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

Virology Journal
Jelena Ivancic-JeleckiDubravko Forcic

Abstract

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. We sequenced 198 clinical samples collected within a limited area and time frame. In this HRSV collection, rapid and significant changes in HVR2 occurred. 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 stra...Continue Reading

References

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Jun 25, 2016·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Anamarija SlovicDubravko Forcic

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Citations

Sep 16, 2019·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·M JagusicD Forcic

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Datasets Mentioned

BETA
KX765891

Methods Mentioned

BETA
genotyping
PCR
glycosylation

Software Mentioned

Datamonkey
ClustalX
NetOGlyc
HyPhy
BioEdit
MEGA
jModeltest

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