Abstract
Human respiratory syncytial virus (HRSV) is a major cause of acute lower respiratory tract infections in infants and children worldwide. We performed molecular analysis of HRSV among infants and children with clinical diagnosis of severe pneumonia in four study sites in the Philippines, including Biliran, Leyte, Palawan, and Metro Manila from June 2012 to July 2013. Nasopharyngeal swabs were collected and screened for HRSV using real-time polymerase chain reaction (PCR). Positive samples were tested by conventional PCR and sequenced for the second hypervariable region (2nd HVR) of the G gene. Among a total of 1,505 samples, 423 samples were positive for HRSV (28.1%), of which 305 (72.1%) and 118 (27.9%) were identified as HRSV-A and HRSV-B, respectively. Two genotypes of HRSV-A, NA1 and ON1, were identified during the study period. The novel ON1 genotype with a 72-nucleotide duplication in 2nd HVR of the G gene increased rapidly and finally became the predominant genotype in 2013 with an evolutionary rate higher than the NA1 genotype. Moreover, in the ON1 genotype, we found positive selection at amino acid position 274 (p<0.05) and massive O- and N-glycosylation in the 2nd HVR of the G gene. Among HRSV-B, BA9 was the predominant genotype circulating in the Philippines. However, two sporadic cases of GB2 genotype were found, which might share a common ancestor with other Asian strains. These findings suggest that HRSV is an important cause of severe acute respiratory infection among children in the Philippines and revealed the emergence and subsequent predominance of the ON1 genotype and the sporadic detection of the GB2 genotype. Both genotypes were detected for the first time in the Philippines.
Highlights
Acute lower respiratory tract infection (ALRI) is a severe disease that leads to the morbidity and mortality in infants and children worldwide
A total of 1,505 nasopharyngeal swabs (NPS) were collected from children aged less than 14 years who sought hospital care or referred to the hospital with clinical diagnosis of severe pneumonia based on the Integrated Management of Childhood Illness (IMCI) guidelines [26] from June 2012 to July 2013 from four study sites in the Philippines, including 549 samples from the Eastern Visayas Regional Medical Center (EVRMC) in Tacloban City of Leyte Island, 456 from the Ospital Ng Palawan (ONP) in Puerto Princesa City of Palawan Island, 431 from the Biliran Provincial Hospital (BPH) in Naval City of Biliran Island, and 69 from the Research Institute for Tropical Medicine (RITM) in Metro Manila
From 2008 to 2012, an etiological study on acute respiratory infection in the Philippines showed that human respiratory syncytial virus (HRSV) (19.3%) was one of the most common virus detected from hospitalized children with severe pneumonia [7]
Summary
Acute lower respiratory tract infection (ALRI) is a severe disease that leads to the morbidity and mortality in infants and children worldwide. One of the most common causes of ALRI is human respiratory syncytial virus (HRSV). 2.8 to 4.3 million children are admitted to hospitals and approximately 66,000 to 199,000 children infected with HRSV aged less than 5 years old die annually, in developing countries [1]. The HRSV virion is 100–350 nm in diameter. It has an envelope and a linear, negative-sense, and single-stranded RNA genome of approximately 15.2 kb with helical nucleocapsid. The genome has genes, which encodes proteins. The G gene encodes for the G protein, a type II glycoprotein on the virus envelope involved in attachment during virus entry. The G protein, which is heavily glycosylated with N-linked and, especially, O-linked sugars [2], contains two hypervariable regions (HVR), the 1st HVR and 2nd HVR, flanking a central conserved region
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