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Xu J, He J, Yang J, Wang F, Huo Y, Guo Y, Si Y, Gao Y, Wang F, Cheng H, Cheng T, Yu J, Wang X, Ma Y. REDH: A database of RNA editome in hematopoietic differentiation and malignancy. Chin Med J (Engl) 2024; 137:283-293. [PMID: 37386732 PMCID: PMC10836905 DOI: 10.1097/cm9.0000000000002782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Indexed: 07/01/2023] Open
Abstract
BACKGROUND The conversion of adenosine (A) to inosine (I) through deamination is the prevailing form of RNA editing, impacting numerous nuclear and cytoplasmic transcripts across various eukaryotic species. Millions of high-confidence RNA editing sites have been identified and integrated into various RNA databases, providing a convenient platform for the rapid identification of key drivers of cancer and potential therapeutic targets. However, the available database for integration of RNA editing in hematopoietic cells and hematopoietic malignancies is still lacking. METHODS We downloaded RNA sequencing (RNA-seq) data of 29 leukemia patients and 19 healthy donors from National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database, and RNA-seq data of 12 mouse hematopoietic cell populations obtained from our previous research were also used. We performed sequence alignment, identified RNA editing sites, and obtained characteristic editing sites related to normal hematopoietic development and abnormal editing sites associated with hematologic diseases. RESULTS We established a new database, "REDH", represents RNA editome in hematopoietic differentiation and malignancy. REDH is a curated database of associations between RNA editome and hematopoiesis. REDH integrates 30,796 editing sites from 12 murine adult hematopoietic cell populations and systematically characterizes more than 400,000 edited events in malignant hematopoietic samples from 48 cohorts (human). Through the Differentiation, Disease, Enrichment, and knowledge modules, each A-to-I editing site is systematically integrated, including its distribution throughout the genome, its clinical information (human sample), and functional editing sites under physiological and pathological conditions. Furthermore, REDH compares the similarities and differences of editing sites between different hematologic malignancies and healthy control. CONCLUSIONS REDH is accessible at http://www.redhdatabase.com/ . This user-friendly database would aid in understanding the mechanisms of RNA editing in hematopoietic differentiation and malignancies. It provides a set of data related to the maintenance of hematopoietic homeostasis and identifying potential therapeutic targets in malignancies.
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Affiliation(s)
- Jiayue Xu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Jiahuan He
- Key Laboratory of RNA and Hematopoietic Regulation, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Jiabin Yang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, China
- Department of Biochemistry and Molecular Biology, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Fengjiao Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Yue Huo
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Yuehong Guo
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Yanmin Si
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Yufeng Gao
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Fang Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Hui Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Jia Yu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, China
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, Sichuan 610052, China
| | - Xiaoshuang Wang
- Department of Biochemistry and Molecular Biology, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Yanni Ma
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, China
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Mehedi M, Ricklefs S, Takada A, Sturdevant D, Porcella SF, Marzi A, Feldmann H. RNA Editing as a General Trait of Ebolaviruses. J Infect Dis 2023; 228:S498-S507. [PMID: 37348869 PMCID: PMC10651210 DOI: 10.1093/infdis/jiad228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/06/2023] [Accepted: 06/20/2023] [Indexed: 06/24/2023] Open
Abstract
RNA editing has been discovered as an essential mechanism for the transcription of the glycoprotein (GP) gene of Ebola virus but not Marburg virus. We developed a rapid transcript quantification assay (RTQA) to analyze RNA transcripts generated through RNA editing and used immunoblotting with a pan-ebolavirus monoclonal antibody to confirm different GP gene-derived products. RTQA successfully quantified GP gene transcripts during infection with representative members of 5 ebolavirus species. Immunoblotting verified expression of the soluble GP and the transmembrane GP. Our results defined RNA editing as a general trait of ebolaviruses. The degree of editing, however, varies among ebolaviruses with Reston virus showing the lowest and Bundibugyo virus the highest degree of editing.
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Affiliation(s)
| | - Stacy Ricklefs
- Genomics Unit, Research Technology Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Dan Sturdevant
- Genomics Unit, Research Technology Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana
| | - Stephen F Porcella
- Genomics Unit, Research Technology Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana
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3
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Douglas J, Drummond AJ, Kingston RL. Evolutionary history of cotranscriptional editing in the paramyxoviral phosphoprotein gene. Virus Evol 2021; 7:veab028. [PMID: 34141448 PMCID: PMC8204654 DOI: 10.1093/ve/veab028] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The phosphoprotein gene of the paramyxoviruses encodes multiple protein products. The P, V, and W proteins are generated by transcriptional slippage. This process results in the insertion of non-templated guanosine nucleosides into the mRNA at a conserved edit site. The P protein is an essential component of the viral RNA polymerase and is encoded by a faithful copy of the gene in the majority of paramyxoviruses. However, in some cases, the non-essential V protein is encoded by default and guanosines must be inserted into the mRNA in order to encode P. The number of guanosines inserted into the P gene can be described by a probability distribution, which varies between viruses. In this article, we review the nature of these distributions, which can be inferred from mRNA sequencing data, and reconstruct the evolutionary history of cotranscriptional editing in the paramyxovirus family. Our model suggests that, throughout known history of the family, the system has switched from a P default to a V default mode four times; complete loss of the editing system has occurred twice, the canonical zinc finger domain of the V protein has been deleted or heavily mutated a further two times, and the W protein has independently evolved a novel function three times. Finally, we review the physical mechanisms of cotranscriptional editing via slippage of the viral RNA polymerase.
