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Cheng WY, Chen BS, Wang HC, Liu MT. Genetic Characteristics of Measles Viruses Isolated in Taiwan between 2015 and 2020. Viruses 2023; 15:211. [PMID: 36680251 PMCID: PMC9863581 DOI: 10.3390/v15010211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
A genetic analysis of circulating measles virus (MeV) provides strong evidence of an interruption in endemic measles and supports the elimination status of this disease. This study investigated 219 MeVs isolated between 2015 and 2020. Based on the 450 nucleotide sequences of the nucleoprotein gene (N-450), three genotypes of the H1, D8 and B3 with 8, 18 and 6 different N-450 sequences, respectively, were identified. The H1 genotype virus has not circulated in Taiwan since 2017, and the D8 and B3 genotype MeVs became dominant between 2018 and 2019. Different D8 genotype variants were imported from neighboring countries, and the majority of MeV variants were detected only for a short period. However, MVs/Gir Somnath.IND/42.16[D8], a named strain designated by the World Health Organization (WHO), was detected over 2 years. To explore whether the endemic transmission of measles has been underestimated, another sequence window of the hypervariable, noncoding regions between the matrix (M) and fusion (F) genes (MF-NCR) was introduced to clarify the transmission chain. From the chronological sequence analysis of MeVs with N-450 and MF-NCR sequence windows, no endemic MeV variants lasted over 4 weeks, providing strong evidence to support the contention that Taiwan has reached the status for measles elimination.
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Affiliation(s)
- Wen-Yueh Cheng
- Center for Research, Diagnostic and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei 11561, Taiwan
| | | | | | - Ming-Tsan Liu
- Center for Research, Diagnostic and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei 11561, Taiwan
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2
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Liu F, Lin J, Wang Q, Zhang Y, Shan H. Recovery of Recombinant Canine Distemper Virus That Expresses CPV-2a VP2: Uncovering the Mutation Profile of Recombinant Undergoing 50 Serial Passages In Vitro. Front Cell Infect Microbiol 2022; 11:770576. [PMID: 35096636 PMCID: PMC8795682 DOI: 10.3389/fcimb.2021.770576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 12/16/2021] [Indexed: 12/15/2022] Open
Abstract
Canine distemper and canine parvoviral enteritis are infections caused by the canine distemper virus (CDV) and canine parvovirus type 2 (CPV-2), respectively. They are two common infectious diseases that cause high morbidity and mortality in affected dogs. Combination vaccines have been broadly used to protect dogs from infections of CDV, CPV-2, and other viruses. VP2 is the most abundant protein of the CPV-2 capsid. It elicits potent immunity in animals and, therefore, is widely used for designing subunit antigen-based vaccines. In this study, we rescued a recombinant CDV (QN vaccine strain) using reverse genetics. The recombinant CDV (rCDV-VP2) was demonstrated to express stably the VP2 in cells for at least 33 serial passages in vitro. Unfortunately, a nonsense mutation was initially identified in the VP2 open reading frame (ORF) at passage-34 (P34) and gradually became predominant in rCDV-VP2 quasispecies with passaging. Neither test strip detection nor indirect immunofluorescence assay demonstrated the expression of the VP2 at P50. The P50 rCDV-VP2 was subjected to next-generation sequencing, which totally identified 17 single-nucleotide variations (SNVs), consisting of 11 transitions and 6 transversions. Out of the 17 SNVs, 1 and 9 were identified as nonsense and missense mutations, respectively. Since the nonsense mutation arose in the VP2 ORF as early as P34, an earlier rCDV-VP2 progeny should be selected for the vaccination of animals in future experiments.
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Affiliation(s)
- Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
- *Correspondence: Hu Shan, ; Fuxiao Liu,
| | - Jiahui Lin
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Qianqian Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Hu Shan
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
- *Correspondence: Hu Shan, ; Fuxiao Liu,
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3
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Liu F, Wang N, Lin J, Wang Q, Huang Y, Zhang Y, Shan H. Rescuing eGFP-Tagged Canine Distemper Virus for 40 Serial Passages Separately in Ribavirin- and Non-Treated Cells: Comparative Analysis of Viral Mutation Profiles. Front Cell Infect Microbiol 2021; 11:746926. [PMID: 34604118 PMCID: PMC8481889 DOI: 10.3389/fcimb.2021.746926] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/01/2021] [Indexed: 02/05/2023] Open
Abstract
Due to lacking a proofreading mechanism in their RNA-dependent RNA polymerases (RdRp), RNA viruses generally possess high mutation frequencies, making them evolve rapidly to form viral quasispecies during serial passages in cells, especially treated with mutagens, like ribavirin. Canine distemper virus (CDV) belongs to the genus Morbillivirus. Its L protein functions as an RdRp during viral replication. In this study, a recombinant enhanced green fluorescence protein-tagged CDV (rCDV-eGFP) was rescued from its cDNA clone, followed by viral identification and characterization at passage-7 (P7). This recombinant was independently subjected to extra 40 serial passages (P8 to 47) in ribavirin- and non-treated cells. Two viral progenies, undergoing passages in ribavirin- and non-treated VDS cells, were named rCDV-eGFP-R and -N, respectively. Both progenies were simultaneously subjected to next-generation sequencing (NGS) at P47 for comparing their quasispecies diversities with each other. The rCDV-eGFP-R and -N showed 62 and 23 single-nucleotide mutations (SNMs) in individual antigenomes, respectively, suggesting that the ribavirin conferred a mutagenic effect on the rCDV-eGFP-R. The spectrum of 62 SNMs contained 26 missense and 36 silent mutations, and that of 23 SNMs was composed of 17 missense and 6 silent mutations. Neither the rCDV-eGFP-R nor -N exhibited nonsense mutation in individual antigenomes. We speculate that the rCDV-eGFP-R may contain at least one P47 sub-progeny characterized by high-fidelity replication in cells. If such a sub-progeny can be purified from the mutant swarm, its L protein would elucidate a molecular mechanism of CDV high-fidelity replication.
