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Külekci B, Mollik M, Schwarz S, Perkmann-Nagele N, Geleff S, Jaksch P, Hoetzenecker K, Lambers C, Puchhammer-Stöckl E, Goerzer I. Bidirectional transfer of human cytomegalovirus strains in donor and recipient seropositive lung transplant patients. J Med Virol 2024; 96:e29770. [PMID: 38949200 DOI: 10.1002/jmv.29770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/29/2024] [Accepted: 06/11/2024] [Indexed: 07/02/2024]
Abstract
Donor and recipient human cytomegalovirus (HCMV) seropositive (D+R+) lung transplant recipients (LTRs) often harbor multiple strains of HCMV, likely due to transmitted donor (D) strains and reactivated recipient (R) strains. To date, the extent and timely occurrence of each likely source in shaping the post-transplantation (post-Tx) strain population is unknown. Here, we deciphered the D and R origin of the post-Tx HCMV strain composition in blood, bronchoalveolar lavage (BAL), and CD45+ BAL cell subsets. We investigated either D and/or R formalin-fixed paraffin-embedded blocks or fresh D lung tissue from four D+R+ LTRs obtained before transplantation. HCMV strains were characterized by short amplicon deep sequencing. In two LTRs, we show that the transplanted lung is reseeded by R strains within the first 6 months after transplantation, likely by infiltrating CD14+ CD163+/- alveolar macrophages. In three LTRs, we demonstrate both rapid D-strain dissemination and persistence in the transplanted lung for >1 year post-Tx. Broad inter-host diversity contrasts with intra-host genotype sequence stability upon transmission, during follow-up and across compartments. In D+R+ LTRs, HCMV strains of both, D and R origin can emerge first and dominate long-term in subsequent episodes of infection, indicating replication of both sources despite pre-existing immunity.
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Affiliation(s)
- Büsra Külekci
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Madlen Mollik
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Stefan Schwarz
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Nicole Perkmann-Nagele
- Divison of Clinical Virology, Department of Laboratory Medicine, University of Vienna, Vienna, Austria
| | - Silvana Geleff
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Peter Jaksch
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Konrad Hoetzenecker
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | - Christopher Lambers
- Department of Thoracic Surgery, Medical University of Vienna, Vienna, Austria
| | | | - Irene Goerzer
- Center for Virology, Medical University of Vienna, Vienna, Austria
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Külekci B, Schwarz S, Brait N, Perkmann-Nagele N, Jaksch P, Hoetzenecker K, Puchhammer-Stöckl E, Goerzer I. Human cytomegalovirus strain diversity and dynamics reveal the donor lung as a major contributor after transplantation. Virus Evol 2022; 8:veac076. [PMID: 36128049 PMCID: PMC9477073 DOI: 10.1093/ve/veac076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 07/05/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Mixed human cytomegalovirus (HCMV) strain infections are frequent in lung transplant recipients (LTRs). To date, the influence of the donor (D) and recipient (R) HCMV serostatus on intra-host HCMV strain composition and viral population dynamics after transplantation is only poorly understood. Here, we investigated ten pre-transplant lungs from HCMV-seropositive donors and 163 sequential HCMV-DNA-positive plasma and bronchoalveolar lavage samples from fifty LTRs with multiviremic episodes post-transplantation. The study cohort included D+R+ (38 per cent), D+R- (36 per cent), and D-R+ (26 per cent) patients. All samples were subjected to quantitative genotyping by short amplicon deep sequencing, and twenty-four of them were additionally PacBio long-read sequenced for genotype linkages. We find that D+R+ patients show a significantly elevated intra-host strain diversity compared to D+R- and D-R+ patients (P = 0.0089). Both D+ patient groups display significantly higher viral population dynamics than D- patients (P = 0.0061). Five out of ten pre-transplant donor lungs were HCMV DNA positive, whereof three multiple HCMV strains were detected, indicating that multi-strain transmission via lung transplantation is likely. Using long reads, we show that intra-host haplotypes can share distinctly linked genotypes, which limits overall intra-host diversity in mixed infections. Together, our findings demonstrate donor-derived strains as the main source of increased HCMV strain diversity and dynamics post-transplantation. These results foster strategies to mitigate the potential transmission of the donor strain reservoir to the allograft, such as ex vivo delivery of HCMV-selective immunotoxins prior to transplantation to reduce latent HCMV.
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Affiliation(s)
- Büsra Külekci
- Center for Virology, Medical University of Vienna, Kinderspitalgasse 15, Vienna 1090, Austria
| | - Stefan Schwarz
- Department of Thoracic Surgery, Medical University of Vienna, Währinger Gürtel 18-20, Vienna 1090, Austria
| | - Nadja Brait
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands
| | - Nicole Perkmann-Nagele
- Division of Clinical Virology, Medical University of Vienna, Währinger Gürtel 18-20, Vienna 1090, Austria
| | - Peter Jaksch
- Department of Thoracic Surgery, Medical University of Vienna, Währinger Gürtel 18-20, Vienna 1090, Austria
| | - Konrad Hoetzenecker
- Department of Thoracic Surgery, Medical University of Vienna, Währinger Gürtel 18-20, Vienna 1090, Austria
| | | | - Irene Goerzer
- Center for Virology, Medical University of Vienna, Kinderspitalgasse 15, Vienna 1090, Austria
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Complexity of Human Cytomegalovirus Infection in South African HIV-Exposed Infants with Pneumonia. Viruses 2022; 14:v14050855. [PMID: 35632596 PMCID: PMC9147013 DOI: 10.3390/v14050855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/11/2022] [Accepted: 04/19/2022] [Indexed: 02/01/2023] Open
Abstract
Human cytomegalovirus (HCMV) can cause significant end-organ diseases such as pneumonia in HIV-exposed infants. Complex viral factors may influence pathogenesis including: a large genome with a sizeable coding capacity, numerous gene regions of hypervariability, multiple-strain infections, and tissue compartmentalization of strains. We used a whole genome sequencing approach to assess the complexity of infection by comparing high-throughput sequencing data obtained from respiratory and blood specimens of HIV-exposed infants with severe HCMV pneumonia with those of lung transplant recipients and patients with hematological disorders. There were significantly more specimens from HIV-exposed infants showing multiple HCMV strain infection. Some genotypes, such as UL73 G4B and UL74 G4, were significantly more prevalent in HIV-exposed infants with severe HCMV pneumonia. Some genotypes were predominant in the respiratory specimens of several patients. However, the predominance was not statistically significant, precluding firm conclusions on anatomical compartmentalization in the lung.
