug and determine when to initiate therapy, alter drug dosage, or switch medication. This review critically examines HCMV diagnostics approaches, particularly for immunocompromised patients, and the development of genotypic techniques to rapidly diagnose drug resistance mutations. The current standard method to identify prevalent and well-known resistance mutations involves polymerase chain reaction amplification of UL97, UL54, and UL56 gene regions, followed by Sanger sequencing. This method can confirm clinical suspicion of drug resistance as well as determine the level of drug resistance and range of cross-resistance with other drugs. Despite the effectiveness of this approach, there remains an urgent need for more rapid and point-of-care HCMV diagnosis, allowing for timely lifesaving intervention.
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Affiliation(s)
- Madain S. Alsanea
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia; (M.S.A.); (A.A.A.-Q.); (M.A.A.); (B.M.A.); (D.O.); (F.A.A.)
| | - Ahmed A. Al-Qahtani
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia; (M.S.A.); (A.A.A.-Q.); (M.A.A.); (B.M.A.); (D.O.); (F.A.A.)
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Reem S. Almaghrabi
- Organ Transplant Center of Excellence, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia;
| | - Maha A. AlAbdulkareem
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia; (M.S.A.); (A.A.A.-Q.); (M.A.A.); (B.M.A.); (D.O.); (F.A.A.)
| | - Basma M. Alahideb
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia; (M.S.A.); (A.A.A.-Q.); (M.A.A.); (B.M.A.); (D.O.); (F.A.A.)
| | - Dalia Obeid
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia; (M.S.A.); (A.A.A.-Q.); (M.A.A.); (B.M.A.); (D.O.); (F.A.A.)
- Organ Transplant Center of Excellence, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia;
| | - Feda A. Alsuwairi
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia; (M.S.A.); (A.A.A.-Q.); (M.A.A.); (B.M.A.); (D.O.); (F.A.A.)
| | - Fatimah S. Alhamlan
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia; (M.S.A.); (A.A.A.-Q.); (M.A.A.); (B.M.A.); (D.O.); (F.A.A.)
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11564, Saudi Arabia
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Pérez AB, Santos Bravo M, Vidal-Verdú E, Páez-Vega A, Vaquero-Barrios JM, Montero JL, Marcos MÁ, Torre-Cisneros J. Real-life experience in two cases of secondary prophylaxis with letermovir for CMV infection in solid organ transplantation. Microbiol Spectr 2023; 11:e0163023. [PMID: 37902387 PMCID: PMC10714737 DOI: 10.1128/spectrum.01630-23] [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: 04/24/2023] [Accepted: 09/26/2023] [Indexed: 10/31/2023] Open
Abstract
IMPORTANCE This observation provides comprehensive data on the clinical correlates of both cytomegalovirus (CMV) genotypic follow-up and clinical monitoring and outcomes for two different solid organ transplantation recipients that received letermovir as secondary prophylaxis. Our study emphasizes that monitoring of CMV disease in the patient and early genotypic detection of resistance mutations are essential when using new antiviral drugs for off-label indication in patients experiencing CMV relapses or not responding to standard antiviral therapy. These cases and the bibliography reviewed can be helpful for other researchers and clinicians working in the field to optimize the use of new treatments for transplant recipients since drug-resistant CMV infection is an important emerging problem even with new developments in antiviral treatment.
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Affiliation(s)
- Ana-Belén Pérez
- Microbiology Service, Reina Sofia University Hospital, Cordoba, Spain
- Maimónides Institute for Biomedical Research (IMIBIC), Cordoba, Spain
- Centre of Biomedical Research for Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, Madrid, Spain
| | - Marta Santos Bravo
- Centre of Biomedical Research for Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, Madrid, Spain
- Microbiology Service, Hospital Clínic, Barcelona, Spain
| | - Elisa Vidal-Verdú
- Centre of Biomedical Research for Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, Madrid, Spain
- Infectious Diseases Service, Reina Sofia University Hospital, Cordoba, Spain
- Maimónides Institute for Biomedical Research (IMIBIC), Cordoba, Spain
- Departament of Medicine (Medicine, Dermatology and Otorhinolaryngology), University of Cordoba, Spain
| | - Aurora Páez-Vega
- Centre of Biomedical Research for Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, Madrid, Spain
- Maimónides Institute for Biomedical Research (IMIBIC), Cordoba, Spain
| | - José-Manuel Vaquero-Barrios
- Maimónides Institute for Biomedical Research (IMIBIC), Cordoba, Spain
- Lung Transplantation Section, Reina Sofia University Hospital, Cordoba, Spain
| | - José-Luis Montero
- Maimónides Institute for Biomedical Research (IMIBIC), Cordoba, Spain
- Liver Transplantation Section, Reina Sofia University Hospital, Cordoba, Spain
| | - María-Ángeles Marcos
- Centre of Biomedical Research for Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, Madrid, Spain
- Microbiology Service, Hospital Clínic, Barcelona, Spain
| | - Julián Torre-Cisneros
- Maimónides Institute for Biomedical Research (IMIBIC), Cordoba, Spain
- Centre of Biomedical Research for Infectious Diseases (CIBERINFEC), Institute of Health Carlos III, Madrid, Spain
- Infectious Diseases Service, Reina Sofia University Hospital, Cordoba, Spain
- Departament of Medicine (Medicine, Dermatology and Otorhinolaryngology), University of Cordoba, Spain
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Li KK, Lau B, Suárez NM, Camiolo S, Gunson R, Davison AJ, Orton RJ. Direct Nanopore Sequencing of Human Cytomegalovirus Genomes from High-Viral-Load Clinical Samples. Viruses 2023; 15:1248. [PMID: 37376548 DOI: 10.3390/v15061248] [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: 04/19/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
Nanopore sequencing is becoming increasingly commonplace in clinical settings, particularly for diagnostic assessments and outbreak investigations, due to its portability, low cost, and ability to operate in near real-time. Although high sequencing error rates initially hampered the wider implementation of this technology, improvements have been made continually with each iteration of the sequencing hardware and base-calling software. Here, we assess the feasibility of using nanopore sequencing to determine the complete genomes of human cytomegalovirus (HCMV) in high-viral-load clinical samples without viral DNA enrichment, PCR amplification, or prior knowledge of the sequences. We utilised a hybrid bioinformatic approach that involved assembling the reads de novo, improving the consensus sequence by aligning reads to the best-matching genome from a collated set of published sequences, and polishing the improved consensus sequence. The final genomes from a urine sample and a lung sample, the former with an HCMV to human DNA load approximately 50 times greater than the latter, achieved 99.97 and 99.93% identity, respectively, to the benchmark genomes obtained independently by Illumina sequencing. Thus, we demonstrated that nanopore sequencing is capable of determining HCMV genomes directly from high-viral-load clinical samples with a high accuracy.
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Affiliation(s)
- Kathy K Li
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
- Regional Virus Laboratory, Belfast Health and Social Care Trust, Belfast BT12 6BA, UK
| | - Betty Lau
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Nicolás M Suárez
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Salvatore Camiolo
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Rory Gunson
- West of Scotland Specialist Virology Centre, NHS Greater Glasgow & Clyde, Glasgow G31 2ER, UK
| | - Andrew J Davison
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Richard J Orton
- Medical Research Council, University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
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5
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Reischig T, Vlas T, Kacer M, Pivovarcikova K, Lysak D, Nemcova J, Drenko P, Machova J, Bouda M, Sedivcova M, Kormunda S. A Randomized Trial of Valganciclovir Prophylaxis Versus Preemptive Therapy in Kidney Transplant Recipients. J Am Soc Nephrol 2023; 34:920-934. [PMID: 36749127 PMCID: PMC10125645 DOI: 10.1681/asn.0000000000000090] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 12/26/2022] [Indexed: 02/08/2023] Open
Abstract
SIGNIFICANCE STATEMENT Although cytomegalovirus (CMV) infection is an important factor in the pathogenesis of kidney allograft rejection, previous studies have not determined the optimal CMV prevention strategy to avoid indirect effects of the virus. In this randomized trial involving 140 kidney transplant recipients, incidence of acute rejection at 12 months was not lower with valganciclovir prophylaxis (for at least 3 months) compared with preemptive therapy initiated after detection of CMV DNA in whole blood. However, prophylaxis was associated with a lower risk of subclinical rejection at 3 months. Although both regimens were effective in preventing CMV disease, the incidence of CMV DNAemia (including episodes with higher viral loads) was significantly higher with preemptive therapy. Further research with long-term follow-up is warranted to better compare the two approaches. BACKGROUND The optimal regimen for preventing cytomegalovirus (CMV) infection in kidney transplant recipients, primarily in reducing indirect CMV effects, has not been defined. METHODS This open-label, single-center, randomized clinical trial of valganciclovir prophylaxis versus preemptive therapy included kidney transplant recipients recruited between June 2013 and May 2018. After excluding CMV-seronegative recipients with transplants from seronegative donors, we randomized 140 participants 1:1 to receive valganciclovir prophylaxis (900 mg, daily for 3 or 6 months for CMV-seronegative recipients who received a kidney from a CMV-seropositive donor) or preemptive therapy (valganciclovir, 900 mg, twice daily) that was initiated after detection of CMV DNA in whole blood (≥1000 IU/ml) and stopped after two consecutive negative tests (preemptive therapy patients received weekly CMV PCR tests for 4 months). The primary outcome was the incidence of biopsy-confirmed acute rejection at 12 months. Key secondary outcomes included subclinical rejection, CMV disease and DNAemia, and neutropenia. RESULTS The incidence of acute rejection was lower with valganciclovir prophylaxis than with preemptive therapy (13%, 9/70 versus 23%, 16/70), but the difference was not statistically significant. Subclinical rejection at 3 months was lower in the prophylaxis group (13% versus 29%, P = 0.027). Both regimens prevented CMV disease (in 4% of patients in both groups). Compared with prophylaxis, preemptive therapy resulted in significantly higher rates of CMV DNAemia (44% versus 75%, P < 0.001) and a higher proportion of patients experiencing episodes with higher viral load (≥2000 IU/ml), but significantly lower valganciclovir exposure and neutropenia. CONCLUSION Among kidney transplant recipients, the use of valganciclovir prophylaxis did not result in a significantly lower incidence of acute rejection compared with the use of preemptive therapy. CLINICAL TRIAL REGISTRY NAME AND REGISTRATION NUMBER Optimizing Valganciclovir Efficacy in Renal Transplantation (OVERT Study), ACTRN12613000554763 .