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Affiliation(s)
- Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Ning Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Jiahui Lin
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Qianqian Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Yilan Huang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Hu Shan
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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4
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Liu F, Zou Y, Li L, Liu C, Wu X. Mutation Profiles of eGFP-Tagged Small Ruminant Morbillivirus During 45 Serial Passages in Ribavirin-Treated Cells. Front Vet Sci 2021; 8:690204. [PMID: 34368277 PMCID: PMC8333274 DOI: 10.3389/fvets.2021.690204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/09/2021] [Indexed: 11/17/2022] Open
Abstract
Small ruminant morbillivirus (SRMV), formerly known as peste-des-petits-ruminants virus, classified into the genus Morbillivirus in the family Paramyxoviridae. Its L protein functions as the RNA-dependent RNA polymerases (RdRp) during viral replication. Due to the absence of efficient proofreading activity in their RdRps, various RNA viruses reveal high mutation frequencies, making them evolve rapidly during serial passages in cells, especially treated with a certain mutagen, like ribavirin. We have previously rescued a recombinant enhanced green fluorescence protein-tagged SRMV (rSRMV-eGFP) using reverse genetics. In this study, the rSRMV-eGFP was subjected to serial passages in ribavirin-treated cells. Due to the ribavirin-exerted selective pressure, it was speculated that viral progenies would form quasispecies after dozens of passages. Viral progenies at passage-10, -20, -30, -40, and -50 were separately subjected to next-generation sequencing (NGS), consequently revealing a total of 34 single-nucleotide variations, including five synonymous, 21 missense, and one non-sense mutations. The L sequence was found to harbor eight missense mutations during serial passaging. It was speculated that at least one high-fidelity variant was present in viral quasispecies at passage-50. If purified from the population of viral progenies, this putative variant would contribute to clarifying a molecular mechanism in viral high-fidelity replication in vitro.
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Affiliation(s)
- Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Yanli Zou
- OIE Reference Laboratory for Peste des Petits Ruminants, China Animal Health and Epidemiology Center, Qingdao, China
| | - Lin Li
- OIE Reference Laboratory for Peste des Petits Ruminants, China Animal Health and Epidemiology Center, Qingdao, China
| | - Chunju Liu
- OIE Reference Laboratory for Peste des Petits Ruminants, China Animal Health and Epidemiology Center, Qingdao, China
| | - Xiaodong Wu
- OIE Reference Laboratory for Peste des Petits Ruminants, China Animal Health and Epidemiology Center, Qingdao, China
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5
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Mohammadi E, Shafiee F, Shahzamani K, Ranjbar MM, Alibakhshi A, Ahangarzadeh S, Beikmohammadi L, Shariati L, Hooshmandi S, Ataei B, Javanmard SH. Novel and emerging mutations of SARS-CoV-2: Biomedical implications. Biomed Pharmacother 2021; 139:111599. [PMID: 33915502 PMCID: PMC8062574 DOI: 10.1016/j.biopha.2021.111599] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/18/2021] [Accepted: 03/27/2021] [Indexed: 12/31/2022] Open
Abstract
Coronavirus disease-19 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 virus strains has geographical diversity associated with diverse severity, mortality rate, and response to treatment that were characterized using phylogenetic network analysis of SARS-CoV-2 genomes. Although, there is no explicit and integrative explanation for these variations, the genetic arrangement, and stability of SARS-CoV-2 are basic contributing factors to its virulence and pathogenesis. Hence, understanding these features can be used to predict the future transmission dynamics of SARS-CoV-2 infection, drug development, and vaccine. In this review, we discuss the most recent findings on the mutations in the SARS-CoV-2, which provide valuable information on the genetic diversity of SARS-CoV-2, especially for DNA-based diagnosis, antivirals, and vaccine development for COVID-19.