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Brait N, Külekçi B, Goerzer I. Long range PCR-based deep sequencing for haplotype determination in mixed HCMV infections. BMC Genomics 2022; 23:31. [PMID: 34991471 PMCID: PMC8735729 DOI: 10.1186/s12864-021-08272-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 12/03/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Short read sequencing has been used extensively to decipher the genome diversity of human cytomegalovirus (HCMV) strains, but falls short to reveal individual genomes in mixed HCMV strain populations. Novel third-generation sequencing platforms offer an extended read length and promise to resolve how distant polymorphic sites along individual genomes are linked. In the present study, we established a long amplicon PacBio sequencing workflow to identify the absolute and relative quantities of unique HCMV haplotypes spanning over multiple hypervariable sites in mixtures. Initial validation of this approach was performed with defined HCMV DNA templates derived from cell-culture enriched viruses and was further tested for its suitability on patient samples carrying mixed HCMV infections. RESULTS Total substitution and indel error rate of mapped reads ranged from 0.17 to 0.43% depending on the stringency of quality trimming. Artificial HCMV DNA mixtures were correctly determined down to 1% abundance of the minor DNA source when the total HCMV DNA input was 4 × 104 copies/ml. PCR products of up to 7.7 kb and a GC content < 55% were efficiently generated when DNA was directly isolated from patient samples. In a single sample, up to three distinct haplotypes were identified showing varying relative frequencies. Alignments of distinct haplotype sequences within patient samples showed uneven distribution of sequence diversity, interspersed by long identical stretches. Moreover, diversity estimation at single polymorphic regions as assessed by short amplicon sequencing may markedly underestimate the overall diversity of mixed haplotype populations. CONCLUSIONS Quantitative haplotype determination by long amplicon sequencing provides a novel approach for HCMV strain characterisation in mixed infected samples which can be scaled up to cover the majority of the genome by multi-amplicon panels. This will substantially improve our understanding of intra-host HCMV strain diversity and its dynamic behaviour.
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Affiliation(s)
- Nadja Brait
- Center for Virology, Medical University of Vienna, Vienna, Austria
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Büşra Külekçi
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Irene Goerzer
- Center for Virology, Medical University of Vienna, Vienna, Austria.
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Galitska G, Coscia A, Forni D, Steinbrueck L, De Meo S, Biolatti M, De Andrea M, Cagliani R, Leone A, Bertino E, Schulz T, Santoni A, Landolfo S, Sironi M, Cerboni C, Dell'Oste V. Genetic Variability of Human Cytomegalovirus Clinical Isolates Correlates With Altered Expression of Natural Killer Cell-Activating Ligands and IFN-γ. Front Immunol 2021; 12:532484. [PMID: 33897679 PMCID: PMC8062705 DOI: 10.3389/fimmu.2021.532484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 03/23/2021] [Indexed: 01/03/2023] Open
Abstract
Human cytomegalovirus (HCMV) infection often leads to systemic disease in immunodeficient patients and congenitally infected children. Despite its clinical significance, the exact mechanisms contributing to HCMV pathogenesis and clinical outcomes have yet to be determined. One of such mechanisms involves HCMV-mediated NK cell immune response, which favors viral immune evasion by hindering NK cell-mediated cytolysis. This process appears to be dependent on the extent of HCMV genetic variation as high levels of variability in viral genes involved in immune escape have an impact on viral pathogenesis. However, the link between viral genome variations and their functional effects has so far remained elusive. Thus, here we sought to determine whether inter-host genetic variability of HCMV influences its ability to modulate NK cell responses to infection. For this purpose, five HCMV clinical isolates from a previously characterized cohort of pediatric patients with confirmed HCMV congenital infection were evaluated by next-generation sequencing (NGS) for genetic polymorphisms, phylogenetic relationships, and multiple-strain infection. We report variable levels of genetic characteristics among the selected clinical strains, with moderate variations in genome regions associated with modulation of NK cell functions. Remarkably, we show that different HCMV clinical strains differentially modulate the expression of several ligands for the NK cell-activating receptors NKG2D, DNAM-1/CD226, and NKp30. Specifically, the DNAM-1/CD226 ligand PVR/CD155 appears to be predominantly upregulated by fast-replicating (“aggressive”) HCMV isolates. On the other hand, the NGK2D ligands ULBP2/5/6 are downregulated regardless of the strain used, while other NK cell ligands (i.e., MICA, MICB, ULBP3, Nectin-2/CD112, and B7-H6) are not significantly modulated. Furthermore, we show that IFN-γ; production by NK cells co-cultured with HCMV-infected fibroblasts is directly proportional to the aggressiveness of the HCMV clinical isolates employed. Interestingly, loss of NK cell-modulating genes directed against NK cell ligands appears to be a common feature among the “aggressive” HCMV strains, which also share several gene variants across their genomes. Overall, even though further studies based on a higher number of patients would offer a more definitive scenario, our findings provide novel mechanistic insights into the impact of HCMV genetic variability on NK cell-mediated immune responses.
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Affiliation(s)
- Ganna Galitska
- Laboratory of Pathogenesis of Viral Infections, 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
| | - Diego Forni
- Laboratory of Bioinformatics, Scientific Institute IRCCS E. Medea, Bosisio Parini, Italy
| | - Lars Steinbrueck
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Simone De Meo
- Laboratory of Molecular Immunology and Immunopathology, Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Matteo Biolatti
- Laboratory of Pathogenesis of Viral Infections, Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Marco De Andrea
- Laboratory of Pathogenesis of Viral Infections, Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy.,Center for Translational Research on Autoimmune and Allergic Disease - CAAD, University of Piemonte Orientale, Novara, Italy
| | - Rachele Cagliani
- Laboratory of Bioinformatics, Scientific Institute IRCCS E. Medea, Bosisio Parini, Italy
| | - Agata Leone
- Neonatal Unit, Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Enrico Bertino
- Neonatal Unit, Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Thomas Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Angela Santoni
- Laboratory of Molecular Immunology and Immunopathology, Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Santo Landolfo
- Laboratory of Pathogenesis of Viral Infections, Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Manuela Sironi
- Laboratory of Bioinformatics, Scientific Institute IRCCS E. Medea, Bosisio Parini, Italy
| | - Cristina Cerboni
- Laboratory of Molecular Immunology and Immunopathology, Department of Molecular Medicine, "Sapienza" University of Rome, Rome, Italy
| | - Valentina Dell'Oste
- Laboratory of Pathogenesis of Viral Infections, Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
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Baldo F, Suárez NM, Davison AJ, Zanon D, Barbi E, Maximova N. Post-HSCT graft failure due to refractory human cytomegalovirus successfully treated with haploidentical donor-derived immunoglobulins and stem cell graft infusion: A case report. Antiviral Res 2021; 188:105024. [PMID: 33577809 PMCID: PMC9188265 DOI: 10.1016/j.antiviral.2021.105024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/23/2021] [Accepted: 01/25/2021] [Indexed: 11/05/2022]
Abstract
Background Human cytomegalovirus (HCMV) remains an important cause of transplant-related morbidity and mortality. The incidence of HCMV recurrence in the donor seronegative (D-)/recipient seropositive (R+) group is significantly higher than in other serostatus combinations as a result of a lack of pre-existing HCMV-specific memory T-lymphocytes in the donor, coupled with the eradication of the recipient's cellular immunity due to the conditioning regimen. Case presentation We describe the case of an 8-year-old βE-thalassemic girl from Bangladesh who was seropositive for human cytomegalovirus (HCMV) and underwent hematopoietic stem cell transplantation from a HLA-matched, unrelated, HCMV-seronegative donor. Despite administering antiviral prophylaxis with commercial pooled anti-HCMV immunoglobulin (Ig) from day +1, the post-transplant course was complicated by prompt viral reactivation, and foscarnet therapy was initiated. The virus was refractory to treatment, leading rapidly to complete bone marrow failure, and targeted immunotherapy was proposed as a second-line therapy. Hypothesizing that the patient and her relatives may have been exposed to similar HCMV strains, we selected the patient's mother, who presented a high HCMV antibody titer, as the donor of virus strain-specific anti-HCMV Ig and T-lymphocytes. Complete viral clearance was achieved after two transfusions of the mother's plasma. Subsequently, the patient underwent a haploidentical rescue transplant, promptly reaching full hematological recovery. Conclusion These findings suggest that treatment with virus strain-specific Ig may offer a new therapeutic option for critically ill patients. Human cytomegalovirus (HCMV) remains an important cause of transplant-related morbidity and mortality. Reactivation of multiple viral strains is particularly challenging to eradicate. . Virus strain-specific Ig is an inexpensive, non-toxic therapy to treat HCMV reactivation and improve transplant outcomes. . The efficacy of this approach as a means of prevention has only been demonstrated previously in mouse models.
