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Updated: Jan 23, 2026
Generation and Assembly of Virus-Specific Nucleocapsids of the Respiratory Syncytial Virus
Published on: July 27, 2021
Molecular characterization of circulating respiratory syncytial virus genotypes in Pakistani children, 2010-2013
Uzma Bashir Aamir1, Muhammad Salman2, Nadia Nisar2
1World Health Organization, Pakistan Country Office, Chak Shehzad, Islamabad, Pakistan.
Insights
Human respiratory syncytial virus (RSV) significantly impacts Pakistani children under five. This study identified diverse RSV genotypes, including a new BA-13 subtype, emphasizing the need for ongoing surveillance.
Area of Science:
- Virology
- Epidemiology
- Public Health
Background:
- Limited data exists on viral causes of acute lower respiratory infections in Pakistan.
- Human respiratory syncytial virus (RSV) is a major cause of childhood illness, with no current vaccine or antiviral treatments.
- Understanding local RSV genotypes is crucial for future vaccine development and public health strategies.
Purpose of the Study:
- To determine the molecular epidemiology of Human respiratory syncytial virus (RSV) genotypes A and B in Pakistani children under five years old.
- To provide baseline data for future vaccine efficacy studies and public health interventions.
- To identify prevalent and emerging RSV strains in Pakistan.
Main Methods:
- Children under five presenting with influenza-like illness (ILI) or severe acute respiratory illness (SARI) were enrolled from 2010-2013.
- Nasopharyngeal/throat swabs were analyzed using real-time polymerase chain reaction (PCR) for RSV A and B.
- G protein sequencing and phylogenetic analysis were performed for RSV subtyping.
Main Results:
- Out of 1941 samples, RSV was detected in 472 (24%) children.
- RSV A was detected in 367 (78%) and RSV B in 105 (22%) of positive cases.
- RSV A strains belonged to the NA1/GA2 genotype, while RSV B strains showed a 60-nucleotide duplication, falling into BA-9, BA-10, and a novel BA-13 genotype.
Conclusions:
- Human respiratory syncytial virus (RSV) is a significant cause of acute respiratory infections in Pakistani children.
- The study revealed genetic diversity among circulating RSV strains, including a new genotype.
- Continuous molecular surveillance is essential for tracking RSV epidemiology and emerging genotypes in Pakistan.
Background:
Data on the viral etiology of acute lower respiratory infections are scarce in Pakistan. Human respiratory syncytial virus (RSV) is an important cause of morbidity in children but no effective vaccine or antiviral therapy is currently available. As vaccines are expected to become available in the future, it is important to understand the epidemiology of locally prevalent RSV subtypes. This study aimed to define the molecular epidemiology of RSV (A and B) genotypes in Pakistani children under 5 years.
Methods:
World Health Organization case definitions for influenza-like illness (ILI) and severe acute respiratory illness (SARI) were used for case selection. Children under 5 years who presented with ILI or SARI at tertiary care hospitals from all provinces/regions, including the eight influenza sentinel sites, during October-April each year between 2010 and 2013 were enrolled. Demographic and clinical data of the children were recorded and nasopharyngeal/throat swabs taken for analysis. All samples were tested for RSV A and B using real-time polymerase chain reaction for non-influenza respiratory viruses. Specific oligonucleotide primers for RSV A and B were used for subtyping and sequencing of the G protein, followed by phylogenetic analysis.
Results:
A total of 1941 samples were included. RSV was detected in 472 (24%) children, with RSV A detected in 367 (78%) and RSV B in 105 (22%). The G protein of all RSV A strains clustered in the NA1/GA2 genotype while RSV B strains carried the signature 60 nucleotide duplication and were assigned to three BA genotypes: BA-9, BA-10 and the new BA-13 genotype.
Conclusions:
This study highlights the importance of RSV as a viral etiologic agent of acute respiratory infections in children in Pakistan, and the diversity of RSV viruses. Continued molecular surveillance for early detection of prevalent and newly emerging genotypes is needed to understand the epidemiology of RSV infections in Pakistan.
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