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Gazali FM, Wijayanti N, Hakim MS, Supriyati E, Arguni E, Daniwijaya MEW, Nuryastuti T, Nuhamunada M, Nabilla R, Haryana SM, Wibawa T. The high mutation rate at the D614G hotspot-furin cleavage site region increases the priming efficiency of the Spike protein by furin protease: analysis of Indonesian SARS-CoV-2 G614 variants obtained during the early COVID-19 pandemic. Virusdisease 2023:1-10. [PMID: 37363361 PMCID: PMC10231289 DOI: 10.1007/s13337-023-00827-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 05/08/2023] [Indexed: 06/28/2023] Open
Abstract
D614G mutation plays a significant role in the transmissibility of SARS-CoV-2. Identification of other mutations related to D614G mutation within the Spike protein is pivotal as they might contribute to the pathogenicity of SARS-CoV-2. This study aims to analyze the mutation rate of furin cleavage site (FCS) region of Indonesian origin SARS-CoV-2 and to predict the effect of mutation against Spike priming efficiency by furin. A total of 375 sequences of Indonesian isolates obtained during the early pandemic were used for mutation analysis. Mutation analysis includes mutation pattern, variability, frequency of mutation, amino acid conservation, and mutation rate. The effect of mutation against Spike priming efficiency by furin protease from eight sequences with mutation in the FCS region was analyzed by protein-protein docking. We showed that mutations related to the G614 variant were increasing through time, in contrast to the D614 variant. The FCS region at the position 675-692 contained the most variable (66.67%) as well as the highest mutation frequency (85.92%) and has been observed to be the hotspot mutations linked to the D614G mutation. The D614G hotspot-FCS region (residue 600-700) had the highest amino acid change per site (20.8%) as well as the highest mutation rate as 1.34 × 10-2 substitution per site per year (95% CI 1.79 × 10-3-2.74 × 10-2), compared with other Spike protein regions. Mutations in the FCS region were the most common mutation found after the D614G mutation. These mutations were predicted to increase the Spike priming efficiency by furin. Thus, this study elucidates the importance of D614G mutation to other mutations located in the FCS region and their significance to Spike priming efficiency by furin. Supplementary Information The online version contains supplementary material available at 10.1007/s13337-023-00827-w.
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Affiliation(s)
- Faris Muhammad Gazali
- Master Program in Biotechnology, Postgraduate School, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Nastiti Wijayanti
- Animal Physiology Laboratory, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Mohamad Saifudin Hakim
- Department of Microbiology, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Endah Supriyati
- Centre for Tropical Medicine, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Eggi Arguni
- Department of Child Health, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | - Titik Nuryastuti
- Department of Microbiology, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Matin Nuhamunada
- Biotechnology Laboratory, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Rahma Nabilla
- Graduate Program in Biology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Sofia Mubarika Haryana
- Department of Histology and Cell Biology, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tri Wibawa
- Department of Microbiology, Faculty of Medicine Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
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2
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Cui X, Li Y, Yang Y, Tang W, Li Z, Chen H, Li Y, Cui X, Huang Z, Sun X, Xu S, Zhang Y, Li C, Zhang X. Characteristics and Genomic Diversity of Measles Virus From Measles Cases With Known Vaccination Status in Shanghai, China. Front Med (Lausanne) 2022; 9:841650. [PMID: 35847814 PMCID: PMC9281471 DOI: 10.3389/fmed.2022.841650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Although the highly effective measles vaccine has dramatically reduced the incidence of measles, measles, and outbreaks continue to occur in individuals who received the measles vaccine because of immunization failure. In this study, patients who have definite records of immunization were enrolled based on measles surveillance in Shanghai, China, from 2009 to 2017, and genomic characteristics regarding viruses retrieved from these cases provided insights into immunization failure. A total of 147 complete genomes of measles virus (MV) were obtained from the laboratory-confirmed cases through Illumina MiSeq. Epidemiological, and genetic characteristics of the MV were focused on information about age, gender, immunization record, variation, and evolution of the whole genome. Furthermore, systematic genomics using phylogeny and selection pressure approaches were analyzed. Our analysis based on the whole genome of 147 isolates revealed 4 clusters: 2 for the genotype H1 (clusters named H1-A, including 73 isolates; H1-B, including 72 isolates) and the other 2 for D8 and B3, respectively. Estimated nucleotide substitution rates of genotype H1 MV derived using genome and individual genes are lower than other genotypes. Our study contributes to global measles epidemiology and proves that whole-genome sequencing was a useful tool for more refined genomic characterization. The conclusion indicates that vaccination may have an effect on virus evolution. However, no major impact was found on the antigenicity in Shanghai isolates.
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Affiliation(s)
- Xiaoxian Cui
- Division of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Yunyi Li
- Division of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Yuying Yang
- Division of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Wei Tang
- Division of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Zhi Li
- Department of Immunization Program, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Hongyou Chen
- Division of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Yang Li
- Chongqing School, University of Chinese Academy of Sciences, Chongqing, China
| | - Xinyi Cui
- Division of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Zhuoying Huang
- Department of Immunization Program, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Xiaodong Sun
- Department of Immunization Program, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Songtao Xu
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yan Zhang
- National Health Commission (NHC) Key Laboratory of Medical Virology and Viral Diseases, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Chongshan Li
- Division of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Xi Zhang
- Division of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
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3
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Yuan C, Wang C, Zhu K, Li S, Miao Z. Measles Epidemiology and Viral Nucleoprotein Gene Evolution in Shandong Province, China. J Med Virol 2022; 94:4926-4933. [PMID: 35711081 DOI: 10.1002/jmv.27941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/18/2022] [Accepted: 06/14/2022] [Indexed: 11/07/2022]
Abstract
Measles, caused by measles virus (MeV), has not been eradicated in many regions and countries, threatening human health. Thus, it is beneficial for measles elimination to understand measles epidemiology and molecular evolution of key viral genes, such as nucleoprotein (N) gene. Based on public data, measles epidemiological information and MeV N gene sequences reported in Shandong Province, China were comprehensively collected and systematically analyzed. The results showed a positive correlation between population density and measles incidence (r = + 0.31), while negative correlations were found between measles incidence and healthcare condition (r = - 0.21) as well as average routine vaccination rate (r = - 0.11). Additionally, the predominant lineage of MeV in Shandong was formed by genotype H1 strains, and the time of the most recent common ancestor of the N gene of MeV genotype H1 in Shandong traced back to 1987 (95% highest posterior density, 1984-1990) with relatively rapid evolution (mean rate, 1.267×10-3 substitutions/site/year). The genetic diversity of MeV N gene increased with the substantial emergence of major divergent clades of genotype H1 before 2005 and then remained relatively stable. In summary, these findings provided a significant insight into the measles elimination. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Chuang Yuan
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230026, China.,School of Life Sciences, Shandong First Medical University, Tai'an, Shandong, 271000, China
| | - Cheng Wang
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Shandong, 250002, China.,National Institute of Health Data Science of China, Shandong University, Shandong, 250002, China
| | - Kongfu Zhu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Song Li
- School of Basic Medicine, Shandong First Medical University, Tai'an, Shandong, 271000, China
| | - Zengmin Miao
- School of Life Sciences, Shandong First Medical University, Tai'an, Shandong, 271000, China
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4
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Zhou N, Li M, Huang Y, Zhou L, Wang B. Genetic Characterizations and Molecular Evolution of the Measles Virus Genotype B3's Hemagglutinin (H) Gene in the Elimination Era. Viruses 2021; 13:1970. [PMID: 34696400 PMCID: PMC8540759 DOI: 10.3390/v13101970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/10/2021] [Accepted: 09/26/2021] [Indexed: 12/18/2022] Open
Abstract
Measles virus (MeV) genotype B3 is one globally significant circulating genotype. Here, we present a systematic description of long-term evolutionary characterizations of the MeV genotype B3's hemagglutinin (H) gene in the elimination era. Our results show that the B3 H gene can be divided into two main sub-genotypes, and the highest intra-genotypic diversity was observed in 2004. MeV genotype B3's H gene diverged in 1976; its overall nucleotide substitution rate is estimated to be 5.697 × 10-4 substitutions/site/year, and is slowing down. The amino acid substitution rate of genotype B3's H gene is also decreasing, and the mean effective population size has been in a downward trend since 2000. Selection pressure analysis only recognized a few sites under positive selection, and the number of positive selection sites is getting smaller. All of these observations may reveal that genotype B3's H gene is not under strong selection pressure, and is becoming increasingly conservative. MeV H-gene or whole-genome sequencing should be routine, so as to better elucidate the molecular epidemiology of MeV in the future.
