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.