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Affiliation(s)
- Tomas Reischig
- Department of Internal Medicine I, Faculty of Medicine in Pilsen, Charles University, and Teaching Hospital, Pilsen, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Tomas Vlas
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Department of Immunology and Allergology, Faculty of Medicine in Pilsen, Charles University, and Teaching Hospital, Pilsen, Czech Republic
| | - Martin Kacer
- Department of Internal Medicine I, Faculty of Medicine in Pilsen, Charles University, and Teaching Hospital, Pilsen, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Kristyna Pivovarcikova
- Department of Pathology, Faculty of Medicine in Pilsen, Charles University, and Teaching Hospital, Pilsen, Czech Republic
| | - Daniel Lysak
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Department of Hematology and Oncology, Faculty of Medicine in Pilsen, Charles University, and Teaching Hospital, Pilsen, Czech Republic
| | - Jana Nemcova
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Department of Molecular Genetic, Biopticka laboratory, Pilsen, Czech Republic
| | - Petr Drenko
- Department of Internal Medicine I, Faculty of Medicine in Pilsen, Charles University, and Teaching Hospital, Pilsen, Czech Republic
| | - Jana Machova
- Department of Internal Medicine I, Faculty of Medicine in Pilsen, Charles University, and Teaching Hospital, Pilsen, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Mirko Bouda
- Department of Internal Medicine I, Faculty of Medicine in Pilsen, Charles University, and Teaching Hospital, Pilsen, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Monika Sedivcova
- Department of Molecular Genetic, Biopticka laboratory, Pilsen, Czech Republic
| | - Stanislav Kormunda
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- Division of Information Technologies and Statistics, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
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Torii Y, Horiba K, Kawada JI, Haruta K, Yamaguchi M, Suzuki T, Uryu H, Kashiwa N, Goishi K, Ogi T, Ito Y. Detection of antiviral drug resistance in patients with congenital cytomegalovirus infection using long-read sequencing: a retrospective observational study. BMC Infect Dis 2022; 22:568. [PMID: 35733089 PMCID: PMC9219161 DOI: 10.1186/s12879-022-07537-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Congenital human cytomegalovirus (cCMV) infection can cause sensorineural hearing loss and neurodevelopmental disabilities in children. Ganciclovir and valganciclovir (GCV/VGCV) improve long-term audiologic and neurodevelopmental outcomes for patients with cCMV infection; however, antiviral drug resistance has been documented in some cases. Long-read sequencing can be used for the detection of drug resistance mutations. The objective of this study was to develop full-length analysis of UL97 and UL54, target genes with mutations that confer GCV/VGCV resistance using long-read sequencing, and investigate drug resistance mutation in patients with cCMV infection. METHODS Drug resistance mutation analysis was retrospectively performed in 11 patients with cCMV infection treated with GCV/VGCV. UL97 and UL54 genes were amplified using blood DNA. The amplicons were sequenced using a long-read sequencer and aligned with the reference gene. Single nucleotide variants were detected and replaced with the reference sequence. The replaced sequence was submitted to a mutation resistance analyzer, which is an open platform for drug resistance mutations. RESULTS Two drug resistance mutations (UL54 V823A and UL97 A594V) were found in one patient. Both mutations emerged after 6 months of therapy, where viral load increased. Mutation rates subsided after cessation of GCV/VGCV treatment. CONCLUSIONS Antiviral drug resistance can emerge in patients with cCMV receiving long-term therapy. Full-length analysis of UL97 and UL54 via long-read sequencing enabled the rapid and comprehensive detection of drug resistance mutations.
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Affiliation(s)
- Yuka Torii
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan
| | - Kazuhiro Horiba
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan.,Department of Genetics, Research Institute of Environmental Medicine Nagoya University, Furo-cho, Chikusa-ku, 464-8601, Nagoya, Japan.,Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan
| | - Jun-Ichi Kawada
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan
| | - Kazunori Haruta
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan
| | - Makoto Yamaguchi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan
| | - Takako Suzuki
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan
| | - Hideko Uryu
- Department of Pediatrics, National Center for Global Health and Medicine, 1-21-1 Toyama Shinjuku-ku, Tokyo, Japan
| | - Naoyuki Kashiwa
- Department of Pediatrics, National Center for Global Health and Medicine, 1-21-1 Toyama Shinjuku-ku, Tokyo, Japan
| | - Keiji Goishi
- Department of Pediatrics, National Center for Global Health and Medicine, 1-21-1 Toyama Shinjuku-ku, Tokyo, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine Nagoya University, Furo-cho, Chikusa-ku, 464-8601, Nagoya, Japan.,Department of Human Genetics and Molecular Biology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan
| | - Yoshinori Ito
- Department of Pediatrics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, 466-8550, Nagoya, Japan. .,Department of Pediatrics and Child Health, Nihon University School of Medicine, 30-1 Oyaguchi, Kami-cho, Itabashi-ku, 173-8610, Tokyo, Japan.
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7
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Chorlton SD, Ritchie G, Lawson T, McLachlan E, Romney MG, Matic N, Lowe CF. Next-generation sequencing for cytomegalovirus antiviral resistance genotyping in a clinical virology laboratory. Antiviral Res 2021; 192:105123. [PMID: 34174249 DOI: 10.1016/j.antiviral.2021.105123] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 06/16/2021] [Accepted: 06/22/2021] [Indexed: 11/26/2022]
Abstract
INTRODUCTION The identification of CMV antiviral drug resistance (AVDR) is a critical diagnostic test for immunocompromised patients with CMV infection and a failure of virologic response on optimal antiviral treatment. We developed a next-generation sequencing (NGS) assay for CMV AVDR testing and compared the AVDR mutations identified by NGS to Sanger sequencing. METHODS Retrospective review of CMV AVDR testing requests for UL97 and UL54 at our laboratory from 2014 to 2019 was conducted. NGS was performed on the MinION and compared to Sanger sequencing performed at the national reference laboratory. Analysis of the sequences was completed with a novel cloud bioinformatics platform (BugSeq). RESULTS Twenty patient samples previously characterized were included for study on the MinION. NGS captured all of the CMV AVDR mutations identified by Sanger, and identified additional mutations in UL97 and/or UL54 in 8/13 (62%) of the samples. An analysis of the depth of coverage at which we no longer detected minority single nucleotide variants (SNVs) detected in the original data was conducted, estimating a recall of 95% at 1800 fold coverage. CONCLUSION NGS utilizing MinION technology for the detection of CMV AVDR mutations identified additional minority variants in UL97 and UL54 as compared with Sanger sequencing. Through the application of a bioinformatics pipeline available online, our NGS process eliminates barriers associated with the use of the MinION and NGS in clinical laboratories.
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Affiliation(s)
- Samuel D Chorlton
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Gordon Ritchie
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, BC, Canada
| | - Tanya Lawson
- Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, BC, Canada
| | - Elizabeth McLachlan
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Marc G Romney
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, BC, Canada
| | - Nancy Matic
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, BC, Canada
| | - Christopher F Lowe
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Division of Medical Microbiology and Virology, St. Paul's Hospital, Vancouver, BC, Canada.
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Successful Use of Heterologous CMV-Reactive T Lymphocyte to Treat Severe Refractory Cytomegalovirus (CMV) Infection in a Liver Transplanted Patient: Correlation of the Host Antiviral Immune Reconstitution with CMV Viral Load and CMV miRNome. Microorganisms 2021; 9:microorganisms9040684. [PMID: 33810329 PMCID: PMC8066103 DOI: 10.3390/microorganisms9040684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 12/16/2022] Open
Abstract
Cytomegalovirus (CMV) infection is the most significant viral infection in hosts with compromised immune systems as solid organ transplant patients. Despite significant progress being made in the prevention of CMV disease in these patients, further therapeutic strategies for CMV disease and for the CMV reactivation prevention are needed. Here, we describe the outcome of the infusion of in vitro expanded CMV-reactive T-cells, taken from a healthy CMV-seropositive donor, in a liver-transplanted recipient with a refractory recurrent CMV. In this particular case, adoptive transfer of allogenic CMV-reactive T-lymphocytes resulted in the clearance of CMV infection and resolution of the pathological manifestations of the patient. In the study we also investigated circulating miRNAs, both cellular and viral, as potential biomarkers during the course of CMV infection. The results indicate that the infusion of allogenic CMV-reactive T-cells can be an effective strategy to treat CMV infection recurrence when the generation of autologous virus specific T cell clones is not possible.