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Affiliation(s)
- Nan Zhou
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China; (N.Z.); (M.L.); (Y.H.)
| | - Mingma Li
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China; (N.Z.); (M.L.); (Y.H.)
| | - Yue Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China; (N.Z.); (M.L.); (Y.H.)
| | - Lu Zhou
- Jiangsu Provincial Center for Disease Control and Prevention, Department of Acute Infectious Diseases, Nanjing 210009, China;
| | - Bei Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China; (N.Z.); (M.L.); (Y.H.)
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5
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Fall A, Elawar F, Hodcroft EB, Jallow MM, Toure CT, Barry MA, Kiori DE, Sy S, Diaw Y, Goudiaby D, Niang MN, Dia N. Genetic diversity and evolutionary dynamics of respiratory syncytial virus over eleven consecutive years of surveillance in Senegal. INFECTION GENETICS AND EVOLUTION 2021; 91:104864. [PMID: 33866019 DOI: 10.1016/j.meegid.2021.104864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 04/07/2021] [Accepted: 04/12/2021] [Indexed: 11/18/2022]
Affiliation(s)
- Amary Fall
- Virology Department, Institute Pasteur of Dakar, Senegal.
| | - Farah Elawar
- Li Ka Shing Institute of Virology, Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada.
| | - Emma B Hodcroft
- Biozentrum, University of Basel, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland.
| | - Mamadou Malado Jallow
- Virology Department, Institute Pasteur of Dakar, Senegal; University Cheikh Anta Diop of Dakar, Senegal.
| | - Cheikh Talibouya Toure
- Virology Department, Institute Pasteur of Dakar, Senegal; University Cheikh Anta Diop of Dakar, Senegal.
| | - Mamadou A Barry
- Unit Epidemiology of Infectious Diseases, Institute Pasteur of Dakar, Senegal.
| | | | - Sara Sy
- Virology Department, Institute Pasteur of Dakar, Senegal.
| | - Yague Diaw
- Virology Department, Institute Pasteur of Dakar, Senegal.
| | | | | | - Ndongo Dia
- Virology Department, Institute Pasteur of Dakar, Senegal.
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6
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Stepien CA, Niner MD. Evolutionary trajectory of fish Piscine novirhabdovirus (=Viral Hemorrhagic Septicemia Virus) across its Laurentian Great Lakes history: Spatial and temporal diversification. Ecol Evol 2020; 10:9740-9775. [PMID: 33005343 PMCID: PMC7520192 DOI: 10.1002/ece3.6611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/04/2020] [Accepted: 05/10/2020] [Indexed: 02/05/2023] Open
Abstract
Piscine novirhabdovirus = Viral Hemorrhagic Septicemia Virus (VHSV) first appeared in the Laurentian Great Lakes with large outbreaks from 2005 to 2006, as a new and novel RNA rhabdovirus subgenogroup (IVb) that killed >30 fish species. Interlude periods punctuated smaller more localized outbreaks in 2007, 2010, and 2017, although some fishes tested positive in the intervals. There have not been reports of outbreaks or positives from 2018, 2019, or 2020. Here, we employ a combined population genetics and phylogenetic approach to evaluate spatial and temporal evolutionary trajectory on its G-gene sequence variation, in comparison with whole-genome sequences (11,083 bp) from a subset of 44 individual isolates (including 40 newly sequenced ones). Our results show that IVb (N = 184 individual fish isolates) diversified into 36 G-gene haplotypes from 2003 to 2017, stemming from two originals ("a" and "b"). G-gene haplotypes "a" and "b" differed by just one synonymous single-nucleotide polymorphism (SNP) substitution, remained the most abundant until 2011, then disappeared. Group "a" descendants (14 haplotypes) remained most prevalent in the Upper and Central Great Lakes, with eight (51%) having nonsynonymous substitutions. Group "b" descendants primarily have occurred in the Lower Great Lakes, including 22 haplotypes, of which 15 (68%) contained nonsynonymous changes. Evolutionary patterns of the whole-genome sequences (which had 34 haplotypes among 44 isolates) appear congruent with those from the G-gene. Virus populations significantly diverged among the Upper, Central, and Lower Great Lakes, diversifying over time. Spatial divergence was apparent in the overall patterns of nucleotide substitutions, while amino acid changes increased temporally. VHSV-IVb thus significantly differentiated across its less than two decades in the Great Lakes, accompanied by declining outbreaks and virulence. Continuing diversification likely allowed the virus to persist at low levels in resident fish populations, and may facilitate its potential for further and future spread to new habitats and nonacclimated hosts.
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Affiliation(s)
- Carol A. Stepien
- Genetics and Genomics Group (G3)NOAA Pacific Marine Environmental Laboratory (PMEL)SeattleWAUSA
| | - Megan D. Niner
- Genetics and Genomics Group (G3), Department of Environmental SciencesUniversity of ToledoToledoOHUSA
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7
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Düx A, Lequime S, Patrono LV, Vrancken B, Boral S, Gogarten JF, Hilbig A, Horst D, Merkel K, Prepoint B, Santibanez S, Schlotterbeck J, Suchard MA, Ulrich M, Widulin N, Mankertz A, Leendertz FH, Harper K, Schnalke T, Lemey P, Calvignac-Spencer S. Measles virus and rinderpest virus divergence dated to the sixth century BCE. Science 2020; 368:1367-1370. [PMID: 32554594 DOI: 10.1126/science.aba9411] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/30/2020] [Indexed: 12/11/2022]
Abstract
Many infectious diseases are thought to have emerged in humans after the Neolithic revolution. Although it is broadly accepted that this also applies to measles, the exact date of emergence for this disease is controversial. We sequenced the genome of a 1912 measles virus and used selection-aware molecular clock modeling to determine the divergence date of measles virus and rinderpest virus. This divergence date represents the earliest possible date for the establishment of measles in human populations. Our analyses show that the measles virus potentially arose as early as the sixth century BCE, possibly coinciding with the rise of large cities.
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Affiliation(s)
- Ariane Düx
- Epidemiology of Highly Pathogenic Microorganisms Project Group, Robert Koch Institute, Berlin, Germany.,Viral Evolution Project Group, Robert Koch Institute, Berlin, Germany
| | - Sebastian Lequime
- Laboratory of Clinical and Evolutionary Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Livia Victoria Patrono
- Epidemiology of Highly Pathogenic Microorganisms Project Group, Robert Koch Institute, Berlin, Germany.,Viral Evolution Project Group, Robert Koch Institute, Berlin, Germany
| | - Bram Vrancken
- Laboratory of Clinical and Evolutionary Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Sengül Boral
- Institute for Pathology, Charité, Berlin, Germany
| | - Jan F Gogarten
- Epidemiology of Highly Pathogenic Microorganisms Project Group, Robert Koch Institute, Berlin, Germany.,Viral Evolution Project Group, Robert Koch Institute, Berlin, Germany
| | - Antonia Hilbig
- Epidemiology of Highly Pathogenic Microorganisms Project Group, Robert Koch Institute, Berlin, Germany
| | - David Horst
- Institute for Pathology, Charité, Berlin, Germany
| | - Kevin Merkel
- Epidemiology of Highly Pathogenic Microorganisms Project Group, Robert Koch Institute, Berlin, Germany.,Viral Evolution Project Group, Robert Koch Institute, Berlin, Germany
| | - Baptiste Prepoint
- Viral Evolution Project Group, Robert Koch Institute, Berlin, Germany.,Département de Biologie, Ecole Normale Supérieure, PSL Université Paris, Paris, France
| | - Sabine Santibanez
- National Reference Centre for Measles, Mumps, and Rubella, Robert Koch Institute, Berlin, Germany
| | | | - Marc A Suchard
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Markus Ulrich
- Epidemiology of Highly Pathogenic Microorganisms Project Group, Robert Koch Institute, Berlin, Germany
| | - Navena Widulin
- Berlin Museum of Medical History, Charité, Berlin, Germany
| | - Annette Mankertz
- National Reference Centre for Measles, Mumps, and Rubella, Robert Koch Institute, Berlin, Germany
| | - Fabian H Leendertz
- Epidemiology of Highly Pathogenic Microorganisms Project Group, Robert Koch Institute, Berlin, Germany
| | - Kyle Harper
- Department of Classics and Letters, University of Oklahoma, Norman, OK, USA
| | | | - Philippe Lemey
- Laboratory of Clinical and Evolutionary Virology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit (KU) Leuven, Leuven, Belgium
| | - Sébastien Calvignac-Spencer
- Epidemiology of Highly Pathogenic Microorganisms Project Group, Robert Koch Institute, Berlin, Germany. .,Viral Evolution Project Group, Robert Koch Institute, Berlin, Germany
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8
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Vaidya SR, Kasibhatla SM, Bhattad DR, Ramtirthkar MR, Kale MM, Raut CG, Kulkarni-Kale U. Characterization of diversity of measles viruses in India: Genomic sequencing and comparative genomics studies. J Infect 2020; 80:301-309. [DOI: 10.1016/j.jinf.2019.11.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 11/29/2019] [Accepted: 11/30/2019] [Indexed: 10/25/2022]
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9
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Dou Y, Liang Z, Prajapati M, Zhang R, Li Y, Zhang Z. Expanding Diversity of Susceptible Hosts in Peste Des Petits Ruminants Virus Infection and Its Potential Mechanism Beyond. Front Vet Sci 2020; 7:66. [PMID: 32181263 PMCID: PMC7059747 DOI: 10.3389/fvets.2020.00066] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/27/2020] [Indexed: 01/12/2023] Open
Abstract
Peste des petits ruminants (PPR) is a severe respiratory and digestive tract disease of domestic small ruminants caused by PPR virus (PPRV) of the genus Morbillivirus. Although the primary hosts of PPRV are goats and sheep, the host range of PPRV has been continuously expanding and reported to infect various animal hosts over the last decades, which could bring a potential challenge to effectively control and eradicate PPR globally. In this review, we focused on current knowledge about host expansion and interspecies infection of PPRV and discussed the potential mechanisms involved.
