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

Ivančić-Jelečki, Jelena and Slović, Anamarija and Ljubin-Sternak, Sunčanica and Mlinarić Galinović, Gordana and Forčić, Dubravko (2018) Variability analysis and inter-genotype comparison of human respiratory syncytial virus small hydrophobic gene. Virology Journal, 15 (1). p. 109. ISSN 1743-422X

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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.

Item Type: Article
Additional Information: © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
MeSH: Amino Acid Sequence ; Genetic Variation ; Genotype ; Humans ; Phylogeny ; Respiratory Syncytial Virus Infections/virology ; Respiratory Syncytial Virus, Human/classification ; Respiratory Syncytial Virus, Human/genetics ; Sequence Analysis, DNA ; Viral Proteins/genetics
Departments: Katedra za medicinsku mikrobiologiju i parazitologiju
Depositing User: Kristina Berketa
Status: Published
Creators:
CreatorsEmail
Ivančić-Jelečki, JelenaUNSPECIFIED
Slović, AnamarijaUNSPECIFIED
Ljubin-Sternak, SunčanicaUNSPECIFIED
Mlinarić Galinović, GordanaUNSPECIFIED
Forčić, DubravkoUNSPECIFIED
Date: 18 July 2018
Date Deposited: 19 Jul 2019 09:31
Last Modified: 25 Aug 2020 08:07
Subjects: /
Related URLs:
URI: http://medlib.mef.hr/id/eprint/3322

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