1
|
Lohr B, Niemann D, Verheyen J. Bamlanivimab treatment leads to rapid selection of immune escape variant carrying E484K mutation in a B.1.1.7 infected and immunosuppressed patient. Clin Infect Dis 2021; 73:2144-2145. [PMID: 34009286 DOI: 10.1093/cid/ciab392] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Dirk Niemann
- Gemeinschaftsklinikum Mittelrhein - Ev. Stift St. Martin, 56068 Koblenz, Germany
| | - Jens Verheyen
- Institute of Immunology and Genetics, 67655 Kaiserslautern, Germany
| |
Collapse
|
2
|
Salpini R, Battisti A, Piermatteo L, Carioti L, Anastasiou OE, Gill US, Di Carlo D, Colagrossi L, Duca L, Bertoli A, La Rosa KY, Fabeni L, Iuvara A, Malagnino V, Cerva C, Lichtner M, Mastroianni CM, De Sanctis GM, Paoloni M, Marignani M, Pasquazzi C, Iapadre N, Parruti G, Vecchiet J, Sarmati L, Andreoni M, Angelico M, Grelli S, T Kennedy P, Verheyen J, Aquaro S, Silberstein FC, Perno CF, Svicher V. Key mutations in the C-terminus of the HBV surface glycoprotein correlate with lower HBsAg levels in vivo, hinder HBsAg secretion in vitro and reduce HBsAg structural stability in the setting of HBeAg-negative chronic HBV genotype-D infection. Emerg Microbes Infect 2020; 9:928-939. [PMID: 32312174 PMCID: PMC7269061 DOI: 10.1080/22221751.2020.1757998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Increasing evidences suggest that HBsAg-production varies across HBV-genotypes. HBsAg C-terminus plays a crucial role for HBsAg-secretion. Here, we evaluate HBsAg-levels in different HBV-genotypes in HBeAg-negative chronic infection, the correlation of specific mutations in HBsAg C-terminus with HBsAg-levels in-vivo, their impact on HBsAg-secretion in-vitro and on structural stability in-silico. HBsAg-levels were investigated in 323 drug-naïve HBeAg-negative patients chronically infected with HBV genotype-D(N = 228), -A(N = 65) and -E(N = 30). Genotype-D was characterized by HBsAg-levels lower than genotype-A and -E (3.3[2.7–3.8]IU/ml; 3.8[3.5–4.2]IU/ml and 3.9[3.7–4.2]IU/ml, P < 0.001). Results confirmed by multivariable analysis correcting for patients’demographics, HBV-DNA, ALT and infection-status. In genotype-D, specific C-terminus mutations (V190A-S204N-Y206C-Y206F-S210N) significantly correlate with HBsAg<1000IU/ml(P-value from <0.001 to 0.04). These mutations lie in divergent pathways involving other HBsAg C-terminus mutations: V190A + F220L (Phi = 0.41, P = 0.003), S204N + L205P (Phi = 0.36, P = 0.005), Y206F + S210R (Phi = 0.47, P < 0.001) and S210N + F220L (Phi = 0.40, P = 0.006). Notably, patients with these mutational pairs present HBsAg-levels 1log lower than patients without them(P-value from 0.003 to 0.02). In-vitro, the above-mentioned mutational pairs determined a significant decrease in HBsAg secretion-efficiency compared to wt(P-value from <0.001 to 0.02). Structurally, these mutational pairs reduced HBsAg C-terminus stability and determined a rearrangement of this domain. In conclusion, HBsAg-levels in genotype-D are significantly lower than in genotype-A and -E in HBeAg-negative patients. In genotype-D, specific mutational clusters in HBsAg C-terminus correlate with lower HBsAg-levels in-vivo, hamper HBsAg-release in-vitro and affect its structural stability, supporting their detrimental role on HBsAg-secretion. In this light, genotypic-testing can be a valuable tool to optimize the clinical interpretation of HBsAg in genotype-D and to provide information on HBV-pathogenicity and disease-progression.
Collapse
Affiliation(s)
- Romina Salpini
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Arianna Battisti
- Barts Liver Centre, Blizard Institute, Barts and The London SMD, QMUL, London, UK
| | - Lorenzo Piermatteo
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Luca Carioti
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Olympia E Anastasiou
- Institute of Virology, University-Hospital, University Duisburg-Essen, Essen, Germany
| | - Upkar S Gill
- Barts Liver Centre, Blizard Institute, Barts and The London SMD, QMUL, London, UK
| | - Domenico Di Carlo
- Paediatric Clinical Research Center "Romeo and Enrica Invernizzi", University of Milan, Milan, Italy
| | - Luna Colagrossi
- Microbiology and Virology Unit, University of Milan, Milan, Italy
| | - Leonardo Duca
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Ada Bertoli
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Katia Yu La Rosa
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Lavinia Fabeni
- Laboratory of Virology, National Institute for Infectious Diseases "Lazzaro Spallanzani" -IRCCS, Rome, Italy
| | - Alessandra Iuvara
- Microbiology and Virology Unit, Tor Vergata University Hospital, Rome, Italy
| | | | - Carlotta Cerva
- Infectious Diseases Unit, Tor Vergata University Hospital, Rome, Italy
| | - Miriam Lichtner
- Public Health and Infectious Disease Department, "Sapienza" University, Rome, Italy
| | | | | | - Maurizio Paoloni
- Infectious Disease Unit, "S.S. Filippo e Nicola" Hospital, Avezzano, Italy
| | | | | | | | - Giustino Parruti
- Infectious Disease Unit, Pescara General Hospital, Pescara, Italy
| | - Jacopo Vecchiet
- Department of Medicine and Science of Aging, Clinic of Infectious Diseases, University "G. d'Annunzio" Chieti-Pescara, Chieti, Italy
| | - Loredana Sarmati
- Infectious Diseases Unit, Tor Vergata University Hospital, Rome, Italy
| | - Massimo Andreoni
- Infectious Diseases Unit, Tor Vergata University Hospital, Rome, Italy
| | - Mario Angelico
- Hepatology Unit, Tor Vergata University Hospital, Rome, Italy
| | - Sandro Grelli
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy.,Microbiology and Virology Unit, Tor Vergata University Hospital, Rome, Italy
| | - Patrick T Kennedy
- Barts Liver Centre, Blizard Institute, Barts and The London SMD, QMUL, London, UK
| | - Jens Verheyen
- Institute of Virology, University-Hospital, University Duisburg-Essen, Essen, Germany
| | - Stefano Aquaro
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | | | | | - Valentina Svicher
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy
| |
Collapse
|
3
|
Verheyen J, Thielen A, Lübke N, Dirks M, Widera M, Dittmer U, Kordelas L, Däumer M, de Jong DCM, Wensing AMJ, Kaiser R, Nijhuis M, Esser S. Rapid Rebound of a Preexisting CXCR4-tropic Human Immunodeficiency Virus Variant After Allogeneic Transplantation With CCR5 Δ32 Homozygous Stem Cells. Clin Infect Dis 2020; 68:684-687. [PMID: 30020413 DOI: 10.1093/cid/ciy565] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 07/06/2018] [Indexed: 11/12/2022] Open
Abstract
Allogeneic stem cell transplantation (alloSCT) of homozygous CCR5 Δ32 stem cells once resulted in the cure of human immunodeficiency virus (HIV) infection. We have recently reported a viral breakthrough in a similar setting. Here, we demonstrate that the rapid rebound after alloSCT was related to a highly replicative CXCR4-tropic HIV variant, which could already be detected before alloSCT.
Collapse
Affiliation(s)
- Jens Verheyen
- Institute of Virology, University Hospital, University of Duisburg-Essen.,Institute of Immunology and Genetics, Kaiserslautern
| | | | - Nadine Lübke
- Institute of Virology, Heinrich-Heine-University, University Hospital, Düsseldorf
| | - Miriam Dirks
- Institute of Virology, University Hospital, University of Duisburg-Essen
| | - Marek Widera
- Institute of Virology, University Hospital, University of Duisburg-Essen
| | - Ulf Dittmer
- Institute of Virology, University Hospital, University of Duisburg-Essen
| | - Lambros Kordelas
- Department of Bone Marrow Transplantation, University Hospital, University of Duisburg-Essen, Germany
| | - Martin Däumer
- Institute of Immunology and Genetics, Kaiserslautern
| | - Dorien C M de Jong
- Department of Medical Microbiology, Virology, University Medical Center Utrecht, The Netherlands
| | - Annemarie M J Wensing
- Department of Medical Microbiology, Virology, University Medical Center Utrecht, The Netherlands
| | - Rolf Kaiser
- Institute of Virology, University of Cologne
| | - Monique Nijhuis
- Department of Medical Microbiology, Virology, University Medical Center Utrecht, The Netherlands
| | - Stefan Esser
- Clinic for Dermatology, University Hospital, University of Duisburg-Essen, Germany
| |
Collapse
|
4
|
Salpini R, Piermatteo L, Battisti A, Colagrossi L, Aragri M, Yu La Rosa K, Bertoli A, Saccomandi P, Lichtner M, Marignani M, Maylin S, Delaugerre C, Morisco F, Coppola N, Marrone A, Iapadre N, Cerva C, Aquaro S, Angelico M, Sarmati L, Andreoni M, Verheyen J, Ceccherini-Silberstein F, Levrero M, Perno CF, Belloni L, Svicher V. A Hyper-Glycosylation of HBV Surface Antigen Correlates with HBsAg-Negativity at Immunosuppression-Driven HBV Reactivation in Vivo and Hinders HBsAg Recognition in Vitro. Viruses 2020; 12:v12020251. [PMID: 32102257 PMCID: PMC7077195 DOI: 10.3390/v12020251] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/17/2020] [Accepted: 02/20/2020] [Indexed: 02/07/2023] Open
Abstract
Immune-suppression driven Hepatitis B Virus (HBV)-reactivation poses serious concerns since it occurs in several clinical settings and can result in severe forms of hepatitis. Previous studies showed that HBV strains, circulating in patients with HBV-reactivation, are characterized by an enrichment of immune-escape mutations in HBV surface antigen (HBsAg). Here, we focused on specific immune-escape mutations associated with the acquisition of N-linked glycosylation sites in HBsAg (NLGSs). In particular, we investigated profiles of NLGSs in 47 patients with immunosuppression-driven HBV-reactivation and we evaluated their impact on HBsAg-antigenicity and HBV-replication in vitro. At HBV-reactivation, despite a median serum HBV-DNA of 6.7 [5.3–8.0] logIU/mL, 23.4% of patients remained HBsAg-negative. HBsAg-negativity at HBV-reactivation correlated with the presence of >1 additional NLGSs (p < 0.001). These NLGSs are located in the major hydrophilic region of HBsAg (known to be the target of antibodies) and resulted from the single mutation T115N, T117N, T123N, N114ins, and from the triple mutant S113N+T131N+M133T. In vitro, NLGSs strongly alter HBsAg antigenic properties and recognition by antibodies used in assays for HBsAg-quantification without affecting HBsAg-secretion and other parameters of HBV-replication. In conclusion, additional NLGSs correlate with HBsAg-negativity despite HBV-reactivation, and hamper HBsAg-antigenicity in vitro, supporting the role of NGSs in immune-escape and the importance of HBV-DNA for a proper diagnosis of HBV-reactivation.
Collapse
Affiliation(s)
- Romina Salpini
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (L.P.); (A.B.); (L.C.); (M.A.); (K.Y.L.R.); (A.B.); (P.S.); (F.C.-S.)
| | - Lorenzo Piermatteo
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (L.P.); (A.B.); (L.C.); (M.A.); (K.Y.L.R.); (A.B.); (P.S.); (F.C.-S.)
| | - Arianna Battisti
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (L.P.); (A.B.); (L.C.); (M.A.); (K.Y.L.R.); (A.B.); (P.S.); (F.C.-S.)
| | - Luna Colagrossi
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (L.P.); (A.B.); (L.C.); (M.A.); (K.Y.L.R.); (A.B.); (P.S.); (F.C.-S.)
| | - Marianna Aragri
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (L.P.); (A.B.); (L.C.); (M.A.); (K.Y.L.R.); (A.B.); (P.S.); (F.C.-S.)
| | - Katia Yu La Rosa
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (L.P.); (A.B.); (L.C.); (M.A.); (K.Y.L.R.); (A.B.); (P.S.); (F.C.-S.)
| | - Ada Bertoli
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (L.P.); (A.B.); (L.C.); (M.A.); (K.Y.L.R.); (A.B.); (P.S.); (F.C.-S.)
| | - Patrizia Saccomandi
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (L.P.); (A.B.); (L.C.); (M.A.); (K.Y.L.R.); (A.B.); (P.S.); (F.C.-S.)
| | - Miriam Lichtner
- Public Health and Infectious Disease Department, Sapienza University, 00185 Rome, Italy;
| | - Massimo Marignani
- Department of Gastroenterology, S.Andrea Hospital, 00189 Rome, Italy;
| | - Sarah Maylin
- Laboratoire de Virologie, AP-HP Hopital Saint-Louis, 75010 Paris, France; (S.M.); (C.D.)
| | - Constance Delaugerre
- Laboratoire de Virologie, AP-HP Hopital Saint-Louis, 75010 Paris, France; (S.M.); (C.D.)
| | - Filomena Morisco
- Department of Clinical Medicine and Surgery, Section of Infectious Diseases, University of Naples Federico II, 80138 Naples, Italy;
| | - Nicola Coppola
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, Second University of Naples, 80138 Naples, Italy;
| | - Aldo Marrone
- Internal Medicine and Hepatology Unit, Second University of Naples, 80138 Naples, Italy;
| | - Nerio Iapadre
- Infectious Diseases Unit, San Salvatore Hospital, 67100 L’Aquila, Italy;
| | - Carlotta Cerva
- Infectious Diseases Unit, Tor Vergata University Hospital, 00133 Rome, Italy; (C.C.); (L.S.); (M.A.)
| | - Stefano Aquaro
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy;
| | - Mario Angelico
- Hepatology Unit, Tor Vergata University Hospital, 00133 Rome, Italy;
| | - Loredana Sarmati
- Infectious Diseases Unit, Tor Vergata University Hospital, 00133 Rome, Italy; (C.C.); (L.S.); (M.A.)
| | - Massimo Andreoni
- Infectious Diseases Unit, Tor Vergata University Hospital, 00133 Rome, Italy; (C.C.); (L.S.); (M.A.)
| | - Jens Verheyen
- Institute of Virology, University-Hospital, University Duisburg-Essen, 47057 Essen, Germany;
| | - Francesca Ceccherini-Silberstein
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (L.P.); (A.B.); (L.C.); (M.A.); (K.Y.L.R.); (A.B.); (P.S.); (F.C.-S.)
| | - Massimo Levrero
- Department of Internal Medicine-DMISM, Sapienza University, 00185 Rome, Italy; (M.L.); (L.B.)
- INSERM U1052-Cancer Research Center of Lyon (CRCL), University of Lyon, UMR_S1052, 69008 Lyon, France
| | - Carlo Federico Perno
- Department of Oncology and Haemato-oncology, University of Milan, 20122 Milan, Italy;
| | - Laura Belloni
- Department of Internal Medicine-DMISM, Sapienza University, 00185 Rome, Italy; (M.L.); (L.B.)
