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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-A G protein in 2012–2013.(A) Thirty-one representative unique NA1 amino acid sequences corresponding to position 212 to 301 of the 2nd HVR of G protein were aligned with the prototype NA1 strain, NG-016-04 (AB470478). (B) Fifty-two representative unique ON1 amino acid sequences corresponding to position 212 to 325 of the 2nd HVR of G protein were aligned with the prototype ON1 strain, ON67-1210A (JN257693). 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, boxes for analogous sites/duplication sites, and parenthesis for number of identical strains are indicated.
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pone.0142192.g003: Deduced amino acids of representative HRSV-A G protein in 2012–2013.(A) Thirty-one representative unique NA1 amino acid sequences corresponding to position 212 to 301 of the 2nd HVR of G protein were aligned with the prototype NA1 strain, NG-016-04 (AB470478). (B) Fifty-two representative unique ON1 amino acid sequences corresponding to position 212 to 325 of the 2nd HVR of G protein were aligned with the prototype ON1 strain, ON67-1210A (JN257693). 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, boxes for analogous sites/duplication sites, and parenthesis for number of identical strains are indicated.

Mentions: The G protein is highly variable and heavily glycosylated with N- and O-linked sugars. To investigate the diversity in the 2nd HVR of G protein, representative HRSV strains with unique sequences from the Philippines from 2012–2013 were compared with the prototype strains for genotype NA1 (NG-016-04), ON1 (ON67-1210A), GB2 (CH93-9b), and BA (BA3833/99B). Compared with the NG-016-04 strain, all NA1 strains from the Philippines had N260S amino acid substitution and most had T253I and N273Y amino acid substitutions in the analogous site, the site that corresponds to the duplicated region of the G gene (Fig 3A). The predicted N-linked and O-linked glycosylation were found in 3 and 36 sites, respectively. Forty-three percent (88/204) of the 2012–2013 Philippine ON1 strains had identical deduced amino acid sequence in the 2nd HVR of the G protein as the prototype Canadian strain, ON67-1210A (Fig 3B). Within the 23-amino acid duplication sites, lysine (L) to proline (P) and tyrosine (Y) to histidine (H) substitutions were found in the exact same positions in both sites in several ON1 strains. An additional valine (V) to alanine (A) amino acid change was found in the duplicated site in 11 strains. Outside of the duplication sites, V225A, T245I, H258Q and L310P substitutions were observed in some ON1 strains. N-linked and O-linked glycosylation was predicted in 2 and 45 sites, respectively, which also included the predicted O-linked sugars in the duplication sites. Amino acid mutations within the N-linked glycosylation sites such as Tyr to Ile at position 239 led to a loss of glycosylation while the change Tyr to Ala at position 319 did not. Moreover, amino acid position 274 in the analogous site was found to be positively selected (p<0.05).


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-A G protein in 2012–2013.(A) Thirty-one representative unique NA1 amino acid sequences corresponding to position 212 to 301 of the 2nd HVR of G protein were aligned with the prototype NA1 strain, NG-016-04 (AB470478). (B) Fifty-two representative unique ON1 amino acid sequences corresponding to position 212 to 325 of the 2nd HVR of G protein were aligned with the prototype ON1 strain, ON67-1210A (JN257693). 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, boxes for analogous sites/duplication sites, and parenthesis for number of identical strains are indicated.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0142192.g003: Deduced amino acids of representative HRSV-A G protein in 2012–2013.(A) Thirty-one representative unique NA1 amino acid sequences corresponding to position 212 to 301 of the 2nd HVR of G protein were aligned with the prototype NA1 strain, NG-016-04 (AB470478). (B) Fifty-two representative unique ON1 amino acid sequences corresponding to position 212 to 325 of the 2nd HVR of G protein were aligned with the prototype ON1 strain, ON67-1210A (JN257693). 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, boxes for analogous sites/duplication sites, and parenthesis for number of identical strains are indicated.
Mentions: The G protein is highly variable and heavily glycosylated with N- and O-linked sugars. To investigate the diversity in the 2nd HVR of G protein, representative HRSV strains with unique sequences from the Philippines from 2012–2013 were compared with the prototype strains for genotype NA1 (NG-016-04), ON1 (ON67-1210A), GB2 (CH93-9b), and BA (BA3833/99B). Compared with the NG-016-04 strain, all NA1 strains from the Philippines had N260S amino acid substitution and most had T253I and N273Y amino acid substitutions in the analogous site, the site that corresponds to the duplicated region of the G gene (Fig 3A). The predicted N-linked and O-linked glycosylation were found in 3 and 36 sites, respectively. Forty-three percent (88/204) of the 2012–2013 Philippine ON1 strains had identical deduced amino acid sequence in the 2nd HVR of the G protein as the prototype Canadian strain, ON67-1210A (Fig 3B). Within the 23-amino acid duplication sites, lysine (L) to proline (P) and tyrosine (Y) to histidine (H) substitutions were found in the exact same positions in both sites in several ON1 strains. An additional valine (V) to alanine (A) amino acid change was found in the duplicated site in 11 strains. Outside of the duplication sites, V225A, T245I, H258Q and L310P substitutions were observed in some ON1 strains. N-linked and O-linked glycosylation was predicted in 2 and 45 sites, respectively, which also included the predicted O-linked sugars in the duplication sites. Amino acid mutations within the N-linked glycosylation sites such as Tyr to Ile at position 239 led to a loss of glycosylation while the change Tyr to Ala at position 319 did not. Moreover, amino acid position 274 in the analogous site was found to be positively selected (p<0.05).

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