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9
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Nakamichi K, Shen JZ, Lee CS, Lee A, Roberts EA, Simonson PD, Roychoudhury P, Andriesen J, Randhawa AK, Mathias PC, Greninger AL, Jerome KR, Van Gelder RN. Hospitalization and mortality associated with SARS-CoV-2 viral clades in COVID-19. Sci Rep 2021; 11:4802. [PMID: 33637820 PMCID: PMC7910290 DOI: 10.1038/s41598-021-82850-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 01/20/2021] [Indexed: 02/07/2023] Open
Abstract
The COVID-19 epidemic of 2019-20 is due to the novel coronavirus SARS-CoV-2. Following first case description in December, 2019 this virus has infected over 10 million individuals and resulted in at least 500,000 deaths world-wide. The virus is undergoing rapid mutation, with two major clades of sequence variants emerging. This study sought to determine whether SARS-CoV-2 sequence variants are associated with differing outcomes among COVID-19 patients in a single medical system. Whole genome SARS-CoV-2 RNA sequence was obtained from isolates collected from patients registered in the University of Washington Medicine health system between March 1 and April 15, 2020. Demographic and baseline clinical characteristics of patients and their outcome data including their hospitalization and death were collected. Statistical and machine learning models were applied to determine if viral genetic variants were associated with specific outcomes of hospitalization or death. Full length SARS-CoV-2 sequence was obtained 190 subjects with clinical outcome data. 35 (18.4%) were hospitalized and 14 (7.4%) died from complications of infection. A total of 289 single nucleotide variants were identified. Clustering methods demonstrated two major viral clades, which could be readily distinguished by 12 polymorphisms in 5 genes. A trend toward higher rates of hospitalization of patients with Clade 2 infections was observed (p = 0.06, Fisher's exact). Machine learning models utilizing patient demographics and co-morbidities achieved area-under-the-curve (AUC) values of 0.93 for predicting hospitalization. Addition of viral clade or sequence information did not significantly improve models for outcome prediction. In summary, SARS-CoV-2 shows substantial sequence diversity in a community-based sample. Two dominant clades of virus are in circulation. Among patients sufficiently ill to warrant testing for virus, no significant difference in outcomes of hospitalization or death could be discerned between clades in this sample. Major risk factors for hospitalization and death for either major clade of virus include patient age and comorbid conditions.
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Affiliation(s)
- Kenji Nakamichi
- Department of Ophthalmology, University of Washington School of Medicine, 325 9th Avenue, Campus Box 359608, Seattle, WA, 98104, USA
| | - Jolie Z Shen
- University of Washington School of Medicine, Seattle, WA, USA
| | - Cecilia S Lee
- Department of Ophthalmology, University of Washington School of Medicine, 325 9th Avenue, Campus Box 359608, Seattle, WA, 98104, USA
| | - Aaron Lee
- Department of Ophthalmology, University of Washington School of Medicine, 325 9th Avenue, Campus Box 359608, Seattle, WA, 98104, USA
| | - Emma A Roberts
- University of Washington School of Medicine, Seattle, WA, USA
| | - Paul D Simonson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Pavitra Roychoudhury
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Jessica Andriesen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - April K Randhawa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Patrick C Mathias
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Alex L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Keith R Jerome
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Russell N Van Gelder
- Department of Ophthalmology, University of Washington School of Medicine, 325 9th Avenue, Campus Box 359608, Seattle, WA, 98104, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
- Department of Biological Structure, University of Washington, Seattle, WA, USA.
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10
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Shaga Devan K, Walther P, von Einem J, Ropinski T, A Kestler H, Read C. Improved automatic detection of herpesvirus secondary envelopment stages in electron microscopy by augmenting training data with synthetic labelled images generated by a generative adversarial network. Cell Microbiol 2020; 23:e13280. [PMID: 33073426 DOI: 10.1111/cmi.13280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/01/2020] [Accepted: 10/14/2020] [Indexed: 12/16/2022]
Abstract
Detailed analysis of secondary envelopment of the herpesvirus human cytomegalovirus (HCMV) by transmission electron microscopy (TEM) is crucial for understanding the formation of infectious virions. Here, we present a convolutional neural network (CNN) that automatically recognises cytoplasmic capsids and distinguishes between three HCMV capsid envelopment stages in TEM images. 315 TEM images containing 2,610 expert-labelled capsids of the three classes were available for CNN training. To overcome the limitation of small training datasets and thus poor CNN performance, we used a deep learning method, the generative adversarial network (GAN), to automatically increase our labelled training dataset with 500 synthetic images and thus to 9,192 labelled capsids. The synthetic TEM images were added to the ground truth dataset to train the Faster R-CNN deep learning-based object detector. Training with 315 ground truth images yielded an average precision (AP) of 53.81% for detection, whereas the addition of 500 synthetic training images increased the AP to 76.48%. This shows that generation and additional use of synthetic labelled images for detector training is an inexpensive way to improve detector performance. This work combines the gold standard of secondary envelopment research with state-of-the-art deep learning technology to speed up automatic image analysis even when large labelled training datasets are not available.
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Affiliation(s)
| | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, Ulm, Germany
| | - Jens von Einem
- Institute of Virology, Ulm University Medical Center, Ulm, Germany
| | - Timo Ropinski
- Institute of Media Informatics, Ulm University, Ulm, Germany
| | | | - Clarissa Read
- Central Facility for Electron Microscopy, Ulm University, Ulm, Germany.,Institute of Virology, Ulm University Medical Center, Ulm, Germany
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11
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Nakamichi K, Shen JZ, Lee CS, Lee AY, Roberts EA, Simonson PD, Roychoudhury P, Andriesen JG, Randhawa AK, Mathias PC, Greninger A, Jerome KR, Van Gelder RN. Outcomes associated with SARS-CoV-2 viral clades in COVID-19. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.09.24.20201228. [PMID: 32995827 PMCID: PMC7523168 DOI: 10.1101/2020.09.24.20201228] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Background The COVID-19 epidemic of 2019-20 is due to the novel coronavirus SARS-CoV-2. Following first case description in December, 2019 this virus has infected over 10 million individuals and resulted in at least 500,000 deaths world-wide. The virus is undergoing rapid mutation, with two major clades of sequence variants emerging. This study sought to determine whether SARS-CoV-2 sequence variants are associated with differing outcomes among COVID-19 patients in a single medical system. Methods Whole genome SARS-CoV-2 RNA sequence was obtained from isolates collected from patients registered in the University of Washington Medicine health system between March 1 and April 15, 2020. Demographic and baseline medical data along with outcomes of hospitalization and death were collected. Statistical and machine learning models were applied to determine if viral genetic variants were associated with specific outcomes of hospitalization or death. Findings Full length SARS-CoV-2 sequence was obtained 190 subjects with clinical outcome data. 35 (18.4%) were hospitalized and 14 (7.4%) died from complications of infection. A total of 289 single nucleotide variants were identified. Clustering methods demonstrated two major viral clades, which could be readily distinguished by 12 polymorphisms in 5 genes. A trend toward higher rates of hospitalization of patients with Clade 2 was observed (p=0.06). Machine learning models utilizing patient demographics and co-morbidities achieved area-under-the-curve (AUC) values of 0.93 for predicting hospitalization. Addition of viral clade or sequence information did not significantly improve models for outcome prediction. Conclusion SARS-CoV-2 shows substantial sequence diversity in a community-based sample. Two dominant clades of virus are in circulation. Among patients sufficiently ill to warrant testing for virus, no significant difference in outcomes of hospitalization or death could be discerned between clades in this sample. Major risk factors for hospitalization and death for either major clade of virus include patient age and comorbid conditions.
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12
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Suárez NM, Blyth E, Li K, Ganzenmueller T, Camiolo S, Avdic S, Withers B, Linnenweber-Held S, Gwinner W, Dhingra A, Heim A, Schulz TF, Gunson R, Gottlieb D, Slobedman B, Davison AJ. Whole-Genome Approach to Assessing Human Cytomegalovirus Dynamics in Transplant Patients Undergoing Antiviral Therapy. Front Cell Infect Microbiol 2020; 10:267. [PMID: 32612959 PMCID: PMC7308726 DOI: 10.3389/fcimb.2020.00267] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/05/2020] [Indexed: 12/16/2022] Open
Abstract
Human cytomegalovirus (HCMV) is the most frequent cause of opportunistic viral infection following transplantation. Viral factors of potential clinical importance include the selection of mutants resistant to antiviral drugs and the occurrence of infections involving multiple HCMV strains. These factors are typically addressed by analyzing relevant HCMV genes by PCR and Sanger sequencing, which involves independent assays of limited sensitivity. To assess the dynamics of viral populations with high sensitivity, we applied high-throughput sequencing coupled with HCMV-adapted target enrichment to samples collected longitudinally from 11 transplant recipients (solid organ, n = 9, and allogeneic hematopoietic stem cell, n = 2). Only the latter presented multiple-strain infections. Four cases presented resistance mutations (n = 6), two (A594V and L595S) at high (100%) and four (V715M, V781I, A809V, and T838A) at low (<25%) frequency. One allogeneic hematopoietic stem cell transplant recipient presented up to four resistance mutations, each at low frequency. The use of high-throughput sequencing to monitor mutations and strain composition in people at risk of HCMV disease is of potential value in helping clinicians implement the most appropriate therapy.