- Center for Life NanoSciences (CLNS), IIT-Sapienza, 00133 Rome, Italy
| | - Valentina Svicher
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (L.P.); (A.B.); (L.C.); (M.A.); (K.Y.L.R.); (A.B.); (P.S.); (F.C.-S.)
- Correspondence:
| |
Collapse
|
5
|
Anastasiou OE, Theissen M, Verheyen J, Bleekmann B, Wedemeyer H, Widera M, Ciesek S. Clinical and Virological Aspects of HBV Reactivation: A Focus on Acute Liver Failure. Viruses 2019; 11:v11090863. [PMID: 31527514 PMCID: PMC6784066 DOI: 10.3390/v11090863] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/03/2019] [Accepted: 09/10/2019] [Indexed: 02/07/2023] Open
Abstract
Hepatitis B virus (HBV) reactivation in immunosuppressed patients can cause considerable morbidity and mortality. The aim of our study was to evaluate factors associated with acute liver failure (ALF) in HBV reactivation. Clinical, laboratory, and virological data of 87 patients with HBV reactivation were analyzed retrospectively. Teno torque virus (TTV) plasma loads were measured as a measure of immune competence. HBV genomes isolated from 47 patients were analyzed by next-generation sequencing. A functional analysis of identified HBsAg mutants was performed. In patients with ALF the diagnosis was significantly later confirmed than in the non-ALF group. Patients diagnosed during immunosuppression had a milder clinical course compared to later diagnosed patients (p = 0.018, OR = 4.17). TTV viral loads did not differ significantly between the two groups. The HBV genomes isolated from ALF patients had higher viral complexity. A mutation in C-region of HBsAg (L216*), was associated with reduced HBsAg production and secretion. Patients diagnosed with HBV reactivation during immunosuppression had a milder clinical course compared to patients diagnosed during immune reconstitution. ALF was associated with higher viral complexity. An HBsAg mutation (L216*) was found to be more frequent in ALF patients and was associated with reduced HBsAg production and secretion.
Collapse
Affiliation(s)
- Olympia E Anastasiou
- Institute of Virology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany.
| | - Martin Theissen
- Department of Bioinformatics and Computational Biophysics, University of Duisburg-Essen, 45117 Essen, Germany.
| | - Jens Verheyen
- Institute of Virology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany.
| | - Barbara Bleekmann
- Institute of Virology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany.
| | - Heiner Wedemeyer
- Department of Gastroenterology and Hepatology, University Hospital Essen, 45147 Essen, Germany.
- German Center for Infection Research, DZIF, 38124 Braunschweig, Germany.
| | - Marek Widera
- Institute of Virology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany.
| | - Sandra Ciesek
- Institute of Virology, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany.
- German Center for Infection Research, DZIF, 38124 Braunschweig, Germany.
- Institute of Medical Virology, University Hospital Frankfurt, 60596 Frankfurt am Main, Germany.
| |
Collapse
|
6
|
Anastasiou OE, Widera M, Westhaus S, Timmer L, Korth J, Gerken G, Canbay A, Todt D, Steinmann E, Schwarz T, Timm J, Verheyen J, Ciesek S. Clinical Outcome and Viral Genome Variability of Hepatitis B Virus-Induced Acute Liver Failure. Hepatology 2019; 69:993-1003. [PMID: 30229977 DOI: 10.1002/hep.30279] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 09/01/2018] [Indexed: 12/29/2022]
Abstract
Acute hepatitis B virus (HBV) infection remains a frequent cause of acute liver failure (ALF) worldwide. ALF occurs in 0.1%-0.5% of infected patients. The aim of this study was to scrutinize the outcome of patients with HBV-induced ALF and mutational patterns of HBV variants, which might contribute to ALF. From 2005 to 2016, 42 patients were treated for HBV-induced ALF in the University Hospital Essen, Germany. Clinical and virological data from these patients were collected. As a control, 38 patients with acute hepatitis B (AHB) without liver failure were included. The HBV genome was sequenced by next-generation sequencing (NGS). Mutations that were found by NGS were analyzed in vitro. Of 42 patients, 8 had ALF without spontaneous recovery (NSR): Seven patients underwent liver transplantation (LT) and one patient died before LT. Of 42 patients, 34 (81%) had spontaneous recovery (SR) and cleared the infection, achieving either anti-HBs seroconversion or hepatitis B surface antigen (HBsAg) loss. HBV genotype (GT)-D was the most frequent GT in patients with ALF. Mutations in HBV core, preS2, and small hepatitis B surface antigen (SHB) were more frequent in patients with ALF-NSR compared with those with ALF-SR or AHB. Amino acid deletions (del; 16-22 and 20-22) in preS2 and SHB mutation L49R were exclusively detected in patients with ALF-NSR. In vitro analyses reveal that these mutations did not influence HBsAg secretion or infectivity. Conclusion: HBV GT-D and increased variability in HBV core, preS2 region, and SHB are associated with a worse clinical outcome of acute HBV infection.
Collapse
Affiliation(s)
- Olympia E Anastasiou
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany.,Department of Gastroenterology and Hepatology, University Hospital of Essen, Essen, Germany
| | - Marek Widera
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Sandra Westhaus
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Lejla Timmer
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Johannes Korth
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Guido Gerken
- Department of Gastroenterology and Hepatology, University Hospital of Essen, Essen, Germany
| | - Ali Canbay
- Department of Gastroenterology and Hepatology, University Hospital of Magdeburg, Magdeburg, Germany
| | - Daniel Todt
- Department of Molecular and Medical Virology, Ruhr University, Bochum, Germany
| | - Eike Steinmann
- Department of Molecular and Medical Virology, Ruhr University, Bochum, Germany
| | - Tatjana Schwarz
- Institute of Virology, University Hospital of Düsseldorf, University of Düsseldorf, Düsseldorf, Germany
| | - Jörg Timm
- Institute of Virology, University Hospital of Düsseldorf, University of Düsseldorf, Düsseldorf, Germany
| | - Jens Verheyen
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Sandra Ciesek
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| |
Collapse
|
7
|
Korth J, Anastasiou OE, Bräsen JH, Brinkhoff A, Lehmann U, Kribben A, Dittmer U, Verheyen J, Wilde B, Ciesek S, Witzke O, Widera M. The detection of BKPyV genotypes II and IV after renal transplantation as a simple tool for risk assessment for PyVAN and transplant outcome already at early stages of BKPyV reactivation. J Clin Virol 2019; 113:14-19. [PMID: 30771597 DOI: 10.1016/j.jcv.2019.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 01/07/2019] [Accepted: 02/08/2019] [Indexed: 12/25/2022]
Abstract
BACKGROUND After reactivation the BK-polyomavirus (BKPyV) associated nephropathy (PyVAN) is observed in 1-10% of renal transplant recipients, of which up to 80% undergo graft failure. BKPyV reactivation after renal transplantation was associated with donor-derived serotypes against which the recipient has no immunological protection. However, PyVAN risk assessment seroactivity testing is a time-consuming and cost intensive process. OBJECTIVES Since BKPyV serotypes can be attributed to distinct genotypes I to IV, in the present study we retrospectively analyzed whether a simple PCR-based BKPyV genotyping assay might be a fast and inexpensive method to assess the risk for PyVAN and transplant outcome already at early stages of BKPyV reactivation. STUDY DESIGN 56 patients who were renal transplanted and tested positive for BKPyV viremia were included into the study. The BKPyV-VP1-coding sequences were PCR-amplified, sequenced, and subjected to genotyping. For group specific analysis patients were grouped in genotype I (n = 46) and a second group including genotype II and IV (n = 10) and associated with their clinical outcomes. RESULTS The most abundant genotype I was detected in 46 of 56 (82%) patients, however, in the genotype II and IV group PyVAN was twice as frequent as compared to the genotype I group 24 months after transplantation (8 of 10 (80%) vs. 17 of 46 (37%); p = 0.001). Accordingly, graft failure was significantly more frequent in the genotype II and IV group (3 of 10 (30%) vs. 2 of 46 (4%); p = 0.007). CONCLUSION PCR-based BKPyV genotyping might represent a fast and inexpensive method to assess the risk for PyVAN and transplant outcome already at early stages of BKPyV reactivation even if matched samples of the donor are not available.
Collapse
Affiliation(s)
- Johannes Korth
- Department of Nephrology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147, Essen, Germany; Institute for Virology, University Hospital Essen, University of Duisburg-Essen Virchowstr. 179, 45147, Essen, Germany.
| | - Olympia Evdoxia Anastasiou
- Department of Gastroenterology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147, Essen, Germany
| | - Jan Hinrich Bräsen
- Institute for Pathology, Hanover Medical School, Carl-Neuberg-Str. 1, 30625, Hanover, Germany
| | - Alexandra Brinkhoff
- Department of Nephrology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147, Essen, Germany
| | - Ulrich Lehmann
- Institute for Pathology, Hanover Medical School, Carl-Neuberg-Str. 1, 30625, Hanover, Germany
| | - Andreas Kribben
- Department of Nephrology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147, Essen, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen Virchowstr. 179, 45147, Essen, Germany
| | - Jens Verheyen
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen Virchowstr. 179, 45147, Essen, Germany
| | - Benjamin Wilde
- Department of Nephrology, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147, Essen, Germany
| | - Sandra Ciesek
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen Virchowstr. 179, 45147, Essen, Germany
| | - Oliver Witzke
- Department of Infectious Diseases, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45147, Essen, Germany
| | - Marek Widera
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen Virchowstr. 179, 45147, Essen, Germany
| |
Collapse
|
8
|
Korth J, Anastasiou OE, Verheyen J, Dickow J, Sertznig H, Frericks N, Bleekmann B, Kribben A, Brinkhoff A, Wilde B, Sutter K, Dittmer U, Ciesek S, Witzke O, Widera M. Impact of immune suppressive agents on the BK-Polyomavirus non coding control region. Antiviral Res 2018; 159:68-76. [PMID: 30268912 DOI: 10.1016/j.antiviral.2018.09.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 04/23/2018] [Accepted: 09/26/2018] [Indexed: 02/08/2023]
Abstract
BACKGROUND Reactivation of the BK-Polyomavirus (BKPyV) can cause a polyomavirus associated nephropathy in approx. 10% of kidney transplant recipients. In these cases, current therapy is based on the reduction of immunosuppression. Since BKPyV-transcription is driven by the Non-Coding-Control-Region (NCCR) we were interested whether NCCR-activity is affected by immunosuppressive agents. METHODS Plasma samples from 45 BKPyV-positive patients after renal transplantation were subjected to PCR-analysis. NCCR-amplicons were cloned into a plasmid that allows the quantification of early and late NCCR-activity by tdTomato and eGFP expression, respectively. HEK293T-cells were transfected with the reporter-plasmids, treated with immunosuppressive agents, and subjected to FACS-analysis. In addition, H727-cells were infected with patient derived BKPyV, treated with mTOR-inhibitors, and NCCR activity was analysed using qRT-PCR. RESULTS While tacrolimus and cyclosporine-A did not affect NCCR-promoter-activity, treatment with mTOR1-inhibitor rapamycin resulted in the reduction of early, but not late-NCCR-promoter-activity. Treatment with dual mTOR1/2 inhibitors (INK128 or pp242) led to significant inhibition of early, however, concomitantly enhanced late-promoter-activity. In BKPyV infected cells both rapamycin and INK128 reduced early expression, however, INK128 resulted in higher late-mRNA levels when compared to rapamycin treatment. CONCLUSIONS Our results demonstrate that mTOR1-inhibitors are able to reduce early-expression of wildtype and rearranged NCCRs, which might contribute to previously described inhibition of BKPyV-replication. Dual mTOR1/2-inhibitors, however, additionally might shift viral early into late-expression promoting synthesis of viral structural proteins and particle production.
Collapse
Affiliation(s)
- Johannes Korth
- Department of Nephrology, University of Duisburg-Essen, University Hospital Essen, Hufelandstr. 55, 45147, Essen, Germany; Institute for Virology, University of Duisburg-Essen, University Hospital Essen, Virchowstr. 179, 45147, Essen, Germany
| | - Olympia E Anastasiou
- Institute for Virology, University of Duisburg-Essen, University Hospital Essen, Virchowstr. 179, 45147, Essen, Germany; Department of Gastroenterology, University of Duisburg-Essen, University Hospital Essen, Hufelandstr. 55, 45147, Essen, Germany
| | - Jens Verheyen
- Institute for Virology, University of Duisburg-Essen, University Hospital Essen, Virchowstr. 179, 45147, Essen, Germany
| | - Julia Dickow
- Institute for Virology, University of Duisburg-Essen, University Hospital Essen, Virchowstr. 179, 45147, Essen, Germany
| | - Helene Sertznig
- Institute for Virology, University of Duisburg-Essen, University Hospital Essen, Virchowstr. 179, 45147, Essen, Germany
| | - Nicola Frericks
- Institute for Virology, University of Duisburg-Essen, University Hospital Essen, Virchowstr. 179, 45147, Essen, Germany
| | - Barbara Bleekmann
- Institute for Virology, University of Duisburg-Essen, University Hospital Essen, Virchowstr. 179, 45147, Essen, Germany
| | - Andreas Kribben
- Department of Nephrology, University of Duisburg-Essen, University Hospital Essen, Hufelandstr. 55, 45147, Essen, Germany
| | - Alexandra Brinkhoff
- Department of Nephrology, University of Duisburg-Essen, University Hospital Essen, Hufelandstr. 55, 45147, Essen, Germany
| | - Benjamin Wilde
- Department of Nephrology, University of Duisburg-Essen, University Hospital Essen, Hufelandstr. 55, 45147, Essen, Germany
| | - Kathrin Sutter
- Institute for Virology, University of Duisburg-Essen, University Hospital Essen, Virchowstr. 179, 45147, Essen, Germany
| | - Ulf Dittmer
- Institute for Virology, University of Duisburg-Essen, University Hospital Essen, Virchowstr. 179, 45147, Essen, Germany
| | - Sandra Ciesek
- Institute for Virology, University of Duisburg-Essen, University Hospital Essen, Virchowstr. 179, 45147, Essen, Germany
| | - Oliver Witzke
- Department of Infectious Diseases, University of Duisburg-Essen, University Hospital Essen, Hufelandstr. 55, 45147, Essen, Germany
| | - Marek Widera
- Institute for Virology, University of Duisburg-Essen, University Hospital Essen, Virchowstr. 179, 45147, Essen, Germany.