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Affiliation(s)
- Francesco Baldo
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy.
| | - Nicolás M Suárez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom.
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom.
| | - Davide Zanon
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste, Italy.
| | - Egidio Barbi
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy; Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste, Italy.
| | - Natalia Maximova
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo, Trieste, Italy.
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Leleu I, Jhanji V, Touhami S, Westcott M, Angi M, Titah C, Rousseau A, Hamard P, Brasnu E, Manicom T, Blumen-Ohana E, Rozenberg F, Vauloup-Fellous C, Deback C, Labetoulle M, Sahel JA, Bodaghi B, Merabet L, Kobal A, Brignole-Baudouin F, Errera MH. Clinical Features and Diagnosis of Anterior Segment Inflammation Related to Cytomegalovirus in Immunocompetent African, Asian, and Caucasian Patients. Ocul Immunol Inflamm 2021; 29:160-168. [PMID: 31642720 DOI: 10.1080/09273948.2019.1662059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 08/27/2019] [Accepted: 08/27/2019] [Indexed: 12/11/2022]
Abstract
Objective: To report the clinical features and treatment outcomes in immunocompetent patients with anterior segment inflammation (ASI) related to human cytomegalovirus (HCMV) depending on their ethnic origin.Material and Methods: Multicenter retrospective study of 38 patients with at least one test, either HCMV-positive PCR or GWc.Results: Features of Posner-Schlossman syndrome were observed in 50% of the eyes, Fuchs heterochromic iridocyclitis in 13% of the eyes, chronic nonspecific anterior uveitis in 21% of the eyes, and corneal endotheliitis in 18% of the eyes. PCR and GWc were positive for HCMV in 50% and 96.2% of the eyes, respectively. Glaucoma was diagnosed in 50% of eyes. Treatment was oral valganciclovir in about half of the patients. Other treatments were intravenous ganciclovir and/or ganciclovir topical ointment and/or intravitreal ganciclovir.Conclusions: No obvious association of specific clinical features with individual ethnicity could be identified. We found a high rate of glaucoma in all ethnic groups. There was a delay in diagnosis and specific treatment of HCMV in most patients.
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Affiliation(s)
- Igor Leleu
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Ophthalmology Department and Laboratory and DHU Sight Restore, Paris, France
| | | | - Sara Touhami
- Department of Ophthalmology, Hôpital de la Pitié-Salpêtrière, Paris, France
- Department of Ophthalmology, Hôpital de Lariboisière, Paris, France
| | - Mark Westcott
- Department of Medical Retina, Moorfields Eye Hospital, NHS Foundation Trust, London, UK
- Biomedical Research Centre, UCL Institute of Ophthalmology, London, UK
| | - Martina Angi
- Department of Ophthalmology, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Cherif Titah
- Department of Ophthalmology, Fondation Ophthalmologique de Rothschild, Paris, France
| | - Antoine Rousseau
- Department of Ophthalmology, Hôpital Bicêtre, Université Paris Sud, APHP, Paris, France
| | - Pascale Hamard
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Ophthalmology Department and Laboratory and DHU Sight Restore, Paris, France
| | - Emmanuelle Brasnu
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Ophthalmology Department and Laboratory and DHU Sight Restore, Paris, France
| | - Thomas Manicom
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Ophthalmology Department and Laboratory and DHU Sight Restore, Paris, France
| | - Esther Blumen-Ohana
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Ophthalmology Department and Laboratory and DHU Sight Restore, Paris, France
| | - Flore Rozenberg
- Université Paris Descartes, Paris, France
- Virology Department, Hôpital Cochin, Université Paris V, Paris, France
| | | | - Claire Deback
- Virology Department, Université Paris Sud, APHP, Villejuif, France
| | - Marc Labetoulle
- Department of Ophthalmology, Hôpital Bicêtre, Université Paris Sud, APHP, Paris, France
| | - Jose-Alain Sahel
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Ophthalmology Department and Laboratory and DHU Sight Restore, Paris, France
- Sorbonne Universités, UPMC Univ Paris VI, Paris, France
| | - Bahram Bodaghi
- Department of Ophthalmology, Hôpital de la Pitié-Salpêtrière, Paris, France
- Sorbonne Universités, UPMC Univ Paris VI, Paris, France
| | - Lilia Merabet
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Ophthalmology Department and Laboratory and DHU Sight Restore, Paris, France
| | - Alfred Kobal
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Ophthalmology Department and Laboratory and DHU Sight Restore, Paris, France
| | - Françoise Brignole-Baudouin
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Ophthalmology Department and Laboratory and DHU Sight Restore, Paris, France
- Virology Department, Hôpital Cochin, Université Paris V, Paris, France
| | - Marie-Hélène Errera
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Ophthalmology Department and Laboratory and DHU Sight Restore, Paris, France
- Pittsburgh University Hospital, Pittsburgh, PA, USA
- Sorbonne Universités, UPMC Univ Paris VI, Paris, France
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Camiolo S, Suárez NM, Chalka A, Venturini C, Breuer J, Davison AJ. GRACy: A tool for analysing human cytomegalovirus sequence data. Virus Evol 2020; 7:veaa099. [PMID: 33505707 PMCID: PMC7816668 DOI: 10.1093/ve/veaa099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Modern DNA sequencing has instituted a new era in human cytomegalovirus (HCMV) genomics. A key development has been the ability to determine the genome sequences of HCMV strains directly from clinical material. This involves the application of complex and often non-standardized bioinformatics approaches to analysing data of variable quality in a process that requires substantial manual intervention. To relieve this bottleneck, we have developed GRACy (Genome Reconstruction and Annotation of Cytomegalovirus), an easy-to-use toolkit for analysing HCMV sequence data. GRACy automates and integrates modules for read filtering, genotyping, genome assembly, genome annotation, variant analysis, and data submission. These modules were tested extensively on simulated and experimental data and outperformed generic approaches. GRACy is written in Python and is embedded in a graphical user interface with all required dependencies installed by a single command. It runs on the Linux operating system and is designed to allow the future implementation of a cross-platform version. GRACy is distributed under a GPL 3.0 license and is freely available at https://bioinformatics.cvr.ac.uk/software/ with the manual and a test dataset.