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Affiliation(s)
- Yongxi Dou
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Lanzhou, China.,CAAS-ILRI Joint Laboratory for Ruminant Disease Control, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Lanzhou, China
| | - Zhongxiang Liang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Lanzhou, China
| | - Meera Prajapati
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Lanzhou, China.,CAAS-ILRI Joint Laboratory for Ruminant Disease Control, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Lanzhou, China.,Animal Health Research Division, Nepal Agricultural Research Council, Lalitpur, Nepal
| | - Rui Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Lanzhou, China
| | - Yanmin Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Lanzhou, China
| | - Zhidong Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Lanzhou, China.,CAAS-ILRI Joint Laboratory for Ruminant Disease Control, Lanzhou Veterinary Research Institute, Chinese Academy of Agriculture Sciences, Lanzhou, China.,College of Life Science and Technology, Southwest Minzu University, Chengdu, China
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10
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Yoshihara K, Minh LN, Okada T, Toizumi M, Nguyen HA, Vo HM, Hashizume M, Dang DA, Kimura H, Yoshida LM. Evolutionary dynamics of influenza B strains detected from paediatric acute respiratory infections in central Vietnam. INFECTION GENETICS AND EVOLUTION 2020; 81:104264. [PMID: 32105864 DOI: 10.1016/j.meegid.2020.104264] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/07/2020] [Accepted: 02/22/2020] [Indexed: 11/28/2022]
Abstract
Influenza virus B belongs to the family Orthomyxoviridae with segmented negative-sense RNA genomes. Since 1970s, influenza B has diverged intoVictoria and Yamagata, which differs in antigenic and evolutionary characteristics. Yet, molecular-epidemiological information of influenza B from developing nations is limited. In central Vietnam, influenza A subtype-specific circulation pattern and clinical characteristics were previously described. However, molecular evolutionary characteristics of influenza B has not been discussed to date. We utilized the influenza B positives obtained from paediatric ARI surveillance during 2007-2013. Influenza B HA and NA genes were amplified, sequenced, and phylogenetic/molecular evolutionary analysis was performed using Maximum Likelihood and Bayesian MCMC. Phylodynamics analysis was performed with Bayesian Skyline Plot (BSP). Furthermore, we performed selection pressure analysis and estimated N-glycosylation sites. In the current study, overall positive rate for influenza B was 3.0%, and Victoria lineage immediately became predominant in post-A/H1N1pdm09 period. The noticeable shift in Victoria lineage WHO Group occurred. With respect to the evolutionary rate (substitutions/site/year), Victoria lineage HA gene was evolving faster than Yamagata lineage (2.43 × 10-3 vs 2.00 × 10-3). Furthermore, the evolutionary rate of Victoria Group 5 was greater than Group 1. BSP presented the rapid growth in Effective Population Size (EPS) of Victoria lineage occurred soon after the 1st A/H1N1pdm09 case was detected whereas the EPS of Yamagata lineage was stable for both genes. N-glycosylation pattern between lineages and among WHO Groups were slightly different, and HA gene had a total of 6 amino acid substitutions under positive section pressure (4 for Victoria and 2 for Yamagata). The current results highlight the importance of Victoria lineage in post-A/H1N1pdm09 period. Difference in evolutionary characteristics and phylodynamics may indicate lineage and WHO Group-specific evolutionary dynamics. It is necessary to further continue the molecular-epidemiological surveillance in local setting to gain a better understanding of local evolutionary characteristics of influenza B strains.
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Affiliation(s)
- Keisuke Yoshihara
- Department of Paediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
| | - Le Nhat Minh
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Viet Nam
| | - Takashi Okada
- Department of Paediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
| | - Michiko Toizumi
- Department of Paediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
| | - Hien Anh Nguyen
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Viet Nam
| | - Hien Minh Vo
- Department of Paediatrics, Khanh Hoa General Hospital, Nha Trang 650000, Viet Nam
| | - Masahiro Hashizume
- Department of Paediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
| | - Duc Anh Dang
- National Institute of Hygiene and Epidemiology, Hanoi 100000, Viet Nam
| | - Hirokazu Kimura
- School of Medical Technology, Gunma Paz University, Takasaki-shi, Gunma, 370-0006, Japan
| | - Lay-Myint Yoshida
- Department of Paediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan.
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11
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Azarm KD, Lee B. Differential Features of Fusion Activation within the Paramyxoviridae. Viruses 2020; 12:v12020161. [PMID: 32019182 PMCID: PMC7077268 DOI: 10.3390/v12020161] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/25/2020] [Accepted: 01/29/2020] [Indexed: 12/13/2022] Open
Abstract
Paramyxovirus (PMV) entry requires the coordinated action of two envelope glycoproteins, the receptor binding protein (RBP) and fusion protein (F). The sequence of events that occurs during the PMV entry process is tightly regulated. This regulation ensures entry will only initiate when the virion is in the vicinity of a target cell membrane. Here, we review recent structural and mechanistic studies to delineate the entry features that are shared and distinct amongst the Paramyxoviridae. In general, we observe overarching distinctions between the protein-using RBPs and the sialic acid- (SA-) using RBPs, including how their stalk domains differentially trigger F. Moreover, through sequence comparisons, we identify greater structural and functional conservation amongst the PMV fusion proteins, as compared to the RBPs. When examining the relative contributions to sequence conservation of the globular head versus stalk domains of the RBP, we observe that, for the protein-using PMVs, the stalk domains exhibit higher conservation and find the opposite trend is true for SA-using PMVs. A better understanding of conserved and distinct features that govern the entry of protein-using versus SA-using PMVs will inform the rational design of broader spectrum therapeutics that impede this process.
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12
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Aso J, Kimura H, Ishii H, Saraya T, Kurai D, Nagasawa K, Matsushima Y, Ryo A, Takizawa H. Molecular evolution of the hemagglutinin-neuraminidase (HN) gene in human respirovirus 3. Virus Res 2019; 277:197824. [PMID: 31783038 DOI: 10.1016/j.virusres.2019.197824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 11/08/2019] [Accepted: 11/25/2019] [Indexed: 12/15/2022]
Abstract
Human respirovirus 3 (HRV3) is a major causative agent of acute respiratory infections in humans. HRV3 can manifest as a recurrent infection, although exactly how is not known. In the present study, we conducted detailed molecular evolutionary analyses of the major antigen-coding hemagglutinin-neuraminidase (HN) gene of this virus detected/isolated in various countries. We performed analyses of time-scaled evolution, similarity, selective pressure, phylodynamics, and conformational epitope prediction by mapping to HN protein models. In this way, we estimated that a common ancestor of the HN gene of HRV3 and bovine respirovirus 3 diverged around 1815 and formed many lineages in the phylogenetic tree. The evolutionary rates of the HN gene were 1.1 × 10-3 substitutions/site/year, although the majority of these substitutions were synonymous. Some positive and many negative selection sites were predicted in the HN protein. Phylodynamic fluctuations of the gene were observed, and these were different in each lineage. Furthermore, most of the predicted B cell epitopes did not correspond to the neutralization-related mouse monoclonal antibody binding sites. The lack of a link between the conformational epitopes and neutralization sites may explain the naturally occurring HRV3 reinfection.