| |
Collapse
|
9
|
Colagrossi L, Hermans LE, Salpini R, Di Carlo D, Pas SD, Alvarez M, Ben-Ari Z, Boland G, Bruzzone B, Coppola N, Seguin-Devaux C, Dyda T, Garcia F, Kaiser R, Köse S, Krarup H, Lazarevic I, Lunar MM, Maylin S, Micheli V, Mor O, Paraschiv S, Paraskevis D, Poljak M, Puchhammer-Stöckl E, Simon F, Stanojevic M, Stene-Johansen K, Tihic N, Trimoulet P, Verheyen J, Vince A, Lepej SZ, Weis N, Yalcinkaya T, Boucher CAB, Wensing AMJ, Perno CF, Svicher V. Immune-escape mutations and stop-codons in HBsAg develop in a large proportion of patients with chronic HBV infection exposed to anti-HBV drugs in Europe. BMC Infect Dis 2018; 18:251. [PMID: 29859062 PMCID: PMC5984771 DOI: 10.1186/s12879-018-3161-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 05/23/2018] [Indexed: 12/27/2022] Open
Abstract
Background HBsAg immune-escape mutations can favor HBV-transmission also in vaccinated individuals, promote immunosuppression-driven HBV-reactivation, and increase fitness of drug-resistant strains. Stop-codons can enhance HBV oncogenic-properties. Furthermore, as a consequence of the overlapping structure of HBV genome, some immune-escape mutations or stop-codons in HBsAg can derive from drug-resistance mutations in RT. This study is aimed at gaining insight in prevalence and characteristics of immune-associated escape mutations, and stop-codons in HBsAg in chronically HBV-infected patients experiencing nucleos(t)ide analogues (NA) in Europe. Methods This study analyzed 828 chronically HBV-infected European patients exposed to ≥ 1 NA, with detectable HBV-DNA and with an available HBsAg-sequence. The immune-associated escape mutations and the NA-induced immune-escape mutations sI195M, sI196S, and sE164D (resulting from drug-resistance mutation rtM204 V, rtM204I, and rtV173L) were retrieved from literature and examined. Mutations were defined as an aminoacid substitution with respect to a genotype A or D reference sequence. Results At least one immune-associated escape mutation was detected in 22.1% of patients with rising temporal-trend. By multivariable-analysis, genotype-D correlated with higher selection of ≥ 1 immune-associated escape mutation (OR[95%CI]:2.20[1.32–3.67], P = 0.002). In genotype-D, the presence of ≥ 1 immune-associated escape mutations was significantly higher in drug-exposed patients with drug-resistant strains than with wild-type virus (29.5% vs 20.3% P = 0.012). Result confirmed by analysing drug-naïve patients (29.5% vs 21.2%, P = 0.032). Strong correlation was observed between sP120T and rtM204I/V (P < 0.001), and their co-presence determined an increased HBV-DNA. At least one NA-induced immune-escape mutation occurred in 28.6% of patients, and their selection correlated with genotype-A (OR[95%CI]:2.03[1.32–3.10],P = 0.001). Finally, stop-codons are present in 8.4% of patients also at HBsAg-positions 172 and 182, described to enhance viral oncogenic-properties. Conclusions Immune-escape mutations and stop-codons develop in a large fraction of NA-exposed patients from Europe. This may represent a potential threat for horizontal and vertical HBV transmission also to vaccinated persons, and fuel drug-resistance emergence. Electronic supplementary material The online version of this article (10.1186/s12879-018-3161-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Luna Colagrossi
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Via Montpellier, 1, 00133, Rome, Italy
| | - Lucas E Hermans
- Virology, Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands.,Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Romina Salpini
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Via Montpellier, 1, 00133, Rome, Italy
| | - Domenico Di Carlo
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Via Montpellier, 1, 00133, Rome, Italy
| | - Suzan D Pas
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Marta Alvarez
- Servicio de Microbiología, Hospital San Cecilio, Instituto de Investigación Biosanitaria ibs.GRANADA, Hospitales Universitarios de Granada, Granada, Spain
| | - Ziv Ben-Ari
- Liver Disease Centre, Sheba Medical Centre, Ramat Gan, Israel
| | - Greet Boland
- Virology, Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | | | - Nicola Coppola
- Malattie Infettive, Seconda Università degli studi di Napoli, Naples, Italy
| | | | - Tomasz Dyda
- Molecular Diagnostics Laboratory, Hospital of Infectious Diseases, Warsaw, Poland
| | - Federico Garcia
- Servicio de Microbiología, Hospital San Cecilio, Instituto de Investigación Biosanitaria ibs.GRANADA, Hospitales Universitarios de Granada, Granada, Spain
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Sukran Köse
- Izmir Tepecik Education and Research Hospital, Clinic of Infectious Diseases and Clinical Microbiology, Izmir, Turkey
| | - Henrik Krarup
- Section of Molecular Diagnostics, Clinical Biochemistry, Aalborg University Hospital, Aalborg, Denmark
| | - Ivana Lazarevic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Maja M Lunar
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Sarah Maylin
- Service de Microbiologie, University Paris Diderot, Hôpital Saint Louis, Paris, France
| | | | - Orna Mor
- National HIV Reference Laboratory, Central Virology Laboratory, Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Simona Paraschiv
- Molecular Diagnostics Laboratory, National Institute for Infectious Diseases "Matei Bals", Bucharest, Romania
| | - Dimitros Paraskevis
- National Retrovirus Reference Centre, Department of Hygiene, Epidemiology and Medical Statistics, Faculty of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | | | - François Simon
- Service de Microbiologie, University Paris Diderot, Hôpital Saint Louis, Paris, France
| | - Maja Stanojevic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | | | - Nijaz Tihic
- Institute of Microbiology, Polyclinic for Laboratory Diagnostics, University Clinical Centre Tuzla, Tuzla, Bosnia and Herzegovina
| | - Pascale Trimoulet
- Virology Laboratory, Centre Hospitalier Régional et Université "Victor Segalen", Bordeaux, France
| | - Jens Verheyen
- Institute of Virology, University-Hospital, University Duisburg-Essen, Essen, Germany
| | - Adriana Vince
- University of Zagreb School of Medicine and University Hospital for Infectious Diseases, Zagreb, Croatia
| | - Snjezana Zidovec Lepej
- University of Zagreb School of Medicine and University Hospital for Infectious Diseases, Zagreb, Croatia
| | - Nina Weis
- Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Copenhagen, Denmark
| | | | - Charles A B Boucher
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Annemarie M J Wensing
- Virology, Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Carlo F Perno
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Via Montpellier, 1, 00133, Rome, Italy.
| | - Valentina Svicher
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Via Montpellier, 1, 00133, Rome, Italy.
| | | |
Collapse
|
10
|
Storim J, Verheyen J, Wolff E, Wohlschlaeger J, Heintschel von Heinegg E, Schadendorf D, Esser S. Antiretroviral therapy suppresses rectal HIV-RNA shedding despite inflammation in MSM with rectal C. trachomatis and N. gonorrhoeae infections-a cross-sectional, single-center study. Sex Transm Infect 2018; 95:95-98. [PMID: 29431149 DOI: 10.1136/sextrans-2017-053409] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 01/04/2018] [Accepted: 01/15/2018] [Indexed: 11/03/2022] Open
Abstract
OBJECTIVES Rectal infections with Chlamydia trachomatis and/or Neisseria gonorrhoeae (CT/NG) are common in men who have sex with men (MSM) and are linked to HIV transmission. However, rectal CT/NG infections are often asymptomatic and it is not known how they contribute to HIV transmission. We assessed clinical and cytological signs of inflammation as well as rectal HIV-RNA in HIV-infected MSM with and without CT/NG infection. METHODS 112 HIV-positive MSM with or without rectal symptoms and with or without antiretroviral therapy who underwent high-resolution anoscopy (HRA) at the proctological outpatient centre of the University Hospital Essen, Germany, between November 2013 and February 2014 were included in this cross-sectional study. During the examination, rectal swabs for the assessment of CT/NG, HIV-RNA and inflammatory cells (granulocytes, lymphocytes, histiocytes) were collected. 110 patients were assessed according to the study protocol, and no imputation of missing data was performed. RESULTS Rectal infections with CT or NG were detected in 17 participants, and 4 participants were coinfected. Only symptomatic CT/NG infections (8/17) showed signs of inflammation in HRA. Symptomatic CT/NG infections were also associated with the detection of lymphocytes and histiocytes in rectal cytology (both P<0.001). In contrast, asymptomatic CT/NG infections neither resulted in clinical nor cytological signs of inflammation. Rectal HIV-RNA was undetectable in all participants with rectal CT/NG infections who received combined antiretroviral therapy (ART) when plasma HIV-RNA was below the limit of detection (n=13). Besides rectal CT/NG infections, syphilis (n=4) and HPV-associated lesions (n=37) were frequently detected, and proctological symptoms were associated with simultaneous infection with ≥2 STDs. CONCLUSIONS Only symptomatic but not asymptomatic rectal infections with CT and/or NG were associated with clinical and cytological signs of inflammation. Rectal HIV shedding was not promoted by CT/NG infections in patients receiving ART with suppressed plasma HIV-RNA. TRIAL REGISTRATION NUMBER UTN: U1111-1150-4804. German Clinical Trials Register (DRKS): DRKS00005468.
Collapse
Affiliation(s)
- Julian Storim
- Department of Dermatology, University Hospital, University of Duisburg-Essen, Essen, Germany.,Global Drug Development, Immunology & Dermatology, Novartis Pharma AG, Basel, Switzerland
| | - Jens Verheyen
- Institute of Virology, University Hospital, University of Duisburg-Essen, Essen, Germany.,Institute of Immunology and Genetics, Kaiserslautern, Germany
| | - Eva Wolff
- Department of Dermatology, University Hospital, University of Duisburg-Essen, Essen, Germany.,Department of Internal Medicine, Evangelisches Krankenhaus Oberhausen, Oberhausen, Germany
| | - Jeremias Wohlschlaeger
- Institute of Pathology, University Hospital, University of Duisburg-Essen, Essen, Germany.,Institute for Pathology, Evangelisch-Lutherische Diakonissenanstalt Flensburg, Flensburg, Schleswig-Holstein, Germany
| | | | - Dirk Schadendorf
- Department of Dermatology, University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Stefan Esser
- Department of Dermatology, University Hospital, University of Duisburg-Essen, Essen, Germany
| |
Collapse
|
11
|
Korth J, Widera M, Dolff S, Guberina H, Bienholz A, Brinkhoff A, Anastasiou OE, Kribben A, Dittmer U, Verheyen J, Wilde B, Witzke O. Impact of low-level BK polyomavirus viremia on intermediate-term renal allograft function. Transpl Infect Dis 2018; 20. [PMID: 29156086 DOI: 10.1111/tid.12817] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 07/10/2017] [Accepted: 08/13/2017] [Indexed: 12/29/2022]
Abstract
BACKGROUND BK polyomavirus (BKPyV)-associated nephropathy (PyVAN) is a significant cause of premature renal transplant failure. High-level BKPyV viremia is predictive for PyVAN; however, low-level BKPyV viremia does not necessarily exclude the presence of PyVAN. As data are limited regarding whether or not low-level BKPyV viremia has an effect on intermediate-term graft outcome, this study analyzes the impact of low-level BKPyV viremia on intermediate-term graft function and outcome compared with high-level viremia and non-viremic patients. METHODS All renal transplant patients received follow-up examinations at the Department of Nephrology, University Hospital Essen. Patients were screened for BKPyV viremia and stratified into three groups according to their maximum BKPyV load in serum (low-level viremia, high-level viremia, and no viremia). RESULTS In 142 of 213 (67%) patients, BKPyV was never detected in serum; 42 of 213 (20%) patients were found positive for low-level viremia (≤104 copies/mL); and 29 of 213 (13%) patients showed high-level viremia (>104 copies/mL). No significant differences regarding transplant function and graft failure were observed between patients without BKPyV viremia (delta estimated glomerular filtration rate [eGFR] +0.1 mL/min [month 1 vs last visit at month 44]) and patients with low-level BKPyV viremia (delta eGFR -1.7 mL/min). In patients with high-level viremia, transplant function was significantly restricted (delta eGFR -6.5 mL/min) compared with low-level viremia until the last visit at 44 ± 9.7 months after transplantation. Although the graft function and graft loss were worse in the high-level viremia group compared with no viremia (eGFR 37 vs 45 mL/min), the difference was not significant. CONCLUSIONS High-level viremia was associated with impaired graft function. In contrast, low-level BKPyV viremia had no significant impact on intermediate-term graft function.
Collapse
Affiliation(s)
- Johannes Korth
- Department of Nephrology, University Hospital Essen, University Duisburg-Essen, Essen, Germany.,Institute of Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Marek Widera
- Institute of Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Sebastian Dolff
- Department of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Hana Guberina
- Department of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Anja Bienholz
- Department of Nephrology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Alexandra Brinkhoff
- Department of Nephrology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Olympia Evdoxia Anastasiou
- Institute of Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany.,Department of Gastroenterology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Andreas Kribben
- Department of Nephrology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Ulf Dittmer
- Institute of Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Jens Verheyen
- Institute of Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Benjamin Wilde
- Department of Nephrology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Oliver Witzke
- Department of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| |
Collapse
|
12
|
Kletenkov K, Hoffmann D, Böni J, Yerly S, Aubert V, Schöni-Affolter F, Struck D, Verheyen J, Klimkait T. Role of Gag mutations in PI resistance in the Swiss HIV cohort study: bystanders or contributors? J Antimicrob Chemother 2017; 72:866-875. [PMID: 27999036 DOI: 10.1093/jac/dkw493] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/15/2016] [Indexed: 12/24/2022] Open
Abstract
Background HIV Gag mutations have been reported to confer PI drug resistance. However, clinical implications are still controversial and most current genotyping algorithms consider solely the protease gene for assessing PI resistance. Objectives Our goal was to describe for HIV infections in Switzerland the potential role of the C-terminus of Gag (NC-p6) in PI resistance. We aimed to characterize resistance-relevant mutational patterns in Gag and protease and their possible interactions. Methods Resistance information on plasma samples from 2004-12 was collected for patients treated by two diagnostic centres of the Swiss HIV Cohort Study. Sequence information on protease and the C-terminal Gag region was paired with the corresponding patient treatment history. The prevalence of Gag and protease mutations was analysed for PI treatment-experienced patients versus PI treatment-naive patients. In addition, we modelled multiple paths of an assumed ordered accumulation of genetic changes using random tree mixture models. Results More than half of all PI treatment-experienced patients in our sample set carried HIV variants with at least one of the known Gag mutations, and 17.9% (66/369) carried at least one Gag mutation for which a phenotypic proof of PI resistance by in vitro mutagenesis has been reported. We were able to identify several novel Gag mutations that are associated with PI exposure and therapy failure. Conclusions Our analysis confirmed the association of Gag mutations, well known and new, with PI exposure. This could have clinical implications, since the level of potential PI drug resistance might be underestimated.
