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Philomenadin FS, Mohammed S, Jayagandan S, Ramamurthy N, Ratchagadasse VR, Chandrasekaran V, Dhodapkar R. Characterizing human respiratory syncytial virus among children admitted with acute respiratory tract infections from 2019 to 2022. J Med Virol 2024; 96:e29896. [PMID: 39206836 DOI: 10.1002/jmv.29896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 08/08/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
Respiratory syncytial virus is a major causative agent of lower respiratory tract infection in children, especially infants with substantial morbidity and mortality implications. The virus undergoes continuous evolution documented by accumulation of mutations in the glycoprotein gene necessitating vigilant surveillance to provide essential data to epidemiologists and researchers involved in development of vaccines. This study was aimed to perform molecular characterization of respiratory syncytial virus (RSV) among children ≤ 5 years admitted in hospital. In the current study we observed RSV-A (2019 (n = 95) and 2021 (n = 61) seasons) and RSV-B (2022 season (n = 68)). Phylogenetic analysis revealed all RSV-A strains (n = 47) to be GA.2.3.5 and RSV-B (n = 22) were classified as GB.5.0.5a. Selection pressure analysis identified one positive (P274L/V) and one negative site (P230T) in RSV-A, while in RSV-B there was only one negatively selected site (S295). This study spanning over three seasons contributes to RSV evolutionary dynamics in India emphasizing the importance of on-going surveillance to inform effective public health strategies and vaccine development efforts.
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Affiliation(s)
| | - Shameema Mohammed
- Regional Virus Research and Diagnostic Laboratory (RVRDL), Department of Microbiology, JIPMER, Pondicherry, India
| | - Sangitha Jayagandan
- Regional Virus Research and Diagnostic Laboratory (RVRDL), Department of Microbiology, JIPMER, Pondicherry, India
| | - Narayan Ramamurthy
- Regional Virus Research and Diagnostic Laboratory (RVRDL), Department of Microbiology, JIPMER, Pondicherry, India
| | - Vimal Raj Ratchagadasse
- Regional Virus Research and Diagnostic Laboratory (RVRDL), Department of Microbiology, JIPMER, Pondicherry, India
| | | | - Rahul Dhodapkar
- Regional Virus Research and Diagnostic Laboratory (RVRDL), Department of Microbiology, JIPMER, Pondicherry, India
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Hamid S, Grajeda L, de Leon O, Lopez M, Maldonado H, Gomez A, Lopman B, Clasen T, McCracken J. Variability in the Timing of Respiratory Syncytial Virus Epidemics in Guatemala, 2008-2018. Influenza Other Respir Viruses 2024; 18:e13334. [PMID: 38980961 PMCID: PMC11232890 DOI: 10.1111/irv.13334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 05/12/2024] [Accepted: 05/19/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND The description of local seasonality patterns in respiratory syncytial virus (RSV) incidence is important to guide the timing of administration of RSV immunization products. METHODS We characterized RSV seasonality in Guatemala using the moving epidemic method (MEM) with absolute counts of RSV-associated acute respiratory infections (ARI) from hospital surveillance in Santa Rosa and Quetzaltenango departments of Guatemala. RESULTS From Week 17 of 2008 through Week 16 of 2018, 8487 ARI cases tested positive for RSV by rRT-PCR. Season onsets varied up to 5 months; early seasons starting in late May to early August and finishing in September to November were most common, but late seasons starting in October to November and finishing in March to April were also observed. Both epidemic patterns had similar durations ranging from 4 to 6 months. Epidemic thresholds (the levels of virus activity that signal the onset and end of a seasonal epidemic) calculated prospectively using previous seasons' data captured between 70% and 99% of annual RSV detections. Onset weeks differed by 2-10 weeks, and offset weeks differed by 2-16 weeks between the two surveillance sites. CONCLUSIONS Variability in the timing of seasonal RSV epidemics in Guatemala demonstrates the difficulty in precisely predicting the timing of seasonal RSV epidemics based on onset weeks from past seasons and suggests that maximal reduction in RSV disease burden would be achieved through year-round vaccination and immunoprophylaxis administration to at-risk infants.
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Affiliation(s)
- Sarah Hamid
- Department of Epidemiology, Rollins School of Public HealthEmory UniversityAtlantaGeorgiaUSA
| | - Laura M. Grajeda
- Centro de Estudios en SaludUniversidad del Valle de GuatemalaGuatemala CityGuatemala
- Global Health Institute, College of Public HealthUniversity of GeorgiaAthensGeorgiaUSA
| | - Oscar de Leon
- Department of Epidemiology, Rollins School of Public HealthEmory UniversityAtlantaGeorgiaUSA
- Centro de Estudios en SaludUniversidad del Valle de GuatemalaGuatemala CityGuatemala
- Gangarosa Department of Environmental Health, Rollins School of Public HealthEmory UniversityAtlantaGeorgiaUSA
| | - Maria Renee Lopez
- Centro de Estudios en SaludUniversidad del Valle de GuatemalaGuatemala CityGuatemala
| | - Herberth Maldonado
- Centro de Estudios en SaludUniversidad del Valle de GuatemalaGuatemala CityGuatemala
| | - Ana Beatriz Gomez
- Centro de Estudios en SaludUniversidad del Valle de GuatemalaGuatemala CityGuatemala
| | - Benjamin Lopman
- Department of Epidemiology, Rollins School of Public HealthEmory UniversityAtlantaGeorgiaUSA
| | - Thomas F. Clasen
- Department of Epidemiology, Rollins School of Public HealthEmory UniversityAtlantaGeorgiaUSA
- Gangarosa Department of Environmental Health, Rollins School of Public HealthEmory UniversityAtlantaGeorgiaUSA
| | - John P. McCracken
- Centro de Estudios en SaludUniversidad del Valle de GuatemalaGuatemala CityGuatemala
- Global Health Institute, College of Public HealthUniversity of GeorgiaAthensGeorgiaUSA
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Pangesti KNA, Ansari HR, Bayoumi A, Kesson AM, Hill-Cawthorne GA, Abd El Ghany M. Genomic characterization of respiratory syncytial virus genotypes circulating in the paediatric population of Sydney, NSW, Australia. Microb Genom 2023; 9:001095. [PMID: 37656160 PMCID: PMC10569731 DOI: 10.1099/mgen.0.001095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 08/03/2023] [Indexed: 09/02/2023] Open
Abstract
Respiratory syncytial virus (RSV), or human orthopneumovirus, is a major cause of acute lower respiratory infection (ALRI), particularly in young children, causing significant morbidity and mortality. We used pathogen genomics to characterize the population structure and genetic signatures of RSV isolates circulating in children in New South Wales between 2016 and 2018 and to understand the evolutionary dynamics of these strains in the context of publicly available RSV genomes from the region and globally. Whole-genome phylogenetic analysis demonstrated the co-circulation of a few major RSV clades in the paediatric population from Sydney. The whole-genome-based genotypes A23 (RSV-A ON1-like genotype) and B6 (RSV-B BA9-like genotype) were the predominant RSV-A and RSV-B genotypes circulating during the study period, respectively. These genotypes were characterized with high levels of diversity of predicted N- and O-linked glycosylation patterns in both the G and F glycoproteins. Interestingly, a novel 72-nucleotide triplication in the sequence that corresponds to the C-terminal region of the G gene was identified in four of the A23 genotype sequenced in this study. Consistently, the population dynamics analysis demonstrated a continuous increase in the effective population size of A23 and B6 genotypes globally. Further investigations including functional mapping of mutations and identifying the impact of sequence changes on virus fitness are highly required. This study highlights the potential impact of an integrated approach that uses WG-based phylogeny and studying selective pressure events in understanding the emergence and dissemination of RSV genotypes.
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Affiliation(s)
- Krisna N. A. Pangesti
- School of Public Health, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Hifzur R. Ansari
- King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Ali Bayoumi
- The Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia
| | - Alison M. Kesson
- Department of Infectious Diseases and Microbiology, The Children’s Hospital at Westmead, Sydney, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Sydney, Australia
- Discipline of Child and Adolescent Health, The University of Sydney, Sydney, Australia
| | - Grant A. Hill-Cawthorne
- School of Public Health, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Moataz Abd El Ghany
- School of Public Health, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- The Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia
- Sydney Infectious Diseases Institute, The University of Sydney, Sydney, Australia
- The Westmead Clinical School, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
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Zhao X, Wang C, Jiang H, Zhang H, Fang F, Chen M, Yuan Z, Teng Z, Liu J, Zhang X. Analysis of circulating respiratory syncytial virus A strains in Shanghai, China identified a new and increasingly prevalent lineage within the dominant ON1 genotype. Front Microbiol 2022; 13:966235. [PMID: 36033866 PMCID: PMC9403419 DOI: 10.3389/fmicb.2022.966235] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 07/14/2022] [Indexed: 11/13/2022] Open
Abstract
Respiratory syncytial virus A (RSV-A) is one of the commonest pathogens causing acute respiratory tract infections in infants and children globally. The currently dominant circulating genotype of RSV-A, ON1, was first detected in Shanghai, China in 2011, but little data are available regarding its subsequent circulation and clinical impact here. In this work, we analyzed RSV-A infection in a cohort of patients hospitalized for acute respiratory infections in Shanghai Children’s Hospital, and RSV-A was detected in ~10% of these cases. RSV-A G gene sequencing revealed that all successfully sequenced strains belonged to ON1 genotype, but in phylogenetic analysis, the majority of these sequences formed a clade separate from the four previously established lineages within ON1. The new lineage, denoted ON1-5, was supported by phylogenetic analyses using additional G gene sequences from RSV-A strains isolated in Shanghai and elsewhere. ON1-5 first appeared in 2015 in China and the Netherlands, and has since spread to multiple continents and gained dominance in Asia. In our cohort, ON1-5 was not associated with markedly different clinical presentations compared to other ON1 lineages. ON1-5 strains are characterized by four amino acid variations in the two mucin-like regions of G protein, and one variation (N178G) within the highly conserved CCD domain that is involved in receptor binding. These data highlight the continuous evolution of RSV-A, and suggest the possibility of the virus acquiring variations in domains traditionally considered to be conserved for fitness gain.
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Affiliation(s)
- Xue Zhao
- Virus Testing Laboratory, Pathogen Testing Center, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Chun Wang
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Hui Jiang
- Virus Testing Laboratory, Pathogen Testing Center, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Hong Zhang
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Fanghao Fang
- Virus Testing Laboratory, Pathogen Testing Center, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Min Chen
- Virus Testing Laboratory, Pathogen Testing Center, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Zhengan Yuan
- Virus Testing Laboratory, Pathogen Testing Center, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Zheng Teng
- Virus Testing Laboratory, Pathogen Testing Center, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
- *Correspondence: Zheng Teng,
| | - Jing Liu
- Key Laboratory of Medical Molecular Virology (MOE/MOH/CAMS) and Shanghai Key Laboratory of Medical Epigenetics, Department of Microbiology and Parasitology and Institutes of Biomedical Sciences, School of Basic Medical Sciences and Shanghai Institute of Infectious Diseases and Biosecurity, Shanghai Medical College, Fudan University, Shanghai, China
- Jing Liu,
| | - Xi Zhang
- Virus Testing Laboratory, Pathogen Testing Center, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
- Xi Zhang,
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Molecular epidemiology of respiratory syncytial virus among children and adults in India 2016 to 2018. Virus Genes 2021; 57:489-501. [PMID: 34524602 PMCID: PMC8440155 DOI: 10.1007/s11262-021-01859-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 06/25/2021] [Indexed: 11/21/2022]
Abstract
Respiratory syncytial virus (RSV) is a common cause of respiratory tract infections among children less than 5 years of age and the elderly. This study intended to determine the circulating genotypes of RSV among severe acute respiratory illness (SARI) cases during the period 2016–2018 in India, among hospitalized acute febrile illness cases of age ranging from 1 to 65 years. Throat/nasopharyngeal swab samples were subjected for testing RSV and subgroups by real-time reverse transcriptase polymerase chain reaction (RT-PCR), further sequencing and phylogenetic analysis were performed for the second hypervariable region of the G gene. RSV-A and B subtypes co-circulated during the years 2016, 2017, and 2018, with RSV-A as the dominant subtype in 2016, and RSV-B as the dominant subgroup in 2017 and 2018. Phylogenetic analysis revealed that the circulating genotypes of RSV were GA2 (16/16), of RSV-A, and GB5 (23/23) of RSV-B in the South, North, and Northeast region of India during the period between 2016 and 2018. Here we report the first study comprising the distribution of RSV-A and B genotypes in the different geographic regions of India among children and adults during the year 2016 to 2018. We also report GA2.3.7 lineage of GA2 genotype for the first time in India to the best of our knowledge.