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Affiliation(s)
- Elmira Mohammadi
- Applied Physiology Research Center, Cardiovascular Research Institute, Department of Physiology, Isfahan University of Medical Sciences, Isfahan, Iran; Core Research Facilities, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Fatemeh Shafiee
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Kiana Shahzamani
- Isfahan Gastroenterology and Hepatology Research Center (lGHRC), Isfahan University of medical sciences, Isfahan, Iran
| | - Mohammad Mehdi Ranjbar
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran
| | - Abbas Alibakhshi
- Molecular Medicine Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Shahrzad Ahangarzadeh
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Leila Beikmohammadi
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Laleh Shariati
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, The Netherlands; Stem Cell and Regenerative Medicine Center of Excellence, Tehran University of Medical Sciences, 14155-6559 Tehran, Iran
| | - Soodeh Hooshmandi
- Rajaie Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Behrooz Ataei
- Infectious Diseases and Tropical Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
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6
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Leber MF, Hoyler B, Prien S, Neault S, Engeland CE, Förster JM, Bossow S, Springfeld C, von Kalle C, Jäger D, Bell JC, Ungerechts G. Sequencing of serially passaged measles virus affirms its genomic stability and reveals a nonrandom distribution of consensus mutations. J Gen Virol 2020; 101:399-409. [PMID: 32053093 DOI: 10.1099/jgv.0.001395] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Oncolytic virotherapy is an emerging treatment option for numerous cancers, with several virus families currently being evaluated in clinical trials. More specifically, vaccine-strain measles virus has arisen as a promising candidate for the treatment of different tumour types in several early clinical trials. Replicating viruses, and especially RNA viruses without proofreading polymerases, can rapidly adapt to varying environments by selecting quasispecies with advantageous genetic mutations. Subsequently, these genetic alterations could potentially weaken the safety profile of virotherapy. In this study, we demonstrate that, following an extended period of virus replication in producer or cancer cell lines, the quasispecies consensus sequence of vaccine strain-derived measles virus accrues a remarkably small number of mutations throughout the nonsegmented negative-stranded RNA genome. Interestingly, we detected a nonrandom distribution of genetic alterations within the genome, with an overall decreasing frequency of mutations from the 3' genome start to its 5' end. Comparing the serially passaged viruses to the parental virus on producer cells, we found that the acquired consensus mutations did not drastically change viral replication kinetics or cytolytic potency. Collectively, our data corroborate the genomic stability and excellent safety profile of oncolytic measles virus, thus supporting its continued development and clinical translation as a promising viro-immunotherapeutic.
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Affiliation(s)
- Mathias Felix Leber
- German Cancer Research Center (DKFZ), Clinical Cooperation Unit Virotherapy, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,Heidelberg University Hospital, Department of Medical Oncology, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany.,Ottawa Hospital Research Institute, Cancer Therapeutics Program, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada
| | - Birgit Hoyler
- Heidelberg University Hospital, Department of Medical Oncology, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ), Clinical Cooperation Unit Virotherapy, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Stefanie Prien
- Heidelberg University Hospital, Department of Medical Oncology, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ), Clinical Cooperation Unit Virotherapy, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Serge Neault
- Ottawa Hospital Research Institute, Cancer Therapeutics Program, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada
| | - Christine E Engeland
- Heidelberg University Hospital, Department of Medical Oncology, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ), Clinical Cooperation Unit Virotherapy, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Judith M Förster
- Heidelberg University, Faculty of Biosciences, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ), Clinical Cooperation Unit Virotherapy, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Sascha Bossow
- Heidelberg University Hospital, Department of Medical Oncology, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Christoph Springfeld
- Heidelberg University Hospital, Department of Medical Oncology, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Christof von Kalle
- Sidra Medical and Research Center, Al Luqta Street, Education City, North Campus, 26999, Doha, Qatar.,Berlin Institute of Health and Charité, Universitätsmedizin, Anna-Louisa-Karsch-Straße 2, 10178 Berlin, Germany.,German Cancer Research Center (DKFZ), Division of Translational Oncology, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Dirk Jäger
- Heidelberg University Hospital, Department of Medical Oncology, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - John C Bell
- Ottawa Hospital Research Institute, Cancer Therapeutics Program, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada
| | - Guy Ungerechts
- Ottawa Hospital Research Institute, Cancer Therapeutics Program, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada.,Heidelberg University Hospital, Department of Medical Oncology, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany.,German Cancer Research Center (DKFZ), Clinical Cooperation Unit Virotherapy, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
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7