Collapse
Affiliation(s)
- K Kletenkov
- Molecular Virology, Department of Biomedicine - Petersplatz, University of Basel, Basel, Switzerland
| | - D Hoffmann
- Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology, University of Duisburg-Essen, Duisburg, Germany
| | - J Böni
- Institute of Medical Virology, National Reference Center for Retroviruses, University of Zurich, Zurich, Switzerland
| | - S Yerly
- Laboratory of Virology, University Hospital Geneva, University of Geneva, Geneva, Switzerland
| | - V Aubert
- Division of Immunology and Allergy, University Hospital Lausanne, University of Lausanne, Lausanne, Switzerland
| | - F Schöni-Affolter
- Swiss HIV Cohort Study, Data Centre, Institute for Social and Preventive Medicine, University of Lausanne, Lausanne, Switzerland
| | - D Struck
- Department of Population Health, Luxembourg Institute of Health, Luxembourg
| | - J Verheyen
- Institute of Virology, University Hospital Essen, University Duisburg-Essen, Duisburg, Germany
| | - T Klimkait
- Molecular Virology, Department of Biomedicine - Petersplatz, University of Basel, Basel, Switzerland
| | | |
Collapse
|
13
|
Anastasiou OE, Widera M, Korth J, Kefalakes H, Katsounas A, Hilgard G, Gerken G, Canbay A, Ciesek S, Verheyen J. Clinical patterns associated with the concurrent detection of anti-HBs and HBV DNA. J Med Virol 2017; 90:282-290. [PMID: 28892166 DOI: 10.1002/jmv.24942] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 08/28/2017] [Indexed: 01/16/2023]
Abstract
Simultaneous detection of anti-HBs and HBV DNA is a rare serological combination and has been described in acute and chronic HBV infection. To scrutinize viral and clinical patterns associated with concurrent detection of anti-HBs and HBV DNA. Simultaneous detection of anti-HBs and HBV DNA was observed in 64/1444 (4.4%) patients treated for HBV infection at the University Hospital of Essen from 2006 to 2016 (8 with acute, 20 with reactivated, and 36 chronic HBV infection). Clinical data and laboratory parameters were analyzed. Regions of the small hepatitis B surface antigen (SHB) and the reverse transcriptase (RT) were sequenced using next generation sequencing (NGS). Among the 64 patients with detectable HBV DNA and anti-HBs, 17 were HBsAg negative (HBsAg[-]), and two had acute liver failure. Patients with acute HBV infection had fewer genotype specific amino acid substitutions in the SHB region than patients with reactivated HBV infection (4 [4.5] vs 9 [16.25], P = 0.043). However, we could observe a significantly higher number of mutations in the a-determinant region when comparing chronically infected patients to patients with acute infection (0 [1] vs 1 [1], P = 0.044). The ratio of nonsynonymous to synonymous mutations (Ka/Ks) was on average >1 for the SHB region and <1 for the RT region. The Ka/Ks ratio (>1) in the SHB region indicates that anti-HBs might have exerted selection pressure on the HBsAg. In three cases the diagnosis of acute HBV infection would have been at least delayed by only focusing on HBsAg testing.
Collapse
Affiliation(s)
- Olympia E Anastasiou
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany.,Department of Gastroenterology and Hepatology, University Hospital of Essen, Essen, Germany
| | - Marek Widera
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Johannes Korth
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Helenie Kefalakes
- Department of Gastroenterology and Hepatology, University Hospital of Essen, Essen, Germany.,Immunology Section, Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland
| | - Antonios Katsounas
- Department of Gastroenterology and Hepatology, University Hospital of Essen, Essen, Germany
| | - Gudrun Hilgard
- Department of Gastroenterology and Hepatology, University Hospital of Essen, Essen, Germany
| | - Guido Gerken
- Department of Gastroenterology and Hepatology, University Hospital of Essen, Essen, Germany
| | - Ali Canbay
- Department of Gastroenterology and Hepatology, University Hospital of Magdeburg, Magdeburg, Germany
| | - Sandra Ciesek
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Jens Verheyen
- Institute of Virology, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| |
Collapse
|
14
|
Salpini R, Surdo M, Warner N, Cortese MF, Colledge D, Soppe S, Bellocchi MC, Armenia D, Carioti L, Continenza F, Di Carlo D, Saccomandi P, Mirabelli C, Pollicita M, Longo R, Romano S, Cappiello G, Spanò A, Trimoulet P, Fleury H, Vecchiet J, Iapadre N, Barlattani A, Bertoli A, Mari T, Pasquazzi C, Missale G, Sarrecchia C, Orecchini E, Michienzi A, Andreoni M, Francioso S, Angelico M, Verheyen J, Ceccherini-Silberstein F, Locarnini S, Perno CF, Svicher V. Novel HBsAg mutations correlate with hepatocellular carcinoma, hamper HBsAg secretion and promote cell proliferation in vitro. Oncotarget 2017; 8:15704-15715. [PMID: 28152517 PMCID: PMC5362517 DOI: 10.18632/oncotarget.14944] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 12/27/2016] [Indexed: 02/07/2023] Open
Abstract
Background An impaired HBsAg-secretion can increase HBV oncogenic-properties. Here, we investigate genetic-determinants in HBsAg correlated with HBV-induced hepatocellular carcinoma (HCC), and their impact on HBsAg-secretion and cell-proliferation. Methods This study included 128 chronically HBV-infected patients: 23 with HCC (73.9% D; 26.1% A HBV-genotype), and 105 without cirrhosis/HCC (72.4% D, 27.6% A) as reference-group. The impact of mutations on HBsAg-secretion was assessed by measuring the ratio [secreted/intracellular HBsAg] until day 5 post-transfection. The impact of mutations on cell-cycle advancement was assessed by flow-cytometry. Results Two HBsAg mutations significantly correlated with HCC: P203Q (17.4% [4/23] in HCC vs 1.0% [1/105] in non-HCC, P=0.004); S210R (34.8% [8/23] in HCC vs 3.8% [4/105] in non-HCC, P <0.001); P203Q+S210R (17.4% [4/23] in HCC vs 0% [0/110] in non-HCC, P=0.001). Both mutations reside in trans-membrane C-terminal domain critical for HBsAg-secretion. In in-vitro experiments, P203Q, S210R and P203Q+S210R significantly reduced the ratio [secreted/intracellular HBsAg] compared to wt at each time-point analysed (P <0.05), supporting an impaired HBsAg-secretion. Furthermore, P203Q and P203Q+S210R increased the percentage of cells in S-phase compared to wt, indicating cell-cycle progression (P203Q:26±13%; P203Q+S210R:29±14%; wt:18%±9, P <0.01. Additionally, S210R increased the percentage of cells in G2/M-phase (26±8% for wt versus 33±6% for S210R, P <0.001). Conclusions Specific mutations in HBsAg C-terminus significantly correlate with HBV-induced HCC. They hamper HBsAg-secretion and are associated with increased cellular proliferation, supporting their involvement in HCC-development. The identification of viral genetic markers associated with HCC is critical to identify patients at higher HCC-risk that may deserve intensive liver monitoring, and/or early anti-HBV therapy.
Collapse
Affiliation(s)
- Romina Salpini
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata" Rome, Italy
| | - Matteo Surdo
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata" Rome, Italy
| | - Nadia Warner
- Research and Molecular Development, Victorian Infectious Diseases Reference Laboratory, North Melbourne, Victoria, Australia
| | - Maria Francesca Cortese
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata" Rome, Italy
| | - Danny Colledge
- Research and Molecular Development, Victorian Infectious Diseases Reference Laboratory, North Melbourne, Victoria, Australia
| | - Sally Soppe
- Research and Molecular Development, Victorian Infectious Diseases Reference Laboratory, North Melbourne, Victoria, Australia
| | | | - Daniele Armenia
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata" Rome, Italy
| | - Luca Carioti
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata" Rome, Italy
| | - Fabio Continenza
- Laboratory of Monitoring Antiviral Drugs, National Institute for Infectious Diseases (INMI) "Lazzaro Spallanzani" Rome, Italy
| | - Domenico Di Carlo
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata" Rome, Italy
| | - Patrizia Saccomandi
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata" Rome, Italy
| | - Carmen Mirabelli
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata" Rome, Italy.,Institut Pasteur, Unité de Biologie des Virus Entériques, Paris, France
| | - Michela Pollicita
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata" Rome, Italy
| | - Roberta Longo
- Unit of Microbiology, "S. Pertini Hospital", Rome, Italy
| | - Sara Romano
- Unit of Microbiology, "S. Pertini Hospital", Rome, Italy
| | | | - Alberto Spanò
- Unit of Microbiology, "S. Pertini Hospital", Rome, Italy
| | - Pascale Trimoulet
- Laboratoire de Microbiologie Fondamentale et Pathogénicité, Hôpital Pellegrin Tripode, Bordeaux, France
| | - Herve Fleury
- Laboratoire de Microbiologie Fondamentale et Pathogénicité, Hôpital Pellegrin Tripode, Bordeaux, France
| | - Jacopo Vecchiet
- Department of Medicine and Aging Sciences, "SS Annunziata" Hospital, Chieti, Italy
| | - Nerio Iapadre
- Infectious Diseases Unit, "S Salvatore" Hospital, L'Aquila, Italy
| | | | - Ada Bertoli
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata" Rome, Italy
| | - Terenzio Mari
- Hepatology Unit, "Regina Margherita" Hospital, Rome, Italy
| | | | | | - Cesare Sarrecchia
- Tor Vergata University Hospital, Infectious Diseases Unit, Rome, Italy
| | - Elisa Orecchini
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata" Rome, Italy
| | - Alessandro Michienzi
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata" Rome, Italy
| | - Massimo Andreoni
- Tor Vergata University Hospital, Infectious Diseases Unit, Rome, Italy
| | | | - Mario Angelico
- Tor Vergata University Hospital, Hepatology Unit, Rome, Italy
| | - Jens Verheyen
- Tor Vergata University Hospital, Hepatology Unit, Rome, Italy
| | | | - Stephen Locarnini
- Research and Molecular Development, Victorian Infectious Diseases Reference Laboratory, North Melbourne, Victoria, Australia
| | - Carlo Federico Perno
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata" Rome, Italy
| | - Valentina Svicher
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata" Rome, Italy
| |
Collapse
|
15
|
Anastasiou OE, Widera M, Verheyen J, Korth J, Gerken G, Helfritz FA, Canbay A, Wedemeyer H, Ciesek S. Clinical course and core variability in HBV infected patients without detectable anti-HBc antibodies. J Clin Virol 2017. [DOI: 10.1016/j.jcv.2017.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
16
|
Widera M, Dirks M, Bleekmann B, Jablonka R, Däumer M, Walter H, Ehret R, Verheyen J, Esser S. HIV-1 persistent viremia is frequently followed by episodes of low-level viremia. Med Microbiol Immunol 2017; 206:203-215. [PMID: 28220254 PMCID: PMC5409919 DOI: 10.1007/s00430-017-0494-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 01/24/2017] [Indexed: 12/13/2022]
Abstract
After the start of antiretroviral therapy (ART), plasma HIV-RNA levels should fall below the limit of detection (LOD) within 24 weeks. Hence, the prolonged decline of HIV-RNA after ART initiation is defined as persistent viremia (PV). In this retrospective study, we analyzed factors associated with PV. Next-generation sequencing of viral RNA/DNA was performed to study viral evolution and the emergence of drug-resistance mutations in HIV-infected patients with PV (n = 20). In addition, HIV-DNA species, immunological parameters, and clinical data of the patients were analyzed. We found that the possible causes for PV were divers, and both virologic and host parameters of this particular cohort were heterogeneous. We identified viruses with therapy-associated DRMs in six patients (30%); two of these were detected as minority variants. Five patients had sub-optimal drug levels (25%) and the baseline plasma viral loads were relatively high. Strikingly, we observed that >40% of the PV patients finally reaching HIV levels below the LOD later on showed up with episodes of low-level viremia (LLV). However, the amount of PBMC derived HIV-DNA species was not correlated with the likelihood of LLV after PV. According to our data, we conclude that drug-resistant viruses, sub-optimal drug level, and high baseline viral loads might be probable reasons for the prolonged RNA decline only in a sub-set of patients. In the absence of emerging DRMs and/or compliance issues, the clinical implications of PV remain unclear; however, PV appears to be a risk factor for episodes of LLV.
Collapse
Affiliation(s)
- Marek Widera
- Institute of Virology, University Hospital, University of Duisburg-Essen, Virchowstr. 179, 45147, Essen, Germany.
| | - Miriam Dirks
- Institute of Virology, University Hospital, University of Duisburg-Essen, Virchowstr. 179, 45147, Essen, Germany
| | - Barbara Bleekmann
- Institute of Virology, University Hospital, University of Duisburg-Essen, Virchowstr. 179, 45147, Essen, Germany
| | - Robert Jablonka
- Clinic of Dermatology, University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Martin Däumer
- Institut für Immunologie und Genetik, Kaiserslautern, Germany
| | - Hauke Walter
- Laboratory MIB, Medical Infectiology Center Berlin, Berlin, Germany
| | - Robert Ehret
- Laboratory MIB, Medical Infectiology Center Berlin, Berlin, Germany
| | - Jens Verheyen
- Institute of Virology, University Hospital, University of Duisburg-Essen, Virchowstr. 179, 45147, Essen, Germany
| | - Stefan Esser
- Clinic of Dermatology, University Hospital, University of Duisburg-Essen, Essen, Germany
| |
Collapse
|
17
|
Jochum C, Maischack F, Anastasiou OE, Verheyen J, Timm J, Bechmann L, Gerken G, Canbay A. Treatment of fulminant acute Hepatitis B with nucles(t)id analogues is safe and does not lead to secondary chronification of Hepatitis B. Z Gastroenterol 2016; 54:1306-1311. [PMID: 27936480 DOI: 10.1055/s-0042-120418] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Background: Acute hepatitis B virus (HBV) infection is still a major cause of acute liver failure (ALF), necessitating a high rate of emergency liver transplantation (LTx). Acute infection is followed by high viral replication rates leading to hepatocyte death and, ultimately, ALF. The objective of treating HBV-induced ALF thus is to eliminate, or significantly suppress, HBV replication and therefore reduce cell death and support regeneration. Objective: In this retrospective study, we want to evaluate the timing, the safety, and the long-term virological outcome of this approach. Methods/results: In this study, we included 32 patients (16 female and 16 males; median age 39.5 years) with ALF due to hepatitis B, who were transferred to the university hospital Essen, Germany between January 2009 and December 2013. Before treatment, transaminases were highly elevated, bilirubin was increased, and elevated international normalized ratio (INR) revealed impaired liver function. HBV-DNA and HBsAg were positive. All 32 patients received oral antiviral treatment (3 lamivudine, 21 entecavir, and 8 tenofovir) between 1 day and 4 months after diagnosis of acute hepatitis B. One patient died, 2 were transplanted, one died shortly after LTx the other patient survived after LTx. These 3 patients received treatment in a state of advanced liver failure, and 1 patient 4 months after initial diagnosis of hepatitis B. Twenty-nine patients survived without LTx. Five patients were discharged without further follow-up. All 24 remaining patients became HBV-DNA negative in median of 100 days. Twenty-two patients were followed further, and all patients lost their HBsAg in median of 108 days. Sixteen of the 22 patients experienced a seroconversion to anti-HBs in median of 137 days. Four patients who were followed for 1 more year after HBsAg did not develop anti-HBs. None of the patients developed chronic hepatitis B. Conclusion: Immediate treatment of HBV-induced ALF with nucleos(t)id-analogues (NUCs) appears save and prevents LTx and death, and there is no indication for increased chronicity.