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Affiliation(s)
- Nicolás M Suárez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Emily Blyth
- Westmead Institute for Medical Research, Sydney, NSW, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Blood and Bone Marrow Transplant Unit, Westmead Hospital, Sydney, NSW, Australia.,Sydney Cellular Therapies Laboratory, Westmead Hospital, Sydney, NSW, Australia
| | - Kathy Li
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Tina Ganzenmueller
- Institute for Medical Virology, University Hospital Tübingen, Tübingen, Germany.,Institute of Virology, Hannover Medical School, Hanover, Germany
| | - Salvatore Camiolo
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Selmir Avdic
- Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - Barbara Withers
- Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - Silvia Linnenweber-Held
- Department of Nephrology, Hannover Medical School, Hanover, Germany.,Public Health Agency of Lower Saxony, Hanover, Germany
| | - Wilfried Gwinner
- Department of Nephrology, Hannover Medical School, Hanover, Germany
| | - Akshay Dhingra
- Institute of Virology, Hannover Medical School, Hanover, Germany
| | - Albert Heim
- Institute of Virology, Hannover Medical School, Hanover, Germany
| | - Thomas F Schulz
- Institute of Virology, Hannover Medical School, Hanover, Germany.,German Center for Infection Research, Hanover, Germany
| | - Rory Gunson
- West of Scotland Specialist Virology Centre, Glasgow Royal Infirmary, Glasgow, United Kingdom
| | - David Gottlieb
- Westmead Institute for Medical Research, Sydney, NSW, Australia.,Blood and Bone Marrow Transplant Unit, Westmead Hospital, Sydney, NSW, Australia
| | - Barry Slobedman
- Discipline of Infectious Diseases and Immunology, Faculty of Medicine and Health, Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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13
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Guiu A, López-Aladid R, Cardeñoso L, Mosquera MM, de la Cámara R, Marcos MA. Study of cytomegalovirus resistance in allogeneic hematopoietic cell transplant recipients. Med Clin (Barc) 2020; 154:433-439. [PMID: 31785805 DOI: 10.1016/j.medcli.2019.07.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/21/2019] [Accepted: 07/31/2019] [Indexed: 11/16/2022]
Abstract
INTRODUCTION Cytomegalovirus (CMV) is the most important opportunistic pathogen associated with transplant. The objective of this study was the characterization of CMV resistance mutations in allogeneic haematopoietic cell transplant recipients (allo-TPH) and the study of associated factors. METHODS A retrospective study of a cohort of allo-TPH recipients with post-transplant CMV reactivations with stable or increasing viral loads (CV), despite adequate antiviral treatment for at least 2weeks. The study of resistance mutations of the UL97 and UL54 genes was carried out by Sanger sequencing. RESULTS Refractory CMV infection in our group of allo-TPH patients corresponded with a 21.43% rate of resistant virus infection (3 of 14 patients). All patients with resistance mutations had multiple reactivation episodes (P-value .01). The mutations found were A594V and H520Q in the UL97 gene that confers high-grade resistance to ganciclovir (GCV). One of the 3 cases with antiviral resistance was documented with a low VL (< 1000 copies/ml) and short accumulated GCV treatment (41 days). CONCLUSION Most of the failures in the treatment of CMV were possibly due to clinical resistance; the lack of satisfactory response to antiviral treatment is not always accompanied by virological resistance. However, the appearance of resistances can occur early after the start of the treatment and with VL below 1000 copies / ml. The number of episodes of reactivation was higher among patients with virological resistance than those who did not.
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Affiliation(s)
- Alba Guiu
- Servicio de Microbiología, Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria, Hospital Universitario de La Princesa, Madrid, España.
| | - Rubén López-Aladid
- Servicio de Microbiología, Hospital Clínic, ISGlobal (Instituto de Salud Global de Barcelona), Barcelona, España
| | - Laura Cardeñoso
- Servicio de Microbiología, Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria, Hospital Universitario de La Princesa, Madrid, España
| | - Maria Mar Mosquera
- Servicio de Microbiología, Hospital Clínic, ISGlobal (Instituto de Salud Global de Barcelona), Barcelona, España
| | - Rafael de la Cámara
- Servicio de Hematología, Hospital Universitario de la Princesa, Instituto de Investigación Sanitaria, Hospital Universitario de La Princesa, Madrid, España
| | - Maria Angeles Marcos
- Servicio de Microbiología, Hospital Clínic, ISGlobal (Instituto de Salud Global de Barcelona), Barcelona, España
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14
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Bogožalec Košir A, Cvelbar T, Kammel M, Grunert HP, Zeichhardt H, Milavec M. Digital PCR method for detection and quantification of specific antimicrobial drug-resistance mutations in human cytomegalovirus. J Virol Methods 2020; 281:113864. [PMID: 32380093 DOI: 10.1016/j.jviromet.2020.113864] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/06/2020] [Accepted: 04/08/2020] [Indexed: 12/18/2022]
Abstract
Antimicrobial drug resistance is one of the biggest threats to human health worldwide. Timely detection and quantification of infectious agents and their susceptibility to antimicrobial drugs are crucial for efficient management of resistance to antiviral drugs. In clinical settings, viral drug resistance is most often associated with prolonged treatment of chronic infections, and assessed by genotyping methods; e.g., sequencing and PCR. These approaches have limitations: sequencing can be expensive and does not provide quantification; and qPCR quantification is hampered by a lack of reference materials for standard curves. In recent years, digital PCR has been introduced, which provides absolute quantification without the need for reference materials for standard curves. Using digital PCR, we have developed a rapid, sensitive and accurate method for genotyping and quantification of the most prevalent mutations that cause human cytomegalovirus resistance to ganciclovir.
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Affiliation(s)
- Alexandra Bogožalec Košir
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000 Ljubljana, Slovenia
| | - Tašja Cvelbar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Martin Kammel
- INSTAND, Gesellschaft Zur Förderung Der Qualitätssicherung in Medizinischen Laboratorien e.V. Ubierstr.20, 40223 Düsseldorf, Germany; IQVD GmbH, Institut Für Qualitätssicherung in Der Virusdiagnostik, Potsdamer Chaussee 80, 14129 Berlin, Germany
| | - Hans-Peter Grunert
- GBD Gesellschaft Für Biotechnologische Diagnostik mbH, Potsdamer Chaussee 80, 14129 Berlin, Germany
| | - Heinz Zeichhardt
- INSTAND, Gesellschaft Zur Förderung Der Qualitätssicherung in Medizinischen Laboratorien e.V. Ubierstr.20, 40223 Düsseldorf, Germany; IQVD GmbH, Institut Für Qualitätssicherung in Der Virusdiagnostik, Potsdamer Chaussee 80, 14129 Berlin, Germany; GBD Gesellschaft Für Biotechnologische Diagnostik mbH, Potsdamer Chaussee 80, 14129 Berlin, Germany
| | - Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000 Ljubljana, Slovenia.
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15
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Phoompoung P, Ferreira VH, Tikkanen J, Husain S, Viswabandya A, Kumar D, Humar A. Letermovir as Salvage Therapy for Cytomegalovirus Infection in Transplant Recipients. Transplantation 2020; 104:404-409. [PMID: 32000236 DOI: 10.1097/tp.0000000000002785] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Letermovir, a new viral terminase complex inhibitor, has been approved for the prevention of cytomegalovirus (CMV) infection in hematopoietic stem cell transplant patients. However, data on the efficacy and safety of letermovir for the treatment of CMV infection in transplant recipients remain scarce. METHODS We performed a single-center retrospective study of stem cell and organ transplant recipients who received letermovir for the treatment of CMV infection from November 2017 to October 2018. RESULTS Six patients were included, and 5 were evaluable. All received letermovir in the context of a refractory or resistant CMV infection including asymptomatic CMV viremia (n = 3), CMV syndrome (n = 1), and CMV pneumonitis and colitis (n = 1). The 3 asymptomatic patients experienced a decrease of the viral load (VL) to <200 IU/mL after letermovir therapy. One patient displayed a partial VL response (2-log of VL reduction) but a good clinical response, and one who received a suboptimal dose of letermovir experienced an increase of viremia. There were no treatment-related adverse effects. CONCLUSIONS We demonstrate mixed efficacy in patients with refractory CMV infection suggesting that letermovir may be a useful therapeutic adjunct, potentially in combination with other antivirals.
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Affiliation(s)
- Pakpoom Phoompoung
- Transplant Infectious Diseases, University Health Network, Toronto, ON, Canada
- Division of Infectious Disease and Tropical Medicine, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Victor H Ferreira
- Transplant Infectious Diseases, University Health Network, Toronto, ON, Canada
| | - Jussi Tikkanen
- Transplant Infectious Diseases, University Health Network, Toronto, ON, Canada
| | - Shahid Husain
- Transplant Infectious Diseases, University Health Network, Toronto, ON, Canada
| | - Auro Viswabandya
- Hans Messner Allogeneic Transplant Program, University Health Network, Toronto, ON, Canada
| | - Deepali Kumar
- Transplant Infectious Diseases, University Health Network, Toronto, ON, Canada
| | - Atul Humar
- Transplant Infectious Diseases, University Health Network, Toronto, ON, Canada
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16
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Global estimate of phenotypic and genotypic ganciclovir resistance in cytomegalovirus infections among HIV and organ transplant patients; A systematic review and meta-analysis. Microb Pathog 2020; 141:104012. [PMID: 32004622 DOI: 10.1016/j.micpath.2020.104012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/25/2020] [Accepted: 01/27/2020] [Indexed: 11/21/2022]
Abstract
Human cytomegalovirus (CMV), an opportunistic pathogen belonging to Herpesviridae family, is considered as one of the major causes of morbidity and mortality among wide variety of patients, particularly in transplant recipients and HIV positive patients. As this virus can be resistant to treatment, frequency of CMV in patients who receive organ transplantation and people suffering from AIDS was studied between 1980 and 2019. Medline (via PubMed), Embase, Web of Science, and the Iranian Database were reviewed, and Comprehensive Meta-Analysis (V2.0, Biostat) software analyzed all data. Finally, we used Cochran's Q-statistic to encounter heterogeneity between different studies. Meta-analyses indicated, GCV resistance was 14.1% (95% CI 11.2-17.7); however, in patients suffering from AIDS and organ transplantation were 19.5% (95% CI 14.7-25.4) and 11.4% (95% CI 8.1-15.8), respectively. There were increasing rates in the prevalence of GCV resistance in CMV among transplant recipients, and HIV positive patients. Therefore, evaluation of these refractory infections is beneficial.