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Affiliation(s)
- Jumpei Aso
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Hirokazu Kimura
- Department of Health Science, Gunma Paz University Graduate School of Health Science, Gunma, Japan; Department of Microbiology, Yokohama City University School of Medicine, Kanagawa, Japan.
| | - Haruyuki Ishii
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Takeshi Saraya
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Daisuke Kurai
- Department of General Medicine, Division of Infectious Diseases, Kyorin University School of Medicine, Tokyo, Japan
| | - Koo Nagasawa
- Department of Pediatrics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Yuki Matsushima
- Division of Virology, Kawasaki City Institute for Public Health, Kanagawa, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University School of Medicine, Kanagawa, Japan
| | - Hajime Takizawa
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
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13
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Ciceri G, Canuti M, Bianchi S, Gori M, Piralla A, Colzani D, Libretti M, Frati ER, Baggieri M, Lai A, Rovida F, Zehender G, Baldanti F, Magurano F, Tanzi E, Amendola A. Genetic variability of the measles virus hemagglutinin gene in B3 genotype strains circulating in Northern Italy. INFECTION GENETICS AND EVOLUTION 2019; 75:103943. [PMID: 31255832 DOI: 10.1016/j.meegid.2019.103943] [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] [Received: 03/01/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 11/18/2022]
Abstract
Sequencing the whole measles virus hemagglutinin (H) gene, in conjunction with a 450-nucleotide region of the nucleoprotein gene (N-450), is helpful for the identification of new genotypes and as an auxiliary in outbreak characterization. In addition, it is essential to be able to predict the antigenic changes of the H protein to gain a better monitoring of the response to the vaccine. In this study, we obtained the full-length H gene sequences from 19 measles virus (MV) strains belonging to two B3 genotype variants circulating in Lombardy (Northern Italy) between July 2015 and February 2016 and evaluated the variability of the whole MV-H gene. Furthermore, we compared the obtained H amino acid sequences to all MV sequences available in the GenBank database (n = 1152 in total) and analyzed the amino acid substitutions in the H protein within clades where the Italian strains were included. We identified a higher variability in the H gene compared to the N-450 region and our results support previous studies, highlighting that the H gene is more informative for characterizing the MV B3 genotype than the N-450 sequence. Some of the amino acid substitutions were fixed in the viral population and, remarkably, some of the amino acid substitutions were typically present only in the Italian sequences. Accumulating further molecular information about MV-H gene will be necessary to enable in-depth analyses of the variability of this gene in the vaccinated population.
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Affiliation(s)
- G Ciceri
- Department of Biomedical Sciences for Health, University of Milan, via Carlo Pascal, 36, 20133 Milan, Italy.
| | - M Canuti
- Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John's, NL A1B 3X9, Canada
| | - S Bianchi
- Department of Biomedical Sciences for Health, University of Milan, via Carlo Pascal, 36, 20133 Milan, Italy.
| | - M Gori
- Department of Biomedical Sciences for Health, University of Milan, via Carlo Pascal, 36, 20133 Milan, Italy
| | - A Piralla
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, via Taramelli, 5, 27100 Pavia, Italy.
| | - D Colzani
- Department of Biomedical Sciences for Health, University of Milan, via Carlo Pascal, 36, 20133 Milan, Italy.
| | - M Libretti
- Department of Biomedical Sciences for Health, University of Milan, via Carlo Pascal, 36, 20133 Milan, Italy
| | - E R Frati
- Department of Biomedical Sciences for Health, University of Milan, via Carlo Pascal, 36, 20133 Milan, Italy
| | - M Baggieri
- Department of Infectious Parasitic and Immune-Mediated Diseases, National Reference Laboratory for Measles and Rubella, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy.
| | - A Lai
- Department of Biomedical and Clinical Sciences "Luigi Sacco", Section of Infectious Diseases, University of Milan, Via Gian Battista Grassi, 74, 20157 Milan, Italy.
| | - F Rovida
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, via Taramelli, 5, 27100 Pavia, Italy.
| | - G Zehender
- Department of Biomedical and Clinical Sciences "Luigi Sacco", Section of Infectious Diseases, University of Milan, Via Gian Battista Grassi, 74, 20157 Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, via Carlo Pascal, 36, 20133 Milan, Italy.
| | - F Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, via Taramelli, 5, 27100 Pavia, Italy.
| | - F Magurano
- Department of Infectious Parasitic and Immune-Mediated Diseases, National Reference Laboratory for Measles and Rubella, Istituto Superiore di Sanità, Viale Regina Elena, 299, 00161 Rome, Italy.
| | - E Tanzi
- Department of Biomedical Sciences for Health, University of Milan, via Carlo Pascal, 36, 20133 Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, via Carlo Pascal, 36, 20133 Milan, Italy.
| | - A Amendola
- Department of Biomedical Sciences for Health, University of Milan, via Carlo Pascal, 36, 20133 Milan, Italy; Coordinated Research Center "EpiSoMI", University of Milan, via Carlo Pascal, 36, 20133 Milan, Italy.
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14
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Ozaki K, Matsushima Y, Nagasawa K, Motoya T, Ryo A, Kuroda M, Katayama K, Kimura H. Molecular Evolutionary Analyses of the RNA-Dependent RNA Polymerase Region in Norovirus Genogroup II. Front Microbiol 2018; 9:3070. [PMID: 30619155 PMCID: PMC6305289 DOI: 10.3389/fmicb.2018.03070] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/28/2018] [Indexed: 12/13/2022] Open
Abstract
Noroviruses are the leading cause of viral gastroenteritis in humans across the world. RNA-dependent RNA polymerase (RdRp) plays a critical role in the replication of the viral genome. Although there have been some reports on a limited number of genotypes with respect to the norovirus evolution of the RdRp region, no comprehensive molecular evolution examination of the norovirus GII genotype has yet been undertaken. Therefore, we conducted an evolutionary analysis of the 25 genotypes of the norovirus GII RdRp region (full-length), collected globally using different bioinformatics technologies. The time-scaled phylogenetic tree, generated using the Bayesian Markov Chain Monte Carlo (MCMC) method, indicated that the common ancestor of GII diverged from GIV around 1443 CE [95% highest posterior density (HPD), 1336–1542]. The GII RdRp region emerged around 1731 CE (95% HPD, 1703–1757), forming three lineages. The evolutionary rate of the RdRp region of the norovirus GII strains was estimated at over 10−3 substitutions/site/year. The evolutionary rates were significantly distinct in each genotype. The composition of the phylogenetic distances differed among the strains for each genotype. Furthermore, we mapped the negative selection sites on the RdRp protein and many of these were predicted in the GII.P4 RdRp proteins. The phylodynamics of GII.P4, GII.P12, GII.P16, and GII.Pe showed that their effective population sizes increased during the period from 2003 to 2014. Our results cumulatively suggest that the RdRp region of the norovirus GII rapidly and uniquely evolved with a high divergence similar to that of the norovirus VP1 gene.