Collapse
Affiliation(s)
- C Jochum
- Gastroenterology and Hepatology, University Hospital Essen, Germany
| | - F Maischack
- Gastroenterology and Hepatology, University Hospital Essen, Germany
| | - O E Anastasiou
- Gastroenterology and Hepatology, University Hospital Essen, Germany
| | - J Verheyen
- Institute for Virology, University Hospital Essen, Germany
| | - J Timm
- Institut für Virologie, Universitatsklinikum Dusseldorf, Germany
| | - L Bechmann
- Gastroenterology and Hepatology, University Hospital Essen, Germany
| | - G Gerken
- Gastroenterology and Hepatology, University Hospital Essen, Germany
| | - A Canbay
- Gastroenterology and Hepatology, University Hospital Essen, Germany
| |
Collapse
|
18
|
Punzel M, Medd P, Hunter H, Cunningham R, Pottinger B, Burde B, Widera M, Quade A, Ehninger G, Kozlova A, Schmidt H, Buhrmann K, Schüttler CG, Glebe D, Billen A, Schmidt AH, Mengling T, Verheyen J. Detection of hepatitis b virus DNA in the blood of a stem cell donor after granulocyte colony-stimulating factor treatment. Hepatology 2016; 64:1803-1805. [PMID: 27240006 DOI: 10.1002/hep.28667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 05/27/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Michael Punzel
- Cellex Apheresis and Collection Center, MediaPark Klinik, Cologne, Germany
| | - Patrick Medd
- Department of Haematology, Plymouth Hospitals NHS Trust, Derriford Hospital, Plymouth, UK
| | - Hannah Hunter
- Department of Haematology, Plymouth Hospitals NHS Trust, Derriford Hospital, Plymouth, UK
| | - Richard Cunningham
- Department of Haematology Virology, Plymouth Hospitals NHS Trust, Derriford Hospital, Plymouth, UK
| | - Bryson Pottinger
- Department of Haematology, Royal Cornwall Hospitals NHS Trust, Truro, UK
| | - Bernd Burde
- MVZ Labor Dr. Quade & Kollegen, Cologne, Germany
| | - Marek Widera
- Institute of Virology, University Hospital, University of Duisburg-Essen, Essen, Germany
| | | | - Gerhard Ehninger
- Cellex Apheresis and Collection Center, MediaPark Klinik, Cologne, Germany
| | - Anna Kozlova
- Cellex Apheresis and Collection Center, MediaPark Klinik, Cologne, Germany
| | - Helmuth Schmidt
- Cellex Apheresis and Collection Center, MediaPark Klinik, Cologne, Germany
| | - Karin Buhrmann
- Cellex Apheresis and Collection Center, MediaPark Klinik, Cologne, Germany
| | - Christian G Schüttler
- Institute of Medical Virology, Justus Liebig University Giessen, National Reference Center for Hepatitis B and D Viruses, Biomedical Research Center Seltersberg, Giessen, Germany
| | - Dieter Glebe
- Institute of Medical Virology, Justus Liebig University Giessen, National Reference Center for Hepatitis B and D Viruses, Biomedical Research Center Seltersberg, Giessen, Germany
| | - Annelies Billen
- Anthony Nolan, National Donor Registry of the UK, London, UK
| | | | - Thilo Mengling
- DKMS, German Bone Marrow Donor Registry, Tübingen, Germany
| | - Jens Verheyen
- Institute of Virology, University Hospital, University of Duisburg-Essen, Essen, Germany.
| |
Collapse
|
19
|
Abstract
BACKGROUND Viral hepatitis is still one of the key causes of acute liver failure (ALF) in the world. METHODS A selective literature search of the PubMed database was conducted, including current studies, reviews, meta-analyses, and guidelines. We obtained an overview of ALF due to viral hepatitis in terms of epidemiology, course, and treatment options. RESULTS Most fulminant viral courses are reported after infection with hepatitis A, B, and B/D, but not with hepatitis C. Hepatitis E is also known to cause ALF but has not gained much attention in recent years. However, more and more autochthonous hepatitis E virus infections have been recently observed in Europe. Reactivation of hepatitis B virus (HBV) under immunosuppressive conditions, such as after intensive chemotherapy, is also an increasing problem. For most viral-induced cases of ALF, liver transplantation represented the only therapeutic option in the past. Today, immediate treatment of HBV-induced ALF with nucleotide or nucleoside analogs is well tolerated and beneficially affects the course of the disease. CONCLUSION Although numbers in Western European countries are decreasing rapidly, reliable diagnostic screening for hepatitis A-E is necessary to identify the etiology and to determine those most at risk of developing ALF.
Collapse
Affiliation(s)
- Paul Manka
- Department of Gastroenterology and Hepatology, University Hospital Essen, Essen, Germany
- Regeneration and Repair Group, The Institute of Hepatology, Foundation for Liver Research, London, UK
- Division of Transplantation Immunology and Mucosal Biology, King's College, London, UK
| | - Jens Verheyen
- Institute of Virology, University Hospital, University Duisburg-Essen, Essen, Germany
| | - Guido Gerken
- Department of Gastroenterology and Hepatology, University Hospital Essen, Essen, Germany
| | - Ali Canbay
- Department of Gastroenterology and Hepatology, University Hospital Essen, Essen, Germany
| |
Collapse
|
20
|
Joedicke JJ, Dirks M, Esser S, Verheyen J, Dittmer U. Reduced Frequencies and Activation of Regulatory T Cells After the Treatment of HIV-1-Infected Individuals with the CCR5 Antagonist Maraviroc Are Associated with a Reduction in Viral Loads Rather Than a Direct Effect of the Drug on Regulatory T Cells. Viral Immunol 2016; 29:192-6. [PMID: 27035639 DOI: 10.1089/vim.2015.0046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Regulatory T cells (Tregs) play an important role in the pathogenesis of HIV-1 infection and they frequently express the chemokine receptor CCR5. We therefore investigated whether antiretroviral treatment with the CCR5 antagonist Maraviroc affected Tregs in chronically HIV-1-infected individuals. HIV-1-infected patients with high viral loads had elevated frequencies of activated Tregs in the peripheral blood compared with healthy controls. In patients successfully treated with antiretroviral drugs (undetectable viral loads), the frequency and the activation status of Tregs were comparable with healthy controls without any specific effect related to the treatment with Maraviroc. These results indicate that the control of viral replication in general rather than a direct binding of Maraviroc to CCR5-positive Tregs influences Treg responses in successfully treated chronically HIV-1-infected individuals.
Collapse
Affiliation(s)
- Jara J Joedicke
- 1 Institute for Virology, University Hospital Essen, University of Duisburg-Essen , Essen, Germany
| | - Miriam Dirks
- 1 Institute for Virology, University Hospital Essen, University of Duisburg-Essen , Essen, Germany
| | - Stefan Esser
- 2 Clinic for Dermatology, University Hospital Essen, University of Duisburg-Essen , Essen, Germany
| | - Jens Verheyen
- 1 Institute for Virology, University Hospital Essen, University of Duisburg-Essen , Essen, Germany
| | - Ulf Dittmer
- 1 Institute for Virology, University Hospital Essen, University of Duisburg-Essen , Essen, Germany
| |
Collapse
|
21
|
Van Dis ES, Moore TC, Lavender KJ, Messer RJ, Keppler OT, Verheyen J, Dittmer U, Hasenkrug KJ. No SEVI-mediated enhancement of rectal HIV-1 transmission of HIV-1 in two humanized mouse cohorts. Virology 2015; 488:88-95. [PMID: 26609939 DOI: 10.1016/j.virol.2015.11.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 10/14/2015] [Accepted: 11/06/2015] [Indexed: 11/28/2022]
Abstract
Amyloid fibrils from semen-derived peptide (SEVI) enhance HIV-1 infectivity in vitro but the ability of SEVI to mediate enhancement of HIV infection in vivo has not been tested. In this study we used immunodeficient mice reconstituted with human immune systems to test for in vivo enhancement of HIV-1 transmission. This mouse model supports mucosal transmission of HIV-1 via the intrarectal route leading to productive infection. In separate experiments with humanized mouse cohorts reconstituted with two different donor immune systems, high dose HIV-1JR-CSF that had been incubated with SEVI amyloid fibrils at physiologically relevant concentrations did not show an increased incidence of infection compared to controls. In addition, SEVI failed to enhance rectal transmission with a reduced concentration of HIV-1. Although we confirmed potent SEVI-mediated enhancement of HIV infectivity in vitro, this model showed no evidence that it plays a role in the much more complex situation of in vivo transmission.
Collapse
Affiliation(s)
- Erik S Van Dis
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT 59840, USA
| | - Tyler C Moore
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT 59840, USA
| | - Kerry J Lavender
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT 59840, USA
| | - Ronald J Messer
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT 59840, USA
| | - Oliver T Keppler
- Institute of Medical Virology, National Reference Center for Retroviruses, University of Frankfurt, Frankfurt, Germany
| | - Jens Verheyen
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany
| | - Kim J Hasenkrug
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, NIAID, NIH, Hamilton, MT 59840, USA.
| |
Collapse
|
22
|
Gibbert K, Lavender KJ, Peterson KE, Münch J, Piehler J, Santiago ML, Verheyen J, Hasenkrug K, Dittmer U. ID: 41. Cytokine 2015. [DOI: 10.1016/j.cyto.2015.08.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
23
|
Manka P, Bechmann LP, Coombes JD, Thodou V, Schlattjan M, Kahraman A, Syn WK, Saner F, Gerken G, Baba H, Verheyen J, Timm J, Canbay A. Hepatitis E Virus Infection as a Possible Cause of Acute Liver Failure in Europe. Clin Gastroenterol Hepatol 2015; 13:1836-1842.e2; quiz e157-8. [PMID: 25912835 DOI: 10.1016/j.cgh.2015.04.014] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 04/01/2015] [Accepted: 04/03/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS In Western countries, infection with the hepatitis E virus (HEV) is considered to be rare and imported from endemic regions. However, the prevalence of HEV infection has increased among adults in central Europe. HEV infection can cause acute liver failure (ALF), but there have been only a few confirmed cases of HEV-associated ALF in Europe. We investigated the number of cases of indeterminate ALF associated with HEV infection. METHODS We performed a retrospective analysis of 80 patients diagnosed with ALF or acute hepatitis at the University Hospital Essen in Germany from November 2006 through December 2013. Clinical data were collected from the hospital databases; archived sera were tested for IgG and IgM against HEV, as well as HEV RNA. RESULTS Sera from 12 patients (15%) tested positive for IgG against HEV IgG; 7 of these samples did not test positive for HEV IgM or HEV RNA. Sera from 64 patients (80%) did not test positive for IgG or IgM against HEV or HEV RNA. Sera from 8 patients (10%) tested positive for HEV RNA (only 4 of these were positive for HEV IgG) and had clinical findings to support acute HEV infection. CONCLUSIONS In a hospital in Germany, approximately 10% to 15% of patients with ALF had evidence for HEV infection. Serologic tests for IgG against HEV are insufficient to identify or exclude HEV infection; tests for HEV RNA also should be performed on patients with ALF of ambiguous etiology.
Collapse
Affiliation(s)
- Paul Manka
- Department of Gastroenterology and Hepatology, University Hospital, University Duisburg-Essen, Essen, Germany
| | - Lars P Bechmann
- Department of Gastroenterology and Hepatology, University Hospital, University Duisburg-Essen, Essen, Germany
| | - Jason D Coombes
- Regeneration and Repair Group, Foundation for Liver Research, The Institute of Hepatology, London, United Kingdom
| | - Viktoria Thodou
- Department of Gastroenterology and Hepatology, University Hospital, University Duisburg-Essen, Essen, Germany
| | - Martin Schlattjan
- Department of Gastroenterology and Hepatology, University Hospital, University Duisburg-Essen, Essen, Germany
| | - Alisan Kahraman
- Department of Gastroenterology and Hepatology, University Hospital, University Duisburg-Essen, Essen, Germany
| | - Wing-Kin Syn
- Regeneration and Repair Group, Foundation for Liver Research, The Institute of Hepatology, London, United Kingdom; Department of Hepatology, Barts Health NHS Trust, London, United Kingdom
| | - Fuat Saner
- Department of General, Visceral and Transplantation Surgery, University Hospital, University Duisburg-Essen, Essen, Germany
| | - Guido Gerken
- Department of Gastroenterology and Hepatology, University Hospital, University Duisburg-Essen, Essen, Germany
| | - Hideo Baba
- Institute of Pathology and Neuropathology, University Hospital, University Duisburg-Essen, Essen, Germany
| | - Jens Verheyen
- Institute of Virology, University Hospital, University Duisburg-Essen, Essen, Germany
| | - Jörg Timm
- Institute for Virology, Düsseldorf University Hospital, Heinrich-Heine-University, Düsseldorf, Germany
| | - Ali Canbay
- Department of Gastroenterology and Hepatology, University Hospital, University Duisburg-Essen, Essen, Germany.
| |
Collapse
|
24
|
Kefalakes H, Jochum C, Hilgard G, Kahraman A, Bohrer AM, El Hindy N, Heinemann FM, Verheyen J, Gerken G, Roggendorf M, Timm J. Decades after recovery from hepatitis B and HBsAg clearance the CD8+ T cell response against HBV core is nearly undetectable. J Hepatol 2015; 63:13-9. [PMID: 25646888 DOI: 10.1016/j.jhep.2015.01.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 01/16/2015] [Accepted: 01/23/2015] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS CD8(+) T cells are an essential component of a successful immune response against hepatitis B virus (HBV). Patients who spontaneously clear HBsAg after acute HBV infection have a strong CD8(+) T cell immune response, predominantly directed against the HBV core protein (HBcAg). However, the fate and phenotype of HBcAg-specific CD8(+) T cells after immune control are unclear. METHODS The CD8(+) T cell immune response against HBV core was determined in 65 patients with chronic HBV infection, 16 patients after recovery from acute HBV infection, and four patients with acute HBV infection utilizing overlapping peptides and HLA class I/peptide-multimers. RESULTS Patients who had cleared HBsAg >30 years ago had significantly weaker CD8(+) T cell responses after antigen-specific expansion compared to patients who had cleared the virus <10 years ago and patients with HBeAg negative chronic infection and low viral load (<2000 IU/ml; p<0.01). Also directly ex vivo, patients who had cleared the HBsAg >30 years ago had less HBV-specific CD8(+) T cells compared to patients with HBeAg negative chronic infection (p=0.0025). In patients with acute HBV infection, the frequency of HBc-specific CD8(+) T cells continued to decline after clearance of HBV-DNA and HBsAg even at a time when ALT levels had already normalized (p=0.0313). CONCLUSIONS The frequency of HBcAg-specific CD8(+) T cells continuously declines after HBsAg clearance. In line with clinical observations, this suggests that humoral and not CD8(+) T cell immune responses mainly contribute to prevention of HBV reactivation decades after HBsAg clearance.