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17
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Adamson CS, Nevels MM. Bright and Early: Inhibiting Human Cytomegalovirus by Targeting Major Immediate-Early Gene Expression or Protein Function. Viruses 2020; 12:v12010110. [PMID: 31963209 PMCID: PMC7019229 DOI: 10.3390/v12010110] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 12/11/2022] Open
Abstract
The human cytomegalovirus (HCMV), one of eight human herpesviruses, establishes lifelong latent infections in most people worldwide. Primary or reactivated HCMV infections cause severe disease in immunosuppressed patients and congenital defects in children. There is no vaccine for HCMV, and the currently approved antivirals come with major limitations. Most approved HCMV antivirals target late molecular processes in the viral replication cycle including DNA replication and packaging. “Bright and early” events in HCMV infection have not been exploited for systemic prevention or treatment of disease. Initiation of HCMV replication depends on transcription from the viral major immediate-early (IE) gene. Alternative transcripts produced from this gene give rise to the IE1 and IE2 families of viral proteins, which localize to the host cell nucleus. The IE1 and IE2 proteins are believed to control all subsequent early and late events in HCMV replication, including reactivation from latency, in part by antagonizing intrinsic and innate immune responses. Here we provide an update on the regulation of major IE gene expression and the functions of IE1 and IE2 proteins. We will relate this insight to experimental approaches that target IE gene expression or protein function via molecular gene silencing and editing or small chemical inhibitors.
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18
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Advances in the genotypic diagnosis of cytomegalovirus antiviral drug resistance. Antiviral Res 2020; 176:104711. [PMID: 31940472 DOI: 10.1016/j.antiviral.2020.104711] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/22/2019] [Accepted: 01/09/2020] [Indexed: 12/20/2022]
Abstract
Cytomegalovirus (CMV) drug resistance mutation maps are updated with recent information for polymerase inhibitors, the terminase inhibitor letermovir and the UL97 kinase inhibitor maribavir. Newly mapped mutations and their phenotypes provide more detail on cross-resistance properties and suggest the need to expand the CMV gene regions covered in diagnostic testing. Next-generation deep sequencing technology offers a more sensitive, higher resolution view of emerging antiviral resistance and is recommended for use in clinical trials. Issues of standardization and diagnostic utility in comparison with traditional Sanger sequencing remain unresolved. Quality control is important for the accurate and reproducible detection of mutant viral populations in clinical specimens.
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19
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Leung PYM, Tran T, Testro A, Paizis K, Kwong J, Whitlam JB. Ganciclovir-resistant post-transplant cytomegalovirus infection due to combined deletion mutation at codons 595-596 of the UL97 gene. Transpl Infect Dis 2019; 21:e13168. [PMID: 31498954 DOI: 10.1111/tid.13168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/23/2019] [Accepted: 08/25/2019] [Indexed: 12/26/2022]
Abstract
The development of antiviral-resistant cytomegalovirus (CMV) infection complicates the management of transplant recipients. We describe the case of a 65-year-old male who developed CMV disease on valganciclovir prophylaxis (donor CMV IgG positive, recipient CMV IgG indeterminate) 30 days after combined liver-kidney transplantation for alcoholic cirrhosis and hepato-renal syndrome. After an initial complete response to treatment dose oral valganciclovir, he developed recurrent CMV viraemia. Resistance testing revealed a UL97 mutation with in-frame deletions of codons 595-596. He was treated successfully with foscarnet and reduction in immunosuppression. This mutation has not been described previously and was suspected to confer ganciclovir resistance. Ganciclovir resistance occurs most commonly due to mutations in the UL97 or UL54 genes, which encode a protein kinase and a DNA polymerase, respectively. The UL97-encoded protein kinase phosphorylates ganciclovir to ganciclovir triphosphate, which competitively inhibits viral replication. Mutations in the UL97 gene are typically point mutations or deletions. We describe a new mutation, del595-596 in the CMV UL97 gene, occurring in the context of clinical treatment failure with standard and double-dose ganciclovir, and successful virological control achieved with foscarnet. This mutation is likely to result in ganciclovir resistance, although recombinant phenotyping is required for confirmation.
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Affiliation(s)
- Po Yee Mia Leung
- Department of Nephrology, Austin Health, Melbourne, Vic., Australia
| | - Thomas Tran
- Virus Identification Laboratory, Victorian Infectious Diseases Reference Laboratory, The Peter Doherty Institute for Infection and Immunity, Melbourne, Vic., Australia
| | - Adam Testro
- Liver Transplant Unit, Austin Health, Melbourne, Vic., Australia
| | - Kathy Paizis
- Department of Nephrology, Austin Health, Melbourne, Vic., Australia
| | - Jason Kwong
- Department of Infectious Diseases, Austin Health, Melbourne, Vic., Australia
| | - John B Whitlam
- Department of Nephrology, Austin Health, Melbourne, Vic., Australia.,Department of Medicine, University of Melbourne, Melbourne, Vic., Australia
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20
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The Third International Consensus Guidelines on the Management of Cytomegalovirus in Solid-organ Transplantation. Transplantation 2019; 102:900-931. [PMID: 29596116 DOI: 10.1097/tp.0000000000002191] [Citation(s) in RCA: 691] [Impact Index Per Article: 138.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite recent advances, cytomegalovirus (CMV) infections remain one of the most common complications affecting solid organ transplant recipients, conveying higher risks of complications, graft loss, morbidity, and mortality. Research in the field and development of prior consensus guidelines supported by The Transplantation Society has allowed a more standardized approach to CMV management. An international multidisciplinary panel of experts was convened to expand and revise evidence and expert opinion-based consensus guidelines on CMV management including prevention, treatment, diagnostics, immunology, drug resistance, and pediatric issues. Highlights include advances in molecular and immunologic diagnostics, improved understanding of diagnostic thresholds, optimized methods of prevention, advances in the use of novel antiviral therapies and certain immunosuppressive agents, and more savvy approaches to treatment resistant/refractory disease. The following report summarizes the updated recommendations.
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21
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Galitska G, Biolatti M, De Andrea M, Leone A, Coscia A, Bertolotti L, Ala U, Bertino E, Dell'Oste V, Landolfo S. Biological relevance of Cytomegalovirus genetic variability in congenitally and postnatally infected children. J Clin Virol 2018; 108:132-140. [PMID: 30312910 DOI: 10.1016/j.jcv.2018.09.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/24/2018] [Accepted: 09/28/2018] [Indexed: 12/30/2022]
Abstract
BACKGROUND Human cytomegalovirus (HCMV) is the leading cause of congenital infections resulting in severe morbidity and mortality among infected children. Although the virus is highly polymorphic, particularly in genes contributing to immune evasion, the mechanisms underlying its genetic variability and pathogenicity are only partially understood. OBJECTIVES We aimed to characterize different HCMV clinical strains isolated from 21 congenitally- or postnatally-infected children for in vitro growth properties and genetic polymorphisms. STUDY DESIGN The growth of various HCMV isolates was analyzed in different cell culture models. Genetic polymorphism was assessed by genetic and phylogenetic analysis of viral genes involved in virulence (UL144, US28, and UL18), latency (UL133-138), or drug resistance (UL54 and UL97). RESULTS Here, we report a high degree of genetic and phenotypic diversity in distinct HCMV clinical isolates, as shown by their in vitro growth properties. In particular, HCMV isolates displayed the highest degree of genetic variability in the UL144 gene, where we were able to define four distinct genotypes within the cohort based on UL144 heterogeneity. Lastly, among all isolates we were able to identify 36 mutations in UL54 and 2 in UL97. CONCLUSIONS Our findings indicate that surprisingly high levels of genetic HCMV variability correlate with a high degree of phenotypic polymorphism, which in turn might differentially influence the growth, fitness, and drug susceptibility of HCMV.
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Affiliation(s)
- Ganna Galitska
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Matteo Biolatti
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Marco De Andrea
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy; Department of Translational Medicine, Novara Medical School, Novara, Italy
| | - Agata Leone
- Neonatal Unit, Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Alessandra Coscia
- Neonatal Unit, Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Luigi Bertolotti
- Department of Veterinary Science, University of Turin, Grugliasco, Italy
| | - Ugo Ala
- Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin, Italy
| | - Enrico Bertino
- Neonatal Unit, Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Valentina Dell'Oste
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy.
| | - Santo Landolfo
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy.
