scholarly journals Early Evolution of Human Respiratory Syncytial Virus ON1 Strains: Analysis of the Diversity in the C-Terminal Hypervariable Region of Glycoprotein Gene within the First 3.5 Years since Their Detection

Intervirology ◽  
2015 ◽  
Vol 58 (3) ◽  
pp. 172-180 ◽  
Author(s):  
Jelena Ivancic-Jelecki ◽  
Dubravko Forcic ◽  
Gordana Mlinaric-Galinovic ◽  
Goran Tesovic ◽  
Ana Nikic Hecer
Keyword(s):  
Respiratory Syncytial Virus ◽  
Hypervariable Region ◽  
Human Respiratory Syncytial Virus ◽  
Early Evolution ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Multiple Sequence Alignments ◽  
Glycoprotein Gene ◽  
Glycosylation Sites ◽  
Syncytial Virus

Objective: Characterization of the phylogeny and diversity of human respiratory syncytial virus (HRSV) genotype ON1 that occurred during its early evolution (within the first 3.5 years since the detection of the first ON1 strains). ON1 strains have a 72-nucleotide-long in-frame duplication within the second hypervariable domain of the glycoprotein gene (HVR2). Methods: All available HVR2 sequences of strains belonging to the ON1 genotype published prior to June 20, 2014 were collected. Multiple sequence alignments, phylogeny, phylogeography, sequence clustering and putative protein analyses were performed. Results: The worldwide spread and diversification of ON1 strains are presented. Only in a minority of ON1 strains do the two replicas remain identical, and various ON1 strains possess common differences between the first and the second copy (segments A and B). Mutations of the progenitor sequence were more frequent in segment B, a higher overall diversity on the protein level and more putative glycosylation sites exist in segment B, and, unlike in segment A, positive selection acts on that protein region. Conclusions: The fast spread of the novel HRSV genotype ON1 has been accompanied by its rapid concurrent diversification. Differences in variability of the two replicas within HVR2 were detected, with C-terminal replica being more variable.

scholarly journals Genetic Diversity and Molecular Epidemiology of Circulating Respiratory Syncytial Virus in Central Taiwan, 2008–2017

Viruses ◽  
2021 ◽  
Vol 14 (1) ◽  
pp. 32
Author(s):  
Chun-Yi Lee ◽  
Yu-Ping Fang ◽  
Li-Chung Wang ◽  
Teh-Ying Chou ◽  
Hsin-Fu Liu
Keyword(s):  
Respiratory Syncytial Virus ◽  
Amino Acid ◽  
Temporal Evolution ◽  
Local Level ◽  
Hypervariable Region ◽  
Amino Acid Sequences ◽  
Sequence Alignments ◽  
Glycosylation Sites ◽  
Syncytial Virus ◽  
Central Taiwan

In this study, we investigated the molecular evolution and phylodynamics of respiratory syncytial virus (RSV) over 10 consecutive seasons (2008–2017) and the genetic variability of the RSV genotypes ON1 and BA in central Taiwan. The ectodomain region of the G gene was sequenced for genotyping. The nucleotide and deduced amino acid sequences of the second hypervariable region of the G protein in RSV ON1 and BA were analyzed. A total of 132 RSV-A and 81 RSV-B isolates were obtained. Phylogenetic analysis revealed that the NA1, ON1, and BA9 genotypes were responsible for the RSV epidemics in central Taiwan in the study period. For RSV-A, the NA1 genotype predominated during the 2008–2011 seasons. The ON1 genotype was first detected in 2011 and replaced NA1 after 2012. For RSV-B, the BA9 and BA10 genotypes cocirculated from 2008 to 2010, but the BA9 genotype has predominated since 2012. Amino acid sequence alignments revealed the continuous evolution of the G gene in the ectodomain region. The predicted N-glycosylation sites were relatively conserved in the ON1 (site 237 and 318) and BA9 (site 296 and 310) genotype strains. Our results contribute to the understanding and prediction of the temporal evolution of RSV at the local level.

scholarly journals Respiratory syncytial virus B sequence analysis reveals a novel early genotype

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Juan C. Muñoz-Escalante ◽  
Andreu Comas-García ◽  
Sofía Bernal-Silva ◽  
Daniel E. Noyola
Keyword(s):  
Molecular Markers ◽  
Respiratory Syncytial Virus ◽  
Maximum Likelihood ◽  
Respiratory Infections ◽  
Phylogenetic Analyses ◽  
Detection Methods ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Individual Gene ◽  
Syncytial Virus

AbstractRespiratory syncytial virus (RSV) is a major cause of respiratory infections and is classified in two main groups, RSV-A and RSV-B, with multiple genotypes within each of them. For RSV-B, more than 30 genotypes have been described, without consensus on their definition. The lack of genotype assignation criteria has a direct impact on viral evolution understanding, development of viral detection methods as well as vaccines design. Here we analyzed the totality of complete RSV-B G gene ectodomain sequences published in GenBank until September 2018 (n = 2190) including 478 complete genome sequences using maximum likelihood and Bayesian phylogenetic analyses, as well as intergenotypic and intragenotypic distance matrices, in order to generate a systematic genotype assignation. Individual RSV-B genes were also assessed using maximum likelihood phylogenetic analyses and multiple sequence alignments were used to identify molecular markers associated to specific genotypes. Analyses of the complete G gene ectodomain region, sequences clustering patterns, and the presence of molecular markers of each individual gene indicate that the 37 previously described genotypes can be classified into fifteen distinct genotypes: BA, BA-C, BA-CC, CB1-THB, GB1-GB4, GB6, JAB1-NZB2, SAB1, SAB2, SAB4, URU2 and a novel early circulating genotype characterized in the present study and designated GB0.