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Affiliation(s)
- Jordan Douglas
- Centre for Computational Evolution, University of Auckland, Auckland 1010, New Zealand
- School of Computer Science, University of Auckland, Auckland 1010, New Zealand
| | - Alexei J Drummond
- Centre for Computational Evolution, University of Auckland, Auckland 1010, New Zealand
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Richard L Kingston
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
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4
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Chen X, Jia Y, Ren S, Chen S, Wang X, Gao X, Wang C, Adam FEA, Wang X, Yang Z. Identification of Newcastle disease virus P-gene editing using next-generation sequencing. J Vet Med Sci 2020; 82:1231-1235. [PMID: 32624548 PMCID: PMC7468068 DOI: 10.1292/jvms.18-0707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Avian paramyxoviruses 1 has the ability to edit its P gene to generate three
amino-coterminal proteins (P, V and W), but its kinetic change is unclear. In this study,
next-generation sequencing (NGS) was used to analyze the P-gene editing of Newcastle
disease virus (NDV). Transcriptome analysis of chicken embryonic tissues and bursa of
fabricius showed the P-gene editing frequencies were 45.46–52.70%. To investigate the
rules of P-gene editing along time, the ratio of PVW was determined by PCR based deep
sequencing at multiple time points in cells infected with velogenic and lentogenic strain
respectively. The results confirmed similar editing frequencies with transcriptome data
and the PVW ratios were stable along time among different NDVs, but had a greater V-gene
transcript on velogenic strain infection (P<0.001), which were
different from previous reports. Also, it was shown that the number of inserted G residues
in P-derived transcripts was not limited to +9G, and +10G transcripts were identified.
These results confirmed the NDV P-gene editing frequencies and provided a novel point of
view on NDV P-gene editing with NDV virulence.
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Affiliation(s)
- Xi Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, P.R. China
| | - Yanqing Jia
- Department of Animal Engineering, Yangling Vocational & Technical College, Yangling, Shaanxi Province 712100, P.R. China
| | - Shanhui Ren
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, P.R. China
| | - Siqi Chen
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, P.R. China
| | - Xiangwei Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, P.R. China
| | - Xiaolong Gao
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, P.R. China
| | - Chongyang Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, P.R. China
| | - Fathalrhman E A Adam
- Department of Preventive Medicine and Public Health, Faculty of Veterinary Science, University of Nyala, P.O. Box: 155 Nyala, Sudan
| | - Xinglong Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, P.R. China
| | - Zengqi Yang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province 712100, P.R. China
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5
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Niu G, Zou D, Li M, Zhang Y, Sang J, Xia L, Li M, Liu L, Cao J, Zhang Y, Wang P, Hu S, Hao L, Zhang Z. Editome Disease Knowledgebase (EDK): a curated knowledgebase of editome-disease associations in human. Nucleic Acids Res 2020; 47:D78-D83. [PMID: 30357418 PMCID: PMC6323952 DOI: 10.1093/nar/gky958] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/17/2018] [Indexed: 12/26/2022] Open
Abstract
RNA editing, as an essential co-/post-transcriptional RNA modification type, plays critical roles in many biological processes and involves with a variety of human diseases. Although several databases have been developed to collect RNA editing data in both model and non-model animals, there still lacks a resource integrating associations between editome and human disease. In this study, we present Editome-Disease Knowledgebase (EDK; http://bigd.big.ac.cn/edk), an integrated knowledgebase of RNA editome-disease associations manually curated from published literatures. In the current version, EDK incorporates 61 diseases associated with 248 experimentally validated abnormal editing events located in 32 mRNAs, 16 miRNAs, 1 lncRNA and 11 viruses, and 44 aberrant activities involved with 6 editing enzymes, which together are curated from more than 200 publications. In addition, to facilitate standardization of editome-disease knowledge integration, we propose a data curation model in EDK, factoring an abundance of relevant information to fully capture the context of editome-disease associations. Taken together, EDK is a comprehensive collection of editome-disease associations and bears the great utility in aid of better understanding the RNA editing machinery and complex molecular mechanisms associated with human diseases.
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Affiliation(s)
- Guangyi Niu
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zou
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Mengwei Li
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuansheng Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Sang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Xia
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Man Li
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Liu
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiabao Cao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pei Wang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Songnian Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lili Hao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- To whom correspondence should be addressed. Tel: +86 10 84097261; Fax: +86 10 84097720; . Correspondence may also be addressed to Lili Hao.
| | - Zhang Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
- To whom correspondence should be addressed. Tel: +86 10 84097261; Fax: +86 10 84097720; . Correspondence may also be addressed to Lili Hao.
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6
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Javelle E, Colson P, Parola P, Raoult D. Measles, the need for a paradigm shift. Eur J Epidemiol 2019; 34:897-915. [DOI: 10.1007/s10654-019-00569-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/03/2019] [Indexed: 01/24/2023]
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7
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Yang Y, Bu Y, Zhao J, Xue J, Xu G, Song Y, Zhao Y, Yang H, Zhang G. Appropriate amount of W protein of avian avulavirus 1 benefits viral replication and W shows strain-dependent subcellular localization. Virology 2019; 538:71-85. [PMID: 31580973 DOI: 10.1016/j.virol.2019.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/17/2019] [Accepted: 09/26/2019] [Indexed: 11/28/2022]
Abstract
In order to confirm the existence of W protein in Avian avulavirus 1 (AAvV-1) infected cells, two monoclonal antibodies were prepared. The presence of W protein in cells infected with lentogenic genotype II strain La Sota or velogenic genotype VII strain SG10 was confirmed with immunofluorescence and western blotting assays. WSG10 localized to the cytoplasm, whereas WLa Sota localized to the nucleus. The influence of W protein was investigated in vitro and in vivo with two AAvV-1 strains defective in the W C-terminus. The growth kinetic curves and pathogenicity tests in 3-week-old SPF chickens both showed that the replication abilities of strains with C-terminally deleted W proteins were lower than that of the parental strain. Restoring the appropriate dose of W protein increased the viral titers of these strains. The expression validation and functional exploration of W protein will facilitate our understanding of pathogenic mechanism of AAvV-1.