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22
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Vejrazkova E, Pliskova L, Hubacek P, Kostal M, Zavrelova A, Radocha J, Kutova R, Stepanova V, Zak P. Clinical and genotypic CMV drug resistance in HSCT recipients: a single center epidemiological and clinical data. Bone Marrow Transplant 2018; 54:146-149. [PMID: 29950664 DOI: 10.1038/s41409-018-0257-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 05/23/2018] [Accepted: 05/28/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Eva Vejrazkova
- 4th Department of Internal Medicine, Haematology, University Hospital and Faculty of Medicine, Hradec Kralove, Czech Republic.
| | - Lenka Pliskova
- Institute of Clinical Biochemistry and Diagnostics, University Hospital and Faculty of Medicine, Hradec Kralove, Czech Republic
| | - Petr Hubacek
- Department of Medical Microbiology of 2nd Medical Faculty, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Milan Kostal
- 4th Department of Internal Medicine, Haematology, University Hospital and Faculty of Medicine, Hradec Kralove, Czech Republic
| | - Alzbeta Zavrelova
- 4th Department of Internal Medicine, Haematology, University Hospital and Faculty of Medicine, Hradec Kralove, Czech Republic
| | - Jakub Radocha
- 4th Department of Internal Medicine, Haematology, University Hospital and Faculty of Medicine, Hradec Kralove, Czech Republic
| | - Radka Kutova
- Institute of Clinical Biochemistry and Diagnostics, University Hospital and Faculty of Medicine, Hradec Kralove, Czech Republic
| | - Vlasta Stepanova
- Institute of Clinical Microbiology, University Hospital and Faculty of Medicine, Hradec Kralove, Czech Republic
| | - Pavel Zak
- 4th Department of Internal Medicine, Haematology, University Hospital and Faculty of Medicine, Hradec Kralove, Czech Republic
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23
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Czarnecka P, Czarnecka K, Tronina O, Durlik M. Cytomegalovirus Disease After Liver Transplant-A Description of a Treatment-Resistant Case: A Case Report and Literature Review. Transplant Proc 2018; 50:4015-4022. [PMID: 30577306 DOI: 10.1016/j.transproceed.2018.05.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 05/23/2018] [Indexed: 12/18/2022]
Abstract
Cytomegalovirus (CMV) infection is a common complication in solid organ transplant recipients. In patients receiving immunosuppressive treatment, CMV may lead to life-threatening organ complications or graft loss. We describe a case of 31-year-old CMV-seronegative patient who underwent liver transplant from a CMV-seropositive donor with an early acute resistant rejection of the transplanted organ followed by primary CMV infection, despite prophylaxis, and its severe organ complications. Routine treatment of acute allograft rejection through increasing the base immunosuppression and then administering methylprednisolone infusions did not yield significant therapeutic effect. This resulted in anti-thymocyte globulin and ultimately proteasome inhibitor introduction. The cholestasis remitted and liver parameters improved. But 4 weeks later the patient was admitted again due to incorrect liver function tests. Blood tests revealed high CMV viral load, and primary CMV infection was diagnosed. On diagnosis the patient was treated with ganciclovir (GCV) intravenously. As GCV resistance was suspected based on clinical premises, foscarnet (FOS) and leflunomide (LFM) were implemented with concomitant cautious immunosuppression reduction due to the history of recent graft rejection. Despite aggressive treatment introduction, viral clearance was not obtained. Ultimately the patient died due to respiratory distress resulting from lung fibrosis, most probably owing to CMV diseases with Pneumocystis jiroveci coinfection. The presented case proves the importance of strictly following the rules of prophylaxis, especially in patients with a high risk factor of CMV infection development. A quick diagnosis, implementation of appropriate treatment, and fast reaction to the lack of satisfying therapeutic effect can be the key to a successful treatment.
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Affiliation(s)
- P Czarnecka
- Department of Transplantation Medicine, Nephrology, and Internal Medicine, Medical University of Warsaw, Warsaw, Poland.
| | - K Czarnecka
- Department of Transplantation Medicine, Nephrology, and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | - O Tronina
- Department of Transplantation Medicine, Nephrology, and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | - M Durlik
- Department of Transplantation Medicine, Nephrology, and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
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24
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Kraus JM, Lausser L, Kuhn P, Jobst F, Bock M, Halanke C, Hummel M, Heuschmann P, Kestler HA. Big data and precision medicine: challenges and strategies with healthcare data. INTERNATIONAL JOURNAL OF DATA SCIENCE AND ANALYTICS 2018. [DOI: 10.1007/s41060-018-0095-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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25
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Bauer D, Keller J, Alt M, Schubert A, Aufderhorst UW, Palapys V, Kasper M, Heilingloh CS, Dittmer U, Laffer B, Eis-Hübinger AM, Verjans GM, Heiligenhaus A, Roggendorf M, Krawczyk A. Antibody-based immunotherapy of aciclovir resistant ocular herpes simplex virus infections. Virology 2017; 512:194-200. [DOI: 10.1016/j.virol.2017.09.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/20/2017] [Accepted: 09/22/2017] [Indexed: 11/29/2022]
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26
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Javid N, Talkhabifard M, Tabarraei A, Moradi A. Human cytomegalovirus UL54 and UL97 mutations for detection of ganciclovir resistance in congenital infection. Future Virol 2017. [DOI: 10.2217/fvl-2017-0018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Aim: Ganciclovir (GCV) is used as an antiviral drug for the treatment of human cytomegalovirus infection. The aim of this study was to demonstrate GCV-resistant human cytomegalovirus in congenitally infected neonates. Patients & methods: DNA of CMV positive newborn samples was extracted and UL97 and UL54 genes were amplified by PCR and real-time PCR. Sequencing of UL97 and UL54 genes were performed and analyzed. Results: UL97 GCV resistance mutation C603W was detected in one newborn. D605E was the most common polymorphism in UL97 observed in 7/13 (53.8%) of samples. N685S, A688V, A885T and N898D were four known common UL54 polymorphisms. Conclusion: The rate of GCV resistance in congenital CMV is low. Common polymorphisms in UL97 and UL54 genes are also reported as new mutations.
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Affiliation(s)
- Naeme Javid
- Department of Microbiology, Golestan University of Medical Sciences, Gorgan, IR Iran
| | - Majid Talkhabifard
- Faculty of Medical Advance technology, Department of Molecular Medicine, Golestan University of Medical Science, Gorgan, IR Iran
| | - Alijan Tabarraei
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, IR Iran
| | - Abdolvahab Moradi
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, IR Iran
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27
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Torre-Cisneros J, Aguado J, Caston J, Almenar L, Alonso A, Cantisán S, Carratalá J, Cervera C, Cordero E, Fariñas M, Fernández-Ruiz M, Fortún J, Frauca E, Gavaldá J, Hernández D, Herrero I, Len O, Lopez-Medrano F, Manito N, Marcos M, Martín-Dávila P, Monforte V, Montejo M, Moreno A, Muñoz P, Navarro D, Pérez-Romero P, Rodriguez-Bernot A, Rumbao J, San Juan R, Vaquero J, Vidal E. Management of cytomegalovirus infection in solid organ transplant recipients: SET/GESITRA-SEIMC/REIPI recommendations. Transplant Rev (Orlando) 2016; 30:119-43. [DOI: 10.1016/j.trre.2016.04.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 04/02/2016] [Accepted: 04/04/2016] [Indexed: 02/06/2023]
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28
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Abstract
Antiviral drug resistance is a matter of great clinical importance that, historically, has been investigated mostly from a virological perspective. Although the proximate mechanisms of resistance can be readily uncovered using these methods, larger evolutionary trends often remain elusive. Recent interest by population geneticists in studies of antiviral resistance has spurred new metrics for evaluating mutation and recombination rates, demographic histories of transmission and compartmentalization, and selective forces incurred during viral adaptation to antiviral drug treatment. We present up-to-date summaries on antiviral resistance for a range of drugs and viral types, and review recent advances for studying their evolutionary histories. We conclude that information imparted by demographic and selective histories, as revealed through population genomic inference, is integral to assessing the evolution of antiviral resistance as it pertains to human health.
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Affiliation(s)
- Kristen K Irwin
- School of Life Sciences, École Polytechnique Fédéral de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Nicholas Renzette
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Timothy F Kowalik
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jeffrey D Jensen
- School of Life Sciences, École Polytechnique Fédéral de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
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29
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Campos AB, Ribeiro J, Boutolleau D, Sousa H. Human cytomegalovirus antiviral drug resistance in hematopoietic stem cell transplantation: current state of the art. Rev Med Virol 2016; 26:161-82. [DOI: 10.1002/rmv.1873] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 01/09/2016] [Accepted: 02/01/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Ana Bela Campos
- Molecular Oncology and Viral Pathology Group (CI-IPOP); Porto Portugal
- Faculty of Medicine; University of Porto; Porto Portugal
| | - Joana Ribeiro
- Molecular Oncology and Viral Pathology Group (CI-IPOP); Porto Portugal
- Virology Service; Portuguese Oncology Institute of Porto; Porto Portugal
- Faculty of Medicine; University of Porto; Porto Portugal
| | - David Boutolleau
- Sorbonne Universités; UPMC Université Paris 06, CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris); Paris France
- INSERM, U1135, CIMI-Paris; Paris France
- AP-HP, Hôpitaux Universitaires La Pitié-Salpêtrière - Charles Foix; Service de Virologie; Paris France
| | - Hugo Sousa
- Molecular Oncology and Viral Pathology Group (CI-IPOP); Porto Portugal
- Virology Service; Portuguese Oncology Institute of Porto; Porto Portugal
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30
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Persistent CMV infection after allogeneic hematopoietic stem cell transplantation in a CMV-seronegative donor-to-positive recipient constellation: Development of multidrug resistance in the absence of anti-viral cellular immunity. J Clin Virol 2016; 74:57-60. [DOI: 10.1016/j.jcv.2015.11.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/23/2015] [Accepted: 11/26/2015] [Indexed: 11/21/2022]
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31
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Slavov SN, Vilar FC, Wagatsuma VMD, Santana RC, Machado AA, Fonseca BALD, Kashima S, Covas DT. Late emergence of A594V and L595W mutations related to ganciclovir resistance in a patient with HCMV retinitis and long-term HIV progression. ACTA ACUST UNITED AC 2015; 48:777-81. [PMID: 26270327 PMCID: PMC4568804 DOI: 10.1590/1414-431x20154507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 03/13/2015] [Indexed: 11/22/2022]
Abstract
The emergence of ganciclovir (GCV) resistance during the treatment of human cytomegalovirus (HCMV) infection is a serious clinical challenge, and is associated with high morbidity and mortality. In this case report, we describe the emergence of two consecutive mutations (A594V and L595W) related to GCV resistance in a patient with HCMV retinitis and long-term HIV progression after approximately 240 days of GCV use. Following the diagnosis of retinitis, the introduction of GCV did not result in viral load reduction. The detected mutations appeared late in the treatment, and we propose that other factors (high initial HCMV load, previous GCV exposure, low CD4+ cell count), in addition to the presence of resistance mutations, may have contributed to the treatment failure of HCMV infection in this patient.
