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. 2022 Dec 5;13(12):2288.
doi: 10.3390/genes13122288.

ON-1 and BA-IX Are the Dominant Sub-Genotypes of Human Orthopneumovirus A&B in Riyadh, Saudi Arabia

Rasha M Alzayed  1   2 , Ibrahim M Aziz  1 , Asma N Alsaleh  1 , Gani Asa Dudin  1 , Anwar A Ahmed  3 , Tajamul Hussain  3 , Abdullah K Alshememry  4 , Ali M Somily  5 , Muslim M Alsaadi  6 , Fahad N Almajhdi  1
Affiliations

ON-1 and BA-IX Are the Dominant Sub-Genotypes of Human Orthopneumovirus A&B in Riyadh, Saudi Arabia

Rasha M Alzayed et al. Genes (Basel). .

Abstract

Human orthopneumovirus (HOPV) is the major viral pathogen responsible for lower respiratory tract infections (LRTIs) in infants and young children in Riyadh, Saudi Arabia. Yet, predominant HOPV subtypes circulating in this region and their molecular and epidemiological characteristics are not fully ascertained. A total of 300 clinical samples involving nasopharyngeal aspirates (NPAs), throat swabs, and sputum were collected during winter seasons of 2019/2020 and 2021/2022 for HOPV subtyping and genotyping. Of the 300 samples, HOPV was identified in 55 samples (18.3%) with a distinct predominance of type A viruses (81.8%) compared to type B viruses (18.2%). Importantly, the ON1 strain of HOPV-A and BA-IX strain of HOPV-B groups were found to be responsible for all the infections. Sequence analysis revealed a duplication region within 2nd HVR of G protein gene of ON1 and BA-IX strains. This nucleotide duplication exerted a profound effect on protein length and affinity towards cell receptors. Further, these modifications may aid the HOPV in immune evasion and recurrent infections. Data from this study showed that ON-1 genotype of HOPV-A and BA-IX genotype of HOPV-B were dominant in Riyadh, Saudi Arabia. Further, a duplication of sequence within 2nd HVR of G protein gene was found.

Keywords: 2nd HVR; BA-IX; HRSV; ON-1; Riyadh; Saudi Arabia; human orthopneumovirus.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Phylogenetic trees for HOPV group A (A) and group B (B). The 270 base nucleotide sequences of the C-terminal fragment of the 2nd HVR of the G protein gene were used for alignment. The phylogeny tree was created using the neighbor-joining method using MEGA11 program. The numbers at the internal nodes of the tree represent the bootstrap values of 1000 replicates. Only values exceeding 60% are shown. Strains of seasons 2019/2020 and 2021/2022 are denoted by red.
Figure 2
Figure 2
Alignment of deduced AA sequences of the 2nd HVR of the G genes of HOPV group A. The AA positions corresponded to AA positions of the relative to the sequences of prototype ON1 strain. Different AAs are marked in different colors, identical residues are presented by dots. The original and duplicated amino-acid region are shown in the green rectangles. Red rectangles color = the AA residues specific to genotype. Predicted N-glycosylation sites are enclosed in black rectangles. Small filled circles correspond to predicted O-glycosylation sites.
Figure 3
Figure 3
Deduced AA sequence alignment of 2nd HVR of G protein gene of the HOPV-B. The alignment was performed by the Clustal W method running within the MegAlign program (DNAstar). Alignment is shown relative to the BA prototype strain from Argentina. Dots are indicated for identical AA residues, while sequence variation is identified in single-letter code. The duplicated regions are shown in the green rectangles. Red rectangles color = the AA residues specific to HOPV-genotype. Predicted N-glycosylation sites are enclosed in black rectangles. Small filled circles = predicted O-glycosylation sites.
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