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Affiliation(s)
| | - Nicolás M Suárez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Antonia Chalka
- Division of Infection & Immunity, Roslin Institute, R(D)SVM, University of Edinburgh, Edinburgh, UK
| | - Cristina Venturini
- Division of Infection and Immunity, University College London, London, UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
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9
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Brait N, Stögerer T, Kalser J, Adler B, Kunz I, Benesch M, Kropff B, Mach M, Puchhammer-Stöckl E, Görzer I. Influence of Human Cytomegalovirus Glycoprotein O Polymorphism on the Inhibitory Effect of Soluble Forms of Trimer- and Pentamer-Specific Entry Receptors. J Virol 2020; 94:e00107-20. [PMID: 32350071 PMCID: PMC7343208 DOI: 10.1128/jvi.00107-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/21/2020] [Indexed: 01/24/2023] Open
Abstract
Human cytomegalovirus (HCMV) envelope glycoprotein complexes, gH/gL/gO trimer and gH/gL/UL128-131 pentamer, are important for cell-free HCMV entry. While soluble NRP2-Fc (sNRP2-Fc) interferes with epithelial/endothelial cell entry through UL128, soluble platelet-derived growth factor receptor α-Fc (sPDGFRα-Fc) interacts with gO, thereby inhibiting infection of all cell types. Since gO is the most variable subunit, we investigated the influence of gO polymorphism on the inhibitory capacities of sPDGFRα-Fc and sNRP2-Fc. Accordingly, gO genotype 1c (GT1c) sequence was fully or partially replaced by gO GT2b, GT3, and GT5 sequences in the bacterial artificial chromosome (BAC) TB40-BAC4-luc background (where luc is luciferase). All mutants were tested for fibroblast and epithelial cell infectivity, for virion content of gB, gH, and gO, and for infection inhibition by sPDGFRα-Fc and sNRP2-Fc. Full-length and partial gO GT swapping may increase epithelial-to-fibroblast ratios due to subtle alterations in fibroblast and/or epithelial infectivity but without substantial changes in gB and gH levels in mutant virions. All gO GT mutants except recombinant gO GT1c/3 displayed a nearly complete inhibition at 1.25 μg/ml sPDGFRα-Fc on epithelial cells (98% versus 91%), and all experienced complete inhibition on fibroblasts (≥99%). While gO GT replacement did not influence sNRP2-Fc inhibition at 1.25 μg/ml on epithelial cells (97% to 99%), it rendered recombinant mutant GT1c/3 moderately accessible to fibroblast inhibition (40%). In contrast to the steep sPDGFRα-Fc inhibition curves (slope of >1.0), sNRP2-Fc dose-response curves on epithelial cells displayed slopes of ∼1.0, suggesting functional differences between these entry inhibitors. Our findings demonstrate that artificially generated gO recombinants rather than the major gO genotypic forms may affect the inhibitory capacities of sPDGFRα and sNRP2 in a cell type-dependent manner.IMPORTANCE Human cytomegalovirus (HCMV) is known for its broad cell tropism, as reflected by the different organs and tissues affected by HCMV infection. Hence, inhibition of HCMV entry into distinct cell types could be considered a promising therapeutic option to limit cell-free HCMV infection. Soluble forms of cellular entry receptor PDGFRα rather than those of entry receptor neuropilin-2 inhibit infection of multiple cell types. sPDGFRα specifically interacts with gO of the trimeric gH/gL/gO envelope glycoprotein complex. HCMV strains may differ with respect to the amounts of trimer in virions and the highly polymorphic gO sequence. In this study, we show that the major gO genotypes of HCMV that are also found in vivo are similarly well inhibited by sPDGFRα. Novel gO genotypic forms potentially emerging through recombination, however, may evade sPDGFRα inhibition on epithelial cells. These findings provide useful additional information for the future development of anti-HCMV therapeutic compounds based on sPDGFRα.
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Affiliation(s)
- Nadja Brait
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Tanja Stögerer
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Julia Kalser
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Barbara Adler
- Max von Pettenkofer Institute for Virology, Ludwig Maximilians University Munich, Munich, Germany
| | - Ines Kunz
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Max Benesch
- Center for Virology, Medical University of Vienna, Vienna, Austria
| | - Barbara Kropff
- Virologisches Institut, Klinische und Molekulare Virologie, Friedrich Alexander Universität Erlangen Nürnberg, Erlangen, Germany
| | - Michael Mach
- Virologisches Institut, Klinische und Molekulare Virologie, Friedrich Alexander Universität Erlangen Nürnberg, Erlangen, Germany
| | | | - Irene Görzer
- Center for Virology, Medical University of Vienna, Vienna, Austria
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10
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Richardson AK, Walker LC, Cox B, Rollag H, Robinson BA, Morrin H, Pearson JF, Potter JD, Paterson M, Surcel HM, Pukkala E, Currie MJ. Breast cancer and cytomegalovirus. Clin Transl Oncol 2019; 22:585-602. [PMID: 31256361 DOI: 10.1007/s12094-019-02164-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 06/14/2019] [Indexed: 12/24/2022]
Abstract
PURPOSE To determine whether cytomegalovirus is causally associated with breast cancer and whether cytomegalovirus should be categorised as an oncogenic virus. METHODS We undertook a review of published epidemiological and laboratory studies, using established causal criteria: Bradford Hill criteria to determine whether cytomegalovirus is associated with breast cancer; and Evans/Mueller criteria to determine whether cytomegalovirus should be categorised as an oncogenic virus. RESULTS Although there are inconsistencies in the findings of published epidemiological and laboratory studies, these may be explained by factors such as: differences in timing of blood samples, differences in selection of cases and controls, or high cytomegalovirus seroprevalence among participants in the epidemiological studies; and, in the laboratory studies, differences in sample preparations, age of sample, whether or not paired breast cancer and normal breast tissue samples were used, differences in the tests, primers and/or antibodies used, differences in histological types of breast cancer studied, and/or features of the virus. CONCLUSIONS Overall, the results of published studies of cytomegalovirus and breast cancer suggest cytomegalovirus is a causal factor for at least some types of breast cancer. If the evidence for a link between cytomegalovirus and breast cancer continues to strengthen, further research could lead to: targeted screening; therapy using antiviral drugs; and, perhaps, primary prevention of a significant proportion of breast cancer. Vaccination against viruses has already been shown to be effective in preventing cervix and liver cancer; cytomegalovirus vaccines are already under development.