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Affiliation(s)
- S N Slavov
- Hemocentro de Ribeirão Preto, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, BR
| | - F C Vilar
- Divisão de Moléstias Infecciosas e Tropicais, Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, BR
| | - V M D Wagatsuma
- Laboratório de Hematologia Experimental, Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, BR
| | - R C Santana
- Divisão de Moléstias Infecciosas e Tropicais, Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, BR
| | - A A Machado
- Divisão de Moléstias Infecciosas e Tropicais, Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, BR
| | - B A L da Fonseca
- Divisão de Moléstias Infecciosas e Tropicais, Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, BR
| | - S Kashima
- Hemocentro de Ribeirão Preto, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, BR
| | - D T Covas
- Hemocentro de Ribeirão Preto, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, BR
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32
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Lischka P, Michel D, Zimmermann H. Characterization of Cytomegalovirus Breakthrough Events in a Phase 2 Prophylaxis Trial of Letermovir (AIC246, MK 8228). J Infect Dis 2015; 213:23-30. [DOI: 10.1093/infdis/jiv352] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 06/17/2015] [Indexed: 11/13/2022] Open
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33
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Goldner T, Zimmermann H, Lischka P. Phenotypic characterization of two naturally occurring human Cytomegalovirus sequence polymorphisms located in a distinct region of ORF UL56 known to be involved in in vitro resistance to letermovir. Antiviral Res 2015; 116:48-50. [DOI: 10.1016/j.antiviral.2015.01.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/15/2015] [Accepted: 01/20/2015] [Indexed: 12/01/2022]
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34
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Drug resistance of clinical varicella-zoster virus strains confirmed by recombinant thymidine kinase expression and by targeted resistance mutagenesis of a cloned wild-type isolate. Antimicrob Agents Chemother 2015; 59:2726-34. [PMID: 25712361 DOI: 10.1128/aac.05115-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/16/2015] [Indexed: 01/02/2023] Open
Abstract
In this study, approaches were developed to examine the phenotypes of nonviable clinical varicella-zoster virus (VZV) strains with amino acid substitutions in the thymidine kinase (TK) (open reading frame 36 [ORF36]) and/or DNA polymerase (Pol) (ORF28) suspected to cause resistance to antivirals. Initially, recombinant TK proteins containing amino acid substitutions described as known or suspected causes of antiviral resistance were analyzed by measuring the TK activity by applying a modified commercial enzyme immunoassay. To examine the effects of these TK and Pol substitutions on the replication of recombinant virus strains, the method of en passant mutagenesis was used. Targeted mutations within ORF36 and/or ORF28 and an autonomously expressed gene of the monomeric red fluorescent protein for plaque identification were introduced into the European wild-type VZV strain HJO. Plaque reduction assays revealed that the amino acid substitutions with unknown functions in TK, Q303stop, N334stop, A163stop, and the deletion of amino acids 7 to 74 aa (Δaa 7 to 74), were associated with resistance against acyclovir (ACV), penciclovir, or brivudine, whereas the L73I substitution and the Pol substitutions T237K and A955T revealed sensitive viral phenotypes. The results were confirmed by quantitative PCR by measuring the viral load under increasing ACV concentrations. In conclusion, analyzing the enzymatic activities of recombinant TK proteins represent a useful tool for evaluating the significance of amino acid substitutions in the antiviral resistance of clinical VZV strains. However, direct testing of replication-competent viruses by the introduction of nonsynonymous mutations in a VZV bacterial artificial chromosome using en passant mutagenesis led to reliable phenotypic characterization results.
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35
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Göhring K, Hamprecht K, Jahn G. Antiviral Drug- and Multidrug Resistance in Cytomegalovirus Infected SCT Patients. Comput Struct Biotechnol J 2015; 13:153-9. [PMID: 25750703 PMCID: PMC4348572 DOI: 10.1016/j.csbj.2015.01.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 01/27/2015] [Accepted: 01/29/2015] [Indexed: 01/23/2023] Open
Abstract
In pediatric and adult patients after stem cell transplantation (SCT) disseminated infections caused by human cytomegalovirus (HCMV) can cause life threatening diseases. For treatment, the three antivirals ganciclovir (GCV), foscarnet (PFA) and cidofovir (CDV) are approved and most frequently used. Resistance to all of these antiviral drugs may induce a severe problem in this patient cohort. Responsible for resistance phenomena are mutations in the HCMV phosphotransferase-gene (UL97) and the polymerase-gene (UL54). Most frequently mutations in the UL97-gene are associated with resistance to GCV. Resistance against all three drugs is associated to mutations in the UL54-gene. Monitoring of drug resistance by genotyping is mostly done by PCR-based Sanger sequencing. For phenotyping with cell culture the isolation of HCMV is a prerequisite. The development of multidrug resistance with mutation in both genes is rare, but it is often associated with a fatal outcome. The manifestation of multidrug resistance is mostly associated with combined UL97/UL54-mutations. Normally, mutations in the UL97 gene occur initially followed by UL54 mutation after therapy switch. The appearance of UL54-mutation alone without any detection of UL97-mutation is rare. Interestingly, in a number of patients the UL97 mutation could be detected in specific compartments exclusively and not in blood.
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Affiliation(s)
- Katharina Göhring
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital of Tübingen, 72076 Tübingen, Germany
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36
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Volfova P, Lengerova M, Lochmanova J, Dvorakova D, Ricna D, Palackova M, Weinbergerova B, Mayer J, Racil Z. Detecting human cytomegalovirus drug resistant mutations and monitoring the emergence of resistant strains using real-time PCR. J Clin Virol 2014; 61:270-4. [DOI: 10.1016/j.jcv.2014.07.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 06/30/2014] [Accepted: 07/15/2014] [Indexed: 10/25/2022]
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37
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Fürstberger A, Maucher M, Kestler HA. Extended pairwise local alignment of wild card DNA/RNA sequences using dynamic programming. J STAT COMPUT SIM 2014. [DOI: 10.1080/00949655.2014.928294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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38
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Piret J, Boivin G. Antiviral drug resistance in herpesviruses other than cytomegalovirus. Rev Med Virol 2014; 24:186-218. [DOI: 10.1002/rmv.1787] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 01/23/2014] [Accepted: 01/29/2014] [Indexed: 12/16/2022]
Affiliation(s)
- Jocelyne Piret
- Research Center in Infectious Diseases; Laval University; Quebec City QC Canada
| | - Guy Boivin
- Research Center in Infectious Diseases; Laval University; Quebec City QC Canada
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39
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Geno- and phenotypic characterization of human cytomegalovirus mutants selected in vitro after letermovir (AIC246) exposure. Antimicrob Agents Chemother 2013; 58:610-3. [PMID: 24189264 DOI: 10.1128/aac.01794-13] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Letermovir is a novel antiviral compound currently in clinical development for the prevention of human cytomegalovirus (HCMV) infections. In contrast to all currently approved anti-HCMV drugs that target the viral DNA polymerase, letermovir acts via a distinct mode of action involving the viral terminase subunit pUL56. To extend our understanding of potential letermovir resistance mechanisms, we used marker transfer to characterize mutations identified in letermovir-resistant HCMV variants that were selected in cell culture.
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40
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Burrel S, Aime C, Hermet L, Ait-Arkoub Z, Agut H, Boutolleau D. Surveillance of herpes simplex virus resistance to antivirals: A 4-year survey. Antiviral Res 2013; 100:365-72. [DOI: 10.1016/j.antiviral.2013.09.012] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 09/09/2013] [Accepted: 09/12/2013] [Indexed: 12/11/2022]
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41
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Kotton CN, Kumar D, Caliendo AM, Asberg A, Chou S, Danziger-Isakov L, Humar A. Updated international consensus guidelines on the management of cytomegalovirus in solid-organ transplantation. Transplantation 2013; 96:333-60. [PMID: 23896556 DOI: 10.1097/tp.0b013e31829df29d] [Citation(s) in RCA: 554] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cytomegalovirus (CMV) continues to be one of the most common infections after solid-organ transplantation, resulting in significant morbidity, graft loss, and adverse outcomes. Management of CMV varies considerably among transplant centers but has been become more standardized by publication of consensus guidelines by the Infectious Diseases Section of The Transplantation Society. An international panel of experts was reconvened in October 2012 to revise and expand evidence and expert opinion-based consensus guidelines on CMV management, including diagnostics, immunology, prevention, treatment, drug resistance, and pediatric issues. The following report summarizes the recommendations.
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Affiliation(s)
- Camille N Kotton
- Transplant and Immunocompromised Host Infectious Diseases, Infectious Diseases Division, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA 02114, USA.