Collapse
Affiliation(s)
- Helenie Kefalakes
- Institute of Virology, University of Duisburg-Essen, University Hospital Essen, Essen, Germany; Department of Gastroenterology, University Hospital Essen, Essen, Germany
| | - Christoph Jochum
- Department of Gastroenterology, University Hospital Essen, Essen, Germany
| | - Gudrun Hilgard
- Department of Gastroenterology, University Hospital Essen, Essen, Germany
| | - Alisan Kahraman
- Department of Gastroenterology, University Hospital Essen, Essen, Germany
| | | | - Nicolai El Hindy
- Department of Neurosurgery, University Hospital Essen, Essen, Germany
| | - Falko Markus Heinemann
- Institute for Transfusion Medicine, University of Duisburg-Essen, University Hospital Essen, Essen, Germany
| | - Jens Verheyen
- Institute of Virology, University of Duisburg-Essen, University Hospital Essen, Essen, Germany
| | - Guido Gerken
- Department of Gastroenterology, University Hospital Essen, Essen, Germany
| | | | - Joerg Timm
- Institute of Virology, University of Duisburg-Essen, University Hospital Essen, Essen, Germany; Institute of Virology, Heinrich-Heine-University, University Hospital, Düsseldorf, Germany.
| |
Collapse
|
25
|
Hermans LE, Svicher V, Pas SD, Salpini R, Alvarez M, Ben Ari Z, Boland G, Bruzzone B, Coppola N, Seguin-Devaux C, Dyda T, Garcia F, Kaiser R, Köse S, Krarup H, Lazarevic I, Lunar MM, Maylin S, Micheli V, Mor O, Paraschiv S, Paraskevis D, Poljak M, Puchhammer-Stöckl E, Simon F, Stanojevic M, Stene-Johansen K, Tihic N, Trimoulet P, Verheyen J, Vince A, Weis N, Yalcinkaya T, Lepej SZ, Perno C, Boucher CAB, Wensing AMJ. Combined Analysis of the Prevalence of Drug-Resistant Hepatitis B Virus in Antiviral Therapy-Experienced Patients in Europe (CAPRE). J Infect Dis 2015; 213:39-48. [PMID: 26136470 DOI: 10.1093/infdis/jiv363] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 06/23/2015] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND European guidelines recommend treatment of chronic hepatitis B virus infection (CHB) with the nucleos(t)ide analogs (NAs) entecavir or tenofovir. However, many European CHB patients have been exposed to other NAs, which are associated with therapy failure and resistance. The CAPRE study was performed to gain insight in prevalence and characteristics of NA resistance in Europe. METHODS A survey was performed on genotypic resistance testing results acquired during routine monitoring of CHB patients with detectable serum hepatitis B virus DNA in European tertiary referral centers. RESULTS Data from 1568 patients were included. The majority (73.8%) were exposed to lamivudine monotherapy. Drug-resistant strains were detected in 52.7%. The most frequently encountered primary mutation was M204V/I (48.7%), followed by A181T/V (3.8%) and N236T (2.6%). In patients exposed to entecavir (n = 102), full resistance was present in 35.3%. Independent risk factors for resistance were age, viral load, and lamivudine exposure (P < .001). CONCLUSIONS These findings support resistance testing in cases of apparent NA therapy failure. This survey highlights the impact of exposure to lamivudine and adefovir on development of drug resistance and cross-resistance. Continued use of these NAs needs to be reconsidered at a pan-European level.
Collapse
Affiliation(s)
- Lucas Etienne Hermans
- Department of Medical Microbiology, University Medical Centre Utrecht Department of Virology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Valentina Svicher
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Italy
| | | | - Romina Salpini
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Italy
| | - Marta Alvarez
- Servicio de Microbiología, Hospital San Cecilio, Instituto de Investigación Biosanitaria ibs. GRANADA, Hospitales Universitarios de Granada, Spain
| | - Ziv Ben Ari
- Liver Disease Centre, Sheba Medical Centre, Ramat Gan, Israel
| | - Greet Boland
- Department of Medical Microbiology, University Medical Centre Utrecht
| | | | - Nicola Coppola
- Malattie Infettive, Seconda Università degli studi di Napoli, Naples, Italy
| | | | - Tomasz Dyda
- Molecular Diagnostics Laboratory, Hospital of Infectious Diseases, Warsaw, Poland
| | - Federico Garcia
- Servicio de Microbiología, Hospital San Cecilio, Instituto de Investigación Biosanitaria ibs. GRANADA, Hospitales Universitarios de Granada, Spain
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Germany
| | - Sukran Köse
- Clinic of Infectious Diseases and Clinical Microbiology, Izmir Tepecik Education and Research Hospital, Turkey
| | - Henrik Krarup
- Section of Molecular Diagnostics, Clinical Biochemistry, Aalborg University Hospital, Denmark
| | - Ivana Lazarevic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Serbia
| | - Maja M Lunar
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenia
| | - Sarah Maylin
- Service de Microbiologie, University Paris Diderot, Hôpital Saint Louis, France
| | | | - Orna Mor
- National HIV Reference Laboratory, Central Virology Laboratory, Ministry of Health, Tel Hashomer, Ramat Gan, Israel
| | - Simona Paraschiv
- Molecular Diagnostics Laboratory, National Institute for Infectious Diseases Matei Bals, Bucharest, Romania
| | - Dimitrios Paraskevis
- National Retrovirus Reference Centre, Department of Hygiene, Epidemiology and Medical Statistics, Faculty of Medicine, National and Kapodistrian University of Athens, Greece
| | - Mario Poljak
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Slovenia
| | | | - François Simon
- Service de Microbiologie, University Paris Diderot, Hôpital Saint Louis, France
| | - Maja Stanojevic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Serbia
| | | | - Nijaz Tihic
- Institute of Microbiology, Polyclinic for Laboratory Diagnostics, University Clinical Centre Tuzla, Bosnia and Herzegovina
| | - Pascale Trimoulet
- Virology Laboratory, Centre Hospitalier Régional et Université Victor Segalen, Bordeaux, France
| | - Jens Verheyen
- Institute of Virology, University-Hospital, University Duisburg-Essen, Germany
| | - Adriana Vince
- University of Zagreb School of Medicine and University Hospital for Infectious Diseases "Dr Fran Mihaljevic", Croatia
| | - Nina Weis
- Department of Infectious Diseases, Copenhagen University Hospital, Denmark
| | | | - Snjezana Zidovec Lepej
- University of Zagreb School of Medicine and University Hospital for Infectious Diseases "Dr Fran Mihaljevic", Croatia
| | - Carlo Perno
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Italy
| | | | | | | |
Collapse
|
26
|
Teutsch K, Schweitzer F, Knops E, Kaiser R, Pfister H, Verheyen J, Göbel H, Cingöz T, Di Cristanziano V. Early identification of renal transplant recipients with high risk of polyomavirus-associated nephropathy. Med Microbiol Immunol 2015; 204:657-64. [DOI: 10.1007/s00430-015-0398-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 02/21/2015] [Indexed: 02/07/2023]
|
27
|
Salpini R, Colagrossi L, Bellocchi MC, Surdo M, Becker C, Alteri C, Aragri M, Ricciardi A, Armenia D, Pollicita M, Di Santo F, Carioti L, Louzoun Y, Mastroianni CM, Lichtner M, Paoloni M, Esposito M, D'Amore C, Marrone A, Marignani M, Sarrecchia C, Sarmati L, Andreoni M, Angelico M, Verheyen J, Perno CF, Svicher V. Hepatitis B surface antigen genetic elements critical for immune escape correlate with hepatitis B virus reactivation upon immunosuppression. Hepatology 2015; 61:823-33. [PMID: 25418031 DOI: 10.1002/hep.27604] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 11/05/2014] [Indexed: 12/12/2022]
Abstract
UNLABELLED Hepatitis B virus (HBV) reactivation during immunosuppression can lead to severe acute hepatitis, fulminant liver failure, and death. Here, we investigated hepatitis B surface antigen (HBsAg) genetic features underlying this phenomenon by analyzing 93 patients: 29 developing HBV reactivation and 64 consecutive patients with chronic HBV infection (as control). HBsAg genetic diversity was analyzed by population-based and ultradeep sequencing (UDS). Before HBV reactivation, 51.7% of patients were isolated hepatitis B core antibody (anti-HBc) positive, 31.0% inactive carriers, 6.9% anti-HBc/anti-HBs (hepatitis B surface antibody) positive, 6.9% isolated anti-HBs positive, and 3.4% had an overt HBV infection. Of HBV-reactivated patients, 51.7% were treated with rituximab, 34.5% with different chemotherapeutics, and 13.8% with corticosteroids only for inflammatory diseases. In total, 75.9% of HBV-reactivated patients (vs. 3.1% of control patients; P<0.001) carried HBsAg mutations localized in immune-active HBsAg regions. Of the 13 HBsAg mutations found in these patients, 8 of 13 (M103I-L109I-T118K-P120A-Y134H-S143L-D144E-S171F) reside in a major hydrophilic loop (target of neutralizing antibodies [Abs]); some of them are already known to hamper HBsAg recognition by humoral response. The remaining five (C48G-V96A-L175S-G185E-V190A) are localized in class I/II-restricted T-cell epitopes, suggesting a role in HBV escape from T-cell-mediated responses. By UDS, these mutations occurred in HBV-reactivated patients with a median intrapatient prevalence of 73.3% (range, 27.6%-100%) supporting their fixation in the viral population as a predominant species. In control patients carrying such mutations, their median intrapatient prevalence was 4.6% (range, 2.5%-11.3%; P<0.001). Finally, additional N-linked glycosylation (NLG) sites within the major hydrophilic loop were found in 24.1% of HBV-reactivated patients (vs. 0% of chronic patients; P<0.001); 5 of 7 patients carrying these sites remained HBsAg negative despite HBV reactivation. NLG can mask immunogenic epitopes, abrogating HBsAg recognition by Abs. CONCLUSION HBV reactivation occurs in a wide variety of clinical settings requiring immune-suppressive therapy, and correlates with HBsAg mutations endowed with enhanced capability to evade immune response. This highlights the need for careful patient monitoring in all immunosuppressive settings at reactivation risk and of establishing a prompt therapy to prevent HBV-related clinical complications.
Collapse
Affiliation(s)
- Romina Salpini
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Verheyen J, Maizus K, Feist E, Tolman Z, Knops E, Saech J, Spengler L, Waterboer T, Burmester GR, Pawlita M, Pfister H, Rubbert-Roth A. Increased frequency of JC-polyomavirus detection in rheumatoid arthritis patients treated with multiple biologics. Med Microbiol Immunol 2015; 204:613-8. [DOI: 10.1007/s00430-015-0390-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 02/02/2015] [Indexed: 11/29/2022]
|
29
|
Li G, Theys K, Verheyen J, Pineda-Peña AC, Khouri R, Piampongsant S, Eusébio M, Ramon J, Vandamme AM. A new ensemble coevolution system for detecting HIV-1 protein coevolution. Biol Direct 2015; 10:1. [PMID: 25564011 PMCID: PMC4332441 DOI: 10.1186/s13062-014-0031-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 12/02/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND A key challenge in the field of HIV-1 protein evolution is the identification of coevolving amino acids at the molecular level. In the past decades, many sequence-based methods have been designed to detect position-specific coevolution within and between different proteins. However, an ensemble coevolution system that integrates different methods to improve the detection of HIV-1 protein coevolution has not been developed. RESULTS We integrated 27 sequence-based prediction methods published between 2004 and 2013 into an ensemble coevolution system. This system allowed combinations of different sequence-based methods for coevolution predictions. Using HIV-1 protein structures and experimental data, we evaluated the performance of individual and combined sequence-based methods in the prediction of HIV-1 intra- and inter-protein coevolution. We showed that sequence-based methods clustered according to their methodology, and a combination of four methods outperformed any of the 27 individual methods. This four-method combination estimated that HIV-1 intra-protein coevolving positions were mainly located in functional domains and physically contacted with each other in the protein tertiary structures. In the analysis of HIV-1 inter-protein coevolving positions between Gag and protease, protease drug resistance positions near the active site mostly coevolved with Gag cleavage positions (V128, S373-T375, A431, F448-P453) and Gag C-terminal positions (S489-Q500) under selective pressure of protease inhibitors. CONCLUSIONS This study presents a new ensemble coevolution system which detects position-specific coevolution using combinations of 27 different sequence-based methods. Our findings highlight key coevolving residues within HIV-1 structural proteins and between Gag and protease, shedding light on HIV-1 intra- and inter-protein coevolution.
Collapse
Affiliation(s)
- Guangdi Li
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium.
| | - Kristof Theys
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium.
| | - Jens Verheyen
- Institute of Virology, University hospital, University Duisburg-Essen, Essen, Germany.
| | - Andrea-Clemencia Pineda-Peña
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium. .,Clinical and Molecular Infectious Disease Group, Faculty of Sciences and Mathematics, Universidad del Rosario, Bogotá, Colombia.
| | - Ricardo Khouri
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium.
| | - Supinya Piampongsant
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium.
| | - Mónica Eusébio
- Centro de Malária e Outras Doenças Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal.
| | - Jan Ramon
- Department of Computer Science, KU Leuven - University of Leuven, Leuven, Belgium.
| | - Anne-Mieke Vandamme
- KU Leuven - University of Leuven, Department of Microbiology and Immunology, Rega Institute for Medical Research, Clinical and Epidemiological Virology, Leuven, Belgium. .,Centro de Malária e Outras Doenças Tropicais and Unidade de Microbiologia, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisboa, Portugal.
| |
Collapse
|
30
|
Range S, Hagmeyer D, Rotan O, Sokolova V, Verheyen J, Siebers B, Epple M. A continuous method to prepare poorly crystalline silver-doped calcium phosphate ceramics with antibacterial properties. RSC Adv 2015. [DOI: 10.1039/c5ra00401b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Silver-doped calcium phosphate ceramics were prepared in discontinuous and continuous processes with different amounts of incorporated silver (up to 1.8 wt% silver).
Collapse
Affiliation(s)
- S. Range
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE)
- University of Duisburg-Essen
- 45117 Essen
- Germany
| | - D. Hagmeyer
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE)
- University of Duisburg-Essen
- 45117 Essen
- Germany
| | - O. Rotan
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE)
- University of Duisburg-Essen
- 45117 Essen
- Germany
| | - V. Sokolova
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE)
- University of Duisburg-Essen
- 45117 Essen
- Germany
| | - J. Verheyen
- Biofilm Centre Molecular Enzyme Technology and Biochemistry
- University of Duisburg-Essen
- 45117 Essen
- Germany
| | - B. Siebers
- Biofilm Centre Molecular Enzyme Technology and Biochemistry
- University of Duisburg-Essen
- 45117 Essen
- Germany
| | - M. Epple
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE)
- University of Duisburg-Essen
- 45117 Essen
- Germany
| |
Collapse
|
31
|
|
32
|
Mirabelli C, Surdo M, Van Hemert F, Lian Z, Salpini R, Cento V, Cortese MF, Aragri M, Pollicita M, Alteri C, Bertoli A, Berkhout B, Micheli V, Gubertini G, Santoro MM, Romano S, Visca M, Bernassola M, Longo R, De Sanctis GM, Trimoulet P, Fleury H, Marino N, Mazzotta F, Cappiello G, Spanò A, Sarrecchia C, Zhang JM, Andreoni M, Angelico M, Verheyen J, Perno CF, Svicher V. Specific mutations in the C-terminus domain of HBV surface antigen significantly correlate with low level of serum HBV-DNA in patients with chronic HBV infection. J Infect 2014; 70:288-98. [PMID: 25452041 DOI: 10.1016/j.jinf.2014.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 09/05/2014] [Accepted: 10/17/2014] [Indexed: 12/19/2022]
Abstract
BACKGROUND To define HBsAg-mutations correlated with different serum HBV-DNA levels in HBV chronically-infected drug-naive patients. METHODS This study included 187 patients stratified into the following ranges of serum HBV-DNA:12-2000 IU/ml, 2000-100,000 IU/ml, and >100,000 IU/ml. HBsAg-mutations were associated with HBV-DNA levels by applying a Bayesian-Partitional-Model and Fisher-exact test. Mutant and wild-type HBV genotype-D genomes were expressed in Huh7 cells and HBsAg-production was determined in cell-supernatants at 3 days-post-transfection. RESULTS Specific HBsAg-mutations (M197T,-S204N-Y206C/H-F220L) were significantly correlated with serum HBV-DNA <2000 IU/ml (posterior-probability>90%, P < 0.05). The presence of Y206C/H and/or F220L was also associated with lower median (IQR) HBsAg-levels and lower median (IQR) transaminases (for HBsAg:250[115-840] IU/ml for Y206C/H and/or F220L versus 4300[640-11,838] IU/ml for wild-type, P = 0.023; for ALT:28[21-40] IU/ml versus 53[34-90] IU/ml, P < 0.001). These mutations were localized in the HBsAg C-terminus, known to be involved in virion and/or HBsAg secretion. The co-occurrence of Y206C + F220L was found significant by cluster-analysis, (P = 0.02). In addition, in an in-vitro model Y206C + F220L determined a 2.8-3.3 fold-reduction of HBsAg-amount released in supernatants compared to single mutants and wt (Y206C + F220L = 5,679 IU/ml; Y206H = 16,305 IU/ml; F220L = 18,368 IU/ml; Y206C = 18,680 IU/ml; wt = 14,280 IU/ml, P < 0.05). CONCLUSIONS Specific HBsAg-mutations (compartmentalized in the HBsAg C-terminus) correlated with low-serum HBV-DNA and HBsAg-levels. These findings can be important to understand mechanisms underlying low HBV replicative potential including the inactive-carrier state.
