About: Variability analysis and inter-genotype comparison of human respiratory syncytial virus small hydrophobic gene

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About: Variability analysis and inter-genotype comparison of human respiratory syncytial virus small hydrophobic gene Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Variability analysis and inter-genotype comparison of human respiratory syncytial virus small hydrophobic gene
Creator	Ljubin-Sternak, Sunčanica Forcic, Dubravko Ivancic-Jelecki, Jelena Mlinarić Galinović, Gordana Slovic, Anamarija
Source	Medline; PMC
abstract	BACKGROUND: Small hydrophobic (SH) gene is one of the mostly diverse genomic regions of human respiratory syncytial virus (HRSV). Its coding region constitutes less than 50% of the complete gene length, enabling SH gene to be highly variable and the SH protein highly conserved. In standard HRSV molecular epidemiology studies, solely sequences of the second hypervariable region of the glycoprotein gene (HVR2) are analyzed. To what extent do the strains identical in HVR2 differ elsewhere in genomes is rarely investigated. Our goal was to investigate whether diversity and inter-genotype differences observed for HVR2 are also present in the SH gene. METHODS: We sequenced 198 clinical samples collected within a limited area and time frame. In this HRSV collection, rapid and significant changes in HVR2 occurred. RESULTS: Over 20% of strains from this pool (containing HRSV genotypes NA1, ON1, GA5, BA9 and BA10) would be incorrectly assumed to be identical to another strain if only the HVR2 region was analysed. The majority of differences found in SH gene were located in the 5′ untranslated region (UTR). Seven indels were detected, one was genotype GA5 specific. An in-frame deletion of 9 nucleotides (coding for amino acids 49–51) was observed in one of group A strains. Fifteen different SH protein sequences were detected; 68% of strains possessed the consensus sequence and most of others differed from the consensus in only one amino acid (only 4 strains differed in 2 amino acids). The majority of differing amino acids in group A viruses had the same identity as the corresponding amino acids in group B strains. When analysis was restricted to strains with identical HVR2 nucleotide sequences and differing SH protein sequences, 75% of differences observed in the SH ectodomain were located within region coding for amino acids 49–51. CONCLUSIONS: Basing HRSV molecular epidemiology studies solely on HVR2 largely underestimates the complexity of circulating virus populations. In strain identification, broadening of the genomic target sequence to SH gene would provide a more comprehensive insight into viral pool versatility and its evolutionary processes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12985-018-1020-9) contains supplementary material, which is available to authorized users.
has issue date	2018-07-18(xsd:dateTime)
bibo:doi	10.1186/s12985-018-1020-9
bibo:pmid	30021648
has license	cc-by
sha1sum (hex)	76779657e67c07cb2632ac07b61146d7664c64a4
schema:url	https://doi.org/10.1186/s12985-018-1020-9
resource representing a document's title	Variability analysis and inter-genotype comparison of human respiratory syncytial virus small hydrophobic gene
has PubMed Central identifier	PMC6052705
has PubMed identifier	30021648
schema:publication	Virol J
resource representing a document's body	covid:76779657e67c07cb2632ac07b61146d7664c64a4#body_text
is schema:about of	named entity 'limited' named entity 'observed' named entity 'amino acids' named entity 'investigate' named entity 'variable' named entity 'located' named entity 'gene' named entity 'protein' named entity 'viruses' named entity 'gene' named entity 'strains' named entity 'strains' named entity 'Fifteen' named entity 'protein' named entity 'group B' named entity 'STUDIES' named entity 'HUMAN RESPIRATORY SYNCYTIAL VIRUS' named entity 'DIVERSITY' named entity 'ASSUMED' named entity 'region' named entity 'Methods' named entity 'strains' named entity 'identical' named entity 'human respiratory syncytial virus' named entity 'located' named entity 'GA5' named entity 'studies' named entity 'strains' named entity 'conserved' named entity 'HVR2' named entity 'amino acids' named entity 'HRSV' named entity 'clinical samples' named entity 'coding region' named entity 'gene' named entity 'genotypes' named entity 'nucleotide sequences' named entity 'protein' named entity 'in-frame deletion' named entity 'consensus sequence' named entity 'amino acid' named entity 'amino acids' named entity 'highly conserved' named entity 'human respiratory syncytial virus' named entity 'hydrophobic' named entity 'genotypes' named entity 'genome sequence' named entity 'amino acid' named entity 'gene' named entity 'BA10' named entity 'Nucleotides' named entity 'poly A tail' named entity 'RNA' named entity 'start codon' named entity 'amino acids' named entity 'HRSV' named entity 'genomic sequences' named entity 'glycoprotein' named entity 'viruses' named entity 'Nasopharyngeal secretions' named entity 'protein' named entity 'synonymous substitutions' named entity 'RSV' named entity '5′ to 3′' named entity 'HRSV' named entity 'nucleotide' named entity 'amino acid' named entity 'mutation' named entity 'RNA' named entity 'gene' named entity 'amino acid' named entity 'BA9' named entity 'maximum-likelihood method' named entity 'HVR2' named entity 'gene' named entity 'protein' named entity 'protein'

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