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Genomic characterization of mumps viruses from a large-scale mumps outbreak in Arkansas, 2016. INFECTION GENETICS AND EVOLUTION 2019; 75:103965. [PMID: 31319177 DOI: 10.1016/j.meegid.2019.103965] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 07/02/2019] [Accepted: 07/12/2019] [Indexed: 11/22/2022]
Abstract
In 2016, a year-long large-scale mumps outbreak occurred in Arkansas among a highly-vaccinated population. A total of 2954 mumps cases were identified during this outbreak. The majority of cases (1676 (57%)) were school-aged children (5-17 years), 1536 (92%) of these children had completed the mumps vaccination schedule. To weigh the possibility that the mumps virus evaded vaccine-induced immunity in the affected Arkansas population, we established a pipeline for genomic characterization of the outbreak strains. Our pipeline produces whole-genome sequences along with phylogenetic analysis of the outbreak mumps virus strains. We collected buccal swab samples of patients who tested positive for the mumps virus during the 2016 Arkansas outbreak, and used the portable Oxford Nanopore Technology to sequence the extracted strains. Our pipeline identified the genotype of the Arkansas mumps strains as genotype G and presented a genome-based phylogenetic tree with superior resolution to a standard small hydrophobic (SH) gene-based tree. We phylogenetically compared the Arkansas whole-genome sequences to all publicly available mumps strains. While these analyses show that the Arkansas mumps strains are evolutionarily distinct from the vaccine strains, we observed no correlation between vaccination history and phylogenetic grouping. Furthermore, we predicted potential B-cell epitopes encoded by the Arkansas mumps strains using a random forest prediction model trained on antibody-antigen protein structures. Over half of the predicted epitopes of the Jeryl-Lynn vaccine strains in the Hemagglutinin-Neuraminidase (HN) surface glycoprotein (a major target of neutralizing antibodies) region are missing in the Arkansas mumps strains. In-silico analyses of potential epitopes may indicate that the Arkansas mumps strains display antigens with reduced immunogenicity, which may contribute to reduced vaccine effectiveness. However, our in-silico findings should be assessed by robust experiments such as cross neutralization assays. Metadata analysis showed that vaccination history had no effect on the evolution of the Arkansas mumps strains during this outbreak. We conclude that the driving force behind the spread of the mumps virus in the 2016 Arkansas outbreak remains undetermined.
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8
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Cattaneo R, Donohue RC, Generous AR, Navaratnarajah CK, Pfaller CK. Stronger together: Multi-genome transmission of measles virus. Virus Res 2019; 265:74-79. [PMID: 30853585 DOI: 10.1016/j.virusres.2019.03.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 12/29/2022]
Abstract
Measles virus (MeV) is an immunosuppressive, extremely contagious RNA virus that remains a leading cause of death among children. MeV is dual-tropic: it replicates first in lymphatic tissue, causing immunosuppression, and then in epithelial cells of the upper airways, accounting for extremely efficient contagion. Efficient contagion is counter-intuitive because the enveloped MeV particles are large and relatively unstable. However, MeV particles can contain multiple genomes, which can code for proteins with different functional characteristics. These proteins can cooperate to promote virus spread in tissue culture, prompting the question of whether multi-genome MeV transmission may promote efficient MeV spread also in vivo. Consistent with this hypothesis, in well-differentiated primary human airway epithelia large genome populations spread rapidly through intercellular pores. In another line of research, it was shown that distinct lymphocytic-adapted and epithelial-adapted genome populations exist; cyclical adaptation studies indicate that suboptimal variants in one environment may constitute a low frequency reservoir for adaptation to the other environment. Altogether, these observations suggest that, in humans, MeV spread relies on en bloc genome transmission, and that genomic diversity is instrumental for rapid MeV dissemination within hosts.
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Affiliation(s)
- Roberto Cattaneo
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, 55905, United States; Mayo Graduate School, Mayo Clinic, Rochester, MN, 55905, United States.
| | - Ryan C Donohue
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, 55905, United States; Mayo Graduate School, Mayo Clinic, Rochester, MN, 55905, United States
| | - Alex R Generous
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, 55905, United States; Mayo Graduate School, Mayo Clinic, Rochester, MN, 55905, United States
| | - Chanakha K Navaratnarajah
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, 55905, United States; Mayo Graduate School, Mayo Clinic, Rochester, MN, 55905, United States
| | - Christian K Pfaller
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, 55905, United States; Paul-Ehrlich-Institute, Division of Veterinary Medicine, Langen, 63225, Germany
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9
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Pauly MD, Procario MC, Lauring AS. A novel twelve class fluctuation test reveals higher than expected mutation rates for influenza A viruses. eLife 2017; 6. [PMID: 28598328 PMCID: PMC5511008 DOI: 10.7554/elife.26437] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 06/09/2017] [Indexed: 12/21/2022] Open
Abstract