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Affiliation(s)
- Keita Ozaki
- Graduate School of Health Sciences, Gunma Paz University, Takasaki, Japan.,Niitaka Co., Ltd., Osaka, Japan
| | - Yuki Matsushima
- Division of Virology, Kawasaki City Institute for Public Health, Kawasaki, Japan
| | - Koo Nagasawa
- Department of Pediatrics, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takumi Motoya
- Ibaraki Prefectural Institute of Public Health, Mito, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection I, Kitasato Institute for Life Sciences Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Hirokazu Kimura
- Graduate School of Health Sciences, Gunma Paz University, Takasaki, Japan.,Department of Microbiology, Yokohama City University School of Medicine, Yokohama, Japan
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15
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Miyoshi M, Komagome R, Yamaguchi H, Ishida S, Nagano H, Okano M. Genetic characterization of hemagglutinin protein of measles viruses in Hokkaido district, Japan, 2006-2015. Microbiol Immunol 2018; 62:411-417. [PMID: 29687918 DOI: 10.1111/1348-0421.12594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 02/08/2018] [Accepted: 04/11/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Masahiro Miyoshi
- Hokkaido Institute of Public Health; North 19 West 12 Kita-ku Sapporo 060-0819 Japan
| | - Rika Komagome
- Hokkaido Institute of Public Health; North 19 West 12 Kita-ku Sapporo 060-0819 Japan
| | - Hiroki Yamaguchi
- Hokkaido Institute of Public Health; North 19 West 12 Kita-ku Sapporo 060-0819 Japan
| | - Setsuko Ishida
- Hokkaido Institute of Public Health; North 19 West 12 Kita-ku Sapporo 060-0819 Japan
| | - Hideki Nagano
- Hokkaido Institute of Public Health; North 19 West 12 Kita-ku Sapporo 060-0819 Japan
| | - Motohiko Okano
- Hokkaido Institute of Public Health; North 19 West 12 Kita-ku Sapporo 060-0819 Japan
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16
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Haider MSH, Khan WH, Deeba F, Ali S, Ahmed A, Naqvi IH, Dohare R, Alsenaidy HA, Alsenaidy AM, Broor S, Parveen S. BA9 lineage of respiratory syncytial virus from across the globe and its evolutionary dynamics. PLoS One 2018; 13:e0193525. [PMID: 29694383 PMCID: PMC5919079 DOI: 10.1371/journal.pone.0193525] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 02/13/2018] [Indexed: 11/29/2022] Open
Abstract
Respiratory syncytial virus (RSV) is an important pathogen of global significance. The BA9 is one of the most predominant lineages of the BA genotype of group B RSV that has acquired a 60bp duplication in its G protein gene. We describe the local and global evolutionary dynamics of the second hyper variable region in the C- terminal of the G protein gene of the BA9 lineage. A total of 418 sequences (including 31 study and 387 GenBank strains) from 29 different countries were used for phylogenetic analysis. This analysis showed that the study strains clustered with BA (BA9 and BA8) and SAB4 genotype of group B RSV. We performed time-scaled evolutionary clock analyses using Bayesian Markov chain Monte Carlo methods. We also carried out glycosylation, selection pressure, mutational, entropy and Network analyses of the BA9 lineage. The time to the most recent common ancestor (tMRCA) of the BA genotype and BA9 lineage were estimated to be the years 1995 (95% HPD; 1987–1997) and 2000 (95% HPD; 1998–2001), respectively. The nucleotide substitution rate of the BA genotype [(4.58×10−3 (95% HPD; 3.89–5.29×10−3) substitution/site/year] was slightly faster than the BA9 lineage [4.03×10−3 (95% HPD; 4.65–5.2492×10−3)]. The BA9 lineage was categorized into 3 sub lineages (I, II and III) based on the Bayesian and Network analyses. The local transmission pattern suggested that BA9 is the predominant lineage of BA viruses that has been circulating in India since 2002 though showing fluctuations in its effective population size. The BA9 lineage established its global distribution with report from 23 different countries over the past 16 years. The present study augments our understanding of RSV infection, its epidemiological dynamics warranting steps towards its overall global surveillance.
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Affiliation(s)
| | - Wajihul Hasan Khan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Farah Deeba
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Sher Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Anwar Ahmed
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
- Centre for Excellence in Biotechnology Research, Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Irshad H. Naqvi
- Dr. M. A. Ansari Health Centre, Jamia Millia Islamia, New Delhi, India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | | | | | - Shobha Broor
- Department of Microbiology, Faculty of Medicine and Health Science, Shree Guru Gobind Singh Tricentenary University, Gurgaon, Haryana, India
| | - Shama Parveen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- * E-mail: ,
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17
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Muñoz-Alía MÁ, Muller CP, Russell SJ. Hemagglutinin-specific neutralization of subacute sclerosing panencephalitis viruses. PLoS One 2018; 13:e0192245. [PMID: 29466428 PMCID: PMC5821319 DOI: 10.1371/journal.pone.0192245] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/18/2018] [Indexed: 12/31/2022] Open
Abstract
Subacute sclerosing panencephalitis (SSPE) is a progressive, lethal complication of measles caused by particular mutants of measles virus (MeV) that persist in the brain despite high levels of neutralizing antibodies. We addressed the hypothesis that antigenic drift is involved in the pathogenetic mechanism of SSPE by analyzing antigenic alterations in the MeV envelope hemagglutinin protein (MeV-H) found in patients with SSPE in relation to major circulating MeV genotypes. To this aim, we obtained cDNA for the MeV-H gene from tissue taken at brain autopsy from 3 deceased persons with SSPE who had short (3-4 months, SMa79), average (3.5 years, SMa84), and long (18 years, SMa94) disease courses. Recombinant MeVs with a substituted MeV-H gene were generated by a reverse genetic system. Virus neutralization assays with a panel of anti-MeV-H murine monoclonal antibodies (mAbs) or vaccine-immunized mouse anti-MeV-H polyclonal sera were performed to determine the antigenic relatedness. Functional and receptor-binding analysis of the SSPE MeV-H showed activity in a SLAM/nectin-4-dependent manner. Similar to our panel of wild-type viruses, our SSPE viruses showed an altered antigenic profile. Genotypes A, G3, and F (SSPE case SMa79) were the exception, with an intact antigenic structure. Genotypes D7 and F (SSPE SMa79) showed enhanced neutralization by mAbs targeting antigenic site IIa. Genotypes H1 and the recently reported D4.2 were the most antigenically altered genotypes. Epitope mapping of neutralizing mAbs BH015 and BH130 reveal a new antigenic site on MeV-H, which we designated Φ for its intermediate position between previously defined antigenic sites Ia and Ib. We conclude that SSPE-causing viruses show similar antigenic properties to currently circulating MeV genotypes. The absence of a direct correlation between antigenic changes and predisposition of a certain genotype to cause SSPE does not lend support to the proposed antigenic drift as a pathogenetic mechanism in SSPE.
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Affiliation(s)
- Miguel Ángel Muñoz-Alía
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Claude P. Muller
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-Sur-Alzette (Grand Duchy of Luxembourg), Luxembourg
- Laboratoire National de Santé, Dudelange, Luxembourg
| | - Stephen J. Russell
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
- Division of Hematology, Mayo Clinic, Rochester, Minnesota, United States of America
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18
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Detailed genetic analyses of the HN gene in human respirovirus 3 detected in children with acute respiratory illness in the Iwate Prefecture, Japan. INFECTION GENETICS AND EVOLUTION 2018; 59:155-162. [PMID: 29408530 DOI: 10.1016/j.meegid.2018.01.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 01/15/2018] [Accepted: 01/24/2018] [Indexed: 12/21/2022]
Abstract
We performed detailed genetic analyses of the partial hemagglutinin-neuraminidase (HN) gene in 34 human respirovirus 3 (HRV3) strains from children with acute respiratory illness during 2013-2015 in Iwate Prefecture, Japan. In addition, we performed analyses of the evolutionary timescale of the gene using the Bayesian Markov chain Monte Carlo (MCMC) method. Furthermore, we analyzed pairwise distances and performed selective pressure analyses followed by linear B-cell epitope mapping and N-glycosylation and phylodynamic analyses. A phylogenetic tree showed that the strains diversified at around 1939, and the rate of molecular evolution was 7.6 × 10-4 substitutions/site/year. Although the pairwise distances were relatively short (0.03 ± 0.018 [mean ± standard deviation, SD]), two positive selection sites (Cys544Trp and Leu555Ser) and no amino acid substitutions were found in the active/catalytic sites. Six epitopes were estimated in this study, and three mouse monoclonal antibody binding sites (amino acid positions 278, 281, and 461) overlapped with two epitopes belonging to subcluster C3 strains. Bayesian skyline plot analyses indicated that subcluster C3 strains have been increasing from 2004, whereas subcluster C1 strains have declined from 2004. Based on these results, Iwate strains were divided into two subclusters and each subcluster evolved independently. Moreover, our results suggested that some predicted linear epitopes (epitopes 3 and 5) are candidates for an HRV3 vaccine motif. To better understand the details of the molecular evolution of HRV, further studies are needed.
