# Tracking Respiratory Viruses in Pakistan (2022–2025): Genomic and Epidemiologic Insights from Sentinel Surveillance of Influenza, SARS-CoV-2, and RSV

## TL;DR

This study tracks respiratory viruses in hospitalized patients in Pakistan from 2022 to 2025, revealing patterns and impacts of influenza, RSV, and SARS-CoV-2.

## Contribution

The study provides genomic and epidemiologic insights into respiratory viruses in Pakistan through multi-center surveillance.

## Key findings

- RSV was the most common virus in children under 2 years, while influenza and SARS-CoV-2 affected adults aged 15–40 years.
- Phylogenetic analysis showed rapid SARS-CoV-2 variant succession and vaccine-matched influenza clades.
- Strong winter seasonality was observed for influenza and RSV, with significant ICU admission rates for RSV and influenza.

## Abstract

Influenza and other respiratory viruses pose significant public health threats among SARI patients, yet comprehensive surveillance data remain limited in Pakistan. This prospective, multi-center study characterized the burden, distribution, and molecular evolution of respiratory viruses among hospitalized SARI patients across seven tertiary hospitals from November 2022 to June 2025. Specimens were tested using RT-PCR for influenza, SARS-CoV-2, and RSV, with 375 samples sequenced via Oxford Nanopore Technology. Among 11,451 specimens, 2818 (24.6%) tested positive: RSV (1648, 14.4%), influenza (855, 7.5%; 45% H1N1pdm09, 35% H3N2, 20% influenza B), and SARS-CoV-2 (315, 2.8%). RSV predominantly affected children under 2 years (63%), while influenza and SARS-CoV-2 primarily impacted adults aged 15–40 years. Male predominance (65–79%) reflected healthcare access barriers. Strong winter seasonality (December–February) was observed for influenza and RSV. ICU admission rates were 17% for influenza, 16% for RSV, and 4% for SARS-CoV-2. Shortness of breath was associated with influenza (OR = 1.62) and RSV (OR = 1.27), while malaise (OR = 2.24) and myalgia (OR = 3.87) was associated with SARS-CoV-2. Phylogenetic analysis revealed vaccine-matched influenza clades and rapid SARS-CoV-2 variant succession (3–4 months). RSV is the primary SARI pathogen in young children, necessitating maternal vaccines and nirsevimab implementation. Sustained genomic surveillance remains essential for pandemic preparedness.