Influenza virus’ low replicative fidelity contributes to its capacity for rapid evolution. Clonal sequencing and fluctuation tests have suggested that the influenza virus mutation rate is 2.7 × 10–6 - 3.0 × 10–5 substitutions per nucleotide per strand copied (s/n/r). However, sequencing assays are biased toward mutations with minimal fitness impacts and fluctuation tests typically investigate only a subset of all possible single nucleotide mutations. We developed a fluctuation test based on reversion to fluorescence in a set of virally encoded mutant green fluorescent proteins, which allowed us to measure the rates of selectively neutral mutations representative of the twelve different mutation types. We measured an overall mutation rate of 1.8 × 10–4 s/n/r for PR8 (H1N1) and 2.5 × 10–4 s/n/r for Hong Kong 2014 (H3N2) and a transitional bias of 2.7–3.6. Our data suggest that each replicated genome will have an average of 2–3 mutations and highlight the importance of mutational load in influenza virus evolution. DOI:http://dx.doi.org/10.7554/eLife.26437.001
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Affiliation(s)
- Matthew D Pauly
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, United States
| | - Megan C Procario
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, United States
| | - Adam S Lauring
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, United States.,Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, United States
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10
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Antigenic Drift Defines a New D4 Subgenotype of Measles Virus. J Virol 2017; 91:JVI.00209-17. [PMID: 28356529 DOI: 10.1128/jvi.00209-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/19/2017] [Indexed: 01/25/2023] Open
Abstract
The measles virus hemagglutinin (MeV-H) protein is the main target of protective neutralizing antibodies. Using a panel of monoclonal antibodies (MAbs) that recognize known major antigenic sites in MeV-H, we identified a D4 genotype variant that escapes neutralization by MAbs targeting the neutralizing epitope (NE) antigenic site. By site-directed mutagenesis, L249P was identified as the critical mutation disrupting the NE in this genotype D4 variant. Forty-two available D4 genotype gene sequences were subsequently analyzed and divided into 2 groups according to the presence or absence of the L249P MeV-H mutation. Further analysis of the MeV-N gene sequences of these 2 groups confirmed that they represent clearly definable, sequence-divergent D4 subgenotypes, which we named subgenotypes D4.1 and D4.2. The subgenotype D4.1 MeVs were isolated predominantly in Kenya and Ethiopia, whereas the MAb-resistant subgenotype D4.2 MeVs were isolated predominantly in France and Great Britain, countries with higher vaccine coverage rates. Interestingly, D4.2 subgenotype viruses showed a trend toward diminished susceptibility to neutralization by human sera pooled from approximately 60 to 80 North American donors. Escape from MAb neutralization may be a powerful epidemiological surveillance tool to monitor the evolution of new MeV subgenotypes.IMPORTANCE Measles virus is a paradigmatic RNA virus, as the antigenic composition of the vaccination has not needed to be updated since its discovery. The vaccine confers protection by inducing neutralizing antibodies that interfere with the function of the hemagglutinin protein. Viral strains are indistinguishable serologically, although characteristic nucleotide sequences differentiate 24 genotypes. In this work, we describe a distant evolutionary branch within genotype D4. Designated subgenotype D4.2, this virus is distinguishable by neutralization with vaccine-induced monoclonal antibodies that target the neutralizing epitope (NE). The subgenotype D4.2 viruses have a higher predominance in countries with intermediary levels of vaccine coverage. Our studies demonstrate that subgenotype D4.2 lacks epitopes associated with half of the known antigenic sites, which significantly impacts our understanding of measles virus evolution.
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11
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Muñoz-Alía MA, Casasnovas JM, Celma ML, Carabaña J, Liton PB, Fernandez-Muñoz R. Measles Virus Hemagglutinin epitopes immunogenic in natural infection and vaccination are targeted by broad or genotype-specific neutralizing monoclonal antibodies. Virus Res 2017; 236:30-43. [PMID: 28465158 DOI: 10.1016/j.virusres.2017.04.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/24/2017] [Accepted: 04/24/2017] [Indexed: 11/27/2022]
Abstract
Measles virus (MV) remains a leading cause of vaccine-preventable deaths in children. Protection against MV is associated with neutralizing antibodies that preferentially recognize the viral hemagglutinin (MV-H), and to a lesser extent, the fusion protein (MV-F). Although MV is serologically monotypic, 24 genotypes have been identified. Here we report three neutralization epitopes conserved in the more prevalent circulating MV genotypes, two located in the MV-H receptor binding site (RBS) (antigenic site III) and a third in MV-H/MV-F interphase (antigenic site Ia) which are essential for MV multiplication. In contrast, two MV-H neutralization epitopes, showed a genotype-specific neutralization escape due to a single amino acid change, that we mapped in the "noose" antigenic site, or an enhanced neutralization epitope (antigenic site IIa). The monoclonal antibody (mAb) neutralization potency correlated with its binding affinity and was mainly driven by kinetic dissociation rate (koff). We developed an immunoassay for mAb binding to MV-H in its native hetero-oligomeric structure with MV-F on the surface of a MV productive steady-state persistently infected (p.i.) human cell lines, and a competitive-binding assay with serum from individuals with past infection by different MV genotypes. Binding assays revealed that a broad neutralization epitope, in RBS antigenic site, a genotype specific neutralization epitopes, in noose and IIa sites, were immunogenic in natural infection and vaccination and may elicit long-lasting humoral immunity that might contribute to explain MV immunogenic stability. These results support the design of improved measles vaccines, broad-spectrum prophylactic or therapeutic antibodies and MV-used in oncolytic therapies.
