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Tushabe P, Bakamutumaho B, Eliku JP, Birungi M, Aine F, Namuwulya P, Bukenya H, Ampeire I, Kisakye A, Byabamazima CR, Bwogi J. Rubella virus genotype 2B endemicity and related utility of serum-based molecular characterization in Uganda. BMC Res Notes 2023; 16:218. [PMID: 37710238 PMCID: PMC10503080 DOI: 10.1186/s13104-023-06499-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/04/2023] [Indexed: 09/16/2023] Open
Abstract
There are 13 globally recognized rubella virus genotypes of which only 2 (1E and 2B) have been detected recently. The largest percentage of all reported rubella virus sequences come from China and Japan with Africa reporting limited data. In a bid to address the lack of rubella genotype data in Uganda and the World Health Organization Africa region, we sought to characterize rubella viruses retrospectively using sera collected from suspected measles patients that turned out rubella IgM positive.Seven sequences belonging to genotype 2B sub-lineage 2B-L2c were obtained. These sequences clustered with other genotype 2B sequences previously reported from Uganda. None of the other genotypes (1E and 1G) reported from Uganda in the earlier years were detected. In addition, none of the sequences were obtained after the introduction of the measles-rubella containing vaccine. The above highlight the need for continuous rubella virological surveillance to confirm interruption of endemic rubella genotype circulation.
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Affiliation(s)
- Phionah Tushabe
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda.
| | | | - James Peter Eliku
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
| | - Molly Birungi
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
| | - Francis Aine
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
| | - Prossy Namuwulya
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
| | - Henry Bukenya
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
| | - Immaculate Ampeire
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
- Ministry of Health Uganda, P.O. Box 7272, Kampala, Uganda
| | - Annet Kisakye
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
- World Health Organization, Uganda Country Office, P.O. Box 24578, Kampala, Uganda
| | - Charles R Byabamazima
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
- WHO Inter-Country Support Team Office for Eastern and Southern Africa (IST/ESA), Harare, Zimbabwe
| | - Josephine Bwogi
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
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Domingo-Calap P, Schubert B, Joly M, Solis M, Untrau M, Carapito R, Georgel P, Caillard S, Fafi-Kremer S, Paul N, Kohlbacher O, González-Candelas F, Bahram S. An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides. PLoS Pathog 2018; 14:e1007368. [PMID: 30335851 PMCID: PMC6207329 DOI: 10.1371/journal.ppat.1007368] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/30/2018] [Accepted: 09/28/2018] [Indexed: 11/18/2022] Open
Abstract
Infection with human BK polyomavirus, a small double-stranded DNA virus, potentially results in severe complications in immunocompromised patients. Here, we describe the in vivo variability and evolution of the BK polyomavirus by deep sequencing. Our data reveal the highest genomic evolutionary rate described in double-stranded DNA viruses, i.e., 10−3–10−5 substitutions per nucleotide site per year. High mutation rates in viruses allow their escape from immune surveillance and adaptation to new hosts. By combining mutational landscapes across viral genomes with in silico prediction of viral peptides, we demonstrate the presence of significantly more coding substitutions within predicted cognate HLA-C-bound viral peptides than outside. This finding suggests a role for HLA-C in antiviral immunity, perhaps through the action of killer cell immunoglobulin-like receptors. The present study provides a comprehensive view of viral evolution and immune escape in a DNA virus. Little is known about the mechanisms of evolution and viral immune escape in double-stranded DNA (dsDNA) viruses. Here, we study the evolution of BK polyomavirus and observe the highest genomic evolutionary rate described so far for a dsDNA virus, in the range of RNA viruses, which usually evolve rapidly. Furthermore, the prediction of viral peptides to determine immune escape suggests a specific role of HLA-C in antiviral immunity. These findings are helpful for future advances in antiviral therapies and provide a step forward in our understanding of in vivo viral evolution in humans.