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Affiliation(s)
- Yanling Yang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Yawen Bu
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Jing Zhao
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Jia Xue
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Gang Xu
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Yang Song
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Ye Zhao
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Huiming Yang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Guozhong Zhang
- Key Laboratory of Animal Epidemiology of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
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8
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Stokholm I, Härkönen T, Harding KC, Siebert U, Lehnert K, Dietz R, Teilmann J, Galatius A, Worsøe Havmøller L, Carroll EL, Hall A, Olsen MT. Phylogenomic insights to the origin and spread of phocine distemper virus in European harbour seals in 1988 and 2002. DISEASES OF AQUATIC ORGANISMS 2019; 133:47-56. [PMID: 31089002 DOI: 10.3354/dao03328] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The 1988 and 2002 phocine distemper virus (PDV) outbreaks in European harbour seals Phoca vitulina are among the largest mass mortality events recorded in marine mammals. Despite its large impact on harbour seal population numbers, and 3 decades of studies, many questions regarding the spread and temporal origin of PDV remain unanswered. Here, we sequenced and analysed 7123 bp of the PDV genome, including the coding and non-coding regions of the entire P, M, F and H genes in tissues from 44 harbour seals to shed new light on the origin and spread of PDV in 1988 and 2002. The phylogenetic analyses trace the origin of the PDV strain causing the 1988 outbreak to between May 1987 and April 1988, while the origin of the strain causing the 2002 outbreak can be traced back to between June 2001 and May 2002. The analyses further point to several independent introductions of PDV in 1988, possibly linked to a southward mass immigration of harp seals in the winter and spring of 1987-1988. The vector for the 2002 outbreak is unknown, but the epidemiological analyses suggest the subsequent spread of PDV from the epicentre in the Kattegat, Denmark, to haul-out sites in the North Sea through several independent introductions.
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Affiliation(s)
- Iben Stokholm
- Section for Evolutionary Genomics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark
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9
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Cyclical adaptation of measles virus quasispecies to epithelial and lymphocytic cells: To V, or not to V. PLoS Pathog 2019; 15:e1007605. [PMID: 30768648 PMCID: PMC6395005 DOI: 10.1371/journal.ppat.1007605] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/28/2019] [Accepted: 01/29/2019] [Indexed: 12/28/2022] Open
Abstract
Measles virus (MeV) is dual-tropic: it replicates first in lymphatic tissues and then in epithelial cells. This switch in tropism raises the question of whether, and how, intra-host evolution occurs. Towards addressing this question, we adapted MeV either to lymphocytic (Granta-519) or epithelial (H358) cells. We also passaged it consecutively in both human cell lines. Since passaged MeV had different replication kinetics, we sought to investigate the underlying genetic mechanisms of growth differences by performing deep-sequencing analyses. Lymphocytic adaptation reproducibly resulted in accumulation of variants mapping within an 11-nucleotide sequence located in the middle of the phosphoprotein (P) gene. This sequence mediates polymerase slippage and addition of a pseudo-templated guanosine to the P mRNA. This form of co-transcriptional RNA editing results in expression of an interferon antagonist, named V, in place of a polymerase co-factor, named P. We show that lymphocytic-adapted MeV indeed produce minimal amounts of edited transcripts and V protein. In contrast, parental and epithelial-adapted MeV produce similar levels of edited and non-edited transcripts, and of V and P proteins. Raji, another lymphocytic cell line, also positively selects V-deficient MeV genomes. On the other hand, in epithelial cells V-competent MeV genomes rapidly out-compete the V-deficient variants. To characterize the mechanisms of genome re-equilibration we rescued four recombinant MeV carrying individual editing site-proximal mutations. Three mutations interfered with RNA editing, resulting in almost exclusive P protein expression. The fourth preserved RNA editing and a standard P-to-V protein expression ratio. However, it altered a histidine involved in Zn2+ binding, inactivating V function. Thus, the lymphocytic environment favors replication of V-deficient MeV, while the epithelial environment has the opposite effect, resulting in rapid and thorough cyclical quasispecies re-equilibration. Analogous processes may occur in natural infections with other dual-tropic RNA viruses. Key questions in infectious disease are how pathogens adapt to different cells of their hosts, and how the interplay between the virus and host factors controls the outcome of infection. Human measles virus (MeV) and related animal morbilliviruses provide important models of pathogenesis because they are dual-tropic: they replicate first in immune cells for spread through the body, and then in epithelial cells for transmission. We sought here to define the underlying molecular and evolutionary processes that allow MeV to spread rapidly in either lymphocytic or epithelial cells. We discovered unexpectedly rapid and thorough genome adaptation to these two tissues. Genome variants that cannot express functional V protein, an innate immunity control protein, are rapidly selected in lymphocytic cells. These variants express only the P protein, a polymerase co-factor, instead of expressing P and V at similar levels. Upon passaging in epithelial cells, V-competent MeV genome variants rapidly re-gain dominance. These results suggest that cyclical quasispecies re-equilibration may occur in acute MeV infections of humans, and that suboptimal variants in one environment constitute a low frequency reservoir for adaptation to the other, where they become dominant.
