Molecular detection and genetic characterization of human metapneumovirus strains circulating in Islamabad, Pakistan

Abstract

Lower respiratory illness is one of the leading causes of death among children in low- and high-income countries. Human metapneumovirus (hMPV) is a key contributor to respiratory illnesses commonly reported among children and causes serious clinical complications ranging from mild respiratory infections to severe lower respiratory tract anomalies mainly in the form of bronchiolitis and pneumonia. However, due to the lack of a national surveillance system, the clinical significance of hMPV remains obscure in the Pakistani population. This study was conducted to screen throat swabs samples collected from 127 children reported with respiratory symptoms at a tertiary care hospital in Islamabad. Out of 127, 21 (16.5%) samples were positive for hMPV with its genotype distribution as A2a (10%), A2b (20%), B1 (10%), and B2 (60%). Phylogenetic analysis showed that the hMPV viruses were closely related to those reported from neighboring countries including India and China. This work will contribute to a better understanding of this virus, its diagnosis, and the handling of patients in clinical setups. Further studies at a large-scale are warranted for a better understanding of the disease burden and epidemiology of hMPV in Pakistan.

Figure 1

Schematic representation of the cleaved hMPV fusion protein. FP fusion peptide, HRA heptad repeat A, HRB heptad repeat B, TM transmembrane domain, CT cytoplasmic tail. The approximate location of a conserved RGD motif (residues 329–331) is indicated as a magenta box. Arrows indicate the three N-linked glycosylation sites. The location of two disulfide bonds that connect the F1 and F2 protein subunits are shown as S–S.

Figure 2

Phylogenetic analysis of partial F gene of 11 hMPV strains identified in this study (filled circles) Empty circles represents the prototypes for the groups or sub-groups using the Maximum Likelihood method.

Figure 3

Sequence alignment of hMPV A2 genotype. The two N-glycosylation sites are highlighted with green squares and substitutions are highlighted with red squares.

Figure 4

Sequence alignment of hMPV B2 genotype. The two N-glycosylation sites are highlighted with green squares and substitutions are highlighted with red squares.

Figure 5

Month-wise distribution of hMPV positive samples.