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Affiliation(s)
- A K Richardson
- Wayne Francis Cancer Epidemiology Research Group, School of Health Sciences, University of Canterbury, Christchurch, New Zealand.
| | - L C Walker
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - B Cox
- Hugh Adam Cancer Epidemiology Unit, Department of Preventive and Social Medicine, University of Otago, Dunedin, New Zealand
| | - H Rollag
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - B A Robinson
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - H Morrin
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
| | - J F Pearson
- Department of the Dean, University of Otago Christchurch, Christchurch, New Zealand
| | - J D Potter
- Wayne Francis Cancer Epidemiology Research Group, School of Health Sciences, University of Canterbury, Christchurch, New Zealand.,Centre for Public Health Research, Massey University, Wellington, New Zealand.,Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - M Paterson
- University of Canterbury Library, University of Canterbury, Christchurch, New Zealand
| | - H-M Surcel
- European Science Infrastructure Services, University of Oulu, Oulu, Finland
| | - E Pukkala
- Finnish Cancer Registry Institute for Statistical and Epidemiological Cancer Research, Helsinki, Finland.,Faculty of Social Sciences, University of Tampere, Tampere, Finland
| | - M J Currie
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago Christchurch, Christchurch, New Zealand
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11
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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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12
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Sackman AM, Pfeifer SP, Kowalik TF, Jensen JD. On the Demographic and Selective Forces Shaping Patterns of Human Cytomegalovirus Variation within Hosts. Pathogens 2018; 7:pathogens7010016. [PMID: 29382090 PMCID: PMC5874742 DOI: 10.3390/pathogens7010016] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 01/23/2018] [Accepted: 01/25/2018] [Indexed: 02/08/2023] Open
Abstract
Human cytomegalovirus (HCMV) is a member of the β -herpesvirus subfamily within Herpesviridae that is nearly ubiquitous in human populations, and infection generally results only in mild symptoms. However, symptoms can be severe in immunonaive individuals, and transplacental congenital infection of HCMV can result in serious neurological sequelae. Recent work has revealed much about the demographic and selective forces shaping the evolution of congenitally transmitted HCMV both on the level of hosts and within host compartments, providing insight into the dynamics of congenital infection, reinfection, and evolution of HCMV with important implications for the development of effective treatments and vaccines.
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Affiliation(s)
- Andrew M Sackman
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA.
| | - Susanne P Pfeifer
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA.
| | - Timothy F Kowalik
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA.
| | - Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA.
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13
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Vinuesa V, Bracho MA, Albert E, Solano C, Torres-Puente M, Giménez E, González-Candelas F, Navarro D. The impact of virus population diversity on the dynamics of cytomegalovirus DNAemia in allogeneic stem cell transplant recipients. J Gen Virol 2017; 98:2530-2542. [PMID: 28874227 DOI: 10.1099/jgv.0.000916] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Mixed cytomegalovirus (CMV) infections are associated with delayed viral clearance in solid organ transplant recipients. We investigated whether this could be extrapolated to allogeneic stem cell transplant (allo-SCT) recipients. A total of 48 plasma specimens, obtained during 29 episodes of active CMV infection in 25 non-consecutive allo-SCT patients, were analysed. Baseline blood specimens, drawn shortly prior to the inception of pre-emptive antiviral therapy (pre-treatment specimen; n=29), as well as follow-up samples obtained either after the initiation of antiviral therapy (post-treatment specimen; n=15) or during recurrent episodes (n=4) were analysed. Plasma CMV DNA loads were quantified by real-time PCR and the CMV genotyping was performed by ultra-deep sequencing of hypervariable regions in the genes coding for glycoproteins N (gN) and O (gO). A trend towards higher CMV DNA peak loads, longer CMV DNAemia episode durations and slower CMV DNAemia decay rates was observed for episodes with mixed CMV genotype populations compared to those caused by single CMV variants, although the differences did not reach statistical significance. The length of the treatment course required to clear DNAemia was significantly longer in these mixed episodes (P=0.002). Significant changes in the number or frequency of CMV gN or gO genetic variants were documented following the initiation of antiviral therapy or in recurrent episodes. CMV diversity may have a major impact on the kinetics of CMV DNAemia clearance during the treatment of active CMV infection episodes in allo-SCT recipients.
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Affiliation(s)
- Víctor Vinuesa
- Microbiology Service, Hospital Clínico Universitario, Instituto de Investigación INCLIVA, Valencia, Spain
| | - María Alma Bracho
- Unidad Mixta 'Infección y Salud Pública' FISABIO-Salud Pública, Valencia, Spain
| | - Eliseo Albert
- Microbiology Service, Hospital Clínico Universitario, Instituto de Investigación INCLIVA, Valencia, Spain
| | - Carlos Solano
- Hematology Service, Hospital Clínico Universitario, Instituto de Investigación INCLIVA, Valencia, Spain.,Department of Medicine, School of Medicine, University of Valencia, Valencia, Spain
| | | | - Estela Giménez
- Microbiology Service, Hospital Clínico Universitario, Instituto de Investigación INCLIVA, Valencia, Spain
| | - Fernando González-Candelas
- Unidad Mixta 'Infección y Salud Pública' FISABIO-Salud Pública, Valencia, Spain.,CIBER Epidemiología y Salud Pública, Valencia, Spain.,Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Valencia, Spain
| | - David Navarro
- Microbiology Service, Hospital Clínico Universitario, Instituto de Investigación INCLIVA, Valencia, Spain.,Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain
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14
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Kalser J, Adler B, Mach M, Kropff B, Puchhammer-Stöckl E, Görzer I. Differences in Growth Properties among Two Human Cytomegalovirus Glycoprotein O Genotypes. Front Microbiol 2017; 8:1609. [PMID: 28878758 PMCID: PMC5572245 DOI: 10.3389/fmicb.2017.01609] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/07/2017] [Indexed: 11/22/2022] Open
Abstract
Glycoprotein O (gO) of the human cytomegalovirus (HCMV) is the critical subunit of the envelope trimer gH/gL/gO as it interacts with platelet-derived growth factor alpha receptor upon fibroblast entry, and triggers gB-mediated fusion for fibroblast and epithelial cell infection. Eight genotypes (GT) of the highly polymorphic gO gene are described, yet it is unclear whether the distinct GTs differ in their function. Thus, we aimed to elucidate potential functional differences between two highly diverse gO GTs in an otherwise genomically identical HCMV strain. Therefore, resident gO GT1c sequence of strain TB40-BAC4-luc was entirely replaced by gO GT4 of strain Towne and both, GT1c and GT4 viruses, were investigated for their growth properties in fibroblasts and epithelial cells. In addition, two conserved gO cysteines involved in gH/gL/gO stabilization were mutated to serine either in GT1c (C218S and C343S) or GT4 (C216S and C336S) and their effects on cell-free infectivity were assessed. GT4 viruses displayed a significantly enhanced epithelial cell tropism and this resulted in higher virus release upon replication in epithelial cells when compared to GT1c viruses. Further, when the two cysteines were individually mutated in gO GT1c no impairment in cell-free infectivity was observed. This, however, was in sharp contrast to gO GT4, in which both of the corresponding cysteine mutations led to a substantial reduction in cell-free infectivity which was even more pronounced upon mutation of GT4-C336 than of GT4-C216. In conclusion, these findings provide evidence that the two highly diverse gO genotypes, GT1c and GT4, differ in their functional properties as revealed by their different infection capacities for epithelial cells and by their different responsiveness to mutation of strictly conserved cysteine residues. Thus, it is likely that the gO heterogeneity influences cell-free infectivity of HCMV also in vivo which may have important implications for virus host transmission.