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Affiliation(s)
| | | | | | - Juan Carabaña
- Virology Unit, Ramón y Cajal Hospital, Madrid, Spain
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12
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Sanjuán R, Domingo-Calap P. Mechanisms of viral mutation. Cell Mol Life Sci 2016; 73:4433-4448. [PMID: 27392606 PMCID: PMC5075021 DOI: 10.1007/s00018-016-2299-6] [Citation(s) in RCA: 473] [Impact Index Per Article: 59.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 06/20/2016] [Accepted: 06/22/2016] [Indexed: 02/08/2023]
Abstract
The remarkable capacity of some viruses to adapt to new hosts and environments is highly dependent on their ability to generate de novo diversity in a short period of time. Rates of spontaneous mutation vary amply among viruses. RNA viruses mutate faster than DNA viruses, single-stranded viruses mutate faster than double-strand virus, and genome size appears to correlate negatively with mutation rate. Viral mutation rates are modulated at different levels, including polymerase fidelity, sequence context, template secondary structure, cellular microenvironment, replication mechanisms, proofreading, and access to post-replicative repair. Additionally, massive numbers of mutations can be introduced by some virus-encoded diversity-generating elements, as well as by host-encoded cytidine/adenine deaminases. Our current knowledge of viral mutation rates indicates that viral genetic diversity is determined by multiple virus- and host-dependent processes, and that viral mutation rates can evolve in response to specific selective pressures.
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Affiliation(s)
- Rafael Sanjuán
- Department of Genetics and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, C/Catedrático José Beltrán 2, 46980, Paterna, Valencia, Spain.
| | - Pilar Domingo-Calap
- 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
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13
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Deng L, Qin X, Krell P, Lu R, Sharif S, Nagy É. Characterization and functional studies of fowl adenovirus 9 dUTPase. Virology 2016; 497:251-261. [DOI: 10.1016/j.virol.2016.07.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 07/08/2016] [Accepted: 07/21/2016] [Indexed: 01/04/2023]
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14
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Liu F, Wu X, Li L, Zou Y, Liu S, Wang Z. Evolutionary characteristics of morbilliviruses during serial passages in vitro: Gradual attenuation of virus virulence. Comp Immunol Microbiol Infect Dis 2016; 47:7-18. [DOI: 10.1016/j.cimid.2016.05.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 05/22/2016] [Accepted: 05/24/2016] [Indexed: 02/05/2023]
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15
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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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16
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Geller R, Estada Ú, Peris JB, Andreu I, Bou JV, Garijo R, Cuevas JM, Sabariegos R, Mas A, Sanjuán R. Highly heterogeneous mutation rates in the hepatitis C virus genome. Nat Microbiol 2016; 1:16045. [PMID: 27572964 DOI: 10.1038/nmicrobiol.2016.45] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/09/2016] [Indexed: 01/10/2023]
Abstract
Spontaneous mutations are the ultimate source of genetic variation and have a prominent role in evolution. RNA viruses such as hepatitis C virus (HCV) have extremely high mutation rates, but these rates have been inferred from a minute fraction of genome sites, limiting our view of how RNA viruses create diversity. Here, by applying high-fidelity ultradeep sequencing to a modified replicon system, we scored >15,000 spontaneous mutations, encompassing more than 90% of the HCV genome. This revealed >1,000-fold differences in mutability across genome sites, with extreme variations even between adjacent nucleotides. We identify base composition, the presence of high- and low-mutation clusters and transition/transversion biases as the main factors driving this heterogeneity. Furthermore, we find that mutability correlates with the ability of HCV to diversify in patients. These data provide a site-wise baseline for interrogating natural selection, genetic load and evolvability in HCV, as well as for evaluating drug resistance and immune evasion risks.
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Affiliation(s)
- Ron Geller
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, 46980 Paterna, València, Spain
| | - Úrsula Estada
- Unitat de Genómica, Servei Central de Suport a la Investigació Experimental, Universitat de València, 46100 Burjassot, València, Spain
| | - Joan B Peris
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, 46980 Paterna, València, Spain
| | - Iván Andreu
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, 46980 Paterna, València, Spain
| | - Juan-Vicente Bou
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, 46980 Paterna, València, Spain
| | - Raquel Garijo
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, 46980 Paterna, València, Spain
| | - José M Cuevas
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, 46980 Paterna, València, Spain
| | - Rosario Sabariegos
- Regional Center for Biomedical Research, Universidad de Castilla-La Mancha, 02006 Albacete, Spain
| | - Antonio Mas
- Regional Center for Biomedical Research, Universidad de Castilla-La Mancha, 02006 Albacete, Spain
| | - Rafael Sanjuán
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Institute for Integrative Systems Biology (I2SysBio), Universitat de València, 46980 Paterna, València, Spain.,Departament de Genètica, Universitat de València, 46100 Burjassot, València, Spain
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17
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Baldo A, Galanis E, Tangy F, Herman P. Biosafety considerations for attenuated measles virus vectors used in virotherapy and vaccination. Hum Vaccin Immunother 2015; 12:1102-16. [PMID: 26631840 PMCID: PMC4963060 DOI: 10.1080/21645515.2015.1122146] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Attenuated measles virus (MV) is one of the most effective and safe vaccines available, making it attractive candidate vector to prevent infectious diseases. Attenuated MV have acquired the ability to use the complement regulator CD46 as a major receptor to mediate virus entry and intercellular fusion. Therefore, attenuated MV strains preferentially infect and destroy a wide variety of cancer cells making them also attractive oncolytic vectors. The use of recombinant MV vector has to comply with various regulatory requirements, particularly relating to the assessment of potential risks for human health and the environment. The present article highlights the main characteristics of MV and recombinant MV vectors used for vaccination and virotherapy and discusses these features from a biosafety point of view.