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Karsunke J, Heiden S, Murr M, Karger A, Franzke K, Mettenleiter TC, Römer-Oberdörfer A. W protein expression by Newcastle disease virus. Virus Res 2019; 263:207-216. [PMID: 30769123 DOI: 10.1016/j.virusres.2019.02.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 01/23/2019] [Accepted: 02/11/2019] [Indexed: 02/03/2023]
Abstract
Differential editing of transcripts from the Newcastle disease virus (NDV) phosphoprotein gene results in mRNAs capable of encoding the phosphoprotein (P), the V protein, and the W protein which share a common N-terminus but specify different C-termini. Whereas the expression and viral incorporation of the P - and V proteins by NDV has been documented, evidence for the existence of a W protein was lacking. To analyze expression of the NDV W protein, two peptides encompassing predicted antigenic sites of the unique C-terminal W protein amino acid sequence of NDV Clone 30 were used for the generation of W-specific rabbit antisera. One of them detected plasmid-expressed W protein and identified W protein after infection by indirect immunofluorescence and Western blot analyses. W protein was absent in cells infected by a newly generated recombinant NDV lacking W protein expression. Furthermore, Western blot and mass spectrometric analyses indicated the incorporation of W protein into viral particles. Confocal microscopic analyses of infected cells revealed nuclear accumulation of W protein that could be attributed to a bipartite nuclear localization sequence (NLS) within its unique C-terminal part. Redistribution of the W protein to the cytoplasm within transfected cells confirmed functionality of the NLS after mutation of its two basic clusters. This finding was additionally corroborated in cells infected with a recombinant virus expressing the mutated W protein.
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Affiliation(s)
- Julia Karsunke
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
| | - Sandra Heiden
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
| | - Magdalena Murr
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
| | - Axel Karger
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
| | - Kati Franzke
- Institute of Infectology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
| | - Thomas C Mettenleiter
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
| | - Angela Römer-Oberdörfer
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, D-17493 Greifswald-Insel Riems, Germany.
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11
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Abstract
Measles remains an important cause of child morbidity and mortality worldwide despite the availability of a safe and efficacious vaccine. The current measles virus (MeV) vaccine was developed empirically by attenuation of wild-type (WT) MeV by in vitro passage in human and chicken cells and licensed in 1963. Additional passages led to further attenuation and the successful vaccine strains in widespread use today. Attenuation is associated with decreased replication in lymphoid tissue, but the molecular basis for this restriction has not been identified. The immune response is age dependent, inhibited by maternal antibody (Ab) and involves induction of both Ab and T cell responses that resemble the responses to WT MeV infection, but are lower in magnitude. Protective immunity is correlated with levels of neutralizing Ab, but the actual immunologic determinants of protection are not known. Because measles is highly transmissible, control requires high levels of population immunity. Delivery of the two doses of vaccine needed to achieve >90% immunity is accomplished by routine immunization of infants at 9-15 months of age followed by a second dose delivered before school entry or by periodic mass vaccination campaigns. Because delivery by injection creates hurdles to sustained high coverage, there are efforts to deliver MeV vaccine by inhalation. In addition, the safety record for the vaccine combined with advances in reverse genetics for negative strand viruses has expanded proposed uses for recombinant versions of measles vaccine as vectors for immunization against other infections and as oncolytic agents for a variety of tumors.
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Affiliation(s)
- Diane E Griffin
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health , Baltimore, Maryland
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12
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Beaty SM, Lee B. Constraints on the Genetic and Antigenic Variability of Measles Virus. Viruses 2016; 8:109. [PMID: 27110809 PMCID: PMC4848602 DOI: 10.3390/v8040109] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 04/06/2016] [Accepted: 04/14/2016] [Indexed: 01/04/2023] Open
Abstract
Antigenic drift and genetic variation are significantly constrained in measles virus (MeV). Genetic stability of MeV is exceptionally high, both in the lab and in the field, and few regions of the genome allow for rapid genetic change. The regions of the genome that are more tolerant of mutations (i.e., the untranslated regions and certain domains within the N, C, V, P, and M proteins) indicate genetic plasticity or structural flexibility in the encoded proteins. Our analysis reveals that strong constraints in the envelope proteins (F and H) allow for a single serotype despite known antigenic differences among its 24 genotypes. This review describes some of the many variables that limit the evolutionary rate of MeV. The high genomic stability of MeV appears to be a shared property of the Paramyxovirinae, suggesting a common mechanism that biologically restricts the rate of mutation.
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Affiliation(s)
- Shannon M Beaty
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Benhur Lee
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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13
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Millar EL, Rennick LJ, Weissbrich B, Schneider-Schaulies J, Duprex WP, Rima BK. The phosphoprotein genes of measles viruses from subacute sclerosing panencephalitis cases encode functional as well as non-functional proteins and display reduced editing. Virus Res 2015; 211:29-37. [PMID: 26428304 DOI: 10.1016/j.virusres.2015.09.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/22/2015] [Accepted: 09/23/2015] [Indexed: 01/15/2023]
Abstract
Products expressed from the second (P/V/C) gene are important in replication and abrogating innate immune responses during acute measles virus (MV) infection. Thirteen clone sets were derived from the P/V/C genes of measles virus (MV) RNA extracted from brains of a unique collection of seven cases of subacute sclerosing panencephalitis (SSPE) caused by persistent MV in the central nervous system (CNS). Whether these functions are fully maintained when MV replicates in the CNS has not been previously determined. Co-transcriptional editing of the P mRNAs by non-template insertion of guanine (G) nucleotides, which generates mRNAs encoding the viral V protein, occurs much less frequently (9%) in the SSPE derived samples than during the acute infection (30-50%). Thus it is likely that less V protein, which is involved in combatting the innate immune response, is produced. The P genes in MV from SSPE cases were not altered by biased hypermutation but exhibited a high degree of variation within each case. Most but not all SSPE derived phospho-(P) proteins were functional in mini genome replication/transcription assays. An eight amino acid truncation of the carboxyl-terminus made the P protein non-functional while the insertion of an additional glycine residue by insertion of G nucleotides at the editing site had no effect on protein function.