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Komoyo GF, Yambiyo BM, Manirakiza A, Gody JC, Muller CP, Hübschen JM, Nakoune E, Snoeck CJ. Epidemiology and genetic characterization of respiratory syncytial virus in children with acute respiratory infections: Findings from the influenza sentinel surveillance network in Central African Republic, 2015 to 2018. Health Sci Rep 2021; 4:e298. [PMID: 34013070 PMCID: PMC8112815 DOI: 10.1002/hsr2.298] [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: 08/20/2020] [Revised: 03/21/2021] [Accepted: 04/15/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND AND AIMS Respiratory syncytial virus (RSV) is one of the main viral pathogens causing acute respiratory infections in children under 5 years of age but has seldom been studied in Central African Republic (CAF). Taking advantage of the national influenza surveillance network in CAF, this study aimed at providing the first insights into RSV prevalence and seasonality over 4 years of surveillance and the clinical manifestations of RSV in this population in CAF. METHODS A total of 3903 children under 5 years matching the influenza-like illness (ILI, 68.5%) or severe acute respiratory infection (SARI, 31.5%) case definitions were recruited from January 2015 to December 2018. The presence of RSV viral RNA in nasopharyngeal samples was assessed by RT-PCR, followed by RSV-A and RSV-B typing and Sanger sequencing on a subset of samples. Phylogenetic analyses were carried on partial G protein sequences. Associations between RSV and demographic or clinical manifestations were investigated by statistical analyses. RESULTS RSV prevalence was significantly higher in infants <6 months (13.4%), in hospitalized children (13.3% vs 5.5%) and in male patients (9.5% vs 6.4%). An overall prevalence of RSV of 8.0% in the period of 2015 to 2018 was shown, with significant annual (6.4%-10.6%) and seasonal (12.7% in rainy season vs 3.0% in dry season) fluctuations. While RSV seasons in 2015, 2016, and 2018 were relatively similar, 2017 showed deviations from the overall patterns with significantly higher RSV circulation and an outbreak peak 3 to 5 months earlier. Concomitant circulation of RSV-A and RSV-B with an alternating predominance of RSV-A and RSV-B strains and temporal RSV-A genotype replacement from NA1 to ON1 was observed. CONCLUSION This study represents the first in-depth epidemiological analysis of RSV in CAF and provides first insights into RSV genetic diversity and seasonality in the country.
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Affiliation(s)
- Giscard F. Komoyo
- Laboratoire des arbovirus, des fièvres hémorragiques virales, des virus émergents et des zoonosesInstitut Pasteur de BanguiBanguiCentral African Republic
- Ecole Doctorale d'Infectiologie Tropicale de Franceville, GabonFrancevilleGabon
| | - Brice M. Yambiyo
- Service d'épidémiologieInstitut Pasteur de BanguiBanguiCentral African Republic
| | | | - Jean C. Gody
- Complexe pédiatrique de BanguiCentre National Hospitalier Universitaire de BanguiBanguiCentral African Republic
| | - Claude P. Muller
- Clinical and Applied Virology group, Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
| | - Judith M. Hübschen
- Clinical and Applied Virology group, Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
| | - Emmanuel Nakoune
- Laboratoire des arbovirus, des fièvres hémorragiques virales, des virus émergents et des zoonosesInstitut Pasteur de BanguiBanguiCentral African Republic
| | - Chantal J. Snoeck
- Clinical and Applied Virology group, Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
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Ramaekers K, Rector A, Cuypers L, Lemey P, Keyaerts E, Van Ranst M. Towards a unified classification for human respiratory syncytial virus genotypes. Virus Evol 2020; 6:veaa052. [PMID: 33072402 PMCID: PMC7552823 DOI: 10.1093/ve/veaa052] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Since the first human respiratory syncytial virus (HRSV) genotype classification in 1998, inconsistent conclusions have been drawn regarding the criteria that define HRSV genotypes and their nomenclature, challenging data comparisons between research groups. In this study, we aim to unify the field of HRSV genotype classification by reviewing the different methods that have been used in the past to define HRSV genotypes and by proposing a new classification procedure, based on well-established phylogenetic methods. All available complete HRSV genomes (>12,000 bp) were downloaded from GenBank and divided into the two subgroups: HRSV-A and HRSV-B. From whole-genome alignments, the regions that correspond to the open reading frame of the glycoprotein G and the second hypervariable region (HVR2) of the ectodomain were extracted. In the resulting partial alignments, the phylogenetic signal within each fragment was assessed. Maximum likelihood phylogenetic trees were reconstructed using the complete genome alignments. Patristic distances were calculated between all pairs of tips in the phylogenetic tree and summarized as a density plot in order to determine a cutoff value at the lowest point following the major distance peak. Our data show that neither the HVR2 fragment nor the G gene contains sufficient phylogenetic signal to perform reliable phylogenetic reconstruction. Therefore, whole-genome alignments were used to determine HRSV genotypes. We define a genotype using the following criteria: a bootstrap support of ≥ 70 per cent for the respective clade and a maximum patristic distance between all members of the clade of ≤0.018 substitutions per site for HRSV-A or ≤0.026 substitutions per site for HRSV-B. By applying this definition, we distinguish twenty-three genotypes within subtype HRSV-A and six genotypes within subtype HRSV-B. Applying the genotype criteria on subsampled data sets confirmed the robustness of the method.
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Affiliation(s)
- Kaat Ramaekers
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, Herestraat 49 box 1040, BE-3000 Leuven, Belgium
| | - Annabel Rector
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, Herestraat 49 box 1040, BE-3000 Leuven, Belgium
| | - Lize Cuypers
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, Herestraat 49 box 1040, BE-3000 Leuven, Belgium
- University Hospitals Leuven, Department of Laboratory Medicine and National Reference Centre for Respiratory Pathogens, Herestraat 49, BE-3000 Leuven, Belgium
| | - Philippe Lemey
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, Herestraat 49 box 1040, BE-3000 Leuven, Belgium
| | - Els Keyaerts
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, Herestraat 49 box 1040, BE-3000 Leuven, Belgium
- University Hospitals Leuven, Department of Laboratory Medicine and National Reference Centre for Respiratory Pathogens, Herestraat 49, BE-3000 Leuven, Belgium
| | - Marc Van Ranst
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, Herestraat 49 box 1040, BE-3000 Leuven, Belgium
- University Hospitals Leuven, Department of Laboratory Medicine and National Reference Centre for Respiratory Pathogens, Herestraat 49, BE-3000 Leuven, Belgium
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Yun KW, Choi EH, Lee HJ. Molecular epidemiology of respiratory syncytial virus for 28 consecutive seasons (1990-2018) and genetic variability of the duplication region in the G gene of genotypes ON1 and BA in South Korea. Arch Virol 2020; 165:1069-1077. [PMID: 32144544 DOI: 10.1007/s00705-020-04580-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/04/2020] [Indexed: 02/07/2023]
Abstract
We investigated the molecular epidemiology of respiratory syncytial virus (RSV) isolated from children during 28 consecutive seasons (1990-2018) and the genetic variability of the duplication region of RSV genotypes ON1 and BA in South Korea. RSV was identified using culture-based methods in Hep-2 cells and was grouped as RSV-A or RSV-B by an immunofluorescence assay. The second hypervariable region of the G gene was sequenced for genotyping. The nucleotide and deduced amino acid sequences of the duplication region of RSV ON1 and BA were analyzed. A total of 670 RSV-A and 233 RSV-B isolates were obtained. For RSV-A, the NA1 genotype predominated during the 2004/2005-2011/2012 seasons. The ON1 genotype was first detected in 2011 and has since replaced all other genotypes. For RSV-B, the GB3 genotype predominated during the 1999/2000-2005/2006 seasons, but the BA genotype also replaced all other genotypes of RSV-B after the first season in which it was isolated (2005/2006). In ON1 and BA genotype RSV strains, novel sequence types of the duplication region of the G gene were identified in 50-95% and 33-80% of the isolates, respectively, in each season. The ON1 and BA9 genotypes are responsible for the current epidemics of RSV infection in South Korea. The sequences in the duplication region of the G gene have evolved continuously and might be sufficient for the identification of specific strains of the RSV-A ON1 and RSV-B BA genotypes.
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Affiliation(s)
- Ki Wook Yun
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, South Korea
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, 03080, South Korea
| | - Eun Hwa Choi
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, South Korea
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, 03080, South Korea
| | - Hoan Jong Lee
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, 03080, South Korea.
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, 03080, South Korea.
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Broberg EK, Waris M, Johansen K, Snacken R, Penttinen P. Seasonality and geographical spread of respiratory syncytial virus epidemics in 15 European countries, 2010 to 2016. ACTA ACUST UNITED AC 2019; 23. [PMID: 29409569 PMCID: PMC5801642 DOI: 10.2807/1560-7917.es.2018.23.5.17-00284] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Respiratory syncytial virus (RSV) is considered the most common pathogen causing severe lower respiratory tract infections among infants and young children. We describe the seasonality and geographical spread of RSV infection in 15 countries of the European Union and European Economic Area. We performed a retrospective descriptive study of weekly laboratory-confirmed RSV detections between weeks 40/2010 and 20/2016, in patients investigated for influenza-like illness, acute respiratory infection or following the clinician's judgment. Six countries reported 4,230 sentinel RSV laboratory diagnoses from primary care and 14 countries reported 156,188 non-sentinel laboratory diagnoses from primary care or hospitals. The median length of the RSV season based on sentinel and non-sentinel surveillance was 16 (range: 9-24) and 18 (range: 8-24) weeks, respectively. The median peak weeks for sentinel and non-sentinel detections were week 4 (range: 48 to 11) and week 4.5 (range: 49 to 17), respectively. RSV detections peaked later (r = 0.56; p = 0.0360) and seasons lasted longer with increasing latitude (r = 0.57; p = 0.0329). Our data demonstrated regular seasonality with moderate correlation between timing of the epidemic and increasing latitude of the country. This study supports the use of RSV diagnostics within influenza or other surveillance systems to monitor RSV seasonality and geographical spread.