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19
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Motoya T, Nagasawa K, Matsushima Y, Nagata N, Ryo A, Sekizuka T, Yamashita A, Kuroda M, Morita Y, Suzuki Y, Sasaki N, Katayama K, Kimura H. Molecular Evolution of the VP1 Gene in Human Norovirus GII.4 Variants in 1974-2015. Front Microbiol 2017; 8:2399. [PMID: 29259596 PMCID: PMC5723339 DOI: 10.3389/fmicb.2017.02399] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/20/2017] [Indexed: 12/14/2022] Open
Abstract
Human norovirus (HuNoV) is a leading cause of viral gastroenteritis worldwide, of which GII.4 is the most predominant genotype. Unlike other genotypes, GII.4 has created various variants that escaped from previously acquired immunity of the host and caused repeated epidemics. However, the molecular evolutionary differences among all GII.4 variants, including recently discovered strains, have not been elucidated. Thus, we conducted a series of bioinformatic analyses using numerous, globally collected, full-length GII.4 major capsid (VP1) gene sequences (466 strains) to compare the evolutionary patterns among GII.4 variants. The time-scaled phylogenetic tree constructed using the Bayesian Markov chain Monte Carlo (MCMC) method showed that the common ancestor of the GII.4 VP1 gene diverged from GII.20 in 1840. The GII.4 genotype emerged in 1932, and then formed seven clusters including 14 known variants after 1980. The evolutionary rate of GII.4 strains was estimated to be 7.68 × 10−3 substitutions/site/year. The evolutionary rates probably differed among variants as well as domains [protruding 1 (P1), shell, and P2 domains]. The Osaka 2007 variant strains probably contained more nucleotide substitutions than any other variant. Few conformational epitopes were located in the shell and P1 domains, although most were contained in the P2 domain, which, as previously established, is associated with attachment to host factors and antigenicity. We found that positive selection sites for the whole GII.4 genotype existed in the shell and P1 domains, while Den Haag 2006b, New Orleans 2009, and Sydney 2012 variants were under positive selection in the P2 domain. Amino acid substitutions overlapped with putative epitopes or were located around the epitopes in the P2 domain. The effective population sizes of the present strains increased stepwise for Den Haag 2006b, New Orleans 2009, and Sydney 2012 variants. These results suggest that HuNoV GII.4 rapidly evolved in a few decades, created various variants, and altered its evolutionary rate and antigenicity.
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Affiliation(s)
- Takumi Motoya
- Ibaraki Prefectural Institute of Public Health, Mito, Japan.,Laboratory of Laboratory Animal Science and Medicine, Faculty of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Koo Nagasawa
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama, Japan
| | - Yuki Matsushima
- Division of Virology, Kawasaki City Institute for Public Health, Kawasaki, Japan
| | - Noriko Nagata
- Ibaraki Prefectural Institute of Public Health, Mito, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Musashimurayama, Japan
| | - Akifumi Yamashita
- Pathogen Genomics Center, National Institute of Infectious Diseases, Musashimurayama, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Musashimurayama, Japan
| | - Yukio Morita
- Department of Food and Nutrition, Tokyo Kasei University, Itabashi-ku, Japan
| | - Yoshiyuki Suzuki
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan
| | - Nobuya Sasaki
- Laboratory of Laboratory Animal Science and Medicine, Faculty of Veterinary Medicine, Kitasato University, Towada, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection I, Kitasato Institute for Life Sciences, Kitasato University, Minato-ku, Japan
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama, Japan.,Department of Microbiology, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,School of Medical Technology, Faculty of Health Sciences, Gunma Paz University, Takasaki, Japan
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20
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Wang J, Qiu J, Zhu Y, Zhou H, Yu L, Ding Y, Zhang L, Guo Z, Dong C. Molecular evolution of hepatitis B vaccine escape variants in China, during 2000-2016. Vaccine 2017; 35:5808-5813. [PMID: 28939157 DOI: 10.1016/j.vaccine.2017.09.030] [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: 06/24/2017] [Revised: 09/02/2017] [Accepted: 09/08/2017] [Indexed: 02/07/2023]
Abstract
Hepatitis B vaccine escape variants are the main threat to hepatitis B virus (HBV) infection in vaccination era worldwide. With 215 genotype B HBV and 313 genotype C HBV vaccine escape variants isolated from China during 2000-2016, we reported that genotype B HBV vaccine escape strains diverged in ∼1997 (95% HPD; 1987-2005), while genotype C HBV vaccine escape strains diverged in ∼1976 (95% HPD; 1955-2003). Additionally, the p-distance of genotype C HBV vaccine escape strains was 0.0291±0.0169, which was significantly higher than that in the genotype B HBV (t=131.02, p<0.05). However, genotype B HBV vaccine escape strains evolved more rapidly than genotype C HBV (2.103×10-3 vs 1.083×10-3 substitutions/site/year). Bayesian skyline plot analysis showed that the populations of genotype C HBV vaccine escape strains fluctuated more than those in genotype B HBV. Four sites (A5T/S, L21S, T/A126S and T/N131I/A) and 13 sites (N3S, T5A, G10Q/R/E, L21S, T47K/A/V, L98V/P, I/S126N/V/T, Q129H/R/L, T131P/I/N/A, G145A/R, L175S/F, L213I/S, V224A/G) were found to be under positive selection in genotype B and C HBV vaccine escape strains, respectively. More importantly, N3S, L21S, T47K, L98V, I/S126T and L213I mutations were detected in 1 (2.5%), 1 (2.5%), 1 (2.5%), 3 (7.5%), 1 (2.5%), 1 (2.5%) genotype C HBV infected Chinese younger with neonatal HBV vaccination, respectively. Therefore, our results should be valuable in further understanding the molecular evolution of HBV and providing new ideas for the elimination of HBV infection.
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Affiliation(s)
- Jie Wang
- Department of Epidemiology and Statistics, School of Public Health, Jiangsu Key Laboratory and Translational Medicine for Geriatric Disease, Medical College of Soochow University, Suzhou, Jiangsu, China
| | - Jing Qiu
- Department of Epidemiology and Statistics, School of Public Health, Jiangsu Key Laboratory and Translational Medicine for Geriatric Disease, Medical College of Soochow University, Suzhou, Jiangsu, China
| | - Yinwei Zhu
- Department of Epidemiology and Statistics, School of Public Health, Jiangsu Key Laboratory and Translational Medicine for Geriatric Disease, Medical College of Soochow University, Suzhou, Jiangsu, China
| | - Hui Zhou
- Suzhou Industrial Park Centers for Disease Control and Prevention, Suzhou 215123, China
| | - Lugang Yu
- Suzhou Industrial Park Centers for Disease Control and Prevention, Suzhou 215123, China
| | - Yi Ding
- Suzhou Industrial Park Centers for Disease Control and Prevention, Suzhou 215123, China
| | - Lige Zhang
- Department of Epidemiology and Statistics, School of Public Health, Jiangsu Key Laboratory and Translational Medicine for Geriatric Disease, Medical College of Soochow University, Suzhou, Jiangsu, China
| | - Zhirong Guo
- Department of Epidemiology and Statistics, School of Public Health, Jiangsu Key Laboratory and Translational Medicine for Geriatric Disease, Medical College of Soochow University, Suzhou, Jiangsu, China
| | - Chen Dong
- Department of Epidemiology and Statistics, School of Public Health, Jiangsu Key Laboratory and Translational Medicine for Geriatric Disease, Medical College of Soochow University, Suzhou, Jiangsu, China.
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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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Kimura H, Nagasawa K, Kimura R, Tsukagoshi H, Matsushima Y, Fujita K, Hirano E, Ishiwada N, Misaki T, Oishi K, Kuroda M, Ryo A. Molecular evolution of the fusion protein (F) gene in human respiratory syncytial virus subgroup B. INFECTION GENETICS AND EVOLUTION 2017; 52:1-9. [PMID: 28414106 DOI: 10.1016/j.meegid.2017.04.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 04/09/2017] [Accepted: 04/12/2017] [Indexed: 11/19/2022]
Abstract
In this study, we examined the molecular evolution of the fusion protein (F) gene in human respiratory syncytial virus subgroup B (HRSV-B). First, we performed time-scale evolution analyses using the Bayesian Markov chain Monte Carlo (MCMC) method. Next, we performed genetic distance, linear B-cell epitope prediction, N-glycosylation, positive/negative selection site, and Bayesian skyline plot analyses. We also constructed a structural model of the F protein and mapped the amino acid substitutions and the predicted B-cell epitopes. The MCMC-constructed phylogenetic tree indicated that the HRSV F gene diverged from the bovine respiratory syncytial virus gene approximately 580years ago and had a relatively low evolutionary rate (7.14×10-4substitutions/site/year). Furthermore, a common ancestor of HRSV-A and -B diverged approximately 290years ago, while HRSV-B diverged into three clusters for approximately 60years. The genetic similarity of the present strains was very high. Although a maximum of 11 amino acid substitutions were observed in the structural model of the F protein, only one strain possessed an amino acid substitution located within the palivizumab epitope. Four epitopes were predicted, although these did not correspond to the neutralization sites of the F protein including the palivizumab epitope. In addition, five N-glycosylation sites of the present HRSV-B strains were inferred. No positive selection sites were identified; however, many sites were found to be under negative selection. The effective population size of the gene has remained almost constant. On the basis of these results, it can be concluded that the HRSV-B F gene is highly conserved, as is the F protein of HRSV-A. Moreover, our prediction of B-cell epitopes does not show that the palivizumab reaction site may be recognized as an epitope during naturally occurring infections.