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Affiliation(s)
- E L Millar
- Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, BT9 7BL Northern Ireland, UK
| | - L J Rennick
- Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, BT9 7BL Northern Ireland, UK; Department of Microbiology, Boston University School of Medicine and National Emerging Infectious Diseases Laboratories, Boston University, 620 Albany Street, Boston, MA 02118, United States
| | - B Weissbrich
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Straβe 7, D-97078 Würzburg, Germany
| | - J Schneider-Schaulies
- Institute for Virology and Immunobiology, University of Würzburg, Versbacher Straβe 7, D-97078 Würzburg, Germany
| | - W P Duprex
- Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, BT9 7BL Northern Ireland, UK; Department of Microbiology, Boston University School of Medicine and National Emerging Infectious Diseases Laboratories, Boston University, 620 Albany Street, Boston, MA 02118, United States
| | - B K Rima
- Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, The Queen's University of Belfast, Belfast, BT9 7BL Northern Ireland, UK.
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14
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Harvala H, Wiman Å, Wallensten A, Zakikhany K, Englund H, Brytting M. Role of Sequencing the Measles Virus Hemagglutinin Gene and Hypervariable Region in the Measles Outbreak Investigations in Sweden During 2013–2014. J Infect Dis 2015; 213:592-9. [DOI: 10.1093/infdis/jiv434] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 08/24/2015] [Indexed: 01/22/2023] Open
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15
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Rota PA, Bankamp B. Whole-Genome Sequencing During Measles Outbreaks. J Infect Dis 2015; 212:1529-30. [PMID: 26153410 DOI: 10.1093/infdis/jiv272] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 05/05/2015] [Indexed: 11/14/2022] Open
Affiliation(s)
- Paul A Rota
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Bettina Bankamp
- Centers for Disease Control and Prevention, Atlanta, Georgia
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16
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Fulton BO, Sachs D, Beaty SM, Won ST, Lee B, Palese P, Heaton NS. Mutational Analysis of Measles Virus Suggests Constraints on Antigenic Variation of the Glycoproteins. Cell Rep 2015; 11:1331-8. [PMID: 26004185 DOI: 10.1016/j.celrep.2015.04.054] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 04/22/2015] [Accepted: 04/25/2015] [Indexed: 10/23/2022] Open
Abstract
Measles virus undergoes error-prone replication like other RNA viruses, but over time, it has remained antigenically monotypic. The constraints on the virus that prevent the emergence of antigenic variants are unclear. As a first step in understanding this question, we subjected the measles virus genome to unbiased insertional mutagenesis, and viruses that could tolerate insertions were rescued. Only insertions in the nucleoprotein, phosphoprotein, matrix protein, as well as intergenic regions were easily recoverable. Insertions in the glycoproteins of measles virus were severely under-represented in our screen. Host immunity depends on developing neutralizing antibodies to the hemagglutinin and fusion glycoproteins; our analysis suggests that these proteins occupy very little evolutionary space and therefore have difficulty changing in the face of selective pressures. We propose that the inelasticity of these proteins prevents the sequence variation required to escape antibody neutralization in the host, allowing for long-lived immunity after infection with the virus.
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Affiliation(s)
- Benjamin O Fulton
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - David Sachs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Shannon M Beaty
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sohui T Won
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicholas S Heaton
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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17
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Improving molecular tools for global surveillance of measles virus. J Clin Virol 2013; 58:176-82. [PMID: 23806666 DOI: 10.1016/j.jcv.2013.05.018] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 05/21/2013] [Accepted: 05/24/2013] [Indexed: 12/21/2022]
Abstract
BACKGROUND The genetic characterization of wild-type measles viruses plays an important role in the description of viral transmission pathways and the verification of measles elimination. The 450 nucleotides that encode the carboxyl-terminus of the nucleoprotein (N-450) are routinely sequenced for genotype analysis. OBJECTIVES The objectives of this study were to develop improved primers and controls for RT-PCR reactions used for genotyping of measles samples and to develop a method to provide a convenient, safe, and inexpensive means to distribute measles RNA for RT-PCR assays and practice panels. STUDY DESIGN A newly designed, genetically defined synthetic RNA and RNA isolated from cells infected with currently circulating genotypes were used to compare the sensitivity of primer pairs in RT-PCR and nested PCR. FTA® cards loaded with lysates of measles infected cells were tested for their ability to preserve viral RNA and destroy virus infectivity. RESULTS A new primer pair, MeV216/MeV214, was able to amplify N-450 from viruses representing 10 currently circulating genotypes and a genotype A vaccine strain and demonstrated 100-fold increased sensitivity compared to the previously used primer set. A nested PCR assay further increased the sensitivity of detection from patient samples. A synthetic positive control RNA was developed that produced PCR products that are distinguishable by size from PCR products amplified from clinical samples. FTA® cards completely inactivated measles virus and stabilized RNA for at least six months. CONCLUSIONS These improved molecular tools will advance molecular characterization of circulating measles viruses globally and provide enhanced quality control measures.
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18
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Rima BK, Duprex WP. New concepts in measles virus replication: Getting in and out in vivo and modulating the host cell environment. Virus Res 2011; 162:47-62. [DOI: 10.1016/j.virusres.2011.09.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 09/13/2011] [Accepted: 09/14/2011] [Indexed: 12/24/2022]
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19
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Biological feasibility of measles eradication. Virus Res 2011; 162:72-9. [PMID: 21963661 DOI: 10.1016/j.virusres.2011.09.023] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 09/16/2011] [Accepted: 09/17/2011] [Indexed: 11/21/2022]
Abstract
Because of the success of global measles control programs, the World Health Organization (WHO), along with its partner agencies, is once again considering the possibility of setting a target date for measles eradication. Measles would be the fourth viral agent to be eradicated joining the successful programs to eradicate smallpox and rinderpest virus, and the continuing effort to eradicate polio virus. A description of the recent progress toward measles eradication was recently published as a supplement in the Journal of Infectious Diseases (15 July, 2011, 204 (Suppl. 1)) and the reader is referred to this document for a detailed summary of the global status of measles control. This review will focus on the biologic and virologic aspects of measles eradication.