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Affiliation(s)
- Eeva K Broberg
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Matti Waris
- Turku University Hospital, Turku, Finland.,University of Turku, Turku, Finland
| | - Kari Johansen
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - René Snacken
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Pasi Penttinen
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
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Abou-El-Hassan H, Massaad E, Soudani N, Assaf-Casals A, Shaker R, Lteif Khoury M, Ghanem S, Karam M, Andary R, Saito R, Dbaibo G, Zaraket H. Detection of ON1 and novel genotypes of human respiratory syncytial virus and emergence of palivizumab resistance in Lebanon. PLoS One 2019; 14:e0212687. [PMID: 30789963 PMCID: PMC6383889 DOI: 10.1371/journal.pone.0212687] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/07/2019] [Indexed: 12/18/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a common cause of respiratory tract infections in children and immunocompromised individuals. A multi-center surveillance of the epidemiologic and molecular characteristics of RSV circulating in Lebanon was performed. The attachment (G) and fusion (F) glycoproteins were analyzed and compared to those reported regionally and globally. 16% (83/519) of the nasopharyngeal swabs collected during the 2016/17 season tested positive for RSV; 50% (27/54) were RSV-A and 50% (27/54) were RSV-B. Phylogenetic analysis of the G glycoprotein revealed predominance of the RSVA ON1 genotype, in addition to two novel Lebanese genotype variants, hereby named LBA1 and LBA2, which descended from the ON1 and NA2 RSV-A genotypes, respectively. RSV-B strains belonged to BA9 genotype except for one BA10. Deduced amino acid sequences depicted several unique substitutions, alteration of glycosylation patterns and the emergence of palivizumab resistance among the Lebanese viruses. The emergence of ON1 and other novel genotypes that are resistant to palivizumab highlights the importance of monitoring RSV globally.
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Affiliation(s)
- Hadi Abou-El-Hassan
- Department of Experimental Pathology, Immunology, and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
| | - Elie Massaad
- Department of Experimental Pathology, Immunology, and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
| | - Nadia Soudani
- Department of Experimental Pathology, Immunology, and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
- Department of Biology, Faculty of Sciences, EDST, Lebanese University, Hadath, Lebanon
| | - Aia Assaf-Casals
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
- Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Rouba Shaker
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
- Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Mireille Lteif Khoury
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
- Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Soha Ghanem
- Department of Pediatrics, Makassed General Hospital, Beirut, Lebanon
| | | | | | - Reiko Saito
- Division of International Health (Public Health), Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Ghassan Dbaibo
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
- Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, American University of Beirut Medical Center, Beirut, Lebanon
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Hassan Zaraket
- Department of Experimental Pathology, Immunology, and Microbiology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
- * E-mail:
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11
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Pangesti KNA, Abd El Ghany M, Walsh MG, Kesson AM, Hill-Cawthorne GA. Molecular epidemiology of respiratory syncytial virus. Rev Med Virol 2018; 28. [PMID: 29377415 DOI: 10.1002/rmv.1968] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 12/11/2017] [Accepted: 12/11/2017] [Indexed: 01/10/2023]
Abstract
Respiratory syncytial virus (RSV) is a major cause of viral acute respiratory tract infections in young children. The virus is characterised by distinct seasonality that is dependent upon the latitude and its ability to cause reinfection. Respiratory syncytial virus demonstrates a complex molecular epidemiology pattern as multiple strains and/or genotypes cocirculate during a single epidemic. Previous studies have investigated the relationship between RSV genetic diversity, reinfection, and clinical features. Here, we review the evidence behind this relationship together with the impact that the advancement of whole genome sequencing will have upon our understanding and the need for reconsidering the classification of RSV genotypes.
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Affiliation(s)
| | - Moataz Abd El Ghany
- Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia.,Marie Bashir Institute of Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
| | - Michael G Walsh
- Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia.,Marie Bashir Institute of Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
| | - Alison M Kesson
- Marie Bashir Institute of Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia.,Discipline of Child and Adolescent Health, The University of Sydney, Sydney, Australia.,Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, Sydney, Australia
| | - Grant A Hill-Cawthorne
- School of Public Health, The University of Sydney, Sydney, Australia.,Marie Bashir Institute of Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
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12
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Bayrakdar F, Kocabas CN, Altas AB, Kavuncuoglu HG, Cosgun Y, Mısırlıoglu ED, Durmaz I, Korukluoglu G, Ozkul A. Genetic variability human respiratory syncytial virus subgroups A and B in Turkey during six successive epidemic seasons, 2009-2015. J Med Virol 2017; 90:456-463. [PMID: 29077212 PMCID: PMC7166824 DOI: 10.1002/jmv.24983] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/12/2017] [Indexed: 01/10/2023]
Abstract
Human respiratory syncytial virus (HRSV) is most important viral respiratory pathogen of acute lower respiratory tract infections in infants and young children worldwide. The circulating pattern and genetic characteristics in the HRSV attachment glycoprotein gene were investigated in Turkey during six consecutive seasons from 2009 to 2015. HRSVA was dominant in the all epidemic seasons except 2011‐2012 season. Partial sequences of the HVR2 region of the G gene of 479 HRSVA and 135 HRSVB were obtained. Most Turkish strains belonged to NA1, ON1, and BA9, which were the predominant genotypes circulating worldwide. Although three novel genotypes, TR‐A, TR‐BA1, and TR‐BA2, were identified, they were not predominant. Clinical data were available for 69 HRSV‐positive patients who were monitored due to acute lower respiratory tract illness. There were no significant differences in the clinical diagnosis, hospitalization rates, laboratory findings and treatment observed between the HRSVA and HRSVB groups, and co‐infections in this study. The major population afflicted by HRSV infections included infants and children between 13 and 24 months of age. We detected that the CB1, GB5, and THB strains clustered in the same branch with a bootstrap value of 100%. CB‐B and BA12 strains clustered in the same branch with a bootstrap value of 65%. The BA11 genotype was clustered in the BA9 genotype in our study. The present study may contribute on the molecular epidemiology of HRSV in Turkey and provide data for HRSV strains circulating in local communities and other regions worldwide.
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Affiliation(s)
- Fatma Bayrakdar
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Can Naci Kocabas
- Pediatric Immunology and Allergy Unit, Faculty of Medicine, Mugla Sitki Koçman Universty, Muğla, Turkey
| | - Ayse Basak Altas
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - H Gokhan Kavuncuoglu
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Yasemin Cosgun
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Emine Dibek Mısırlıoglu
- Department of Pediatric Allergy and Immunology, Ankara Children's Hematology Oncology Training and Research Hospital, Ankara, Turkey
| | - Ihsan Durmaz
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Gulay Korukluoglu
- Virology Reference and Research Laboratory, Public Health Institutions of Turkey, Ankara, Turkey
| | - Aykut Ozkul
- Faculty of Veterinary Medicine, Department of Virology, Ankara University, Ankara, Turkey
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13
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Whelan JN, Reddy KD, Uversky VN, Teng MN. Functional correlations of respiratory syncytial virus proteins to intrinsic disorder. MOLECULAR BIOSYSTEMS 2017; 12:1507-26. [PMID: 27062995 DOI: 10.1039/c6mb00122j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Protein intrinsic disorder is an important characteristic demonstrated by the absence of higher order structure, and is commonly detected in multifunctional proteins encoded by RNA viruses. Intrinsically disordered regions (IDRs) of proteins exhibit high flexibility and solvent accessibility, which permit several distinct protein functions, including but not limited to binding of multiple partners and accessibility for post-translational modifications. IDR-containing viral proteins can therefore execute various functional roles to enable productive viral replication. Respiratory syncytial virus (RSV) is a globally circulating, non-segmented, negative sense (NNS) RNA virus that causes severe lower respiratory infections. In this study, we performed a comprehensive evaluation of predicted intrinsic disorder of the RSV proteome to better understand the functional role of RSV protein IDRs. We included 27 RSV strains to sample major RSV subtypes and genotypes, as well as geographic and temporal isolate differences. Several types of disorder predictions were applied to the RSV proteome, including per-residue (PONDR®-FIT and PONDR® VL-XT), binary (CH, CDF, CH-CDF), and disorder-based interactions (ANCHOR and MoRFpred). We classified RSV IDRs by size, frequency and function. Finally, we determined the functional implications of RSV IDRs by mapping predicted IDRs to known functional domains of each protein. Identification of RSV IDRs within functional domains improves our understanding of RSV pathogenesis in addition to providing potential therapeutic targets. Furthermore, this approach can be applied to other NNS viruses that encode essential multifunctional proteins for the elucidation of viral protein regions that can be manipulated for attenuation of viral replication.
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Affiliation(s)
- Jillian N Whelan
- Division of Allergy and Immunology, Department of Internal Medicine, and the Joy McCann Culverhouse Airway Diseases Research Center, University of South Florida Morsani College of Medicine, Tampa, FL, USA.
| | - Krishna D Reddy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA and Institute for Biological Instrumentation, Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia
| | - Michael N Teng
- Division of Allergy and Immunology, Department of Internal Medicine, and the Joy McCann Culverhouse Airway Diseases Research Center, University of South Florida Morsani College of Medicine, Tampa, FL, USA.
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14
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Durigon EL, Botosso VF, de Oliveira DBL. Human Respiratory Syncytial Virus: Biology, Epidemiology, and Control. HUMAN VIROLOGY IN LATIN AMERICA 2017. [PMCID: PMC7121549 DOI: 10.1007/978-3-319-54567-7_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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15
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Successive Respiratory Syncytial Virus Epidemics in Local Populations Arise from Multiple Variant Introductions, Providing Insights into Virus Persistence. J Virol 2015; 89:11630-42. [PMID: 26355091 PMCID: PMC4645665 DOI: 10.1128/jvi.01972-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 09/01/2015] [Indexed: 11/29/2022] Open
Abstract
Respiratory syncytial virus (RSV) is a global respiratory pathogen of humans, with infection occurring characteristically as recurrent seasonal epidemics. Unlike influenza viruses, little attention has been paid to the mechanism underlying worldwide spread and persistence of RSV and how this may be discerned through an improved understanding of the introduction and persistence of RSV in local communities. We analyzed 651 attachment (G) glycoprotein nucleotide sequences of RSV B collected over 11 epidemics (2002 to 2012) in Kilifi, Kenya, and contemporaneous data collected elsewhere in Kenya and 18 other countries worldwide (2002 to 2012). Based on phylogeny, genetic distance and clustering patterns, we set out pragmatic criteria to classify local viruses into distinct genotypes and variants, identifying those newly introduced and those locally persisting. Three genotypes were identified in the Kilifi data set: BA (n = 500), SAB1 (n = 148), and SAB4 (n = 3). Recurrent RSV epidemics in the local population were composed of numerous genetic variants, most of which have been newly introduced rather than persisting in the location from season to season. Global comparison revealed that (i) most Kilifi variants do not cluster closely with strains from outside Kenya, (ii) some Kilifi variants were closely related to those observed outside Kenya (mostly Western Europe), and (iii) many variants were circulating elsewhere but were never detected in Kilifi. These results are consistent with the hypothesis that year-to-year presence of RSV at the local level (i.e., Kilifi) is achieved primarily, but not exclusively, through introductions from a pool of variants that are geographically restricted (i.e., to Kenya or to the region) rather than global. IMPORTANCE The mechanism by which RSV persists and reinvades local populations is poorly understood. We investigated this by studying the temporal patterns of RSV variants in a rural setting in tropical Africa and comparing these variants with contemporaneous variants circulating in other countries. We found that periodic seasonal RSV transmission at the local level appears to require regular new introductions of variants. However, importantly, the evidence suggests that the source of new variants is mostly geographically restricted, and we hypothesize that year-to-year RSV persistence is at the country level rather than the global level. This has implications for control.