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Affiliation(s)
- Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan; Department of Microbiology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanagawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan.
| | - Koo Nagasawa
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Ryusuke Kimura
- Faculty of Pharmacy, Takasaki University of Health and Welfare, 37-1 Nakaoruimachi, Takasaki-shi, Gunma 370-0033, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Yuki Matsushima
- Kawasaki City Institute for Public Health, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-0821, Japan
| | - Kiyotaka Fujita
- School of Medical Technology, Faculty of Health Science, Gumma Paz College, 1-7-1 Tonyamachi, Takasaki-shi, Gunma 370-0006, Japan
| | - Eiko Hirano
- Fukui Prefectural Institute of Public Health and Environmental Science, 39-4 Harame-cho, Fukui-shi, Fukui 910-8851, Japan
| | - Naruhiko Ishiwada
- Division of Infection Control and Prevention, Medical Mycology Research Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba 260-8677, Japan
| | - Takako Misaki
- Kawasaki City Institute for Public Health, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa 210-0821, Japan
| | - Kazunori Oishi
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanagawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan
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Yoshihara K, Le MN, Nagasawa K, Tsukagoshi H, Nguyen HA, Toizumi M, Moriuchi H, Hashizume M, Ariyoshi K, Dang DA, Kimura H, Yoshida LM. Molecular evolution of respiratory syncytial virus subgroup A genotype NA1 and ON1 attachment glycoprotein (G) gene in central Vietnam. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2016; 45:437-446. [PMID: 27746294 DOI: 10.1016/j.meegid.2016.10.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 10/11/2016] [Accepted: 10/12/2016] [Indexed: 01/08/2023]
Abstract
We performed molecular evolutionary analyses of the G gene C-terminal 3rd hypervariable region of RSV-A genotypes NA1 and ON1 strains from the paediatric acute respiratory infection patients in central Vietnam during the 2010-2012 study period. Time-scaled phylogenetic analyses were performed using Bayesian Markov Chain Monte Carlo (MCMC) method, and pairwise distances (p-distances) were calculated. Bayesian Skyline Plot (BSP) was constructed to analyze the time-trend relative genetic diversity of central Vietnam RSV-A strains. We also estimated the N-glycosylation sites within G gene hypervariable region. Amino acid substitutions under positive and negative selection pressure were examined using Conservative Single Likelihood Ancestor Counting (SLAC), Fixed Effects Likelihood (FEL), Internal Fixed Effects Likelihood (IFEL) and Mixed Effects Model for Episodic Diversifying Selection (MEME) models. The majority of central Vietnam ON1 strains detected in 2012 were classified into lineage 1 with few positively selected substitutions. As for the Vietnamese NA1 strains, four lineages were circulating during the study period with a few positive selection sites. Shifting patterns of the predominantly circulating NA1 lineage were observed in each year during the investigation period. Median p-distance of central Vietnam NA1 strains was wider (p-distance=0.028) than that of ON1 (p-distance=0.012). The molecular evolutionary rate of central Vietnam ON1 strains was estimated to be 2.55×10-2 (substitutions/site/year) and was faster than NA1 (7.12×10-3 (substitutions/site/year)). Interestingly, the evolutionary rates of both genotypes ON1 and NA1 strains from central Vietnam were faster than the global strains respectively. Furthermore, the shifts of N-glycosylation pattern within the G gene 3rd hypervariable region of Vietnamese NA1 strains were observed in each year. BSP analysis indicated the rapid growth of RSV-A effective population size in early 2012. These results suggested that the molecular evolution of RSV-A G gene detected in central Vietnam was fast with unique evolutionary dynamics.
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Affiliation(s)
- Keisuke Yoshihara
- Department of Paediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan; Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan
| | - Minh Nhat Le
- Department of Paediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan; National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Koo Nagasawa
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama, Tokyo 208-0011, Japan
| | - Hiroyuki Tsukagoshi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, Maebashi, Gunma 371-0052, Japan
| | - Hien Anh Nguyen
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Michiko Toizumi
- Department of Paediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
| | - Hiroyuki Moriuchi
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan; Department of Paediatrics, Nagasaki University Hospital, Nagasaki 852-8102, Japan
| | - Masahiro Hashizume
- Department of Paediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
| | - Koya Ariyoshi
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
| | - Duc Anh Dang
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Musashimurayama, Tokyo 208-0011, Japan
| | - Lay-Myint Yoshida
- Department of Paediatric Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan.
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24
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Lin LT, Richardson CD. The Host Cell Receptors for Measles Virus and Their Interaction with the Viral Hemagglutinin (H) Protein. Viruses 2016; 8:v8090250. [PMID: 27657109 PMCID: PMC5035964 DOI: 10.3390/v8090250] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/29/2016] [Accepted: 09/02/2016] [Indexed: 12/14/2022] Open
Abstract
The hemagglutinin (H) protein of measles virus (MeV) interacts with a cellular receptor which constitutes the initial stage of infection. Binding of H to this host cell receptor subsequently triggers the F protein to activate fusion between virus and host plasma membranes. The search for MeV receptors began with vaccine/laboratory virus strains and evolved to more relevant receptors used by wild-type MeV. Vaccine or laboratory strains of measles virus have been adapted to grow in common cell lines such as Vero and HeLa cells, and were found to use membrane cofactor protein (CD46) as a receptor. CD46 is a regulator that normally prevents cells from complement-mediated self-destruction, and is found on the surface of all human cells, with the exception of erythrocytes. Mutations in the H protein, which occur during adaptation and allow the virus to use CD46 as a receptor, have been identified. Wild-type isolates of measles virus cannot use the CD46 receptor. However, both vaccine/laboratory and wild-type strains can use an immune cell receptor called signaling lymphocyte activation molecule family member 1 (SLAMF1; also called CD150) and a recently discovered epithelial receptor known as Nectin-4. SLAMF1 is found on activated B, T, dendritic, and monocyte cells, and is the initial target for infections by measles virus. Nectin-4 is an adherens junction protein found at the basal surfaces of many polarized epithelial cells, including those of the airways. It is also over-expressed on the apical and basal surfaces of many adenocarcinomas, and is a cancer marker for metastasis and tumor survival. Nectin-4 is a secondary exit receptor which allows measles virus to replicate and amplify in the airways, where the virus is expelled from the body in aerosol droplets. The amino acid residues of H protein that are involved in binding to each of the receptors have been identified through X-ray crystallography and site-specific mutagenesis. Recombinant measles “blind” to each of these receptors have been constructed, allowing the virus to selectively infect receptor specific cell lines. Finally, the observations that SLAMF1 is found on lymphomas and that Nectin-4 is expressed on the cell surfaces of many adenocarcinomas highlight the potential of measles virus for oncolytic therapy. Although CD46 is also upregulated on many tumors, it is less useful as a target for cancer therapy, since normal human cells express this protein on their surfaces.
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Affiliation(s)
- Liang-Tzung Lin
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan.
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan.
| | - Christopher D Richardson
- Department of Microbiology and Immunology, Dalhousie University, 5850 College St., Halifax, NS B3H 4R2, Canada.
- Department of Pediatrics and Canadian Center for Vaccinology, Izaak Walton Killam Health Centre, Halifax, NS B3K 6R8, Canada.
