Molecular surveillance of respiratory viruses among outpatients with acute respiratory infections in Yangon, Myanmar, during the 2024 rainy season

Acute respiratory infections (ARI) remain a major public health problem in Myanmar, a tropical Southeast Asian country, yet comprehensive molecular surveillance data are limited. We conducted outpatient surveillance during the 2024 rainy season and characterized pathogen distribution, seasonality, and viral genetic diversity. From June–November 2024, ARI outpatients were enrolled at two Yangon hospitals. Nasopharyngeal swabs were screened by rapid diagnostic tests (RDTs) for influenza, respiratory syncytial virus (RSV), and SARS-CoV-2. RDT-positive specimens underwent confirmation by real-time PCR (RT-PCR). RDT-negative specimens were tested using the BioFire ® FilmArray ® Respiratory 2.1 Panel (BioFire RP). Influenza A(H1N1)pdm09, A(H3N2), and B/Victoria viruses with cycle threshold (Ct) < 32 underwent next-generation sequencing for hemagglutinin (HA) phylogenetics. Human metapneumovirus (hMPV)-positive specimens were sequenced targeting the partial F-gene for genotyping. Among 646 ARI outpatients (median age 3.7 years), at least one pathogen was detected in 548 (84.8%). Of the 331 RDT-positive specimens, influenza A(H3N2) (40.5%), RSV-A (21.5%), and influenza B/Victoria (20.2%) were most frequently detected, alongside a single A(H1N1)pdm09 case (0.3%). Of the 315 RDT-negative specimens analyzed via BioFire RP, rhinovirus/enterovirus (42.5%) and hMPV (15.2%) were the most prevalent. Co-infections were identified in 35 (15.3%) of the 229 BioFire RP-positive specimens. Influenza activity peaked in July–August, while RSV peaked in September. Phylogenetic analysis revealed that influenza A(H3N2) sequences clustered within clades J.2/J.2.1/J.2.2, B/Victoria sequences within V1A.3a.2 (primarily C.5.7), and the single A(H1N1)pdm09 sequence within C.1.9. Notably, partial F-gene sequencing of hMPV revealed a genotype shift from mixed A2/B1 in 2023 to predominantly B2 in 2024. Various respiratory viruses co-circulated during the 2024 rainy season in this setting, displaying distinct seasonal peaks for influenza and RSV. Ongoing viral genetic evolution underscores the need for sustained molecular surveillance.