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Sequencing and analysis of globally obtained human respiratory syncytial virus A and B genomes. PLoS One 2015; 10:e0120098. [PMID: 25793751 PMCID: PMC4368745 DOI: 10.1371/journal.pone.0120098] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 01/19/2015] [Indexed: 11/19/2022] Open
Abstract
Background Human respiratory syncytial virus (RSV) is the leading cause of respiratory tract infections in children globally, with nearly all children experiencing at least one infection by the age of two. Partial sequencing of the attachment glycoprotein gene is conducted routinely for genotyping, but relatively few whole genome sequences are available for RSV. The goal of our study was to sequence the genomes of RSV strains collected from multiple countries to further understand the global diversity of RSV at a whole-genome level. Methods We collected RSV samples and isolates from Mexico, Argentina, Belgium, Italy, Germany, Australia, South Africa, and the USA from the years 1998-2010. Both Sanger and next-generation sequencing with the Illumina and 454 platforms were used to sequence the whole genomes of RSV A and B. Phylogenetic analyses were performed using the Bayesian and maximum likelihood methods of phylogenetic inference. Results We sequenced the genomes of 34 RSVA and 23 RSVB viruses. Phylogenetic analysis showed that the RSVA genome evolves at an estimated rate of 6.72 × 10-4 substitutions/site/year (95% HPD 5.61 × 10-4 to 7.6 × 10-4) and for RSVB the evolutionary rate was 7.69 × 10-4 substitutions/site/year (95% HPD 6.81 × 10-4 to 8.62 × 10-4). We found multiple clades co-circulating globally for both RSV A and B. The predominant clades were GA2 and GA5 for RSVA and BA for RSVB. Conclusions Our analyses showed that RSV circulates on a global scale with the same predominant clades of viruses being found in countries around the world. However, the distribution of clades can change rapidly as new strains emerge. We did not observe a strong spatial structure in our trees, with the same three main clades of RSV co-circulating globally, suggesting that the evolution of RSV is not strongly regionalized.
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Kim YJ, Kim DW, Lee WJ, Yun MR, Lee HY, Lee HS, Jung HD, Kim K. Rapid replacement of human respiratory syncytial virus A with the ON1 genotype having 72 nucleotide duplication in G gene. INFECTION GENETICS AND EVOLUTION 2014; 26:103-12. [PMID: 24820343 PMCID: PMC7106136 DOI: 10.1016/j.meegid.2014.05.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/23/2014] [Accepted: 05/05/2014] [Indexed: 02/01/2023]
Abstract
We investigated the prevalence of HRSV during 2008–2013. Novel HRSV-A ON1 genotype was emerged in August 2011. After 1 year of emergence in 2012–2013, 94.6% was replaced with novel ON1 genotype. Evolutionary dynamics also drastically increased in 2011. The result of epitope prediction shows the possibilities of antigenic variation.
Human respiratory syncytial virus (HRSV) is the main cause of severe respiratory illness in young children and elderly people. We investigated the genetic characteristics of the circulating HRSV subgroup A (HRSV-A) to determine the distribution of genotype ON1, which has a 72-nucleotide duplication in attachment G gene. We obtained 456 HRSV-A positive samples between October 2008 and February 2013, which were subjected to sequence analysis. The first ON1 genotype was discovered in August 2011 and 273 samples were identified as ON1 up to February 2013. The prevalence of the ON1 genotype increased rapidly from 17.4% in 2011–2012 to 94.6% in 2012–2013. The mean evolutionary rate of G protein was calculated as 3.275 × 10−3 nucleotide substitution/site/year and several positively selected sites for amino acid substitutions were located in the predicted epitope region. This basic and important information may facilitate a better understanding of HRSV epidemiology and evolution.
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Affiliation(s)
- You-Jin Kim
- Division of Respiratory Viruses, Center for Infectious Diseases, Korea National Institute of Health, Cheongwon-gun, Chungbuk-do 363-951, Republic of Korea
| | - Dae-Won Kim
- Systems Biology Team, Center for Immunity and Pathology, Korea National Institute of Health, Cheongwon-gun, Chungbuk-do 363-951, Republic of Korea
| | - Wan-Ji Lee
- Division of Respiratory Viruses, Center for Infectious Diseases, Korea National Institute of Health, Cheongwon-gun, Chungbuk-do 363-951, Republic of Korea
| | - Mi-Ran Yun
- Systems Biology Team, Center for Immunity and Pathology, Korea National Institute of Health, Cheongwon-gun, Chungbuk-do 363-951, Republic of Korea
| | - Ho Yeon Lee
- Division of Respiratory Viruses, Center for Infectious Diseases, Korea National Institute of Health, Cheongwon-gun, Chungbuk-do 363-951, Republic of Korea
| | - Han Saem Lee
- Division of Respiratory Viruses, Center for Infectious Diseases, Korea National Institute of Health, Cheongwon-gun, Chungbuk-do 363-951, Republic of Korea
| | - Hee-Dong Jung
- Division of Respiratory Viruses, Center for Infectious Diseases, Korea National Institute of Health, Cheongwon-gun, Chungbuk-do 363-951, Republic of Korea
| | - Kisoon Kim
- Division of Respiratory Viruses, Center for Infectious Diseases, Korea National Institute of Health, Cheongwon-gun, Chungbuk-do 363-951, Republic of Korea.
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Faghihloo E, Yavarian J, Jandaghi NZS, Shadab A, Azad TM. Genotype circulation pattern of human respiratory syncytial virus in Iran. INFECTION GENETICS AND EVOLUTION 2014; 22:130-3. [PMID: 24462624 DOI: 10.1016/j.meegid.2014.01.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/22/2013] [Accepted: 01/13/2014] [Indexed: 11/29/2022]
Abstract
In order to have information on the molecular epidemiology and genetic circulation pattern of human respiratory syncytial virus (HRSV) in Iran, we studied the genetic variability of both group A and B HRSV strains during seven consecutive years by sequencing the hypervariable C-terminal domain of G protein. A total of 485 children <2years of age who were negative for influenza viruses, screened for the presence of HRSV in this research. HRSV was detected in 94 (19.38%) of the samples using nested RT-PCR. Group A viruses were isolated during each year, while group B viruses were isolated during 2009 and 2013. Phylogenetic analysis showed that all HRSV group A viruses belonged to three genotypes: GA1, GA2, GA5 and the group B viruses were in BA genotype.
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Affiliation(s)
- Ebrahim Faghihloo
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Iran.
| | - Jila Yavarian
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Iran.
| | | | - Azadeh Shadab
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Iran.
| | - Talat Mokhtari Azad
- Virology Department, School of Public Health, Tehran University of Medical Sciences, Iran.
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Cui G, Zhu R, Qian Y, Deng J, Zhao L, Sun Y, Wang F. Genetic variation in attachment glycoprotein genes of human respiratory syncytial virus subgroups a and B in children in recent five consecutive years. PLoS One 2013; 8:e75020. [PMID: 24069376 PMCID: PMC3775769 DOI: 10.1371/journal.pone.0075020] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 08/08/2013] [Indexed: 11/19/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) outranks other viral agents as the cause of respiratory tract diseases in children worldwide. Molecular epidemiological study of the virus provides useful information for the development of globally effective vaccine. We investigated the circulating pattern and genetic variation in the attachment glycoprotein genes of HRSV in Beijing during 5 consecutive seasons from 2007 to 2012. Out of 19,942 tested specimens, 3,160 (15.8%) were HRSV antigen-positive. The incidence of HRSV infection in males was significantly higher than in females. Of the total 723 (23.1%) randomly selected HRSV antigen-positive samples, 462 (63.9%) and 239 (33.1%) samples were identified as subgroup A and B, respectively. Subgroups A and B co-circulated in the 5 consecutive HRSV seasons, which showed a shifting mixed pattern of subgroup dominance. Complete G gene sequences were obtained from 190 HRSV-A and 72 HRSV-B by PCR for phylogenetic analysis. Although 4 new genotypes, NA3 and NA4 for HRSV-A and BA-C and CB1 for HRSV-B, were identified here, they were not predominant; NA1 and BA9 were the prevailing HRSV-A and -B genotypes, respectively. We provide the first report of a 9 consecutive nucleotide insertion in 3 CB1 genotype strains. One Beijing strain of ON1 genotype with a 72 nucleotide insertion was found among samples collected in February 2012. The reversion of codon states in glycosylation sites to previous ones were found from HRSV strains in this study, suggesting an immune-escape strategy of this important virus.
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Affiliation(s)
- Guanglin Cui
- Laboratory of Virology, Peking University Capital Institute of Pediatrics Teaching Hospital, Beijing, China
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing, China
| | - Runan Zhu
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing, China
| | - Yuan Qian
- Laboratory of Virology, Peking University Capital Institute of Pediatrics Teaching Hospital, Beijing, China
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing, China
- * E-mail:
| | - Jie Deng
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing, China
| | - Linqing Zhao
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing, China
| | - Yu Sun
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing, China
| | - Fang Wang
- Laboratory of Virology, Capital Institute of Pediatrics, Beijing, China
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Almajhdi FN, Farrag MA, Amer HM. Genetic diversity in the G protein gene of group A human respiratory syncytial viruses circulating in Riyadh, Saudi Arabia. Arch Virol 2013; 159:73-81. [PMID: 23884633 DOI: 10.1007/s00705-013-1792-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 06/07/2013] [Indexed: 11/26/2022]
Abstract
Human respiratory syncytial virus (HRSV) is a frequent cause of hospitalization and mortality in children worldwide. The molecular epidemiology and circulation pattern of HRSV in Saudi Arabia is mostly uncharted. In the current study, the genetic variability and phylogenetic relationships of HRSV type A strains circulating in Riyadh Province were explored. Nasopharyngeal aspirates were collected from hospitalized children with acute respiratory symptoms during the winter-spring seasons of 2007/08 and 2008/09. Among 175 samples analyzed, 39 (22.3 %) were positive for HRSV by one-step RT-PCR (59 % type A and 41 % type B). Propagation of positive samples in HEp-2 cells permitted the recovery of the first Saudi HRSV isolates. Genetic variability among Saudi HRSV-A strains was evaluated by sequence analysis of the complete attachment (G) protein gene. The nucleotide sequence was compared to representatives of the previously identified HRSV-A genotypes. Sequence and phylogenetic analysis showed that the strains examined in this study were very closely related at both the nucleotide and amino acid level, and all of them are clustered in the GA2 genotype (and mostly belonged to the NA-1 subtype). A total of 23 mutation sites, 14 of which resulted in an amino acid change, were recorded only in Saudi strains. This is the first report on genetic diversity of HRSV-A strains in Saudi Arabia. Further analysis of strains on a geographical and temporal basis is needed to fully understand HRSV-A circulation patterns in Saudi Arabia.
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Affiliation(s)
- Fahad N Almajhdi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia,
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Khor CS, Sam IC, Hooi PS, Chan YF. Displacement of predominant respiratory syncytial virus genotypes in Malaysia between 1989 and 2011. INFECTION GENETICS AND EVOLUTION 2013; 14:357-60. [DOI: 10.1016/j.meegid.2012.12.017] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 12/13/2012] [Accepted: 12/14/2012] [Indexed: 10/27/2022]
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Katzov-Eckert H, Botosso VF, Neto EA, Zanotto PMDA. Phylodynamics and dispersal of HRSV entails its permanence in the general population in between yearly outbreaks in children. PLoS One 2012; 7:e41953. [PMID: 23077477 PMCID: PMC3471929 DOI: 10.1371/journal.pone.0041953] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 06/29/2012] [Indexed: 12/22/2022] Open
Abstract
Background Human respiratory syncytial virus (HRSV) is one of the major etiologic agents of respiratory tract infections among children worldwide. Methodology/Principal Findings Here through a comprehensive analysis of the two major HRSV groups A and B (n = 1983) which comprise of several genotypes, we present a complex pattern of population dynamics of HRSV over a time period of 50 years (1956–2006). Circulation pattern of HRSV revealed a series of expansions and fluctuations of co-circulating lineages with a predominance of HRSVA. Positively selected amino acid substitutions of the G glycoprotein occurred upon population growth of GB3 with a 60-nucleotide insertion (GB3 Insert), while other genotypes acquired substitutions upon both population growth and decrease, thus possibly reflecting a role for immune selected epitopes in linkage to the traced substitution sites that may have important relevance for vaccine design. Analysis evidenced the co-circulation and predominance of distinct HRSV genotypes in Brazil and suggested a year-round presence of the virus. In Brazil, GA2 and GA5 were the main culprits of HRSV outbreaks until recently, when the GB3 Insert became highly prevalent. Using Bayesian methods, we determined the dispersal patterns of genotypes through several inferred migratory routes. Conclusions/Significance Genotypes spread across continents and between neighboring areas. Crucially, genotypes also remained at any given region for extended periods, independent of seasonal outbreaks possibly maintained by re-infecting the general population.