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20
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Komarova AV, Combredet C, Meyniel-Schicklin L, Chapelle M, Caignard G, Camadro JM, Lotteau V, Vidalain PO, Tangy F. Proteomic analysis of virus-host interactions in an infectious context using recombinant viruses. Mol Cell Proteomics 2011; 10:M110.007443. [PMID: 21911578 DOI: 10.1074/mcp.m110.007443] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
RNA viruses exhibit small-sized genomes encoding few proteins, but still establish complex networks of interactions with host cell components to achieve replication and spreading. Ideally, these virus-host protein interactions should be mapped directly in infected cell culture, but such a high standard is often difficult to reach when using conventional approaches. We thus developed a new strategy based on recombinant viruses expressing tagged viral proteins to capture both direct and indirect physical binding partners during infection. As a proof of concept, we engineered a recombinant measles virus (MV) expressing one of its virulence factors, the MV-V protein, with a One-STrEP amino-terminal tag. This allowed virus-host protein complex analysis directly from infected cells by combining modified tandem affinity chromatography and mass spectrometry analysis. Using this approach, we established a prosperous list of 245 cellular proteins interacting either directly or indirectly with MV-V, and including four of the nine already known partners of this viral factor. These interactions were highly specific of MV-V because they were not recovered when the nucleoprotein MV-N, instead of MV-V, was tagged. Besides key components of the antiviral response, cellular proteins from mitochondria, ribosomes, endoplasmic reticulum, protein phosphatase 2A, and histone deacetylase complex were identified for the first time as prominent targets of MV-V and the critical role of the later protein family in MV replication was addressed. Most interestingly, MV-V showed some preferential attachment to essential proteins in the human interactome network, as assessed by centrality and interconnectivity measures. Furthermore, the list of MV-V interactors also showed a massive enrichment for well-known targets of other viruses. Altogether, this clearly supports our approach based on reverse genetics of viruses combined with high-throughput proteomics to probe the interaction network that viruses establish in infected cells.
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Affiliation(s)
- Anastassia V Komarova
- Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS URA 3015, Paris, France
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21
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Bankamp B, Takeda M, Zhang Y, Xu W, Rota PA. Genetic characterization of measles vaccine strains. J Infect Dis 2011; 204 Suppl 1:S533-48. [PMID: 21666210 DOI: 10.1093/infdis/jir097] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The complete genomic sequences of 9 measles vaccine strains were compared with the sequence of the Edmonston wild-type virus. AIK-C, Moraten, Rubeovax, Schwarz, and Zagreb are vaccine strains of the Edmonston lineage, whereas CAM-70, Changchun-47, Leningrad-4 and Shanghai-191 were derived from 4 different wild-type isolates. Nucleotide substitutions were found in the noncoding regions of the genomes as well as in all coding regions, leading to deduced amino acid substitutions in all 8 viral proteins. Although the precise mechanisms involved in the attenuation of individual measles vaccines remain to be elucidated, in vitro assays of viral protein functions and recombinant viruses with defined genetic modifications have been used to characterize the differences between vaccine and wild-type strains. Although almost every protein contributes to an attenuated phenotype, substitutions affecting host cell tropism, virus assembly, and the ability to inhibit cellular antiviral defense mechanisms play an especially important role in attenuation.
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Affiliation(s)
- Bettina Bankamp
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA.
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22
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Rota PA, Brown KE, Hübschen JM, Muller CP, Icenogle J, Chen MH, Bankamp B, Kessler JR, Brown DW, Bellini WJ, Featherstone D. Improving Global Virologic Surveillance for Measles and Rubella. J Infect Dis 2011; 204 Suppl 1:S506-13. [DOI: 10.1093/infdis/jir117] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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23
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Rota PA, Brown K, Mankertz A, Santibanez S, Shulga S, Muller CP, Hübschen JM, Siqueira M, Beirnes J, Ahmed H, Triki H, Al-Busaidy S, Dosseh A, Byabamazima C, Smit S, Akoua-Koffi C, Bwogi J, Bukenya H, Wairagkar N, Ramamurty N, Incomserb P, Pattamadilok S, Jee Y, Lim W, Xu W, Komase K, Takeda M, Tran T, Castillo-Solorzano C, Chenoweth P, Brown D, Mulders MN, Bellini WJ, Featherstone D. Global Distribution of Measles Genotypes and Measles Molecular Epidemiology. J Infect Dis 2011; 204 Suppl 1:S514-23. [DOI: 10.1093/infdis/jir118] [Citation(s) in RCA: 199] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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24
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Measles incidence rate and a phylogenetic study of contemporary genotype H1 measles strains in China: is an improved measles vaccine needed? Virus Genes 2011; 43:319-26. [DOI: 10.1007/s11262-011-0638-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Accepted: 06/11/2011] [Indexed: 10/18/2022]
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25
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Kessler JR, Kremer JR, Shulga SV, Tikhonova NT, Santibanez S, Mankertz A, Semeiko GV, Samoilovich EO, Tamfum JJM, Pukuta E, Muller CP. Revealing new measles virus transmission routes by use of sequence analysis of phosphoprotein and hemagglutinin genes. J Clin Microbiol 2011; 49:677-83. [PMID: 21106790 PMCID: PMC3043479 DOI: 10.1128/jcm.01703-10] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Accepted: 11/17/2010] [Indexed: 11/20/2022] Open
Abstract
With improved measles virus (MV) control, the genetic variability of the MV-nucleoprotein hypervariable region (NP-HVR) decreases. Thus, it becomes increasingly difficult to determine the origin of a virus using only this part of the genome. During outbreaks in Europe and Africa, we found MV strains with identical NP-HVR sequences. However, these strains showed considerable diversity within a larger sequencing window based on concatenated MV phosphoprotein and hemagglutinin genes (P/H pseudogenes). In Belarus, Germany, Russia, and the Democratic Republic of Congo, the P/H pseudogenes provided insights into chains of transmission, whereas identical NP-HVR provided none. In Russia, for instance, the P/H pseudogene identified temporal clusters rather than geographical clusters, demonstrating the circulation and importation of independent variants rather than large local outbreaks lasting for several years, as suggested by NP-HVR. Thus, by extending the sequencing window for molecular epidemiology, a more refined picture of MV circulation was obtained with more clearly defined links between outbreaks and transmission chains. Our results also suggested that in contrast to the P gene, the H gene acquired fixed substitutions that continued to be found in subsequent outbreaks, possibly with consequences for its antigenicity. Thus, a longer sequencing window has true benefits both for the epidemiological surveillance of measles and for the better monitoring of viral evolution.
