Genotyping of respiratory syncytial virus among influenza‐like illness and severe acute respiratory infection cases of children in the Philippines from 2006 to 2016

OBJECTIVE: Respiratory syncytial virus (RSV) is a leading cause of severe lower respiratory infection, and therefore, a major threat to global health. This study determined the epidemiological and molecular characteristics of RSV among cases of influenza‐like illness (ILI) and severe acute respiratory infection (SARI) among children in the Philippines. METHOD: The study included archived nasopharyngeal swab and oropharyngeal swab samples collected from patients under the age of five who are presented with ILI or SARI for the period of 2006–2016. Swabs were examined for RSV subgroup by multiplex real‐time qRT‐PCR. Partial genome sequencing and phylogenetic analyses of the second hypervariable region (HVR) of the G gene were used to determine the genotype of RSV isolates. RESULTS: A total of 1036 representative samples from all sites were selected and tested. Of these samples, 122 were RSV‐positive at 11.8% prevalence rate, and 58.2% (71/122) were classified as RSV‐A. Six genotypes were identified, which include NA1 (27/122, 22.1%), ON1 (5/122, 4.1%), GA2 (1/122, 0.8%), and GA5 (1/122, 0.8%) for RSV‐A; and BA2 (13/122, 10.7%) and BA9 (1/122, 0.8%) for RSV‐B. Most RSV‐related cases were significantly associated with clinical characteristics such as runny nose (88.1% RSV vs. 11.9% non‐RSV: p value = 0.021), pneumonia (80.6% RSV vs. 19.4% non‐RSV; p value = 0.015), and bronchitis (71.7% RSV vs. 28.3% non‐RSV; p value < 0.001). Increased RSV‐related cases were observed among children below 24 months old. CONCLUSION: The RSV trend and genetic variability in the Philippines resembles a similar pattern of transmission globally.