Limits...
Molecular Characterization of Human Respiratory Syncytial Virus in the Philippines, 2012-2013.

Malasao R, Okamoto M, Chaimongkol N, Imamura T, Tohma K, Dapat I, Dapat C, Suzuki A, Saito M, Saito M, Tamaki R, Pedrera-Rico GA, Aniceto R, Quicho RF, Segubre-Mercado E, Lupisan S, Oshitani H - PLoS ONE (2015)

Bottom Line: 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.However, two sporadic cases of GB2 genotype were found, which might share a common ancestor with other Asian strains.Both genotypes were detected for the first time in the Philippines.

View Article: PubMed Central - PubMed

Affiliation: Tohoku University Graduate School of Medicine, Sendai, Japan.

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.

No MeSH data available.


Related in: MedlinePlus

Deduced amino acids of representative HRSV-B G protein in 2012–2013.(A) Two GB2 amino acid sequences corresponding to position 213 to 302 of the 2nd HVR of G protein were aligned with the prototype GB2 strain, CH93-9b (AF065251). (B) Forty-nine representative unique BA9 amino acid sequences corresponding to position 213 to 322 of the 2nd HVR of G protein were aligned with the prototype BA strain, BA3833/99B (AY333362) and the other prototypes of BA branches. Gray shading for predicted N-linked sites, gray octagons for predicted O-linked sites, dots for identical residues, asterisks for stop codon positions, star for positive selection position, and boxes for analogous sites/duplication sites are indicated.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4635013&req=5

pone.0142192.g004: Deduced amino acids of representative HRSV-B G protein in 2012–2013.(A) Two GB2 amino acid sequences corresponding to position 213 to 302 of the 2nd HVR of G protein were aligned with the prototype GB2 strain, CH93-9b (AF065251). (B) Forty-nine representative unique BA9 amino acid sequences corresponding to position 213 to 322 of the 2nd HVR of G protein were aligned with the prototype BA strain, BA3833/99B (AY333362) and the other prototypes of BA branches. Gray shading for predicted N-linked sites, gray octagons for predicted O-linked sites, dots for identical residues, asterisks for stop codon positions, star for positive selection position, and boxes for analogous sites/duplication sites are indicated.

Mentions: Two GB2 strains were detected in two study sites, EVRMC in Tacloban City of Leyte Island (TEv-13-0101) and BPH in Naval City of Biliran Island (TBp-13-0088) (Fig 4A). The predicted N-linked and O-linked glycosylation sites were found in 3 and 35 positions, respectively. All of the Philippine HRSV-B BA strains had a premature stop codon at amino acid position 313, except for three strains with a stop codon at position 320 (Fig 4B). Previously reported amino acid substitutions such as K218T, L223P, S247P and I281T, which are located outside of the 20-amino acid duplication sites, and S267P, T270I and V271A substitutions, which are found within the duplication sites, were also observed in almost all of the 2012–2013 strains [6, 37–39]. The amino acid change H287Y was found in 73% (85/117) of BA strains. In addition, the substitution T290I was found in one-third (38%, 44/117) of BA strains while the substitution T302A was found in another one-third (35%, 41/117) of the strains. Some BA strains contain the Ser to Pro substitution at position 267 in the duplication site located exactly in the same position (S247P) as in the analogous site. The predicted N-linked and O-linked glycosylation sites were 3 and 46 positions, respectively, which also included the predicted O-linked sugars found in the duplication site. The amino acid mutation T275N within the duplicated site led to a gain of glycosylation site while the T312I substitution led to a loss of glycosylation site.


Molecular Characterization of Human Respiratory Syncytial Virus in the Philippines, 2012-2013.

Malasao R, Okamoto M, Chaimongkol N, Imamura T, Tohma K, Dapat I, Dapat C, Suzuki A, Saito M, Saito M, Tamaki R, Pedrera-Rico GA, Aniceto R, Quicho RF, Segubre-Mercado E, Lupisan S, Oshitani H - PLoS ONE (2015)

Deduced amino acids of representative HRSV-B G protein in 2012–2013.(A) Two GB2 amino acid sequences corresponding to position 213 to 302 of the 2nd HVR of G protein were aligned with the prototype GB2 strain, CH93-9b (AF065251). (B) Forty-nine representative unique BA9 amino acid sequences corresponding to position 213 to 322 of the 2nd HVR of G protein were aligned with the prototype BA strain, BA3833/99B (AY333362) and the other prototypes of BA branches. Gray shading for predicted N-linked sites, gray octagons for predicted O-linked sites, dots for identical residues, asterisks for stop codon positions, star for positive selection position, and boxes for analogous sites/duplication sites are indicated.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4635013&req=5

pone.0142192.g004: Deduced amino acids of representative HRSV-B G protein in 2012–2013.(A) Two GB2 amino acid sequences corresponding to position 213 to 302 of the 2nd HVR of G protein were aligned with the prototype GB2 strain, CH93-9b (AF065251). (B) Forty-nine representative unique BA9 amino acid sequences corresponding to position 213 to 322 of the 2nd HVR of G protein were aligned with the prototype BA strain, BA3833/99B (AY333362) and the other prototypes of BA branches. Gray shading for predicted N-linked sites, gray octagons for predicted O-linked sites, dots for identical residues, asterisks for stop codon positions, star for positive selection position, and boxes for analogous sites/duplication sites are indicated.
Mentions: Two GB2 strains were detected in two study sites, EVRMC in Tacloban City of Leyte Island (TEv-13-0101) and BPH in Naval City of Biliran Island (TBp-13-0088) (Fig 4A). The predicted N-linked and O-linked glycosylation sites were found in 3 and 35 positions, respectively. All of the Philippine HRSV-B BA strains had a premature stop codon at amino acid position 313, except for three strains with a stop codon at position 320 (Fig 4B). Previously reported amino acid substitutions such as K218T, L223P, S247P and I281T, which are located outside of the 20-amino acid duplication sites, and S267P, T270I and V271A substitutions, which are found within the duplication sites, were also observed in almost all of the 2012–2013 strains [6, 37–39]. The amino acid change H287Y was found in 73% (85/117) of BA strains. In addition, the substitution T290I was found in one-third (38%, 44/117) of BA strains while the substitution T302A was found in another one-third (35%, 41/117) of the strains. Some BA strains contain the Ser to Pro substitution at position 267 in the duplication site located exactly in the same position (S247P) as in the analogous site. The predicted N-linked and O-linked glycosylation sites were 3 and 46 positions, respectively, which also included the predicted O-linked sugars found in the duplication site. The amino acid mutation T275N within the duplicated site led to a gain of glycosylation site while the T312I substitution led to a loss of glycosylation site.

Bottom Line: 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.However, two sporadic cases of GB2 genotype were found, which might share a common ancestor with other Asian strains.Both genotypes were detected for the first time in the Philippines.

View Article: PubMed Central - PubMed

Affiliation: Tohoku University Graduate School of Medicine, Sendai, Japan.

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.

No MeSH data available.


Related in: MedlinePlus