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Affiliation(s)
- Julia R. Kessler
- Institute of Immunology, Centre de Recherche Public-Santé/Laboratoire National de Santé, WHO Regional Reference Laboratory for Measles and Rubella and WHO Collaboration Centre for Measles Research, Luxembourg, Luxembourg
| | - Jacques R. Kremer
- Institute of Immunology, Centre de Recherche Public-Santé/Laboratoire National de Santé, WHO Regional Reference Laboratory for Measles and Rubella and WHO Collaboration Centre for Measles Research, Luxembourg, Luxembourg
| | - Sergey V. Shulga
- WHO Regional Reference Laboratory for Measles and Rubella, Moscow, Russian Federation
| | - Nina T. Tikhonova
- WHO Regional Reference Laboratory for Measles and Rubella, Moscow, Russian Federation
| | - Sabine Santibanez
- WHO Regional Reference Laboratory for Measles and Rubella, Berlin, Germany
| | - Annette Mankertz
- WHO Regional Reference Laboratory for Measles and Rubella, Berlin, Germany
| | - Galina V. Semeiko
- The Republican Research and Practical Centre for Epidemiology and Microbiology, WHO National Measles and Rubella Laboratory, Minsk, Belarus
| | - Elena O. Samoilovich
- The Republican Research and Practical Centre for Epidemiology and Microbiology, WHO National Measles and Rubella Laboratory, Minsk, Belarus
| | | | - Elisabeth Pukuta
- Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
| | - Claude P. Muller
- Institute of Immunology, Centre de Recherche Public-Santé/Laboratoire National de Santé, WHO Regional Reference Laboratory for Measles and Rubella and WHO Collaboration Centre for Measles Research, Luxembourg, Luxembourg
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26
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Knoop V. When you can't trust the DNA: RNA editing changes transcript sequences. Cell Mol Life Sci 2011; 68:567-86. [PMID: 20938709 PMCID: PMC11114842 DOI: 10.1007/s00018-010-0538-9] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 09/13/2010] [Accepted: 09/23/2010] [Indexed: 12/25/2022]
Abstract
RNA editing describes targeted sequence alterations in RNAs so that the transcript sequences differ from their DNA template. Since the original discovery of RNA editing in trypanosomes nearly 25 years ago more than a dozen such processes of nucleotide insertions, deletions, and exchanges have been identified in evolutionarily widely separated groups of the living world including plants, animals, fungi, protists, bacteria, and viruses. In many cases gene expression in mitochondria is affected, but RNA editing also takes place in chloroplasts and in nucleocytosolic genetic environments. While some RNA editing systems largely seem to repair defect genes (cryptogenes), others have obvious functions in modulating gene activities. The present review aims for an overview on the current states of research in the different systems of RNA editing by following a historic timeline along the respective original discoveries.
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Affiliation(s)
- Volker Knoop
- Abteilung Molekulare Evolution, Institut für Zelluläre und Molekulare Botanik (IZMB), Bonn, Germany.
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27
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Kessler JR, Kremer JR, Muller CP. Interplay of measles virus with early induced cytokines reveals different wild type phenotypes. Virus Res 2010; 155:195-202. [PMID: 20950658 DOI: 10.1016/j.virusres.2010.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Revised: 10/05/2010] [Accepted: 10/05/2010] [Indexed: 10/19/2022]
Abstract
Differential effects of measles virus (MV) on the innate immune response may influence virus spread and severity of disease. Using a representative panel of 22 MV strains including 14 different genotypes, we found that wild-type (wt) differ considerably in their sensitivity to type I interferon (IFN). The wt virus production was 2-47-fold lower in IFN-alpha treated Vero/hSLAM cells, whereas vaccine virus production was reduced only 2-3-fold. Sequence analysis of the MV-P/C/V gene, revealed no obvious amino acid mutations that correlated with the different phenotypes. Strains also widely differed in their ability to induce type I IFN, tumor necrosis factor (TNF) alpha and other cytokines in human A549/hSLAM cells. Some wt strains that were highly sensitive to type I IFN induced only low levels of these and other cytokines. In vitro wt strains that produced the 5' copy-back defective interfering RNAs (5'cb-diRNA) characterized by Shingai et al. (2007), induced high levels of cytokines that otherwise were only reached by vaccine strains. These 5'cb-diRNAs emerged only in virus cultures during multiple passaging and were not detectable in clinical samples of measles patients. These subgenomic RNAs are an important confounding parameter in passaged wt viruses which must be carefully assessed in all in vitro studies. The present data show that MV wt strains differ in their sensitivity and their ability to temper with the innate immune response, which may result in differences in virulence.
