Abstract
Background and objectives: The human respiratory syncytial virus (hRSV) is among the important respiratory pathogens affecting children. Genotype-specific attachment (G) gene sequencing is usually used to determine the virus genotype. The reliability of the fusion (F) gene vs. G gene genotype-specific sequencing was screened. Materials and Methods: Archival RNA from Saudi children who tested positive for hRSV-A were used. Samples were subjected to a conventional one-step RT-PCR for both F and G genes and direct gene sequencing of the amplicons using the same primer sets. Phylogeny and mutational analysis of the obtained sequences were conducted. Results: The generic primer set succeeded to amplify target gene sequences. The phylogenetic tree based on partial F gene sequencing resulted in an efficient genotyping of hRSV-A strains equivalent to the partial G gene genotyping method. NA1, ON1, and GA5 genotypes were detected in the clinical samples. The latter was detected for the first time in Saudi Arabia. Different mutations in both conserved and escape-mutant domains were detected in both F and G. Conclusion: It was concluded that a partial F gene sequence can be used efficiently for hRSV-A genotyping.
Highlights
Human respiratory syncytial virus causes considerable respiratory distress with variable severity in infancy and early childhood [1,2]
Direct Sequencing and Phylogenetic Analysis. Both generic primers for F and G genes were successful in amplification of the strains, showing relatively high viral load for 13 of the 59 samples (≥1 × 103.5 copies/mL)
The F gene domains of the human respiratory syncytial virus (hRSV)-A isolates possess about 10% nucleotide variability
Summary
Human respiratory syncytial virus (hRSV) causes considerable respiratory distress with variable severity in infancy and early childhood [1,2]. The G glycoprotein is a type II surface protein which is highly glycosylated and possesses a considerable degree of nucleotide variability [8]. It possesses two hypervariable regions (HVR1 and HVR2); the HVR2 in the C-terminal region is used to screen the G gene variability of different genotypes [9,10]. NA1, ON1, and GA5 genotypes were detected in the clinical samples
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