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Affiliation(s)
- Hagit Katzov-Eckert
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute-ICB-II, University of São Paulo, São Paulo, Brazil
| | | | - Eurico Arruda Neto
- Department of Cell Biology, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil, and the VGDN Consortium
| | - Paolo Marinho de Andrade Zanotto
- Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute-ICB-II, University of São Paulo, São Paulo, Brazil
- * E-mail:
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23
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Agoti CN, Mwihuri AG, Sande CJ, Onyango CO, Medley GF, Cane PA, Nokes DJ. Genetic relatedness of infecting and reinfecting respiratory syncytial virus strains identified in a birth cohort from rural Kenya. J Infect Dis 2012; 206:1532-41. [PMID: 22966119 PMCID: PMC3475639 DOI: 10.1093/infdis/jis570] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Background. Respiratory syncytial virus (RSV) reinfects individuals repeatedly. The extent to which this is a consequence of RSV antigenic diversity is unclear. Methods. Six-hundred thirty-five children from rural Kenya were closely monitored for RSV infection from birth through 3 consecutive RSV epidemics. RSV infections were identified by immunofluorescence testing of nasal washing samples collected during acute respiratory illnesses, typed into group A and B, and sequenced in the attachment (G) protein. A positive sample separated from a previous positive by ≥14 days was defined as a reinfection a priori. Results. Phylogenetic analysis was undertaken for 325 (80%) of 409 identified infections, including 53 (64%) of 83 reinfections. Heterologous group reinfections were observed in 28 episodes, and homologous group reinfections were observed in 25 episodes; 10 involved homologous genotypes, 5 showed no amino acid changes, and 3 were separated by 21–24 days and were potentially persistent infections. The temporal distribution of genotypes among reinfections did not differ from that of single infections. Conclusions. The vast majority of infection and reinfection pairs differed by group, genotype, or G amino acid sequence (ie, comprised distinct viruses). The extent to which this is a consequence of immune memory of infection history or prevalent diversity remains unclear.
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Affiliation(s)
- Charles N Agoti
- Kenya Medical Research Institute, Centre for Geographic Medicine Research, Coast, Kenya.
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Baek YH, Choi EH, Song MS, Pascua PNQ, Kwon HI, Park SJ, Lee JH, Woo SI, Ahn BH, Han HS, Hahn YS, Shin KS, Jang HL, Kim SY, Choi YK. Prevalence and genetic characterization of respiratory syncytial virus (RSV) in hospitalized children in Korea. Arch Virol 2012; 157:1039-50. [DOI: 10.1007/s00705-012-1267-1] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2011] [Accepted: 01/20/2012] [Indexed: 11/29/2022]
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Whole genome sequencing and evolutionary analysis of human respiratory syncytial virus A and B from Milwaukee, WI 1998-2010. PLoS One 2011; 6:e25468. [PMID: 21998661 PMCID: PMC3188560 DOI: 10.1371/journal.pone.0025468] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 09/05/2011] [Indexed: 01/24/2023] Open
Abstract
Background Respiratory Syncytial Virus (RSV) is the leading cause of lower respiratory-tract infections in infants and young children worldwide. Despite this, only six complete genome sequences of original strains have been previously published, the most recent of which dates back 35 and 26 years for RSV group A and group B respectively. Methodology/Principal Findings We present a semi-automated sequencing method allowing for the sequencing of four RSV whole genomes simultaneously. We were able to sequence the complete coding sequences of 13 RSV A and 4 RSV B strains from Milwaukee collected from 1998–2010. Another 12 RSV A and 5 RSV B strains sequenced in this study cover the majority of the genome. All RSV A and RSV B sequences were analyzed by neighbor-joining, maximum parsimony and Bayesian phylogeny methods. Genetic diversity was high among RSV A viruses in Milwaukee including the circulation of multiple genotypes (GA1, GA2, GA5, GA7) with GA2 persisting throughout the 13 years of the study. However, RSV B genomes showed little variation with all belonging to the BA genotype. For RSV A, the same evolutionary patterns and clades were seen consistently across the whole genome including all intergenic, coding, and non-coding regions sequences. Conclusions/Significance The sequencing strategy presented in this work allows for RSV A and B genomes to be sequenced simultaneously in two working days and with a low cost. We have significantly increased the amount of genomic data that is available for both RSV A and B, providing the basic molecular characteristics of RSV strains circulating in Milwaukee over the last 13 years. This information can be used for comparative analysis with strains circulating in other communities around the world which should also help with the development of new strategies for control of RSV, specifically vaccine development and improvement of RSV diagnostics.
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Jang JE, Lee JB, Kim KH, Park SM, Shim BS, Cheon IS, Song MK, Chang J. Evaluation of protective efficacy of respiratory syncytial virus vaccine against A and B subgroup human isolates in Korea. PLoS One 2011; 6:e23797. [PMID: 21915262 PMCID: PMC3168431 DOI: 10.1371/journal.pone.0023797] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2011] [Accepted: 07/26/2011] [Indexed: 01/23/2023] Open
Abstract
Human respiratory syncytial virus (HRSV) is a significant cause of upper and lower respiratory tract illness mainly in infants and young children worldwide. HRSV is divided into two subgroups, HRSV-A and HRSV-B, based on sequence variation within the G gene. Despite its importance as a respiratory pathogen, there is currently no safe and effective vaccine for HRSV. In this study, we have detected and identified the HRSV by RT-PCR from nasopharyngeal aspirates of Korean pediatric patients. Interestingly, all HRSV-B isolates exhibited unique deletion of 6 nucleotides and duplication of 60 nucleotides in the G gene. We successfully amplified two isolates ('KR/A/09-8' belonging to HRSV-A and 'KR/B/10-12' to HRSV-B) on large-scale, and evaluated the cross-protective efficacy of our recombinant adenovirus-based HRSV vaccine candidate, rAd/3xG, by challenging the immunized mice with these isolates. The single intranasal immunization with rAd/3xG protected the mice completely from KR/A/09-8 infection and partially from KR/B/10-12 infection. Our study contributes to the understanding of the genetic characteristics and distribution of subgroups in the seasonal HRSV epidemics in Korea and, for the first time, to the evaluation of the cross-protective efficacy of RSV vaccine against HRSV-A and -B field-isolates.
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Affiliation(s)
- Ji-Eun Jang
- Division of Life and Pharmaceutical Sciences, Center for Cell Signaling and Drug Discovery Research, Ewha Womans University, Seoul, Korea
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Kumaria R, Iyer LR, Hibberd ML, Simões EAF, Sugrue RJ. Whole genome characterization of non-tissue culture adapted HRSV strains in severely infected children. Virol J 2011; 8:372. [PMID: 21794174 PMCID: PMC3166936 DOI: 10.1186/1743-422x-8-372] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Accepted: 07/28/2011] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Human respiratory syncytial virus (HRSV) is the most important virus causing lower respiratory infection in young children. The complete genetic characterization of RSV clinical strains is a prerequisite for understanding HRSV infection in the clinical context. Current information about the genetic structure of the HRSV genome has largely been obtained using tissue culture adapted viruses. During tissue culture adaptation genetic changes can be introduced into the virus genome, which may obscure subtle variations in the genetic structure of different RSV strains. METHODS In this study we describe a novel Sanger sequencing strategy which allowed the complete genetic characterisation of 14 clinical HRSV strains. The viruses were sequenced directly in the nasal washes of severely hospitalized children, and without prior passage of the viruses in tissue culture. RESULTS The analysis of nucleotide sequences suggested that vRNA length is a variable factor among primary strains, while the phylogenetic analysis suggests selective pressure for change. The G gene showed the greatest sequence variation (2-6.4%), while small hydrophobic protein and matrix genes were completely conserved across all clinical strains studied. A number of sequence changes in the F, L, M2-1 and M2-2 genes were observed that have not been described in laboratory isolates. The gene junction regions showed more sequence variability, and in particular the intergenic regions showed a highest level of sequence variation. Although the clinical strains grew slower than the HRSVA2 virus isolate in tissue culture, the HRSVA2 isolate and clinical strains formed similar virus structures such as virus filaments and inclusion bodies in infected cells; supporting the clinical relevance of these virus structures. CONCLUSION This is the first report to describe the complete genetic characterization of HRSV clinical strains that have been sequenced directly from clinical material. The presence of novel substitutions and deletions in the vRNA of clinical strains emphasize the importance of genomic characterization of non-tissue culture adapted primary strains.
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Affiliation(s)
- Rajni Kumaria
- Singapore-MIT Alliance for Research and Technology, Centre for Life Sciences, #05-06M, 28 Medical Drive, 117456, Singapore
| | - Laxmi Ravi Iyer
- Division of Molecular and Cell biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 639798, Singapore
| | - Martin L Hibberd
- Singapore-MIT Alliance for Research and Technology, Centre for Life Sciences, #05-06M, 28 Medical Drive, 117456, Singapore
- Genome Institute of Singapore, #02-01, Genome Building, 60 Biopolis Street, 138672, Singapore
| | - Eric AF Simões
- University of Colorado, Denver and The Division of Infectious Diseases, The Children's Hospital, 13123 East 16th Avenue, Aurora, CO 80045, USA
| | - Richard J Sugrue
- Singapore-MIT Alliance for Research and Technology, Centre for Life Sciences, #05-06M, 28 Medical Drive, 117456, Singapore
- Division of Molecular and Cell biology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 639798, Singapore
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Furuse Y, Suzuki A, Kamigaki T, Mpolya EA, Khandaker I, Oshitani H. Viruses that cross borders: factors responsible for global dissemination of viral infections. Intervirology 2011; 54:246-52. [PMID: 21228540 PMCID: PMC7179521 DOI: 10.1159/000320967] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Accepted: 08/30/2010] [Indexed: 01/04/2023] Open
Abstract
Objective Pandemic viral infections as emerging infectious diseases are of a great global concern. However, for some viruses, particular strains are endemic to specific areas and can be genetically distinguished from strains in other regions. In contrast, for some other viruses, genetically similar strains can spread and circulate all over the world. This study addresses global dissemination of various viral infections. Methods We classified 34 viruses as per their ability to cross borders by review. We also described factors responsible for and the dynamics of global dissemination. We examined biological characteristics of viruses, manners or routes of transmission, host responses and epidemiological factors. Results Factors required for viruses to cross borders include ‘non-blood infection’, ‘short incubation period’, ‘short infectious period’, ’frequent re-infection’, ‘small basic reproductive number (R0)’ and ‘high annual incidence’. Conclusion Knowing the factors responsible for global dissemination of pathogens is useful for controlling and/or containing both classic and emerging infectious diseases.