Collapse
Affiliation(s)
- Carmen Mirabelli
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", 00100 Rome, Italy
| | - Matteo Surdo
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", 00100 Rome, Italy
| | - Formijn Van Hemert
- Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, 1000 Amsterdam, The Netherlands
| | - Zhichao Lian
- Yale University, New Haven, CT 06520 United States
| | - Romina Salpini
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", 00100 Rome, Italy
| | - Valeria Cento
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", 00100 Rome, Italy
| | - Maria Francesca Cortese
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", 00100 Rome, Italy
| | - Marianna Aragri
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", 00100 Rome, Italy
| | - Michela Pollicita
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", 00100 Rome, Italy
| | - Claudia Alteri
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", 00100 Rome, Italy
| | - Ada Bertoli
- University Hospital of Rome "Tor Vergata", 00100 Rome, Italy
| | - Ben Berkhout
- Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, 1000 Amsterdam, The Netherlands
| | | | | | - Maria Mercedes Santoro
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", 00100 Rome, Italy
| | - Sara Romano
- Microbiology and Virology Unit, "S. Pertini" Hospital, 00100 Rome, Italy
| | - Michela Visca
- Microbiology and Virology Unit, "S. Pertini" Hospital, 00100 Rome, Italy
| | - Martina Bernassola
- Microbiology and Virology Unit, "S. Pertini" Hospital, 00100 Rome, Italy
| | - Roberta Longo
- Microbiology and Virology Unit, "S. Pertini" Hospital, 00100 Rome, Italy
| | | | - Pascal Trimoulet
- Virology Laboratory, Centre Hospitalier Régional et Université "Victor Segalen", CHU de Bordeaux, 33300 Bordeaux, France
| | - Hervè Fleury
- Virology Laboratory, Centre Hospitalier Régional et Université "Victor Segalen", CHU de Bordeaux, 33300 Bordeaux, France
| | | | | | | | - Alberto Spanò
- Microbiology and Virology Unit, "S. Pertini" Hospital, 00100 Rome, Italy
| | | | | | | | - Mario Angelico
- University Hospital of Rome "Tor Vergata", 00100 Rome, Italy
| | - Jens Verheyen
- Institute of Virology, University Hospital, 45147 Duisburg-Essen, Germany
| | - Carlo Federico Perno
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", 00100 Rome, Italy; University Hospital of Rome "Tor Vergata", 00100 Rome, Italy
| | - Valentina Svicher
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", 00100 Rome, Italy.
| |
Collapse
|
33
|
Li G, Verheyen J, Theys K, Piampongsant S, Van Laethem K, Vandamme AM. HIV-1 Gag C-terminal amino acid substitutions emerging under selective pressure of protease inhibitors in patient populations infected with different HIV-1 subtypes. Retrovirology 2014; 11:79. [PMID: 25253273 PMCID: PMC4189171 DOI: 10.1186/s12977-014-0079-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 09/01/2014] [Indexed: 11/19/2022] Open
Abstract
HIV-1 Gag amino acid substitutions associated with protease inhibitor (PI) treatment have mainly been reported in subtype B, while information on other subtypes is scarce. Using sequences from 11613 patients infected with different HIV-1 subtypes, we evaluated the prevalence of 93 Gag amino acid substitutions and their association with genotypic PI resistance. A significant association was found for 13 Gag substitutions, including A431V in both subtype B and CRF01_AE. K415R in subtype C and S451G in subtype B were newly identified. Most PI-associated Gag substitutions are located in the flexible C-terminal domain, revealing the key role this region plays in PI resistance.
Collapse
|
34
|
Kordelas L, Verheyen J, Beelen DW, Horn PA, Heinold A, Kaiser R, Trenschel R, Schadendorf D, Dittmer U, Esser S. Shift of HIV tropism in stem-cell transplantation with CCR5 Delta32 mutation. N Engl J Med 2014; 371:880-2. [PMID: 25162903 DOI: 10.1056/nejmc1405805] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
35
|
Yoldaş O, Ağaçfidan A, Lübke N, Somer A, Hançerli S, Verheyen J, Kaiser R, Akgül B. Determination of drug resistance and virus typology in HIV-1-positive pediatric patients in Istanbul, Turkey. Intervirology 2014; 57:297-9. [PMID: 24992950 DOI: 10.1159/000362335] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 03/19/2014] [Indexed: 11/19/2022] Open
Abstract
The aim of the study was to determine the prevalence of drug resistance of HIV-1 in pediatric patients from Istanbul, Turkey. Genotypic drug resistance testing revealed transmission of drug resistance from mother to child in 20%. Due to rising numbers of children with HIV-1, baseline resistance testing is recommended for Turkey.
Collapse
Affiliation(s)
- Ozlem Yoldaş
- Department of Medical Microbiology, Istanbul Faculty of Medicine, Istanbul, Turkey
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Grund S, Gkioule C, Termos T, Pfeifer N, Kobbe G, Verheyen J, Adams O. Primarily oseltamivir-resistant influenza A (H1N1pdm09) virus evolving into a multidrug-resistant virus carrying H275Y and I223R neuraminidase substitutions. Antivir Ther 2014; 20:97-100. [PMID: 24941247 DOI: 10.3851/imp2811] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2014] [Indexed: 10/25/2022]
Abstract
Antiviral susceptibility testing and reporting of viruses carrying amino acid substitutions conferring antiviral drug resistance is essential to assess the spread and clinical impact of these viruses. Here, we report on a patient who was infected with a primarily oseltamivir-resistant influenza A (H1N1pdm09) virus following allogeneic stem cell transplantation and rituximab treatment. Under prolonged virus replication and zanamivir therapy the neuraminidase amino acid substitutions H275Y and I223R were detected conferring high-level resistance to oseltamivir and cross-resistance to zanamivir. The emergence of these amino acid changes has been reported rarely worldwide and has been associated with fatal clinical outcomes. The patient survived the influenza infection after 170 days of follow-up.
Collapse
Affiliation(s)
- Sebastian Grund
- Institute for Virology, Medical Faculty, University of Düsseldorf, Düsseldorf, Germany.
| | | | | | | | | | | | | |
Collapse
|
37
|
Dang S, Wang Y, Budeus B, Verheyen J, Yang R, Hoffmann D. Differential selection in HIV-1 gp120 between subtype B and East Asian variant B'. Virol Sin 2014; 29:40-7. [PMID: 24452536 PMCID: PMC8206395 DOI: 10.1007/s12250-014-3389-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Accepted: 12/20/2013] [Indexed: 11/30/2022] Open
Abstract
HIV-1 evolves strongly and undergoes geographic differentiation as it spreads in diverse host populations around the world. For instance, distinct genomic backgrounds can be observed between the pandemic subtype B, prevalent in Europe and North-America, and its offspring clade B' in East Asia. Here we ask whether this differentiation affects the selection pressure experienced by the virus. To answer this question we evaluate selection pressure on the HIV-1 envelope protein gp120 at the level of individual codons using a simple and fast estimation method based on the ratio k a /k s of amino acid changes to synonymous changes. To validate the approach we compare results to those from a state-of-the-art mixed-effect method. The agreement is acceptable, but the analysis also demonstrates some limitations of the simpler approach. Further, we find similar distributions of codons under stabilizing and directional selection pressure in gp120 for subtypes B and B' with more directional selection pressure in variable loops and more stabilizing selection in the constant regions. Focusing on codons with increased k a /k s values in B', we show that these codons are scattered over the whole of gp120, with remarkable clusters of higher density in regions flanking the variable loops. We identify a significant statistical association of glycosylation sites and codons with increased k a /k s values.
Collapse
Affiliation(s)
- Stefan Dang
- Research Group Bioinformatics, Center of Medical Biotechnology and Faculty of Biology, University of Duisburg-Essen, Essen, 45117 Germany
| | - Yan Wang
- AIDS and HIV Research Group, State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071 China
| | - Bettina Budeus
- Research Group Bioinformatics, Center of Medical Biotechnology and Faculty of Biology, University of Duisburg-Essen, Essen, 45117 Germany
| | - Jens Verheyen
- Institute of Virology, University of Duisburg-Essen, Essen, 45117 Germany
| | - Rongge Yang
- AIDS and HIV Research Group, State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071 China
| | - Daniel Hoffmann
- Research Group Bioinformatics, Center of Medical Biotechnology and Faculty of Biology, University of Duisburg-Essen, Essen, 45117 Germany
| |
Collapse
|
38
|
Beggel B, Neumann-Fraune M, Kaiser R, Verheyen J, Lengauer T. Inferring short-range linkage information from sequencing chromatograms. PLoS One 2013; 8:e81687. [PMID: 24376502 PMCID: PMC3869653 DOI: 10.1371/journal.pone.0081687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 10/24/2013] [Indexed: 12/21/2022] Open
Abstract
Direct Sanger sequencing of viral genome populations yields multiple ambiguous sequence positions. It is not straightforward to derive linkage information from sequencing chromatograms, which in turn hampers the correct interpretation of the sequence data. We present a method for determining the variants existing in a viral quasispecies in the case of two nearby ambiguous sequence positions by exploiting the effect of sequence context-dependent incorporation of dideoxynucleotides. The computational model was trained on data from sequencing chromatograms of clonal variants and was evaluated on two test sets of in vitro mixtures. The approach achieved high accuracies in identifying the mixture components of 97.4% on a test set in which the positions to be analyzed are only one base apart from each other, and of 84.5% on a test set in which the ambiguous positions are separated by three bases. In silico experiments suggest two major limitations of our approach in terms of accuracy. First, due to a basic limitation of Sanger sequencing, it is not possible to reliably detect minor variants with a relative frequency of no more than 10%. Second, the model cannot distinguish between mixtures of two or four clonal variants, if one of two sets of linear constraints is fulfilled. Furthermore, the approach requires repetitive sequencing of all variants that might be present in the mixture to be analyzed. Nevertheless, the effectiveness of our method on the two in vitro test sets shows that short-range linkage information of two ambiguous sequence positions can be inferred from Sanger sequencing chromatograms without any further assumptions on the mixture composition. Additionally, our model provides new insights into the established and widely used Sanger sequencing technology. The source code of our method is made available at http://bioinf.mpi-inf.mpg.de/publications/beggel/linkageinformation.zip.
Collapse
Affiliation(s)
- Bastian Beggel
- Department of Computational Biology and Applied Algorithms, Max Planck Institute for Informatics, Saarbrücken, Germany
| | | | - Rolf Kaiser
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Jens Verheyen
- Institute of Virology, University of Duisburg-Essen, Essen, Germany
| | - Thomas Lengauer
- Department of Computational Biology and Applied Algorithms, Max Planck Institute for Informatics, Saarbrücken, Germany
| |
Collapse
|
39
|
Li G, Verheyen J, Rhee SY, Voet A, Vandamme AM, Theys K. Functional conservation of HIV-1 Gag: implications for rational drug design. Retrovirology 2013; 10:126. [PMID: 24176092 PMCID: PMC4228425 DOI: 10.1186/1742-4690-10-126] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 10/21/2013] [Indexed: 11/25/2022] Open
Abstract
Background HIV-1 replication can be successfully blocked by targeting gag gene products, offering a promising strategy for new drug classes that complement current HIV-1 treatment options. However, naturally occurring polymorphisms at drug binding sites can severely compromise HIV-1 susceptibility to gag inhibitors in clinical and experimental studies. Therefore, a comprehensive understanding of gag natural diversity is needed. Findings We analyzed the degree of functional conservation in 10862 full-length gag sequences across 8 major HIV-1 subtypes and identified the impact of natural variation on known drug binding positions targeted by more than 20 gag inhibitors published to date. Complete conservation across all subtypes was detected in 147 (29%) out of 500 gag positions, with the highest level of conservation observed in capsid protein. Almost half (41%) of the 136 known drug binding positions were completely conserved, but all inhibitors were confronted with naturally occurring polymorphisms in their binding sites, some of which correlated with HIV-1 subtype. Integration of sequence and structural information revealed one drug binding pocket with minimal genetic variability, which is situated at the N-terminal domain of the capsid protein. Conclusions This first large-scale analysis of full-length HIV-1 gag provided a detailed mapping of natural diversity across major subtypes and highlighted the considerable variation in current drug binding sites. Our results contribute to the optimization of gag inhibitors in rational drug design, given that drug binding sites should ideally be conserved across all HIV-1 subtypes.
Collapse
Affiliation(s)
- Guangdi Li
- Rega Institute for Medical Research, Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium.
| | | | | | | | | | | |
Collapse
|
40
|
Cento V, Van Hemert F, Neumann-Fraune M, Mirabelli C, Di Maio VC, Salpini R, Bertoli A, Micheli V, Gubertini G, Romano S, Visca M, De Sanctis GM, Berkhout B, Marino N, Mazzotta F, Cappiello G, Spanò A, Sarrecchia C, Ceccherini-Silberstein F, Andreoni M, Angelico M, Verheyen J, Perno CF, Svicher V. Anti-HBV treatment induces novel reverse transcriptase mutations with reflective effect on HBV S antigen. J Infect 2013; 67:303-12. [PMID: 23796863 DOI: 10.1016/j.jinf.2013.05.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 05/06/2013] [Accepted: 05/24/2013] [Indexed: 12/16/2022]
Abstract
INTRODUCTION The identification of novel reverse-transcriptase (RT) drug-resistance mutations is critical in predicting the probability of success to anti-HBV treatment. Furthermore, due to HBV-RT/HBsAg gene-overlap, they can have an impact on HBsAg-detection and quantification. METHODS 356 full-length HBV-RT sequences from 197 drug-naive patients and 159 patients experiencing virological-breakthrough to nucleoside/nucleotide-analogs (NUCs) were analyzed. Mutants and wild-type HBs-antigens were expressed in HuH7-hepatocytes and quantified in cell-supernatants and cell-lysates by Architect HBsAg-assay. RESULTS Ten novel RT-mutations (rtN53T-rtS78T-rtS85F-rtS135T-rtA181I-rtA200V-rtK212Q-rtL229V/F-rtM309K) correlated with specific NUC-treatments and classical drug-resistance mutations on divergent evolutionary pathways. Some of them reduced RT-binding affinity for anti-HBV drugs and altered S-antigen structure. Indeed, rtS78T (prevalence: 1.1% in drug-naïve and 12.2% in adefovir-failing patients) decreased the RT-affinity for adefovir more than the classical adefovir-resistance mutations rtA181 T/V (WT:-9.63 kcal/mol, rtA181T:-9.30 kcal/mol, rtA181V:-7.96 kcal/mol, rtS78T:-7.37 kcal/mol). Moreover, rtS78T introduced a stop-codon at HBsAg-position 69, and completely abrogated HBsAg-quantification in both supernatants and cell-lysates, indicating an impaired HBsAg-secretion/production. Furthermore, the HBsAg-mutation sP217L, silent in RT, significantly correlated with M204V/I-related virological-breakthrough and increased HBsAg-quantification in cell-lysate. CONCLUSIONS Mutations beyond those classically known can affect drug-binding affinity of mutated HBV-RT, and may have potential effects on HBsAg. Their cumulative effect on resistance and HBV-pathogenicity indicates the importance of preventing therapeutic failures.