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Affiliation(s)
- Julia R Kessler
- Laboratoire National de Santé, Institute of Immunology, Centre de Recherche Public-Santé/WHO Regional Reference, 20A rue Auguste Lumière, L-1950 Luxembourg, Luxembourg
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28
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Canine distemper virus diversity in Lake Baikal seal (Phoca sibirica) population. Vet Microbiol 2010; 144:192-7. [PMID: 20083361 DOI: 10.1016/j.vetmic.2009.12.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Revised: 12/18/2009] [Accepted: 12/21/2009] [Indexed: 11/24/2022]
Abstract
Morbillivirus epizootics in marine mammals have been found in a variety of marine mammal species throughout the world over the past 20 years. The virus epizootic which resulted in significant mortality of Siberian seals (Phoca sibirica) in Lake Baikal during 1987-1988 was caused by the canine distemper virus (CDV). In our previous papers we provided evidence that the CDV similar to strain, identified in 1988, continued to circulate in Lake Baikal seals after 1988. The aim of this study was an up to date detection of CDV in Baikal seals and an evaluation of the genetic diversity of Baikal seal CDVs in comparison with other virus isolates and strains available in the GenBank on the basis of nucleotide sequence analysis of the phosphoprotein gene fragment. The majority of CDVs recovered from 1992 till 2007 were found to be similar to the one responsible for the epizootic of Lake Baikal seals. Phylogenetic analysis revealed that more than one genotype of CDV was circulating in Lake Baikal seals after the epizootic of 1987-1988.
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29
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Minet C, Yami M, Egzabhier B, Gil P, Tangy F, Brémont M, Libeau G, Diallo A, Albina E. Sequence analysis of the large (L) polymerase gene and trailer of the peste des petits ruminants virus vaccine strain Nigeria 75/1: Expression and use of the L protein in reverse genetics. Virus Res 2009; 145:9-17. [DOI: 10.1016/j.virusres.2009.06.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Revised: 06/04/2009] [Accepted: 06/05/2009] [Indexed: 10/20/2022]
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30
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Lo MK, Harcourt BH, Mungall BA, Tamin A, Peeples ME, Bellini WJ, Rota PA. Determination of the henipavirus phosphoprotein gene mRNA editing frequencies and detection of the C, V and W proteins of Nipah virus in virus-infected cells. J Gen Virol 2009; 90:398-404. [PMID: 19141449 DOI: 10.1099/vir.0.007294-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The henipaviruses, Nipah virus (NiV) and Hendra virus (HeV), are highly pathogenic zoonotic paramyxoviruses. Like many other paramyxoviruses, henipaviruses employ a process of co-transcriptional mRNA editing during transcription of the phosphoprotein (P) gene to generate additional mRNAs encoding the V and W proteins. The C protein is translated from the P mRNA, but in an alternate reading frame. Sequence analysis of multiple, cloned mRNAs showed that the mRNA editing frequencies of the P genes of the henipaviruses are higher than those reported for other paramyxoviruses. Antisera to synthetic peptides from the P, V, W and C proteins of NiV were generated to study their expression in infected cells. All proteins were detected in both infected cells and purified virions. In infected cells, the W protein was detected in the nucleus while P, V and C were found in the cytoplasm.
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Affiliation(s)
- Michael K Lo
- The Research Institute at Nationwide Children's Hospital, Center for Vaccines and Immunity, 700 Children's Drive, Columbus, OH 43205, USA.,The Ohio State University, College of Medicine, Department of Pediatrics, Columbus, OH 43205, USA.,Emory University School of Medicine, Department of Microbiology and Immunology, 1510 Clifton Road, Atlanta, GA 30322, USA.,Measles, Mumps, Rubella and Herpesviruses Laboratory Branch, 1600 Clifton Road, MS-C-22, Atlanta, GA 30333, USA
| | - Brian H Harcourt
- Measles, Mumps, Rubella and Herpesviruses Laboratory Branch, 1600 Clifton Road, MS-C-22, Atlanta, GA 30333, USA
| | - Bruce A Mungall
- Commonwealth Scientific Industrial Research Organization, Australian Animal Health Laboratory, 5 Portarlington Road, East Geelong, Victoria, Australia
| | - Azaibi Tamin
- Measles, Mumps, Rubella and Herpesviruses Laboratory Branch, 1600 Clifton Road, MS-C-22, Atlanta, GA 30333, USA
| | - Mark E Peeples
- The Ohio State University, College of Medicine, Department of Pediatrics, Columbus, OH 43205, USA.,The Research Institute at Nationwide Children's Hospital, Center for Vaccines and Immunity, 700 Children's Drive, Columbus, OH 43205, USA
| | - William J Bellini
- Measles, Mumps, Rubella and Herpesviruses Laboratory Branch, 1600 Clifton Road, MS-C-22, Atlanta, GA 30333, USA
| | - Paul A Rota
- Measles, Mumps, Rubella and Herpesviruses Laboratory Branch, 1600 Clifton Road, MS-C-22, Atlanta, GA 30333, USA
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Abstract
Nipah virus (NiV) is predicted to encode four proteins from its P gene (P, V, W, and C) via mRNA editing and an alternate open reading frame. By use of specific antibodies, the expression of the V, W, and C proteins in NiV-infected cells has now been confirmed. Analysis of the P-gene transcripts shows a ratio of P:V:W mRNA of 1:1:1, but this differs over time, with greater proportions of V and W transcripts observed as the infection progresses. Eighty-two percent of transcripts are edited, with up to 11 G insertions observed. This exceptionally high editing frequency ensures expression of the V and W proteins.
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