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Affiliation(s)
- Yuki Furuse
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
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Boonyasuppayakorn S, Kowitdamrong E, Bhattarakosol P. Molecular and demographic analysis of respiratory syncytial virus infection in patients admitted to King Chulalongkorn Memorial Hospital, Thailand, 2007. Influenza Other Respir Viruses 2010; 4:313-23. [PMID: 20716160 PMCID: PMC4634657 DOI: 10.1111/j.1750-2659.2010.00152.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Please cite this paper as: Boonyasuppayakorn et al. (2010) Molecular and demographic analysis of respiratory syncytial virus infection in King Chulalongkorn Memorial Hospital admitted patients, Thailand, 2007. Influenza and Other Respiratory Viruses 4(5), 313–323. Objectives: To preliminary preview the molecular character and its possible clinical correlation of RSV subgroups in Thailand. Design: Cross‐sectional analytic design. Setting: Admitted acute lower respiratory tract infection patients of King Chulalongkorn Memorial Hospital, Bangkok, during Jun–Dec, 2007 were recruited. Sample: Nasopharyngeal aspirations were collected. Main outcome measures: All samples were analyzed for the presence of RSV glycoprotein G gene by reverse transcription PCR. Molecular character of each subgroup was determined by sequencing. Admission records were also analyzed for clinical correlations. Results: Equal infectivity and severity of both RSV subgroups to the patients was shown. Mixed infection was shown to be as common as each single infection, higher than previously reported. GA2 of subgroup A and BA‐IV of subgroup B were the most widespread genotypes and showed their monophyletic origins. From admission records, either type of infection did not show significantly preference in demographic record or clinical severity. Comorbidity, however, was statistically significant that more congenital heart disease was found in negative RSV cases, while more chronic pulmonary disease was in positive cases. Nevertheless, the clinical severity was insignificantly different suggesting that only patients with chronic pulmonary underlying were prone to be infected with RSV. Conclusions: This preliminary RSV study showed prevalence of subgroups, types of infection, and common genotypes in an epidemic, uncorrelated to demography or clinical severity.
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Affiliation(s)
- Siwaporn Boonyasuppayakorn
- Division of Virology, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Human respiratory syncytial virus in children with acute respiratory tract infections in China. J Clin Microbiol 2010; 48:4193-9. [PMID: 20810776 DOI: 10.1128/jcm.00179-10] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
There are limited data on the prevalence and clinical and molecular characterization of human respiratory syncytial virus (HRSV) in children with acute respiratory tract infections (ARTIs) in China. From December 2006 to March 2009, 894 nasopharyngeal aspirates (NPAs) were collected from children under 14 years of age with ARTIs. Samples were screened for HRSV and genotyped by reverse transcription-PCR (RT-PCR) and sequencing. Demographic and clinical information was recorded. A total of 38.14% (341/894) of samples were positive for HRSV. Phylogenetic analysis revealed that 60.4% of the selected 227 RSV strains were GA2, 34.4% were BA, 4.8% were GB2, and 0.4% were GB3. A total of 40.47% of all of the RSV-positive samples were coinfected with other respiratory viruses, and adenovirus was the most common additional respiratory virus. No statistical differences were found in the frequency of diagnosis and symptoms between the coinfection group and monoinfection group. Additionally, no statistical differences were found in epidemiological characterizations or disease severity between genotype BA- and GA2-positive patients, except for a greater frequency of lower respiratory tract infections (LRTIs) (mostly bronchitis)with BA. HRSV is the most important viral pathogen in Chinese children with ARTIs. Four genotypes (i.e., GA2, BA, GB2, and GB3) circulate locally, and the predominant genotype may shift between seasons. Coinfection with other viruses does not affect disease severity. HRSV genotypes were not associated with different epidemiological characterizations or disease severity.
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Positive selection results in frequent reversible amino acid replacements in the G protein gene of human respiratory syncytial virus. PLoS Pathog 2009; 5:e1000254. [PMID: 19119418 PMCID: PMC2603285 DOI: 10.1371/journal.ppat.1000254] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Accepted: 12/04/2008] [Indexed: 11/23/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) is the major cause of lower respiratory tract infections in children under 5 years of age and the elderly, causing annual disease outbreaks during the fall and winter. Multiple lineages of the HRSVA and HRSVB serotypes co-circulate within a single outbreak and display a strongly temporal pattern of genetic variation, with a replacement of dominant genotypes occurring during consecutive years. In the present study we utilized phylogenetic methods to detect and map sites subject to adaptive evolution in the G protein of HRSVA and HRSVB. A total of 29 and 23 amino acid sites were found to be putatively positively selected in HRSVA and HRSVB, respectively. Several of these sites defined genotypes and lineages within genotypes in both groups, and correlated well with epitopes previously described in group A. Remarkably, 18 of these positively selected tended to revert in time to a previous codon state, producing a “flip-flop” phylogenetic pattern. Such frequent evolutionary reversals in HRSV are indicative of a combination of frequent positive selection, reflecting the changing immune status of the human population, and a limited repertoire of functionally viable amino acids at specific amino acid sites. As part of the Viral Genetic Diversity Network (VGDN), we sequenced the second variable region (G2) of the G protein of human respiratory syncytial virus (HRSV) A and B from 568 patients sampled during 11 consecutive HRSV seasons (1995–2005) in the state of São Paulo, Brazil. A total of 933 HRSVA and 673 HRSB time-stamped sequences, including those sampled here and globally, was used for phylogenetic inference and the analysis of selection pressures. We identified 18 positively selected sites in both HRSVA (9 sites) and HRSVB (9 sites) that tended to revert in time to their previous codon state (i.e. exhibited a “flip-flop” pattern). We argue that these common evolutionary reversals are indicative of frequent positive selection, reflecting the changing immune status of the human population, coupled with a limited repertoire of functional viable amino acids at specific sites. This information is of particular importance since the ectodomain of the G protein is also a target site in vaccines that have so far proven unsuccessful and because it constitutes a significant step towards describing and understanding the immune-escape repertoire of this major human pathogen.
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The secreted form of respiratory syncytial virus G glycoprotein helps the virus evade antibody-mediated restriction of replication by acting as an antigen decoy and through effects on Fc receptor-bearing leukocytes. J Virol 2008; 82:12191-204. [PMID: 18842713 DOI: 10.1128/jvi.01604-08] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Respiratory syncytial virus (RSV) readily infects and reinfects during infancy and throughout life, despite maternal antibodies and immunity from prior infection and without the need for significant antigenic change. RSV has two neutralization antigens, the F and G virion glycoproteins. G is expressed in both membrane-bound (mG) and secreted (sG) forms. We investigated whether sG might act as a decoy for neutralizing antibodies by comparing the in vitro neutralization of wild-type (wt) RSV versus recombinant mG RSV expressing only mG. wt RSV indeed was less susceptible than mG RSV to monovalent G-specific and polyvalent RSV-specific antibodies, whereas susceptibility to F-specific antibodies was equivalent. This difference disappeared when the virus preparations were purified to remove sG. Thus, sG appears to function as a neutralization decoy. We evaluated this effect in vivo in mice by comparing the effects of passively transferred antibodies on the pulmonary replication of wt RSV versus mG RSV. Again, wt RSV was less sensitive than mG RSV to G-specific and RSV-specific antibodies; however, a similar difference was also observed with F-specific antibodies. This confirmed that sG helps wt RSV evade the antibody-dependent restriction of replication but indicated that in mice, it is not acting primarily as a decoy for G-specific antibodies, perhaps because sG is produced in insufficient quantities in this poorly permissive animal. Rather, we found that the greater sensitivity of mG versus wt RSV to the antiviral effect of passively transferred RSV antibodies required the presence of inflammatory cells in the lung and was Fc gamma receptor dependent. Thus, sG helps RSV escape the antibody-dependent restriction of replication via effects as an antigen decoy and as a modulator of leukocytes bearing Fc gamma receptors.
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Antoniassi da Silva LH, Spilki FR, Riccetto AGL, de Almeida RS, Baracat ECE, Arns CW. Genetic variability in the G protein gene of human respiratory syncytial virus isolated from the Campinas metropolitan region, Brazil. J Med Virol 2008; 80:1653-60. [DOI: 10.1002/jmv.21249] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Fodha I, Vabret A, Bouslama L, Leroux M, Legrand L, Dina J, Gouarin S, Petitjean J, Dewar J, Trabelsi A, Boujaafar N, Freymuth F. Molecular diversity of the aminoterminal region of the G protein gene of human respiratory syncytial virus subgroup B. ACTA ACUST UNITED AC 2008; 56:50-7. [DOI: 10.1016/j.patbio.2007.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2007] [Accepted: 06/13/2007] [Indexed: 10/22/2022]
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Ostlund MR, Lindell AT, Stenler S, Riedel HM, Wirgart BZ, Grillner L. Molecular epidemiology and genetic variability of respiratory syncytial virus (RSV) in Stockholm, 2002-2003. J Med Virol 2008; 80:159-67. [PMID: 18041002 DOI: 10.1002/jmv.21066] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The epidemiology and genetic variability of circulating respiratory syncytial virus (RSV) strains in Stockholm during the season 2002-2003 were studied in consecutive RSV isolates derived from respiratory samples and diagnosed in the laboratory. Two hundred thirty-four viruses were sequenced. The samples were mainly from children under 1 year old (79%). The phylogeny of the N-terminal part of the G gene was studied after amplification and sequencing. One hundred fifty-two viruses belonged to subgroup B and 82 to subgroup A. The subgroup A viruses could be further divided into genotypes GA2 (25) and GA5 (57) and the subgroup B viruses into GB3 (137) and SAB1 (15) strains. These strains clustered with subgroup A and subgroup B strains from Kenya from the same period, as well as with strains from Great Britain from 1995 to 1998. The dominance of subgroup B strains in Stockholm during 2002-2003 is in agreement with findings from other parts of the world during the same years. Only two genotypes of subgroup A, GA2 and GA5, were circulating during this time, and GA2 has been circulating in Sweden for more than 20 years. Consecutive strains from the same individual displayed no variability in the sequenced region, which was also true of strains that had been passaged in cell cultures.
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Affiliation(s)
- Maria Rotzén Ostlund
- Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden.
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36
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Kim YK, Choi EH, Lee HJ. Genetic variability of the fusion protein and circulation patterns of genotypes of the respiratory syncytial virus. J Med Virol 2007; 79:820-8. [PMID: 17457915 DOI: 10.1002/jmv.20891] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Although antigenic and genetic variations were shown to occur both in the G and F protein of respiratory syncytial virus (RSV), few studies looked at the variation of F gene. The F genotypes were determined by the evaluation of clustering patterns, via the phylogenetic analysis of the nucleotide sequences of a variable region in the F gene. One hundred seventy-nine strains obtained from a children's hospital in Korea over nine consecutive epidemics were included. The relationship between the F and G genotypes was analyzed with the G genotypes previously published by the authors. The phylogenetic analysis of the variable region from the F gene revealed 9 genotypes among 129 group A RSVs and 4 genotypes among 50 group B RSVs. In each of the epidemics, the dominant genotypes were replaced with new genotypes in consecutive epidemics. In each of the epidemics of group B RSVs, the predominant genotype alternated between genotypes. Most of the strains which clustered to a particular F genotype were assigned to particular G genotype(s). By determining the nearly entire sequences of the F genes, we revealed the percentage of the nucleotide differences which resulted in amino acid coding changes was determined to be much great in two distinct variable regions of the F gene. Our results indicated that the F gene of the RSVs may be continuously evolving under selective pressure in a distinct pattern, and that the genetic variability of the F protein is associated with that of the G protein.