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42
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Novel method based on "en passant" mutagenesis coupled with a gaussia luciferase reporter assay for studying the combined effects of human cytomegalovirus mutations. J Clin Microbiol 2013; 51:3216-24. [PMID: 23863570 DOI: 10.1128/jcm.01275-13] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Human cytomegalovirus (HCMV) resistance to antivirals is a major problem in immunocompromised patients. Drug resistance is characterized by phenotypic testing or genotypic analysis of the phosphotransferase (UL97) and DNA polymerase (UL54) genes. However, genotypic assays require further characterization of unknown mutations in the drug resistance phenotype. Here, we describe a novel method for generating single or multiple mutations anywhere in the HCMV genome and for studying their effects on drug susceptibility. This method is based on cloning of the reference AD169 strain in a bacterial artificial chromosome and the use of "en passant" mutagenesis in bacteria to introduce mutations in recombinant HCMV without scar sequences. We also used this methodology to introduce the Gaussia luciferase reporter gene into the genome of the recombinant virus. To validate our system, the well-characterized single mutants with UL97 A594V and UL54 E756K mutations as well as the undescribed A594V/E756K double mutant were generated and their drug susceptibility profiles were determined by measuring the luciferase activity in cell culture supernatants. Drug susceptibility phenotypes for the A594V (8.2-fold increase in ganciclovir 50% effective concentration [EC50]) and E756K (1.9-, 3.9-, and 3.0-fold increases in ganciclovir, foscarnet, and cidofovir EC50s, respectively) mutants were similar to those previously reported, while the double mutant exhibited 10.8-, 4.1-, and 2.0-fold increases in ganciclovir, foscarnet, and cidofovir EC50s, respectively. The combination of the Gaussia luciferase reporter-based assay with the markerless "en passant" mutagenesis methodology constitutes an efficient system for studying phenotypes with single or multiple HCMV mutations.
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Göhring K, Wolf D, Bethge W, Mikeler E, Faul C, Vogel W, Vöhringer MC, Jahn G, Hamprecht K. Dynamics of coexisting HCMV-UL97 and UL54 drug-resistance associated mutations in patients after haematopoietic cell transplantation. J Clin Virol 2013; 57:43-9. [DOI: 10.1016/j.jcv.2013.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 12/18/2012] [Accepted: 01/02/2013] [Indexed: 10/27/2022]
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Le Page AK, Jager MM, Iwasenko JM, Scott GM, Alain S, Rawlinson WD. Clinical Aspects of Cytomegalovirus Antiviral Resistance in Solid Organ Transplant Recipients. Clin Infect Dis 2012; 56:1018-29. [DOI: 10.1093/cid/cis1035] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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Effects of mutations on herpes simplex virus 1 thymidine kinase functionality: An in vitro assay based on detection of monophosphate forms of acyclovir and thymidine using HPLC/DAD. Antiviral Res 2012; 95:224-8. [DOI: 10.1016/j.antiviral.2012.07.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 05/07/2012] [Accepted: 07/03/2012] [Indexed: 11/22/2022]
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Intact survival of refractory CMV limbic encephalitis in a patient with severe aplastic anemia after unrelated bone marrow transplantation. J Pediatr Hematol Oncol 2012; 34:472-4. [PMID: 22430584 DOI: 10.1097/mph.0b013e318243501b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We described a patient of refractory cytomegalovirus (CMV) limbic encephalitis who received matched unrelated bone marrow transplantation. Pyrosequencing study on serial cerebrospinal fluid samples revealed the emergence of resistant strains associated with exposure of antiviral agents. Combinations of antiviral agents had a role in partial suppression of CMV viral load but the clearance of virus mainly relied on the recovery of host's immunity and resulted in intact survival of host. Donor's CMV-seronegative status may contribute to the delay in controlling this serious infection. Prompt identification of drug-resistant mutant helps in selection of antiviral agents.
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Shao PL, Lu MY, Liau YJ, Kao CL, Chang SY, Huang LM. Lack of resistance-associated mutations in UL54 and UL97 genes of circulating Cytomegalovirus strains isolated in a medical center in Taiwan. J Formos Med Assoc 2012; 111:456-60. [DOI: 10.1016/j.jfma.2011.08.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 06/07/2011] [Accepted: 08/22/2011] [Indexed: 11/25/2022] Open
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James SH, Prichard MN. The genetic basis of human cytomegalovirus resistance and current trends in antiviral resistance analysis. Infect Disord Drug Targets 2012; 11:504-13. [PMID: 21827431 DOI: 10.2174/187152611797636668] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Accepted: 06/25/2010] [Indexed: 11/22/2022]
Abstract
Infections due to resistant human cytomegalovirus (CMV) are an emerging problem, particularly in immunocompromised hosts. When managing such patients, clinicians should be aware of the possibility of developing CMV antiviral resistance, especially while on prolonged therapy or if severe immunosuppression is present. CMV resistance to current antiviral agents is mediated by alterations in either the UL97 kinase or DNA polymerase, encoded by the UL97 and UL54 genes, respectively. UL97 mutations are capable of conferring resistance to ganciclovir, while UL54 mutations can impart resistance to ganciclovir, cidofovir, and foscarnet. If treatment failure is suspected to be due to antiviral resistance, CMV resistance analysis should be obtained. Phenotypic resistance assays performed on clinical isolates measure antiviral susceptibilities directly, but are laborious and time-consuming. Therefore, genotypic resistance analysis has become the more common means of diagnosing CMV resistance. Mutations in UL97 or UL54 may be clinically associated with resistance, but their effect on antiviral susceptibility must be confirmed by marker transfer techniques such as recombinant phenotyping.
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Affiliation(s)
- S H James
- University of Alabama at Birmingham, Birmingham, AL 35233-1711, USA.
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Zürcher S, Mooser C, Lüthi AU, Mühlemann K, Barbani MT, Mohacsi P, Garzoni C, Gorgievski-Hrisoho M, Schaller A, Flatz L. Sensitive and rapid detection of ganciclovir resistance by PCR based MALDI-TOF analysis. J Clin Virol 2012; 54:359-63. [PMID: 22633201 DOI: 10.1016/j.jcv.2012.04.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 04/22/2012] [Accepted: 04/27/2012] [Indexed: 11/19/2022]
Abstract
BACKGROUND Cytomegalovirus (CMV) infection is associated with significant morbidity and mortality in transplant recipients. Resistance against ganciclovir is increasingly observed. According to current guidelines, direct drug resistance testing is not always performed due to high costs and work effort, even when resistance is suspected. OBJECTIVES To develop a more sensitive, easy applicable and cost-effective assay as proof of concept for direct drug resistance testing in CMV surveillance of post-transplant patients. STUDY DESIGN Five consecutive plasma samples from a heart transplant patient with a primary CMV infection were analyzed by quantitative real-time polymerase chain reaction (rtPCR) as a surrogate marker for therapy failure, and by direct drug resistance detection assays such as Sanger sequencing and the novel primer extension (PEX) reaction matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) based method. RESULTS This report demonstrates that PEX reaction followed by MALDI-TOF analysis detects the A594V mutation, encoding ganciclovir resistance, ten days earlier compared to Sanger sequencing and more than 30 days prior to an increase in viral load. CONCLUSION The greatly increased sensitivity and rapid turnaround-time combined with easy handling and moderate costs indicate that this procedure could make a major contribution to improve transplantation outcomes.
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Affiliation(s)
- Samuel Zürcher
- Institute for Infectious Diseases, University of Bern, 3010 Bern, Switzerland
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Sauerbrei A, Bohn K, Heim A, Hofmann J, Weissbrich B, Schnitzler P, Hoffmann D, Zell R, Jahn G, Wutzler P, Hamprecht K. Novel resistance-associated mutations of thymidine kinase and DNA polymerase genes of herpes simplex virus type 1 and type 2. Antivir Ther 2012; 16:1297-308. [PMID: 22155911 DOI: 10.3851/imp1870] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
BACKGROUND Studies to verify correlations between phenotypes and genotypes of herpes simplex virus (HSV) are an important tool to establish a database of resistance-associated mutations. METHODS In this study, 32 acyclovir (ACV)-resistant clinical HSV-1 and 4 ACV-resistant clinical HSV-2 isolates were examined in parallel by both phenotypic and genotypic resistance testing. Additionally, five non-viable HSV-1 strains and two non-viable HSV-2 strains with clinical resistance were included in genotypic resistance analysis. RESULTS All ACV-resistant HSV isolates showed cross-resistance to brivudin and penciclovir, and were sensitive to foscarnet and cidofovir. Acyclovir resistance was assigned to frameshift and single non-synonymous mutations of the thymidine kinase (TK) gene in 32 out of 37 HSV-1 strains and in 4 out of 6 HSV-2 strains. In three HSV-1 isolates, there were resistance-associated amino acid substitutions of the DNA polymerase (pol). Six substitutions in the TK and two in the DNA pol gene could not be attributed without doubt to either ACV resistance or natural gene polymorphism. Altogether, 10 resistance-related mutations in the TK and 1 in the DNA pol gene have not been reported previously. CONCLUSIONS The novel non-synonymous mutations found in this study enrich the knowledge about the genetic alterations of TK and DNA pol genes in ACV-resistant clinical HSV strains. Together with data from the literature, the findings justify the generation of a HSV database that contains resistance mutations associated with ACV resistance phenotype.
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Affiliation(s)
- Andreas Sauerbrei
- Institute of Virology and Antiviral Therapy, German Reference Laboratory for HSV and VZV, Jena University Clinic, Jena, Germany.
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