Genomic Surveillance of Respiratory Syncytial Virus among Patients with Acute Respiratory Infection through Hospital-Based Influenza Surveillance Platforms in Bangladesh, August 2024–December 2025
Discuss this preprint
Start a discussion What are Sciety discussions?Listed in
This article is not in any list yet, why not save it to one of your lists.Abstract
Background
RSV is one of the major contributing factors of acute lower respiratory tract infection among younger children who are below five years old; over 95% of the burden falls on low- and middle-income countries. Bangladesh faces a substantial pediatric RSV burden yet lacks post-pandemic whole-genome data. Approval of nirsevimab and maternal vaccines (Arexvy, Abrysvo), underscores the need for region-specific genomic surveillance to inform prevention and control strategies.
Objectives
To conduct the whole-genome sequencing (WGS) study of RSV in Bangladeshi population, characterizing viral genotypic diversity, phylogenetics, F and G protein mutations, glycosylation dynamics, while generating and depositing complete genomes in GISAID.
Methods
Between August 2024 and December 2025, of 1,390 RSV-positive specimens (Ct ≤35), 59 high-viral-load samples (Ct ≤25) were selected for whole-genome sequencing using Oxford Nanopore Technology (ARTIC primers), assembled with MIRA v2.0.0, and analyzed via Augur/Nextstrain, Nextclade, and NetNGlyc/NetOGlyc 4.0.
Results
Of 11,874 patients, 1,390 (11.7%) were RSV-positive (RSV-A 94.6%). From selected 59 RSV-positive cases, 49 high-quality genomes were generated (83.1% pass; 94.7% completeness; median depth 1,500×, range 443-4,948): 43 RSV-A (ON1; A.D.3.7 63%, A.D.3 19%, A.D.3.12 9%, A.D.3.1 7%, A.D.1.11 2%) and 6 RSV-B (BA9/B.D.E.1). S276N at antigenic site II (34.9% RSV-A) and S389P in all RSV-B were detected; neither confers resistance to nirsevimab or palivizumab. An F protein N75 N-glycosylation site was fixed in all RSV-A; RSV-B acquired HVR2 N256 glycan in 67%. All 49 genomes were deposited in GISAID.
Conclusion
This WGS study of RSV in the Bangladeshi population confirms LMIC nanopore surveillance feasibility, multi-lineage co-circulation, and intact conservation of all vaccine and antibody targets. Progressive glycan remodeling warrants monitoring. These findings establish a genomic baseline to guide nirsevimab and maternal vaccine deployment in Bangladesh, with direct relevance for RSV surveillance programs across South Asia.
