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

Human respiratory syncytial virus (HRSV) is a major cause of lower respiratory tract infections, especially among infants and young children. The virus belongs to the Orthopneumovirus genus of the Pneumoviridae family and its molecular epidemiology is characterized by co-circulation of numerous strains. In standard molecular surveillance studies, solely sequences of the 2nd hypervariable region of the glycoprotein (G) gene (HVR2, coding for a region located in the G ectodomain) are analysed. HVR2 is not a representative segment of the HRSV genome, as it is marked by elevated mutation rates due to relaxed selective constraints and frequent flip- flop substitutions. To what extent are strains different in HVR2 different in other genomic regions is rarely investigated. The goal of our study was to investigate whether inter-genotype differences observed for HVR2 are also present in the SH gene, the 2nd mostly diverse HRSV genomic region. We analysed SH genes in a set of 198 clinical samples collected in a limited geographical area (Zagreb region) and time frame (03/2011-03/2014). Within this viral pool, rapid and significant evolutionary changes have occurred in HVR2. The level of genetic diversity observed in SH sequences was not comparable to the one detected in HVR2, especially not in the coding region of the gene. A number of strains identical at HVR2 differed at SH, and vice versa. Seven indels were detected, one was genotype specific. An in-frame deletion of 9 nucleotides (coding for amino acids 49-51) was observed in a single group A strain. SH protein sequence analysis showed that little variability is tolerated, even in the ectodomain which is potentially exposed to antibodies. Fifteen different SH protein sequences were detected ; 68% of strains possessed the consensus sequence and others differed mostly in only one amino acid (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, indicating that it might be under immunological pressure. As evolutionary patterns in SH gene and HVR2 are different, broadening the target sequence for HRSV surveillance to SH would provide better insight into the versatility of the virus.

human respiratory syncytial virus ; HRSV ; small hydrophobic gene ; genetic variability ; molecular epidemiology

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