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Affiliation(s)
- Julia Kalser
- Center for Virology, Medical University of ViennaVienna, Austria
| | - Barbara Adler
- Max von Pettenkofer-Institute for Virology, Ludwig-Maximilians-University MunichMunich, Germany
| | - Michael Mach
- Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-NürnbergErlangen, Germany
| | - Barbara Kropff
- Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-NürnbergErlangen, Germany
| | | | - Irene Görzer
- Center for Virology, Medical University of ViennaVienna, Austria
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15
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Hage E, Wilkie GS, Linnenweber-Held S, Dhingra A, Suárez NM, Schmidt JJ, Kay-Fedorov PC, Mischak-Weissinger E, Heim A, Schwarz A, Schulz TF, Davison AJ, Ganzenmueller T. Characterization of Human Cytomegalovirus Genome Diversity in Immunocompromised Hosts by Whole-Genome Sequencing Directly From Clinical Specimens. J Infect Dis 2017; 215:1673-1683. [PMID: 28368496 DOI: 10.1093/infdis/jix157] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 03/22/2017] [Indexed: 01/19/2023] Open
Abstract
Background Advances in next-generation sequencing (NGS) technologies allow comprehensive studies of genetic diversity over the entire genome of human cytomegalovirus (HCMV), a significant pathogen for immunocompromised individuals. Methods Next-generation sequencing was performed on target enriched sequence libraries prepared directly from a variety of clinical specimens (blood, urine, breast milk, respiratory samples, biopsies, and vitreous humor) obtained longitudinally or from different anatomical compartments from 20 HCMV-infected patients (renal transplant recipients, stem cell transplant recipients, and congenitally infected children). Results De novo-assembled HCMV genome sequences were obtained for 57 of 68 sequenced samples. Analysis of longitudinal or compartmental HCMV diversity revealed various patterns: no major differences were detected among longitudinal, intraindividual blood samples from 9 of 15 patients and in most of the patients with compartmental samples, whereas a switch of the major HCMV population was observed in 6 individuals with sequential blood samples and upon compartmental analysis of 1 patient with HCMV retinitis. Variant analysis revealed additional aspects of minor virus population dynamics and antiviral-resistance mutations. Conclusions In immunosuppressed patients, HCMV can remain relatively stable or undergo drastic genomic changes that are suggestive of the emergence of minor resident strains or de novo infection.
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Affiliation(s)
- Elias Hage
- Institute of Virology
- German Centre for Infection Research, Hannover-Braunschweig, Germany
| | - Gavin S Wilkie
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | | | - Akshay Dhingra
- Institute of Virology
- German Centre for Infection Research, Hannover-Braunschweig, Germany
| | - Nicolás M Suárez
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | | | - Penelope C Kay-Fedorov
- Institute of Virology
- German Centre for Infection Research, Hannover-Braunschweig, Germany
| | - Eva Mischak-Weissinger
- Department of Haematology, Haemostasis and Oncology, Hannover Medical School
- German Centre for Infection Research, Hannover-Braunschweig, Germany
| | - Albert Heim
- Institute of Virology
- German Centre for Infection Research, Hannover-Braunschweig, Germany
| | | | - Thomas F Schulz
- Institute of Virology
- German Centre for Infection Research, Hannover-Braunschweig, Germany
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, United Kingdom
| | - Tina Ganzenmueller
- Institute of Virology
- German Centre for Infection Research, Hannover-Braunschweig, Germany
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16
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Talkhabifard M, Javid N, Moradi A, Ghaemi A, Tabarraei A. Evaluation of a Probe-Based PCR-ELISA System for Simultaneous Semi Quantitative Detection and Genotyping of Human Cytomegalovirus (HCMV) Infection in Clinical Specimens. Open Microbiol J 2017; 11:83-91. [PMID: 28694881 PMCID: PMC5481617 DOI: 10.2174/1874285801711010083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 03/12/2017] [Accepted: 03/19/2017] [Indexed: 12/29/2022] Open
Abstract
Background: Human cytomegalovirus (HCMV) is a common opportunistic pathogen that causes serious complications in immunosuppressed patients and infected newborns. In this study, PCR-ELISA was optimized for semi-quantitative detection of infection in clinical specimens and simultaneous genotyping of glycoprotein B for 4 major genotypes, due to its significance. Method: During DIG-labeling PCR, a pair of primers amplifies a fragment of variable region of the glycoprotein B encoding sequence. Under optimized conditions, labeled Target amplicons hybridize to biotinated specific probes and are detected in an ELISA system. Results: PCR-ELISA system showed specific performance with detection limit of approximately 100 copies of CMV DNA. The linear correlation was observed between the PCR-ELISA results (OD) and logarithmic scale of CMV (r=0.979). Repeatability of PCR-ELISA detection system for intra-assay and inter-assay was evaluated for negative and positive samples. In optimized conditions of hybridization, differentiation between genotypes of glycoprotein B was feasible using genotype-specific probes in PCR-ELISA genotyping system. In comparison with sequencing method, genotyping system was confirmed with kappa index of 1. Conclusion: PCR-ELISA is proposed as an applicable and reliable technique for semi-quantitative diagnosis and typing of the infection. This technique is flexible to apply in a variety of molecular fields.
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Affiliation(s)
- Majid Talkhabifard
- Faculty of Advanced Medical Technologies, Golestan University of Medical Sciences, Gorgan, Iran
| | - Naeme Javid
- Department of Microbiology, Golestan University of Medical Sciences, Gorgan, Iran
| | - Abdolvahab Moradi
- Department of Microbiology, Golestan University of Medical Sciences, Gorgan, Iran
| | - Amir Ghaemi
- Department of Microbiology, Golestan University of Medical Sciences, Gorgan, Iran
| | - Alijan Tabarraei
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, Iran
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17
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Moazen B, Ebrahimi E, Nejatollahi F. Single Chain Antibodies Against gp55 of Human Cytomegalovirus (HCMV) for Prophylaxis and Treatment of HCMV Infections. Jundishapur J Microbiol 2016; 9:e16241. [PMID: 27217918 PMCID: PMC4870390 DOI: 10.5812/jjm.16241] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 07/18/2014] [Accepted: 07/23/2014] [Indexed: 02/06/2023] Open
Abstract
Background: Immunotherapy is a promising prospective new treatment for cytomegalovirus (CMV) infections. Neutralizing effects have been reported using monoclonal antibodies. Recombinant single chain antibodies (scFvs) due to their advantages over monoclonal antibodies are potential alternatives and provide valuable clinical agents. Objectives: The aim of this study was to select specific single chain antibodies against gp55 of CMV and to evaluate their neutralizing effects. In the present study, we selected specific single chain antibodies against glycoprotein 55 (gp55) of CMV for their use in treatment and diagnosis. Materials and Methods: Single chain antibodies specific against an epitope located in the C-terminal part of gp55 were selected from a phage antibody display library. After four rounds of panning, twenty clones were amplified by the polymerase chain reaction (PCR) and fingerprinted by MvaI restriction enzyme. The reactivities of the specific clones were tested by the enzyme-linked immunosorbent assay (ELISA) and the neutralizing effects were evaluated by the plaque reduction assay. Results: Fingerprinting of selected clones revealed three specific single chain antibodies (scFv1, scFv2 and scFv3) with frequencies 25%, 20 and 20%. The clones produced positive ELISA with the corresponding peptide. The percentages of plaque reduction for scFv1, scFv2 and scFv3 were 23.7, 68.8 and 11.6, respectively. Conclusions: Gp55 of human CMV is considered as an important candidate for immunotherapy. In this study, we selected three specific clones against gp55. The scFvs reacted only with the corresponding peptide in a positive ELISA. The scFv2 with 68.8% neutralizing effect showed the potential to be considered for prophylaxis and treatment of CMV infections, especially in solid organ transplant recipients, for whom treatment of CMV is urgently needed. The scFv2 with neutralizing effect of 68.8%, has the potential to be considered for treatment of these patients. The specific scFv1 and scFv3 with lower neutralizing effects can be used for diagnostic purposes.