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Affiliation(s)
- Aline Baldo
- a Scientific Institute of Public Health (WIV-ISP), Biosafety and Biotechnology Unit , Brussels , Belgium
| | - Evanthia Galanis
- b Division of Medical Oncology , Mayo Clinic , Rochester , MN , USA
| | - Frédéric Tangy
- c Institut Pasteur, Viral Genomics and Vaccination Unit, CNRS UMR 3569 , Paris , France
| | - Philippe Herman
- a Scientific Institute of Public Health (WIV-ISP), Biosafety and Biotechnology Unit , Brussels , Belgium
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18
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Muñoz-Alía MÁ, Fernández-Muñoz R, Casasnovas JM, Porras-Mansilla R, Serrano-Pardo Á, Pagán I, Ordobás M, Ramírez R, Celma ML. Measles virus genetic evolution throughout an imported epidemic outbreak in a highly vaccinated population. Virus Res 2014; 196:122-7. [PMID: 25445338 DOI: 10.1016/j.virusres.2014.11.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 11/11/2014] [Accepted: 11/12/2014] [Indexed: 11/25/2022]
Abstract
Measles virus circulates endemically in African and Asian large urban populations, causing outbreaks worldwide in populations with up-to-95% immune protection. We studied the natural genetic variability of genotype B3.1 in a population with 95% vaccine coverage throughout an imported six month measles outbreak. From first pass viral isolates of 47 patients we performed direct sequencing of genomic cDNA. Whilst no variation from index case sequence occurred in the Nucleocapsid gene hyper-variable carboxy end, in the Hemagglutinin gene, main target for neutralizing antibodies, we observed gradual nucleotide divergence from index case along the outbreak (0% to 0.380%, average 0.138%) with the emergence of transient and persistent non-synonymous and synonymous mutations. Little or no variation was observed between the index and last outbreak cases in Phosphoprotein, Nucleocapsid, Matrix and Fusion genes. Most of the H non-synonymous mutations were mapped on the protein surface near antigenic and receptors binding sites. We estimated a MV-Hemagglutinin nucleotide substitution rate of 7.28 × 10-6 substitutions/site/day by a Bayesian phylogenetic analysis. The dN/dS analysis did not suggest significant immune or other selective pressures on the H gene during the outbreak. These results emphasize the usefulness of MV-H sequence analysis in measles epidemiological surveillance and elimination programs, and in detection of potentially emergence of measles virus neutralization-resistant mutants.
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Affiliation(s)
- Miguel Ángel Muñoz-Alía
- Virology Unit and National Reference Laboratory for Measles, Ramón y Cajal Hospital, Madrid, Spain
| | - Rafael Fernández-Muñoz
- Virology Unit and National Reference Laboratory for Measles, Ramón y Cajal Hospital, Madrid, Spain.
| | - José María Casasnovas
- Centro Nacional de Biotecnología, Laboratorio de Estructura de Proteínas. CSIC, Cantoblanco, Madrid, Spain
| | - Rebeca Porras-Mansilla
- Virology Unit and National Reference Laboratory for Measles, Ramón y Cajal Hospital, Madrid, Spain
| | - Ángela Serrano-Pardo
- Virology Unit and National Reference Laboratory for Measles, Ramón y Cajal Hospital, Madrid, Spain
| | - Israel Pagán
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and ETSI Agrónomos, Campus Montegancedo, Madrid, Spain
| | - María Ordobás
- Epidemiology Service, Madrid Health Ministry, Madrid, Spain
| | - Rosa Ramírez
- Epidemiology Service, Madrid Health Ministry, Madrid, Spain
| | - María Luisa Celma
- Virology Unit and National Reference Laboratory for Measles, Ramón y Cajal Hospital, Madrid, Spain
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19
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Wild-type measles viruses with non-standard genome lengths. PLoS One 2014; 9:e95470. [PMID: 24748123 PMCID: PMC3991672 DOI: 10.1371/journal.pone.0095470] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 03/27/2014] [Indexed: 12/13/2022] Open
Abstract
The length of the single stranded, negative sense RNA genome of measles virus (MeV) is highly conserved at 15,894 nucleotides (nt). MeVs can be grouped into 24 genotypes based on the highly variable 450 nucleotides coding for the carboxyl-terminus of the nucleocapsid protein (N-450). Here, we report the genomic sequences of 2 wild-type viral isolates of genotype D4 with genome lengths of 15,900 nt. Both genomes had a 7 nt insertion in the 3′ untranslated region (UTR) of the matrix (M) gene and a 1 nt deletion in the 5′ UTR of the fusion (F) gene. The net gain of 6 nt complies with the rule-of-six required for replication competency of the genomes of morbilliviruses. The insertions and deletion (indels) were confirmed in a patient sample that was the source of one of the viral isolates. The positions of the indels were identical in both viral isolates, even though epidemiological data and the 3 nt differences in N-450 between the two genomes suggested that the viruses represented separate chains of transmission. Identical indels were found in the M-F intergenic regions of 14 additional genotype D4 viral isolates that were imported into the US during 2007–2010. Viral isolates with and without indels produced plaques of similar size and replicated efficiently in A549/hSLAM and Vero/hSLAM cells. This is the first report of wild-type MeVs with genome lengths other than 15,894 nt and demonstrates that the length of the M-F UTR of wild-type MeVs is flexible.