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Affiliation(s)
- Pilar Domingo-Calap
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
- * E-mail: (PDC); (SB)
| | - Benjamin Schubert
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany
- Applied Bioinformatics, Department of Computer Science, Tübingen, Germany
| | - Mélanie Joly
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
- Service de Néphrologie et Transplantation Rénale, Hôpitaux Universitaires de Strasbourg, France
| | - Morgane Solis
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
- Laboratoire de Virologie, Plateau Technique de Microbiologie, Pôle de Biologie, Hôpitaux Universitaires de Strasbourg, France
| | - Meiggie Untrau
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
| | - Raphael Carapito
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
- Laboratoire Central d’Immunologie, Plateau Technique de Biologie, Nouvel Hôpital Civil, France
| | - Philippe Georgel
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
| | - Sophie Caillard
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
- Service de Néphrologie et Transplantation Rénale, Hôpitaux Universitaires de Strasbourg, France
| | - Samira Fafi-Kremer
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
- Laboratoire de Virologie, Plateau Technique de Microbiologie, Pôle de Biologie, Hôpitaux Universitaires de Strasbourg, France
| | - Nicodème Paul
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
| | - Oliver Kohlbacher
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany
- Applied Bioinformatics, Department of Computer Science, Tübingen, Germany
- Quantitative Biology Center, Tübingen, Germany
- Faculty of Medicine, University of Tübingen, Tübingen, Germany
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
| | - Fernando González-Candelas
- Unidad Mixta Infección y Salud Pública FISABIO/Universitat de València, Institute for Integrative Systems Biology I2SysBio (CSIC-UV) and CIBER en Epidemiología y Salud Pública, Valencia, Spain
| | - Seiamak Bahram
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
- Laboratoire Central d’Immunologie, Plateau Technique de Biologie, Nouvel Hôpital Civil, France
- * E-mail: (PDC); (SB)
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Claus C, Bergs S, Emmrich NC, Hübschen JM, Mankertz A, Liebert UG. A sensitive one-step TaqMan amplification approach for detection of rubella virus clade I and II genotypes in clinical samples. Arch Virol 2016; 162:477-486. [PMID: 27807657 DOI: 10.1007/s00705-016-3131-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/24/2016] [Indexed: 12/23/2022]
Abstract
Although teratogenic rubella virus (RV) causes a vaccine-preventable disease, it is still endemic in several countries worldwide. Thus, there is a constant risk of RV importation into non-endemic areas. RV monitoring, especially during measles and Zika virus outbreaks, requires reliable diagnostic tools. For this study, a TaqMan-based one-step reverse transcription-quantitative PCR (RT-qPCR) assay, with the p90 gene as a novel and so far unexplored target for detection of clade I and II genotypes, was developed and evaluated. Automated nucleic acid extraction was carried out. Performance characteristics of the TaqMan RT-qPCR assay were determined for a RV plasmid standard and RNA extracted from virus-infected cell culture supernatants representing clade I and II genotypes. Diagnostic specificity and sensitivity were validated against other RNA and DNA viruses, relevant for RV diagnostic approaches and for RV-positive clinical samples, respectively. The assay is specific and highly sensitive with a limit of detection as low as five to one copies per reaction or 200 infectious virus particles per ml. The coefficients of variation (CV) were specified as intra- (within one run) and inter- (between different runs) assay variation, and calculated based on the standard deviations for the obtained Ct values of the respective samples. Intra- and inter-assay CV values were low, with a maximum of 3.4% and 2.4%, respectively. The assay was shown to be suitable and specific for the analysis of clinical samples. With p90 as a novel target, the highly sensitive and specific TaqMan assay outlined in this study is suitable for RV diagnosis worldwide.
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Affiliation(s)
- C Claus
- Institute of Virology, University of Leipzig, Leipzig, Germany.
| | - S Bergs
- Institute of Virology, University of Leipzig, Leipzig, Germany
| | - N C Emmrich
- Institute of Virology, University of Leipzig, Leipzig, Germany
| | - J M Hübschen
- WHO European Regional Reference Laboratory for Measles and Rubella, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - A Mankertz
- WHO European Regional Reference Laboratory for Measles and Rubella, Robert Koch Institute, Berlin, Germany
| | - U G Liebert
- Institute of Virology, University of Leipzig, Leipzig, Germany
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