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Affiliation(s)
- Bahareh Moazen
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, IR Iran
| | - Elahe Ebrahimi
- Department of Immunology, Recombinant Antibody Laboratory, Shiraz University of Medical Sciences, Shiraz, IR Iran
| | - Foroogh Nejatollahi
- Shiraz HIV/AIDS Research Center, Shiraz University of Medical Sciences, Shiraz, IR Iran
- Department of Immunology, Recombinant Antibody Laboratory, Shiraz University of Medical Sciences, Shiraz, IR Iran
- Corresponding author: Foroogh Nejatollahi, Department of Immunology, Recombinant Antibody Laboratory, Shiraz University of Medical Sciences, Shiraz, IR Iran. Tel: +98-7112351575, Fax: +98-7112351575, E-mail:
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18
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Görzer I, Trajanoski S, Popow-Kraupp T, Puchhammer-Stöckl E. Analysis of human cytomegalovirus strain populations in urine samples of newborns by ultra deep sequencing. J Clin Virol 2015; 73:101-104. [DOI: 10.1016/j.jcv.2015.11.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 10/30/2015] [Accepted: 11/01/2015] [Indexed: 11/26/2022]
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19
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Zhao F, Shen ZZ, Liu ZY, Zeng WB, Cheng S, Ma YP, Rayner S, Yang B, Qiao GH, Jiang HF, Gao S, Zhu H, Xu FQ, Ruan Q, Luo MH. Identification and BAC construction of Han, the first characterized HCMV clinical strain in China. J Med Virol 2015; 88:859-70. [PMID: 26426373 DOI: 10.1002/jmv.24396] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2015] [Indexed: 11/10/2022]
Abstract
Human cytomegalovirus (HCMV) is the leading infectious cause of birth defects, and may lead to severe or lethal diseases in immunocompromised individuals. Several HCMV strains have been identified and widely applied in research, but no isolate from China has been characterized. In the present study, we isolated, characterized and sequenced the first Chinese HCMV clinical strain Han, and constructed the novel and functional HCMV infectious clone Han-BAC-2311. HCMV Han was isolated from the urine sample of a Chinese infant with multiple developmental disorders. It expresses HCMV specific proteins and contains a representative HCMV genome with minor differences compared to other strains. By homologous recombination using mini-F derived BAC vector pUS-F6, the infectious clone Han-BAC-2311 was constructed containing representative viral genes across the HCMV genome. The insertion site and orientation of BAC sequence were confirmed by restriction enzyme digestion and Southern blotting. The reconstituted recombinant virus HanBAC-2311 expresses typical viral proteins with the same pattern as that of wild-type Han, and also displayed a similar growth kinetics to wild-type Han. The identification of the first clinical HCMV strain in China and the construction of its infectious clone will greatly facilitate the pathogenesis studies and vaccine development in China.
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Affiliation(s)
- Fei Zhao
- State Key Laboratory of Virology, CAS Center for Excellence in Brain Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Zhang-Zhou Shen
- State Key Laboratory of Virology, CAS Center for Excellence in Brain Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Zhong-Yang Liu
- Virus Laboratory, The Affiliated Shengjing Hospital, China Medical University, Shenyang, China
| | - Wen-Bo Zeng
- State Key Laboratory of Virology, CAS Center for Excellence in Brain Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Shuang Cheng
- State Key Laboratory of Virology, CAS Center for Excellence in Brain Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yan-Ping Ma
- Virus Laboratory, The Affiliated Shengjing Hospital, China Medical University, Shenyang, China
| | - Simon Rayner
- State Key Laboratory of Virology, CAS Center for Excellence in Brain Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Bo Yang
- State Key Laboratory of Virology, CAS Center for Excellence in Brain Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Guan-Hua Qiao
- State Key Laboratory of Virology, CAS Center for Excellence in Brain Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Hai-Fei Jiang
- State Key Laboratory of Virology, CAS Center for Excellence in Brain Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Shuang Gao
- Virus Laboratory, The Affiliated Shengjing Hospital, China Medical University, Shenyang, China
| | - Hua Zhu
- Department of Microbiology and Molecular Genetics, UMDNJ-New Jersey Medical School, Newark, New Jersey, USA
| | - Fu-Qiang Xu
- Key Laboratory of Magnetic Resonance in Biological Systems and State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, CAS Center for Excellence in Brain Science, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, China
| | - Qiang Ruan
- Virus Laboratory, The Affiliated Shengjing Hospital, China Medical University, Shenyang, China
| | - Min-Hua Luo
- State Key Laboratory of Virology, CAS Center for Excellence in Brain Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
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20
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Renzette N, Kowalik TF, Jensen JD. On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity. Mol Ecol 2015. [PMID: 26211679 DOI: 10.1111/mec.13331] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A central focus of population genetics has been examining the contribution of selective and neutral processes in shaping patterns of intraspecies diversity. In terms of selection specifically, surveys of higher organisms have shown considerable variation in the relative contributions of background selection and genetic hitchhiking in shaping the distribution of polymorphisms, although these analyses have rarely been extended to bacteria and viruses. Here, we study the evolution of a ubiquitous, viral pathogen, human cytomegalovirus (HCMV), by analysing the relationship among intraspecies diversity, interspecies divergence and rates of recombination. We show that there is a strong correlation between diversity and divergence, consistent with expectations of neutral evolution. However, after correcting for divergence, there remains a significant correlation between intraspecies diversity and recombination rates, with additional analyses suggesting that this correlation is largely due to the effects of background selection. In addition, a small number of loci, centred on long noncoding RNAs, also show evidence of selective sweeps. These data suggest that HCMV evolution is dominated by neutral mechanisms as well as background selection, expanding our understanding of linked selection to a novel class of organisms.
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Affiliation(s)
- Nicholas Renzette
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01655, USA
| | - Timothy F Kowalik
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01655, USA.,Immunology and Microbiology Program, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01655, USA
| | - Jeffrey D Jensen
- Swiss Institute of Bioinformatics (SIB), Lausanne, CH-1015, Switzerland.,School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, CH-1015, Switzerland
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Abstract
Human cytomegalovirus (HCMV) exhibits surprisingly high genomic diversity during natural infection although little is known about the limits or patterns of HCMV diversity among humans. To address this deficiency, we analyzed genomic diversity among congenitally infected infants. We show that there is an upper limit to HCMV genomic diversity in these patient samples, with ∼ 25% of the genome being devoid of polymorphisms. These low diversity regions were distributed across 26 loci that were preferentially located in DNA-processing genes. Furthermore, by developing, to our knowledge, the first genome-wide mutation and recombination rate maps for HCMV, we show that genomic diversity is positively correlated with these two rates. In contrast, median levels of viral genomic diversity did not vary between putatively single or mixed strain infections. We also provide evidence that HCMV populations isolated from vascular compartments of hosts from different continents are genetically similar and that polymorphisms in glycoproteins and regulatory proteins are enriched in these viral populations. This analysis provides the most highly detailed map of HCMV genomic diversity in human hosts to date and informs our understanding of the distribution of HCMV genomic diversity within human hosts.