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Affiliation(s)
- Yun-Kyung Kim
- Department of Pediatrics, Korea University College of Medicine, Seoul, Korea
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Zlateva KT, Vijgen L, Dekeersmaeker N, Naranjo C, Van Ranst M. Subgroup prevalence and genotype circulation patterns of human respiratory syncytial virus in Belgium during ten successive epidemic seasons. J Clin Microbiol 2007; 45:3022-30. [PMID: 17609323 PMCID: PMC2045289 DOI: 10.1128/jcm.00339-07] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human respiratory syncytial virus (HRSV) is the leading viral cause of severe respiratory illness for infants and young children worldwide. Two major antigenic groups (A and B) of HRSV exist, and viruses from both subgroups can cocirculate during epidemics; however, their frequencies might differ between seasons. The subgroup prevalence and genotype distribution patterns of HRSV strains were investigated in a community in Belgium during 10 successive epidemic seasons (1996 to 2006). A regular 3-year cyclic pattern of subgroup dominance was observed, consisting of two predominant HRSV-A seasons, followed by a single HRSV-B-dominant year. HRSV infections with both subgroups were more prevalent among children younger than 6 months and had a peak incidence in December. The most frequently detected genotypes were GA5 and GB13, the latter including strains with the 60-nucleotide duplication in the G gene. Furthermore, GA5 remained the dominant HRSV genotype in two consecutive epidemic seasons twice during the study period. Additional variability was detected among the GB13 isolates, due to the usage of a novel termination codon in the G gene. Dual infections with both HRSV subgroups were detected for 9 patients, and subsequent infections with the heterologous HRSV subgroup were documented for 15 patients. Among five patients with homologous reinfections, only one was caused by HRSV-B. Our results support the hypothesis that the overall prevalence of HRSV-A over HRSV-B could be due to a more-transient subgroup A-specific immune protection.
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Affiliation(s)
- Kalina T Zlateva
- Laboratory of Clinical and Epidemiological Virology, Department of Microbiology and Immunology, Rega Institute for Medical Research, University of Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
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Zhang Y, Xu W, Shen K, Xie Z, Sun L, Lu Q, Liu C, Liang G, Beeler JA, Anderson LJ. Genetic variability of group A and B human respiratory syncytial viruses isolated from 3 provinces in China. Arch Virol 2007; 152:1425-34. [PMID: 17510775 DOI: 10.1007/s00705-007-0984-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2006] [Accepted: 04/07/2007] [Indexed: 11/26/2022]
Abstract
The genetic variability of HRSV in China was studied using nucleotide sequencing of the hypervariable C-terminal region of the G protein gene and phylogenetic analysis on 80 isolates obtained from three children's hospitals over a period of three epidemic seasons, 1990/1991, 2000/2001, and 2003/2004. The results showed that 76/80 of these isolates belonged to group A and 4/80 belonged to group B. Phylogenetic analysis revealed that most of the group A isolates were genotype GA2 (74/76 isolates), and the other two isolates were GA3 and GA5. All group B isolates clustered into genotype GB3. There was substantial variation among the GA2 isolates, with nucleotide sequence and amino acid homologies ranging from 88.1-100% and 78.4-100%, respectively, in the hypervariable C-terminal region of the G protein gene. One group B virus, HRSV/Beijing/B/04/11, contained a 60-nucleotide duplication in the C-terminal region of the G protein, which was similar to what has been reported previously for isolates in several countries. This is the first report on the genetic diversity of human respiratory syncytial virus isolated during epidemic periods from children in China. These data provided a preliminary evaluation of patterns of circulation and the genetic diversity of isolates associated with HRSV epidemics within China.
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Affiliation(s)
- Y Zhang
- China Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing, China
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Parveen S, Sullender WM, Fowler K, Lefkowitz EJ, Kapoor SK, Broor S. Genetic variability in the G protein gene of group A and B respiratory syncytial viruses from India. J Clin Microbiol 2006; 44:3055-64. [PMID: 16954227 PMCID: PMC1594720 DOI: 10.1128/jcm.00187-06] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the most commonly identified viral agent of acute respiratory tract infection (ARI) of young children and causes repeat infections throughout life. Limited data are available on the molecular epidemiology of RSV from developing countries, including India. This study reports on the genetic variability in the glycoprotein G gene among RSV isolates from India. Reverse transcription-PCR for a region of the RSV G protein gene was done with nasopharyngeal aspirates (NPAs) collected in a prospective longitudinal study in two rural villages near Delhi and from children with ARI seen in an urban hospital. Nucleotide sequence comparisons among 48 samples demonstrated a higher prevalence of group A (77%) than group B (23%) RSV isolates. The level of genetic variability was higher among the group A viruses (up to 14%) than among the group B viruses (up to 2%). Phylogenetic analysis revealed that both the GA2 and GA5 group A RSV genotypes were prevalent during the 2002-2003 season and that genotype GA5 was predominant in the 2003-2004 season, whereas during the 2004-2005 season both genotype GA5 and genotype BA, a newly identified group B genotype, cocirculated in almost equal proportions. Comparison of the nonsynonymous mutation-to-synonymous mutation ratios (dN/dS) revealed greater evidence for selective pressure between the GA2 and GA5 genotypes (dN/dS, 1.78) than within the genotypes (dN/dS, 0.69). These are among the first molecular analyses of RSV strains from the second most populous country in the world and will be useful for comparisons to candidate vaccine strains.
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Affiliation(s)
- Shama Parveen
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110029, India
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Choi EH, Lee HJ, Kim SJ, Eun BW, Kim NH, Lee JA, Lee JH, Song EK, Park SHKJY, Sung JY. The association of newly identified respiratory viruses with lower respiratory tract infections in Korean children, 2000-2005. Clin Infect Dis 2006; 43:585-92. [PMID: 16886150 PMCID: PMC7107986 DOI: 10.1086/506350] [Citation(s) in RCA: 273] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2006] [Accepted: 05/28/2006] [Indexed: 11/17/2022] Open
Abstract
Background. This study was performed to evaluate the associations of newly recognized viruses, namely, human metapneumovirus (hMPV), human coronavirus (HCoV)–NL63, and human bocavirus (HBoV) with lower respiratory tract infections (LRTIs) in previously healthy children. Methods. To determine the prevalences of 11 viruses—respiratory syncytial virus (RSV), adenovirus, rhinovirus, parainfluenza viruses (PIVs) 1 and 3, influenza viruses A and B, hMPV, HCoV, HCoV-NL63, and HBoV—among infants or children with LRTIs, in association with their epidemiologic characteristics, we performed multiplex reverse-transcriptase polymerase chain reaction on nasopharyngeal aspirates obtained from 515 children 5 years old with LRTIs during the period 2000–2005. Results. Viruses were identified in 312 (60.6%) of the 515 patients. RSV was detected in 122 (23.7%), HBoV in 58 (11.3%), adenovirus in 35 (6.8%), PIV-3 in 32 (6.2%), rhinovirus in 30 (5.8%), hMPV in 24 (4.7%), influenza A in 24 (4.7%), PIV-1 in 9 (1.7%), influenza B in 9 (1.7%), and HCoV-NL63 in 8 (1.6%). Coinfections with 2 viruses were observed in 36 patients (11.5%). Twenty-two patients (37.9%) infected with HBoV had a coinfection. Bronchiolitis was frequently diagnosed in patients who tested positive for RSV, PIV-3, or rhinovirus, whereas influenza A, PIV-1, and HCoV-NL63 were commonly found in patients with croup. The age distributions of patients with viral infections differed; notably, RSV was responsible for 77% of LRTIs that occurred in infants 3 months old. The number of hMPV infections peaked between February and April, whereas the number of HCoV-NL63 infections peaked between April and May. Conclusions. This study describes the features of LRTIs associated with newly identified viruses in children, compared with those associated with known viruses. Additional investigations are required to define the role of HBoV in LRTI.
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Affiliation(s)
- Eun Hwa Choi
- Department of Pediatrics, Seoul National University College of Medicine, Seoul
- Seoul Medical Science Research Institute, Seoul National University Bundang Hospital, Gyeonggi-do, Korea
| | - Hoan Jong Lee
- Department of Pediatrics, Seoul National University College of Medicine, Seoul
- Virus Research Center, Clinical Research Institute, Seoul National University Hospital, Seoul
- Reprints or correspondence: Dr. Hoan Jong Lee, Seoul National University College of Medicine, 28, Yeongeon-dong, Jongno-gu, Seoul, Korea 110-744 ()
| | - Sun Jung Kim
- Seoul Medical Science Research Institute, Seoul National University Bundang Hospital, Gyeonggi-do, Korea
| | - Byung Wook Eun
- Department of Pediatrics, Seoul National University College of Medicine, Seoul
| | - Nam Hee Kim
- Department of Pediatrics, Seoul National University College of Medicine, Seoul
| | - Jin A Lee
- Department of Pediatrics, Seoul National University College of Medicine, Seoul
| | - Jun Ho Lee
- Department of Pediatrics, Seoul National University College of Medicine, Seoul
| | - Eun Kyung Song
- Department of Pediatrics, Seoul National University College of Medicine, Seoul
| | | | - Ji Yeon Sung
- Department of Pediatrics, Seoul National University College of Medicine, Seoul
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Kim YK, Lee HJ. Human metapneumovirus-associated lower respiratory tract infections in korean infants and young children. Pediatr Infect Dis J 2005; 24:1111-2. [PMID: 16371878 DOI: 10.1097/01.inf.0000190042.65120.23] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
To define the role of human metapneumovirus (hMPV) in previously healthy Korean children, a retrospective study was done on 166 children with lower respiratory tract infections and on their stored nasal aspirates. The hMPV gene was detected by reverse transcriptase-polymerase chain reaction. Twenty-six of 166 individuals tested positive for hMPV. The clinical diagnoses of hMPV infection were pneumonia in 15 children and bronchiolitis in 11 children.
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Affiliation(s)
- Yun-Kyung Kim
- Department of Pediatrics, Korea University College of Medicine, Korea
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43
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Galiano MC, Luchsinger V, Videla CM, De Souza L, Puch SS, Palomo C, Ricarte C, Ebekian B, Avendaño L, Carballal G. Intragroup antigenic diversity of human respiratory syncytial virus (group A) isolated in Argentina and Chile. J Med Virol 2005; 77:311-6. [PMID: 16121383 DOI: 10.1002/jmv.20456] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The intragroup antigenic diversity of the G glycoprotein of 226 human respiratory syncytial virus (HRSV) strains isolated in Buenos Aires (Argentina) and Santiago (Chile) between 1995 and 2002 was evaluated by ELISA with a panel of 14 anti-G monoclonal antibodies (MAbs). Out of 226 strains characterized, 172 (76%) belonged to group A and 54 (24%) to group B. Strains from both groups cocirculated throughout the study period in both countries, except in 1996, 2000, and 2002 when only group A strains were isolated. Within group A 23 different antigenic patterns were found as defined by the combination of reactivities with eight strain-specific anti-G MAbs. These antigenic patterns showed different behavior regarding their circulation. Some major patterns were observed in most years with variable proportions; other minor patterns were present in low proportions during 1 or 2 years and then were apparently replaced by new patterns. Some antigenic patterns occurred both in Argentina and Chile during the same epidemics. Since no strain-specific MAbs were available for group B, we could not evidence the antigenic variability within group B. These are the first data on antigenic characterization of HRSV strains isolated in Argentina and Chile. It is shown that the ELISA with MAbs directed against the G protein of RSV is a valuable tool. These results will also provide useful information for further studies to evaluate the antigenic variability of HRSV strains in relation with genetic characteristics.
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Affiliation(s)
- Mónica C Galiano
- Laboratorio de Virología Clínica, Centro de Educación Médica e Investigaciones Clínicas, CEMIC, Hospital Universitario, Buenos Aires, Argentina
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44
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Viegas M, Mistchenko AS. Molecular epidemiology of human respiratory syncytial virus subgroup A over a six-year period (1999-2004) in Argentina. J Med Virol 2005; 77:302-10. [PMID: 16121371 DOI: 10.1002/jmv.20457] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Human respiratory syncytial virus (HRSV) is the main viral cause of acute lower respiratory tract infections in children. Little information about the molecular epidemiology of HRSV in developing countries, such as Argentina, is available. By RT-PCR, we subgrouped 353 HRSV isolates over six consecutive epidemic seasons (1999-2004) and few isolates from 1997. Between them, 232 (65.7%) belonged to subgroup A and 121 (34.3%) to subgroup B. Therefore, the nucleotide, amino-acid variability and phylogenetic relations of 78 HRSV subgroup A isolates, were analyzed using RFLP and sequence analysis of the G-protein gene. The results showed that there were two main restriction patterns (PA1 and PA2) and two previously described genotypes (GA2 and GA5) cocirculating in Buenos Aires, without evidence of alternation between them during the studied period. The Argentine sequences were compared with previously reported molecular data from other countries. It showed that viruses genetically related circulated the same years within neighboring countries and the sequences from long-distant places were closely related to Argentine sequences, but they belonged to different sampling years. The data reported here support the growing database on the molecular diversity of HRSVA circulating in Latin America in children under 2 years of age and contributes to describe the pattern of global spread of this virus.