Collapse
Affiliation(s)
- Valeria Cento
- Department of Experimental Medicine and Surgery, University of Rome "Tor Vergata", 00100 Rome, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Neumann-Fraune M, Beggel B, Pfister H, Kaiser R, Verheyen J. High frequency of complex mutational patterns in lamivudine resistant hepatitis B virus isolates. J Med Virol 2013; 85:775-9. [DOI: 10.1002/jmv.23530] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2012] [Indexed: 12/16/2022]
|
42
|
Cento V, Mirabelli C, Dimonte S, Salpini R, Han Y, Trimoulet P, Bertoli A, Micheli V, Gubertini G, Cappiello G, Spanò A, Longo R, Bernassola M, Mazzotta F, De Sanctis GM, Zhang XX, Verheyen J, D’Arminio Monforte A, Ceccherini-Silberstein F, Perno CF, Svicher V. Overlapping structure of hepatitis B virus (HBV) genome and immune selection pressure are critical forces modulating HBV evolution. J Gen Virol 2013; 94:143-149. [DOI: 10.1099/vir.0.046524-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
Abstract
How the overlap between the hepatitis B virus (HBV) reverse transcriptase (RT) and HBV S antigen (HBsAg) genes modulates the extent of HBV genetic variability is still an open question, and was investigated here. The rate of nucleotide conservation (≤1 % variability) followed an atypical pattern in the RT gene, due to an overlap between RT and HBsAg (69.9 % nucleotide conservation in the overlapping region vs 41.2 % in the non-overlapping region;P<0.001), with a consequently lower rate of synonymous substitution within the overlapping region [median(interquartile range)dS = 3.1(1.5–7.4) vs 20.1(10.6–30.0);P = 3.249×10−22]. The most conserved RT regions were located within the YMDD motif and the N-terminal parts of the palm and finger domains, critical for RT functionality. These regions also corresponded to highly conserved HBsAg domains that are critical for HBsAg secretion. Conversely, the genomic region encoding the HBsAg antigenic loop (where immune-escape mutations are localized) showed a sharp decrease in the extent of conservation (40.6 %), which was less pronounced in the setting of human immunodeficiency virus (HIV)-driven immune suppression (48.8 % in HIV–HBV co-infection vs 21.5 % in mono-infected patients;P = 0.020). In conclusion, the overlapping reading frame and the immune system appear to have shaped the patterns of RT and HBsAg genetic variability. Highly conserved regions in RT and HBsAg may deserve further attention as novel therapeutic targets.
Collapse
Affiliation(s)
- Valeria Cento
- Department of Experimental Medicine and Surgery, University of Rome ‘Tor Vergata’, Rome 00133, Italy
| | - Carmen Mirabelli
- Department of Experimental Medicine and Surgery, University of Rome ‘Tor Vergata’, Rome 00133, Italy
| | - Salvatore Dimonte
- Department of Experimental Medicine and Surgery, University of Rome ‘Tor Vergata’, Rome 00133, Italy
| | - Romina Salpini
- Department of Experimental Medicine and Surgery, University of Rome ‘Tor Vergata’, Rome 00133, Italy
| | - Yue Han
- Department of Infectious Diseases, Rui Jin Hospital, Shanghai Jiao Tong University, Shanghai 200025, PR China
| | - Pascale Trimoulet
- Bordeaux University Hospital, University Victor Segalen, Bordeaux 33076, France
| | - Ada Bertoli
- University Hospital ‘Tor Vergata’, Rome 00133, Italy
| | | | | | | | | | | | | | | | | | - Xin Xin Zhang
- Department of Infectious Diseases, Rui Jin Hospital, Shanghai Jiao Tong University, Shanghai 200025, PR China
| | | | | | | | - Carlo Federico Perno
- Department of Experimental Medicine and Surgery, University of Rome ‘Tor Vergata’, Rome 00133, Italy
| | - Valentina Svicher
- Department of Experimental Medicine and Surgery, University of Rome ‘Tor Vergata’, Rome 00133, Italy
| |
Collapse
|
43
|
Fun A, Wensing AMJ, Verheyen J, Nijhuis M. Human Immunodeficiency Virus Gag and protease: partners in resistance. Retrovirology 2012; 9:63. [PMID: 22867298 PMCID: PMC3422997 DOI: 10.1186/1742-4690-9-63] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 07/17/2012] [Indexed: 12/26/2022] Open
Abstract
Human Immunodeficiency Virus (HIV) maturation plays an essential role in the viral life cycle by enabling the generation of mature infectious virus particles through proteolytic processing of the viral Gag and GagPol precursor proteins. An impaired polyprotein processing results in the production of non-infectious virus particles. Consequently, particle maturation is an excellent drug target as exemplified by inhibitors specifically targeting the viral protease (protease inhibitors; PIs) and the experimental class of maturation inhibitors that target the precursor Gag and GagPol polyproteins. Considering the different target sites of the two drug classes, direct cross-resistance may seem unlikely. However, coevolution of protease and its substrate Gag during PI exposure has been observed both in vivo and in vitro. This review addresses in detail all mutations in Gag that are selected under PI pressure. We evaluate how polymorphisms and mutations in Gag affect PI therapy, an aspect of PI resistance that is currently not included in standard genotypic PI resistance testing. In addition, we consider the consequences of Gag mutations for the development and positioning of future maturation inhibitors.
Collapse
Affiliation(s)
- Axel Fun
- Department of Virology, Medical Microbiology, University Medical Center Utrecht, HP G04,614, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
| | | | | | | |
Collapse
|
44
|
Verheyen J, Kaiser R, Bozic M, Timmen-Wego M, Maier BK, Kessler HH. Extraction of viral nucleic acids: Comparison of five automated nucleic acid extraction platforms. J Clin Virol 2012; 54:255-9. [DOI: 10.1016/j.jcv.2012.03.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 03/13/2012] [Accepted: 03/14/2012] [Indexed: 02/02/2023]
|
45
|
Verheyen J, Neumann-Fraune M, Berg T, Kaiser R, Obermeier M. The detection of HBsAg mutants expressed in vitro using two different quantitative HBsAg assays. J Clin Virol 2012; 54:279-81. [DOI: 10.1016/j.jcv.2012.04.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 04/04/2012] [Accepted: 04/17/2012] [Indexed: 10/28/2022]
|
46
|
Beggel B, Neumann-Fraune M, Döring M, Lawyer G, Kaiser R, Verheyen J, Lengauer T. Genotyping hepatitis B virus dual infections using population-based sequence data. J Gen Virol 2012; 93:1899-1907. [PMID: 22694900 DOI: 10.1099/vir.0.043042-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The hepatitis B virus (HBV) is classified into distinct genotypes A-H that are characterized by different progression of hepatitis B and sensitivity to interferon treatment. Previous computational genotyping methods are not robust enough regarding HBV dual infections with different genotypes. The correct classification of HBV sequences into the present genotypes is impaired due to multiple ambiguous sequence positions. We present a computational model that is able to identify and genotype inter- and intragenotype dual infections using population-based sequencing data. Model verification on synthetic data showed 100 % accuracy for intergenotype dual infections and 36.4 % sensitivity in intragenotype dual infections. Screening patient sera (n = 241) revealed eight putative cases of intergenotype dual infection (one A-D, six A-G and one D-G) and four putative cases of intragenotype dual infection (one A-A, two D-D and one E-E). Clonal experiments from the original patient material confirmed three out of three of our predictions. The method has been integrated into geno2pheno([hbv]), an established web-service in clinical use for analysing HBV sequence data. It offers exact and detailed identification of HBV genotypes in patients with dual infections that helps to optimize antiviral therapy regimens. geno2pheno([hbv]) is available under http://www.genafor.org/g2p_hbv/index.php.
Collapse
Affiliation(s)
- Bastian Beggel
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | | | - Matthias Döring
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Glenn Lawyer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Jens Verheyen
- Institute of Virology, University of Cologne, Cologne, Germany
| | - Thomas Lengauer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, Germany
| |
Collapse
|
47
|
Svicher V, Cento V, Bernassola M, Neumann-Fraune M, Hemert FV, Chen M, Salpini R, Liu C, Longo R, Visca M, Romano S, Micheli V, Bertoli A, Gori C, Ceccherini-Silberstein F, Sarrecchia C, Andreoni M, Angelico M, Ursitti A, Spanò A, Zhang JM, Verheyen J, Cappiello G, Perno CF. Novel HBsAg markers tightly correlate with occult HBV infection and strongly affect HBsAg detection. Antiviral Res 2012; 93:86-93. [DOI: 10.1016/j.antiviral.2011.10.022] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 10/26/2011] [Accepted: 10/30/2011] [Indexed: 02/06/2023]
|
48
|
Svicher V, Cento V, Salpini R, Mercurio F, Fraune M, Beggel B, Han Y, Gori C, Wittkop L, Bertoli A, Micheli V, Gubertini G, Longo R, Romano S, Visca M, Gallinaro V, Marino N, Mazzotta F, De Sanctis GM, Fleury H, Trimoulet P, Angelico M, Cappiello G, Zhang XX, Verheyen J, Ceccherini-Silberstein F, Perno CF. Role of hepatitis B virus genetic barrier in drug-resistance and immune-escape development. Dig Liver Dis 2011; 43:975-83. [PMID: 21831732 DOI: 10.1016/j.dld.2011.07.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Revised: 06/09/2011] [Accepted: 07/01/2011] [Indexed: 12/11/2022]
Abstract
BACKGROUND Impact of hepatitis B virus genetic barrier, defined as the number and type of nucleotide substitutions required to overcome drug/immune selective pressure, on drug-resistance/immune-escape development is unknown. METHODS Genetic barrier was calculated according to Van de Vijver (2006) in 3482 hepatitis B virus-reverse transcriptase/HBV surface antigen sequences from 555 drug-naïve patients and 2927 antiviral-treated patients infected with hepatitis B virus genotypes A-G. RESULTS Despite high natural variability, genetic barrier for drug-resistance development is identical amongst hepatitis B virus genotypes, but varies according to drug-resistance mutation type. Highest genetic barrier is found for secondary/compensatory mutations (e.g. rtL80I/V-rtL180M-rtV173L), whilst most primary mutations (including rtM204V-rtA181T/V-rtI169T-rtA194T) are associated with low genetic barrier. An exception is rtM204I, which can derive from a transition or a transversion. Genotypes A and G are more prone to develop immune/diagnostic-escape mutations sT114R and sG130N. Vaccine-escape associated sT131N-mutation is a natural polymorphism in both A and G genotypes. CONCLUSION Genetic barrier and reverse transcriptase/HBV surface antigen overlapping can synergistically influence hepatitis B virus drug-resistance/immune-escape development. The different immune-escape potential of specific hepatitis B virus genotypes could have important clinical consequences in terms of disease progression, vaccine strategies and correct HBV surface antigen detection.
Collapse
Affiliation(s)
- Valentina Svicher
- Department of Experimental Medicine and Biochemical Science, University of Tor Vergata Rome, Italy
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Dybowski JN, Riemenschneider M, Hauke S, Pyka M, Verheyen J, Hoffmann D, Heider D. Improved Bevirimat resistance prediction by combination of structural and sequence-based classifiers. BioData Min 2011; 4:26. [PMID: 22082002 PMCID: PMC3248369 DOI: 10.1186/1756-0381-4-26] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 11/14/2011] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Maturation inhibitors such as Bevirimat are a new class of antiretroviral drugs that hamper the cleavage of HIV-1 proteins into their functional active forms. They bind to these preproteins and inhibit their cleavage by the HIV-1 protease, resulting in non-functional virus particles. Nevertheless, there exist mutations in this region leading to resistance against Bevirimat. Highly specific and accurate tools to predict resistance to maturation inhibitors can help to identify patients, who might benefit from the usage of these new drugs. RESULTS We tested several methods to improve Bevirimat resistance prediction in HIV-1. It turned out that combining structural and sequence-based information in classifier ensembles led to accurate and reliable predictions. Moreover, we were able to identify the most crucial regions for Bevirimat resistance computationally, which are in line with experimental results from other studies. CONCLUSIONS Our analysis demonstrated the use of machine learning techniques to predict HIV-1 resistance against maturation inhibitors such as Bevirimat. New maturation inhibitors are already under development and might enlarge the arsenal of antiretroviral drugs in the future. Thus, accurate prediction tools are very useful to enable a personalized therapy.
Collapse
Affiliation(s)
- J Nikolaj Dybowski
- Department of Bioinformatics, Center of Medical Biotechnology, University of Duisburg-Essen, Universitaetsstr, 2, 45117 Essen, Germany.
| | | | | | | | | | | | | |
Collapse
|
50
|
Abstract
BACKGROUND Machine learning techniques have been widely applied to biological sequences, e.g. to predict drug resistance in HIV-1 from sequences of drug target proteins and protein functional classes. As deletions and insertions are frequent in biological sequences, a major limitation of current methods is the inability to handle varying sequence lengths. FINDINGS We propose to normalize sequences to uniform length. To this end, we tested one linear and four different non-linear interpolation methods for the normalization of sequence lengths of 19 classification datasets. Classification tasks included prediction of HIV-1 drug resistance from drug target sequences and sequence-based prediction of protein function. We applied random forests to the classification of sequences into "positive" and "negative" samples. Statistical tests showed that the linear interpolation outperforms the non-linear interpolation methods in most of the analyzed datasets, while in a few cases non-linear methods had a small but significant advantage. Compared to other published methods, our prediction scheme leads to an improvement in prediction accuracy by up to 14%. CONCLUSIONS We found that machine learning on sequences normalized by simple linear interpolation gave better or at least competitive results compared to state-of-the-art procedures, and thus, is a promising alternative to existing methods, especially for protein sequences of variable length.
Collapse
Affiliation(s)
- Dominik Heider
- Department of Bioinformatics, Center of Medical Biotechnology, University of Duisburg-Essen, Universitaetsstr. 2, 45117 Essen, Germany
| | - Jens Verheyen
- Institute of Virology, University of Cologne, Fuerst-Pueckler-Str. 56, 50935 Cologne, Germany
| | - Daniel Hoffmann
- Department of Bioinformatics, Center of Medical Biotechnology, University of Duisburg-Essen, Universitaetsstr. 2, 45117 Essen, Germany
| |
Collapse
|