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High-throughput analysis of human cytomegalovirus genome diversity highlights the widespread occurrence of gene-disrupting mutations and pervasive recombination. J Virol 2015; 89:7673-7695. [PMID: 25972543 DOI: 10.1128/jvi.00578-15] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Human cytomegalovirus is a widespread pathogen of major medical importance. It causes significant morbidity and mortality in the immunocompromised and congenital infections can result in severe disabilities or stillbirth. Development of a vaccine is prioritized, but no candidate is close to release. Although correlations of viral genetic variability with pathogenicity are suspected, knowledge about strain diversity of the 235kb genome is still limited. In this study, 96 full-length human cytomegalovirus genomes from clinical isolates were characterized, quadrupling the available information for full-genome analysis. These data provide the first high-resolution map of human cytomegalovirus interhost diversity and evolution. We show that cytomegalovirus is significantly more divergent than all other human herpesviruses and highlight hotspots of diversity in the genome. Importantly, 75% of strains are not genetically intact, but contain disruptive mutations in a diverse set of 26 genes, including immunomodulative genes UL40 and UL111A. These mutants are independent from culture passaging artifacts and circulate in natural populations. Pervasive recombination, which is linked to the widespread occurrence of multiple infections, was found throughout the genome. Recombination density was significantly higher than in other human herpesviruses and correlated with strain diversity. While the overall effects of strong purifying selection on virus evolution are apparent, evidence of diversifying selection was found in several genes encoding proteins that interact with the host immune system, including UL18, UL40, UL142 and UL147. These residues may present phylogenetic signatures of past and ongoing virus-host interactions. IMPORTANCE Human cytomegalovirus has the largest genome of all viruses that infect humans. Currently, there is a great interest in establishing associations between genetic variants and strain pathogenicity of this herpesvirus. Since the number of publicly available full-genome sequences is limited, knowledge about strain diversity is highly fragmented and biased towards a small set of loci. Combined with our previous work, we have now contributed 101 complete genome sequences. We have used these data to conduct the first high-resolution analysis of interhost genome diversity, providing an unbiased and comprehensive overview of cytomegalovirus variability. These data are of major value to the development of novel antivirals and a vaccine and to identify potential targets for genotype-phenotype experiments. Furthermore, they have enabled a thorough study of the evolutionary processes that have shaped cytomegalovirus diversity.
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Sijmons S, Thys K, Corthout M, Van Damme E, Van Loock M, Bollen S, Baguet S, Aerssens J, Van Ranst M, Maes P. A method enabling high-throughput sequencing of human cytomegalovirus complete genomes from clinical isolates. PLoS One 2014; 9:e95501. [PMID: 24755734 PMCID: PMC3995935 DOI: 10.1371/journal.pone.0095501] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 03/26/2014] [Indexed: 12/20/2022] Open
Abstract
Human cytomegalovirus (HCMV) is a ubiquitous virus that can cause serious sequelae in immunocompromised patients and in the developing fetus. The coding capacity of the 235 kbp genome is still incompletely understood, and there is a pressing need to characterize genomic contents in clinical isolates. In this study, a procedure for the high-throughput generation of full genome consensus sequences from clinical HCMV isolates is presented. This method relies on low number passaging of clinical isolates on human fibroblasts, followed by digestion of cellular DNA and purification of viral DNA. After multiple displacement amplification, highly pure viral DNA is generated. These extracts are suitable for high-throughput next-generation sequencing and assembly of consensus sequences. Throughout a series of validation experiments, we showed that the workflow reproducibly generated consensus sequences representative for the virus population present in the original clinical material. Additionally, the performance of 454 GS FLX and/or Illumina Genome Analyzer datasets in consensus sequence deduction was evaluated. Based on assembly performance data, the Illumina Genome Analyzer was the platform of choice in the presented workflow. Analysis of the consensus sequences derived in this study confirmed the presence of gene-disrupting mutations in clinical HCMV isolates independent from in vitro passaging. These mutations were identified in genes RL5A, UL1, UL9, UL111A and UL150. In conclusion, the presented workflow provides opportunities for high-throughput characterization of complete HCMV genomes that could deliver new insights into HCMV coding capacity and genetic determinants of viral tropism and pathogenicity.
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Affiliation(s)
- Steven Sijmons
- Laboratory of Clinical Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
- * E-mail:
| | - Kim Thys
- Janssen Infectious Diseases BVBA, Beerse, Belgium
| | - Michaël Corthout
- Laboratory of Clinical Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | | | - Stefanie Bollen
- Laboratory of Clinical Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Sylvie Baguet
- Laboratory of Clinical Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Marc Van Ranst
- Laboratory of Clinical Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Piet Maes
- Laboratory of Clinical Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
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Sijmons S, Van Ranst M, Maes P. Genomic and functional characteristics of human cytomegalovirus revealed by next-generation sequencing. Viruses 2014; 6:1049-72. [PMID: 24603756 PMCID: PMC3970138 DOI: 10.3390/v6031049] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 02/11/2014] [Accepted: 02/11/2014] [Indexed: 01/08/2023] Open
Abstract
The complete genome of human cytomegalovirus (HCMV) was elucidated almost 25 years ago using a traditional cloning and Sanger sequencing approach. Analysis of the genetic content of additional laboratory and clinical isolates has lead to a better, albeit still incomplete, definition of the coding potential and diversity of wild-type HCMV strains. The introduction of a new generation of massively parallel sequencing technologies, collectively called next-generation sequencing, has profoundly increased the throughput and resolution of the genomics field. These increased possibilities are already leading to a better understanding of the circulating diversity of HCMV clinical isolates. The higher resolution of next-generation sequencing provides new opportunities in the study of intrahost viral population structures. Furthermore, deep sequencing enables novel diagnostic applications for sensitive drug resistance mutation detection. RNA-seq applications have changed the picture of the HCMV transcriptome, which resulted in proof of a vast amount of splicing events and alternative transcripts. This review discusses the application of next-generation sequencing technologies, which has provided a clearer picture of the intricate nature of the HCMV genome. The continuing development and application of novel sequencing technologies will further augment our understanding of this ubiquitous, but elusive, herpesvirus.
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Affiliation(s)
- Steven Sijmons
- Laboratory of Clinical Virology, Rega Institute for Medical Research, K.U.Leuven, Minderbroedersstraat 10, Leuven BE-3000, Belgium.
| | - Marc Van Ranst
- Laboratory of Clinical Virology, Rega Institute for Medical Research, K.U.Leuven, Minderbroedersstraat 10, Leuven BE-3000, Belgium.
| | - Piet Maes
- Laboratory of Clinical Virology, Rega Institute for Medical Research, K.U.Leuven, Minderbroedersstraat 10, Leuven BE-3000, Belgium.
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Ikuta K, Minematsu T, Inoue N, Kubo T, Asano K, Ishibashi K, Imamura T, Nakai H, Yoshikawa T, Moriuchi H, Fujiwara S, Koyano S, Suzutani T. Cytomegalovirus (CMV) glycoprotein H-based serological analysis in Japanese healthy pregnant women, and in neonates with congenital CMV infection and their mothers. J Clin Virol 2013; 58:474-8. [DOI: 10.1016/j.jcv.2013.07.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 06/25/2013] [Accepted: 07/03/2013] [Indexed: 11/30/2022]
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