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Affiliation(s)
- Mariana Viegas
- Laboratorio de Virología, Hospital de Niños Dr. Ricardo Gutiérrez, Buenos Aires, Argentina.
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45
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Galiano MC, Palomo C, Videla CM, Arbiza J, Melero JA, Carballal G. Genetic and antigenic variability of human respiratory syncytial virus (groups a and b) isolated over seven consecutive seasons in Argentina (1995 to 2001). J Clin Microbiol 2005; 43:2266-73. [PMID: 15872254 PMCID: PMC1153737 DOI: 10.1128/jcm.43.5.2266-2273.2005] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genetic and antigenic variability of human respiratory syncytial virus (HRSV) strains isolated in Buenos Aires from 1995 to 2001 was evaluated by partial nucleotide sequencing of the G gene and enzyme-linked immunosorbent assay analysis with anti-G monoclonal antibodies. Phylogenetic analyses showed that 37 group A strains clustered into five genotypes, whereas 20 group B strains clustered into three genotypes. Group A showed more genetic variability than group B. A close correlation between genotypes and antigenic patterns was observed. Changes detected in the G protein of viruses from both groups included (i) amino acid substitutions and(ii) differences in protein length due to either changes in stop codon usage or sequence duplications. Three B strains from 1999 exhibited a duplication of 20 amino acids, while one B strain from 2001 had 2 amino acids duplicated. The comparison among Argentinean HRSV strains and viruses isolated in other geographical areas during different epidemics is discussed.
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Affiliation(s)
- Monica C Galiano
- Laboratorio de Virología Clínica, Centro de Educacion Médica e Investigaciones Clínicas, CEMIC, Hospiatal Universitario, Buenos Aires, Argentina
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Valentova V, Antonis AFG, Kovarcik K. Restriction enzyme analysis of RT-PCR amplicons as a rapid method for detection of genetic diversity among bovine respiratory syncytial virus isolates. Vet Microbiol 2005; 108:1-12. [PMID: 15917131 DOI: 10.1016/j.vetmic.2005.02.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2004] [Revised: 01/31/2005] [Accepted: 02/10/2005] [Indexed: 11/24/2022]
Abstract
Our current knowledge of antigenic variability of the bovine respiratory syncytial virus (BRSV) is quite limited and is mainly dependent on the use of monoclonal antibodies (mAb). In this study, we present not only analysis of the antigenic, but also of the genetic variability of BRSV. Using a panel of BRSV-specific mAb we distinguished five main reactivity patterns, three of which corresponded to the previously established subgroups A, B and AB. A single viral strain yielded the fourth pattern, while four viral strains did not react with any of the used mAbs forming the fifth pattern. To investigate the genetic basis for the antigenic heterogeneity of the BRS virus G protein, DNA of 11 BRSV isolates was directly sequenced. The comparison of the obtained nucleotide or amino acid sequences to those BRSV strains present in the GenBank revealed 88.1-99.4% and 77.7-98.4% similarity, respectively. These results supported the previously stated suggestion to type BRSV isolates according to their genetic relationship. In order to introduce a rapid and simple method to study the genetic variability of BRSV, we utilized the restriction enzyme analysis of RT-PCR products derived from mRNAs corresponding to the most variable region of the BRSV glycoprotein G ectodomain. Using this restriction enzyme analysis we were able to identify genetic variability among BRSV isolates. The detected non-synonymous mutations led frequently to a change in digestion pattern and were predominantly located in two mucin-like regions of the G protein gene. A correlation has been found between grouping of isolates in the phylogenetic tree and their restriction patterns clustering together isolates with the same restriction profiles. However, viruses placed distant in the tree sharing the same restriction patterns were detected supposing that phylogenetic analysis should be necessary for BRSV typing. Thus, we propose to use DNA restriction polymorphism for a rapid detection of genetic variants among BRSV isolates circulating in cattle population and as a preliminary tool for their typing.
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Affiliation(s)
- V Valentova
- Veterinary Research Institute, Hudcova 70, 621 32 Brno, Czech Republic.
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Kuroiwa Y, Nagai K, Okita L, Yui I, Kase T, Nakayama T, Tsutsumi H. A phylogenetic study of human respiratory syncytial viruses group A and B strains isolated in two cities in Japan from 1980-2002. J Med Virol 2005; 76:241-7. [PMID: 15834873 DOI: 10.1002/jmv.20348] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The circulation pattern and genetic evolution of respiratory syncytial virus (RSV) in Japan were examined based on 109 RSV field strains isolated over 20 seasons (1980-2002) in two cities, Sapporo and Tokyo. The second hypervariable region of the large glycoprotein (G) gene was amplified by RT-PCR and the products sequenced directly. The nucleotide sequences were compared to those representatives of RSV genotypes identified previously. Japanese group A and B isolates clustered into five and four genotypes defined previously, respectively. Another one group A and one group B genotypes, which could not be assigned to previous genotypes, were also identified. Although different genotypes usually co-circulated in each season, the isolates in proximate seasons from two communities were usually located in the same branches. Moreover, the strains with genotypes defined previously were usually isolated at the same time as each reference strain of Western countries. Several mutant group B strains with 1-20 longer amino acid G proteins were newly identified in Sapporo. These findings suggest that Japanese RSV strains underwent geographical and also temporal clustering while participating in RSV genetic evolution in a global setting. In addition, Japanese strains, especially group B, might have evolved individually in each community, sometimes changing the length of the G protein.
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Affiliation(s)
- Yuki Kuroiwa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Japan
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Rafiefard F, Johansson B, Tecle T, Orvell C. Molecular epidemiology of respiratory syncytial virus (RSV) of group A in Stockholm, Sweden, between 1965 and 2003. Virus Res 2004; 105:137-45. [PMID: 15351487 DOI: 10.1016/j.virusres.2004.05.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2003] [Revised: 05/13/2004] [Accepted: 05/18/2004] [Indexed: 11/26/2022]
Abstract
The epidemiology of respiratory syncytial virus (RSV) group A was followed by nucleotide sequencing of the variable parts of the glycoprotein (G) gene. The amino acid sequences of an aminoterminal (A-terminal, amino acids 90-132) and carboxyterminal (C-terminal, amino acids 262-298) portion of the G protein in 47 virus strains, collected in Stockholm, between 1965 and 2004, were determined. In phylogenetic analysis jointly with previously described genotypes (GA1 to GA7 and SAA1), 33 virus strains (isolated between 1991 and 2004) belonged to genotype GA5, seven to GA2, three to genotype GA1 (isolated before 1991), one to genotype GA4 (isolated in 1982) and three to genotype GA7 (isolated in 1993 and 2001). Genotype GA5 was predominant in four epidemics, between 2000/2001 and 2003/2004. Little or no variation with time of the C-terminal amino acid sequence of the G protein was found when the virus strains were compared within their own genotype. Identical and nearly identical nucleotide sequences were found between strains isolated more than 10 (GA5) and 25 (GA2) years apart. The A-terminal part of they G protein of genotype GA2 was highly conserved. In contrast, the A-terminal part of the G protein of genotype GA5 exhibited a pronounced variation in its amino acid sequence over time.
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Affiliation(s)
- Farideh Rafiefard
- Department of Clinical Virology, Karolinska Institutet, Karolinska University Hospital, SE-141 86 Stockholm, Sweden
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Kuroiwa Y, Nagai K, Okita L, Tsutsumi H. Genetic variability and molecular epidemiology of respiratory syncytial virus subgroup a strains in Japan determined by heteroduplex mobility assay. J Clin Microbiol 2004; 42:2048-53. [PMID: 15131169 PMCID: PMC404669 DOI: 10.1128/jcm.42.5.2048-2053.2004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We used heteroduplex mobility assay (HMA) to determine the genetic variability of 118 respiratory syncytial virus (RSV) field isolates from 19 epidemics occurring in a Japanese urban area between 1980 and 2000. Nucleotides 1 to 584 of the attachment G glycoprotein gene were amplified by reverse transcription-PCR, and the PCR amplicons were analyzed by HMA by using the earliest isolate from 1980 as the reference throughout. We also performed PCR-restriction fragment length polymorphism (RFLP) analysis and phylogenetic analysis on the same nucleotide sequence. PCR-RFLP revealed 9 patterns, whereas HMA produced 31 distinct patterns. The RFLP patterns were divided into two to seven distinct HMA genotypes. Field strains with similar degrees of G gene nucleotide differences from the reference strain often showed distinct HMA types. The RSV genetic heterogeneity detected by direct sequencing of the PCR amplicon was usually identical to HMA analysis. Analysis of the molecular epidemiology of RSV subgroup A isolates obtained by HMA showed that new RSV variants emerged with each epidemic and that previously dominant variants seldom recurred in subsequent epidemics. HMA is useful in detecting genetic variants of RSV subgroup A and has some advantages over other conventional methods.
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Affiliation(s)
- Yuki Kuroiwa
- Department of Pediatrics, Sapporo Medical University School of Medicine, Sapporo, Hokkaido 060-8543, Japan.
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50
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Elliott MB, Pryharski KS, Yu Q, Parks CL, Laughlin TS, Gupta CK, Lerch RA, Randolph VB, LaPierre NA, Dack KMH, Hancock GE. Recombinant respiratory syncytial viruses lacking the C-terminal third of the attachment (G) protein are immunogenic and attenuated in vivo and in vitro. J Virol 2004; 78:5773-83. [PMID: 15140975 PMCID: PMC415824 DOI: 10.1128/jvi.78.11.5773-5783.2004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The design of attenuated vaccines for respiratory syncytial virus (RSV) historically focused on viruses made sensitive to physiologic temperature through point mutations in the genome. These prototype vaccines were not suitable for human infants primarily because of insufficient attenuation, genetic instability, and reversion to a less-attenuated phenotype. We therefore sought to construct novel attenuated viruses with less potential for reversion through genetic alteration of the attachment G protein. Complete deletion of G protein was previously shown to result in RSV strains overly attenuated for replication in mice. Using reverse genetics, recombinant RSV (rRSV) strains were engineered with truncations at amino acid 118, 174, 193, or 213 and respectively designated rA2cpDeltaG118, rA2cpDeltaG174, rA2cpDeltaG193, and rA2cpDeltaG213. All rA2cpDeltaG strains were attenuated for growth in vitro and in the respiratory tracts of BALB/c mice but not restricted for growth at 37 degrees C. The mutations did not significantly affect nascent genome synthesis in human lung epithelial (A549) cells, but infectious rA2cpDeltaG virus shed into the culture medium was dramatically diminished. Hence, the data suggested that a site within the C-terminal 85 amino acids of G protein is important for efficient genome packaging or budding of RSV from the infected cell. Vaccination with the rA2cpDeltaG strains also generated efficacious immune responses in mice that were similar to those elicited by the temperature-sensitive cpts248/404 strain previously tested in human infants. Collectively, the data indicate that the rA2cpDeltaG strains are immunogenic, not likely to revert to the less-attenuated phenotype, and thus candidates for further development as vaccines against RSV.
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Affiliation(s)
- Matthew B Elliott
- Wyeth Vaccines Research, 401 N. Middletown Rd., Pearl River, NY 10965, USA
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