{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,23]],"date-time":"2026-07-23T05:36:24Z","timestamp":1784784984088,"version":"3.55.0"},"reference-count":27,"publisher":"MDPI AG","issue":"1","license":[{"start":{"date-parts":[[2025,12,23]],"date-time":"2025-12-23T00:00:00Z","timestamp":1766448000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Global Influenza Hospital Surveillance Network","award":["00170286\/EF-2025-59051"],"award-info":[{"award-number":["00170286\/EF-2025-59051"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>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\u201340 years. Male predominance (65\u201379%) reflected healthcare access barriers. Strong winter seasonality (December\u2013February) 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\u20134 months). RSV is the primary SARI pathogen in young children, necessitating maternal vaccines and nirsevimab implementation. Sustained genomic surveillance remains essential for pandemic preparedness.<\/jats:p>","DOI":"10.3390\/v18010026","type":"journal-article","created":{"date-parts":[[2025,12,24]],"date-time":"2025-12-24T09:58:34Z","timestamp":1766570314000},"page":"26","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Tracking Respiratory Viruses in Pakistan (2022\u20132025): Genomic and Epidemiologic Insights from Sentinel Surveillance of Influenza, SARS-CoV-2, and RSV"],"prefix":"10.3390","volume":"18","author":[{"given":"Nazish","family":"Badar","sequence":"first","affiliation":[{"name":"Public Health Laboratories Division, National Institute of Health, Chak Shahzad, Park Road, Islamabad 45500, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abdul","family":"Ahad","sequence":"additional","affiliation":[{"name":"Public Health Laboratories Division, National Institute of Health, Chak Shahzad, Park Road, Islamabad 45500, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hamza Ahmed","family":"Mirza","sequence":"additional","affiliation":[{"name":"Public Health Laboratories Division, National Institute of Health, Chak Shahzad, Park Road, Islamabad 45500, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fazal","family":"Hanan","sequence":"additional","affiliation":[{"name":"Saidu Group of Teaching Hospital, Pathology Department, Saidu Medical College, Swat 19200, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Asghar","family":"Javaid","sequence":"additional","affiliation":[{"name":"Pathology Department, Nishtar Medical University, Multan 66000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aamir","family":"Amanat","sequence":"additional","affiliation":[{"name":"Public Health Laboratories Division, National Institute of Health, Chak Shahzad, Park Road, Islamabad 45500, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zunira","family":"Saghir","sequence":"additional","affiliation":[{"name":"Public Health Laboratories Division, National Institute of Health, Chak Shahzad, Park Road, Islamabad 45500, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad","family":"Salman","sequence":"additional","affiliation":[{"name":"National Institute of Health, Chak Shahzad, Park Road, Islamabad 45500, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,12,23]]},"reference":[{"key":"ref_1","first-page":"101034","article-title":"Performance of the World Health Organization (WHO) severe acute respiratory infection (SARI) case definitions in hospitalized children and youth: Cross-sectional study","volume":"44","author":"Gill","year":"2025","journal-title":"Lancet Reg. 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