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25
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Measles Virus Hemagglutinin Protein Epitopes: The Basis of Antigenic Stability. Viruses 2016; 8:v8080216. [PMID: 27490564 PMCID: PMC4997578 DOI: 10.3390/v8080216] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/19/2016] [Accepted: 07/20/2016] [Indexed: 02/07/2023] Open
Abstract
Globally eliminating measles using available vaccines is biologically feasible because the measles virus (MV) hemagglutinin (H) protein is antigenically stable. The H protein is responsible for receptor binding, and is the main target of neutralizing antibodies. The immunodominant epitope, known as the hemagglutinating and noose epitope, is located near the receptor-binding site (RBS). The RBS also contains an immunodominant epitope. Loss of receptor binding correlates with an escape from the neutralization by antibodies that target the epitope at RBS. Another neutralizing epitope is located near RBS and is shielded by an N-linked sugar in certain genotype strains. However, human sera from vaccinees and measles patients neutralized all MV strains with similar efficiencies, regardless of the N-linked sugar modification or mutations at these epitopes. Two other major epitopes exist at a distance from RBS. One has an unstructured flexible domain with a linear neutralizing epitope. When MV-H forms a tetramer (dimer of dimers), these epitopes may form the dimer-dimer interface, and one of the two epitopes may also interact with the F protein. The neutralization mechanisms of antibodies that recognize these epitopes may involve inhibiting the H-F interaction or blocking the fusion cascade after MV-H binds to its receptors.
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26
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Molecular evolution of the fusion protein gene in human respiratory syncytial virus subgroup A. INFECTION GENETICS AND EVOLUTION 2016; 43:398-406. [PMID: 27291709 DOI: 10.1016/j.meegid.2016.06.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 06/01/2016] [Accepted: 06/07/2016] [Indexed: 12/18/2022]
Abstract
We studied the molecular evolution of the fusion protein (F) gene in the human respiratory syncytial virus subgroup A (HRSV-A). We performed time-scaled phylogenetic analyses using the Bayesian Markov chain Monte Carlo (MCMC) method. We also conducted genetic distance (p-distance), positive/negative selection, and Bayesian skyline plot analyses. Furthermore, we mapped the amino acid substitutions of the protein. The MCMC-constructed tree indicated that the HRSV F gene diverged from the bovine RSV (BRSV) gene approximately 550years ago and had a relatively low substitution rate (7.59×10(-4) substitutions/site/year). Moreover, a common ancestor of HRSV-A and -B diverged approximately 280years ago, which has since formed four distinct clusters. The present HRSV-A strains were assigned six genotypes based on F gene sequences and attachment glycoprotein gene sequences. The present strains exhibited high F gene sequence similarity values and low genetic divergence. No positive selection sites were identified; however, 50 negative selection sites were identified. F protein amino acid substitutions at 17 sites were distributed in the F protein. The effective population size of the gene has remained relatively constant, but the population size of the prevalent genotype (GA2) has increased in the last 10years. These results suggest that the HRSV-AF gene has evolved independently and formed some genotypes.
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27
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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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28
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Liang Z, Yuan R, Chen L, Zhu X, Dou Y. Molecular Evolution and Characterization of Hemagglutinin (H) in Peste des Petits Ruminants Virus. PLoS One 2016; 11:e0152587. [PMID: 27035347 PMCID: PMC4818033 DOI: 10.1371/journal.pone.0152587] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 03/16/2016] [Indexed: 11/24/2022] Open
Abstract
Peste des Petits Ruminants (PPR) is an acute, highly contagious, and febrile viral disease that affects both domestic and wild small ruminants. The disease has become a major obstacle to the development of sustainable Agriculture. Hemagglutinin (H), the envelope glycoprotein of Peste des Petits Ruminants Virus (PPRV), plays a crucial role in regulating viral adsorption and entry, thus determining pathogenicity, and release of newly produced viral particles. In order to accurately understand the epidemic of the disease and the interactions between the virus and host, we launch the work. Here, we examined H gene from all four lineages of the PPRV to investigate evolutionary and epidemiologic dynamics of PPRV by the Bayesian method. In addition, we predicted positive selection sites due to selective pressures. Finally, we studied the interaction between H protein and SLAM receptor based on homology model of the complex. Phylogenetic analysis suggested that H gene can also be used to investigate evolutionary and epidemiologic dynamics of PPRV. Positive selection analysis identified four positive selection sites in H gene, in which only one common site (aa246) was detected by two methods, suggesting strong operation structural and/or functional constraint of changes on the H protein. This target site may be of interest for future mutagenesis studies. The results of homology modeling showed PPRVHv-shSLAM binding interface and MVH-maSLAM binding interface were consistent, wherein the groove in the B4 blade and B5 of the head domain of PPRVHv bound to the AGFCC′ β-sheets of the membrane-distal ectodomain of shSLAM. The binding regions could provide insight on the nature of the protein for epitope vaccine design, novel drug discovery, and rational drug design against PPRV.
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Affiliation(s)
- Zhongxiang Liang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Epizootic Diseases of Grazing Animals of Ministry of Agriculture, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, Gansu, China
| | - Ruyi Yuan
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Epizootic Diseases of Grazing Animals of Ministry of Agriculture, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, Gansu, China
| | - Lei Chen
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Epizootic Diseases of Grazing Animals of Ministry of Agriculture, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, Gansu, China
| | - Xueliang Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Epizootic Diseases of Grazing Animals of Ministry of Agriculture, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, Gansu, China
| | - Yongxi Dou
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Epizootic Diseases of Grazing Animals of Ministry of Agriculture, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, Gansu, China
- * E-mail:
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29
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Nagasawa K, Hirano E, Kobayashi M, Ryo A, Oishi K, Obuchi M, Ishiwada N, Noda M, Kuroda M, Shimojo N, Kimura H. Molecular evolution of the hypervariable region of the attachment glycoprotein gene in human respiratory syncytial virus subgroup B genotypes BA9 and BA10. INFECTION GENETICS AND EVOLUTION 2015; 36:217-223. [PMID: 26408340 DOI: 10.1016/j.meegid.2015.09.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/18/2015] [Accepted: 09/19/2015] [Indexed: 01/18/2023]
Abstract
We studied the molecular evolution of the C-terminal 3rd hypervariable region in the attachment glycoprotein gene of human respiratory syncytial virus subgroup B (HRSV-B) genotypes BA9 and BA10. We performed time-scaled phylogenetic analyses using Bayesian Markov chain Monte Carlo methods. We also performed a genetic distance analysis (p-distance analysis), positive and negative selection analyses, and a Bayesian skyline plot (BSP) analysis. We found that genotype BA9 diverged from the common ancestor of genotypes BA7, BA8, and BA10, while genotype BA10 diverged from the ancestor of genotypes BA7 and BA8. Strains of both genotypes were distributed worldwide. BA9 and BA10 diverged between 1999 and 2001. Both BA9 and BA10 evolved rapidly (about 4.8×10(-3)substitutions/site/year) and formed three distinct lineages in a 10-year period. BA10 strains belonging to lineage 3 had large genetic distances (p-distance>0.07). Thus, it may be possible to classify these strains as a new genotype, BA11. No positive selection site was detected in either genotype. Phylodynamic analyses showed that the effective population size of BA10 decreased gradually since 2010 and BA9 slightly decreased since 2009. The results suggested that the recently prevalent HRSV-B genotypes BA9 and BA10 evolved uniquely, leading to epidemics of HRSV-B worldwide over a 15-year period.
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Affiliation(s)
- Koo Nagasawa
- Department of Pediatrics, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba 260-8677, Japan; Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Eiko Hirano
- Fukui Prefectural Institute of Public Health and Environmental Science 39-4 Harame-cho, Fukui-shi, Fukui 910-8851, Japan
| | - Miho Kobayashi
- Gunma Prefectural Institute of Public Health and Environmental Sciences, 378 Kamioki-machi, Maebashi-shi, Gunma 371-0052, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University, Graduate School of Medicine, 3-9 Fukuura, Kanagawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan
| | - Kazunori Oishi
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Masatsugu Obuchi
- Department of Virology, Toyama Institute of Health, 17-1 Nakataikoyama, Imizu-shi, Toyama 939-0363, Japan
| | - Naruhiko Ishiwada
- Division of Infection Control and Prevention Medical Mycology Research Center, Chiba university, 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba 260-8677, Japan
| | - Masahiro Noda
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1 Toyama Shinjuku-ku, Tokyo 162-8640, Japan
| | - Naoki Shimojo
- Department of Pediatrics, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba 260-8677, Japan
| | - Hirokazu Kimura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama-shi, Tokyo 208-0011, Japan; Department of Microbiology, Yokohama City University, Graduate School of Medicine, 3-9 Fukuura, Kanagawa-ku, Yokohama-shi, Kanagawa 236-0004, Japan.
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