scholarly journals Towards a unified classification for human respiratory syncytial virus genotypes

2020 ◽  
Vol 6 (2) ◽  
Author(s):  
Kaat Ramaekers ◽  
Annabel Rector ◽  
Lize Cuypers ◽  
Philippe Lemey ◽  
Els Keyaerts ◽  
...  
Keyword(s):  
Respiratory Syncytial Virus ◽  
Phylogenetic Trees ◽  
Phylogenetic Signal ◽  
Phylogenetic Reconstruction ◽  
Hypervariable Region ◽  
Human Respiratory Syncytial Virus ◽  
Bootstrap Support ◽  
Whole Genome ◽  
Patristic Distance ◽  
Syncytial Virus

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.

scholarly journals Molecular Evolution and Circulation Patterns of Human Respiratory Syncytial Virus Subgroup A: Positively Selected Sites in the Attachment G Glycoprotein

2004 ◽  
Vol 78 (9) ◽  
pp. 4675-4683 ◽  
Author(s):  
Kalina T. Zlateva ◽  
Philippe Lemey ◽  
Anne-Mieke Vandamme ◽  
Marc Van Ranst
Keyword(s):  
Respiratory Syncytial Virus ◽  
Hypervariable Region ◽  
Human Respiratory Syncytial Virus ◽  
Likelihood Method ◽  
Recent Common Ancestor ◽  
Nucleotide Substitutions ◽  
Most Recent Common Ancestor ◽  
Syncytial Virus ◽  
Positively Selected Sites

ABSTRACT Human respiratory syncytial virus (HRSV) is the most common etiological agent of acute lower respiratory tract disease in infants and can cause repeated infections throughout life. In this study, we have analyzed nucleotide sequences encompassing 629 bp at the carboxy terminus of the G glycoprotein gene for HRSV subgroup A strains isolated over 47 years, including 112 Belgian strains isolated over 19 consecutive years (1984 to 2002). By using a maximum likelihood method, we have tested the presence of diversifying selection and identified 13 positively selected sites with a posterior probability above 0.5. The sites under positive selection correspond to sites of O glycosylation or to amino acids that were previously described as monoclonal antibody-induced in vitro escape mutants. Our findings suggest that the evolution of subgroup A HRSV G glycoprotein is driven by immune pressure operating in certain codon positions located mainly in the second hypervariable region of the ectodomain. Phylogenetic analysis revealed the prolonged cocirculation of two subgroup A lineages among the Belgian population and the possible extinction of three other lineages. The evolutionary rate of HRSV subgroup A isolates was estimated to be 1.83 × 10−3 nucleotide substitutions/site/year, projecting the most recent common ancestor back to the early 1940s.

Identification of Australian human respiratory syncytial virus strains containing a 60-nucleotide duplication within the G glycoprotein gene

Pathology ◽  
2008 ◽  
Vol 40 (6) ◽  
pp. 632-635 ◽  
Author(s):  
Sarah Tozer ◽  
David M. Whiley ◽  
Gary Lum ◽  
William D. Rawlinson ◽  
Leanne M. Sammels ◽  
...  
Keyword(s):  
Respiratory Syncytial Virus ◽  
Human Respiratory Syncytial Virus ◽  
Glycoprotein Gene ◽  
Syncytial Virus ◽  
Virus Strains

scholarly journals Expression of the G glycoprotein gene of human respiratory syncytial virus in Salmonella typhimurium

1993 ◽  
Vol 74 (3) ◽  
pp. 453-458 ◽  
Author(s):  
A. Martin-Gallardo ◽  
E. Fleischer ◽  
S. A. Doyle ◽  
R. Arumugham ◽  
P. L. Collins ◽  
...  
Keyword(s):  
Respiratory Syncytial Virus ◽  
Salmonella Typhimurium ◽  
Human Respiratory Syncytial Virus ◽  
Glycoprotein Gene ◽  
Syncytial Virus

Expression of the F glycoprotein gene from human respiratory syncytial virus inEscherichia coli: Mapping of a fusion inhibiting epitope

Virology ◽  
1991 ◽  
Vol 184 (1) ◽  
pp. 428-432 ◽  
Author(s):  
Antonia Martin-Gallardo* ◽  
Karen A. Fien ◽  
Branda T. Hu ◽  
John F. Farley ◽  
Robert Seid ◽  
...  
Keyword(s):  
Respiratory Syncytial Virus ◽  
Human Respiratory Syncytial Virus ◽  
Inescherichia Coli ◽  
Glycoprotein Gene ◽  
Syncytial Virus
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