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Abstract
INTRODUCTION The measles virus is a major human pathogen responsible for approximately 150,000 deaths annually. The disease is vaccine preventable and eradication of the virus is considered feasible, in principle. However, a herd immunity exceeding 95% is required to prevent sporadic viral outbreaks in a population. Declining disease prevalence, combined with public anxiety over the vaccination's safety, has led to increased vaccine refusal, especially in Europe. This has led to the resurgence of measles in some areas. AREAS COVERED This article discusses whether synergizing effective measles therapeutics with the measles vaccination could contribute to finally eradicating measles. The authors identify key elements in a desirable drug profile and review current disease management strategies and the state of experimental inhibitor candidates. The authors also evaluate the risk associated with viral escape from inhibition, and consider the potential of measles therapeutics in the management of persistent central nervous system (CNS) viral infection. Finally, the authors contemplate the possible impact of therapeutics in controlling the threat imposed by closely related zoonotic pathogens of the same genus as measles. EXPERT OPINION Efficacious therapeutics used for post-exposure prophylaxis of high-risk social contacts of confirmed index cases may aid measles eradication by closing herd immunity gaps; this is due to vaccine refusal or failure in populations with overall good vaccination coverage. The envisioned primarily prophylactic application of measles therapeutics to a predominantly pediatric and/or adolescent population, dictates the drug profile. It also has to be safe and efficacious, orally available, shelf-stable at ambient temperature and amenable to cost-effective manufacturing.
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Affiliation(s)
- Richard K Plemper
- Georgia State University, Center for Inflammation, Immunity & Infection, Petit Science Center, 712 100 Piedmont Av, Atlanta, GA 30303 , USA +1 404 413 3579 ;
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21
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Cell tropism predicts long-term nucleotide substitution rates of mammalian RNA viruses. PLoS Pathog 2014; 10:e1003838. [PMID: 24415935 PMCID: PMC3887100 DOI: 10.1371/journal.ppat.1003838] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 11/04/2013] [Indexed: 02/05/2023] Open
Abstract
The high rates of RNA virus evolution are generally attributed to replication with error-prone RNA-dependent RNA polymerases. However, these long-term nucleotide substitution rates span three orders of magnitude and do not correlate well with mutation rates or selection pressures. This substitution rate variation may be explained by differences in virus ecology or intrinsic genomic properties. We generated nucleotide substitution rate estimates for mammalian RNA viruses and compiled comparable published rates, yielding a dataset of 118 substitution rates of structural genes from 51 different species, as well as 40 rates of non-structural genes from 28 species. Through ANCOVA analyses, we evaluated the relationships between these rates and four ecological factors: target cell, transmission route, host range, infection duration; and three genomic properties: genome length, genome sense, genome segmentation. Of these seven factors, we found target cells to be the only significant predictors of viral substitution rates, with tropisms for epithelial cells or neurons (P<0.0001) as the most significant predictors. Further, one-tailed t-tests showed that viruses primarily infecting epithelial cells evolve significantly faster than neurotropic viruses (P<0.0001 and P<0.001 for the structural genes and non-structural genes, respectively). These results provide strong evidence that the fastest evolving mammalian RNA viruses infect cells with the highest turnover rates: the highly proliferative epithelial cells. Estimated viral generation times suggest that epithelial-infecting viruses replicate more quickly than viruses with different cell tropisms. Our results indicate that cell tropism is a key factor in viral evolvability. RNA viruses are the fastest evolving human pathogens, making their treatment and control difficult. Compared to DNA viruses, RNA viruses replicate with much lower fidelity, which can explain why RNA viruses evolve significantly faster than most DNA viruses. However, there is tremendous variation among the evolutionary rates of different RNA viruses, which is not explained by variation in mutation rates. Here we present a survey of mammalian RNA virus rates of evolution, and a comprehensive comparison of these rates to different properties of virus genomic architecture and ecology. We found that cell tropism is the most significant predictor of long-term rates of mammalian RNA virus evolution. For instance, viruses targeting epithelial cells evolve significantly faster than viruses that target neurons. Our results provide mechanistic insight into why viruses that infect respiratory and gastrointestinal epithelia have been difficult to control.
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