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Genetic variability of attachment (G) and Fusion (F) protein genes of human metapneumovirus strains circulating during 2006-2009 in Kolkata, Eastern India.

Agrawal AS, Roy T, Ghosh S, Chawla-Sarkar M - Virol. J. (2011)

Bottom Line: Sequence analysis also revealed changes in the position of stop codon in G protein, which resulted in variable length (217-231 aa) polypeptides.The study suggests that approximately 5% of ARTI in the region were caused by hMPV.Though the study partially fulfills lacunae of information, further studies from other regions are necessary for better understanding of prevalence, epidemiology and virus evolution in Indian subcontinent.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road Scheme XM, Beliaghata, Kolkata-700010, India.

ABSTRACT

Background: Human metapneumovirus (hMPV) is associated with the acute respiratory tract infection (ARTI) in all the age groups. However, there is limited information on prevalence and genetic diversity of human metapneumovirus (hMPV) strains circulating in India.

Objective: To study prevalence and genomic diversity of hMPV strains among ARTI patients reporting in outpatient departments of hospitals in Kolkata, Eastern India.

Methods: Nasal and/or throat swabs from 2309 patients during January 2006 to December 2009, were screened for the presence of hMPV by RT-PCR of nucleocapsid (N) gene. The G and F genes of representative hMPV positive samples were sequenced.

Results: 118 of 2309 (5.11%) clinical samples were positive for hMPV. The majority (≈80%) of the positive cases were detected during July-November all through the study period. Genetic analysis revealed that 77% strains belong to A2 subgroup whereas rest clustered in B1 subgroup. G sequences showed higher diversity at the nucleotide and amino acid level. In contrast, less than 10% variation was observed in F gene of representative strains of all four years. Sequence analysis also revealed changes in the position of stop codon in G protein, which resulted in variable length (217-231 aa) polypeptides.

Conclusion: The study suggests that approximately 5% of ARTI in the region were caused by hMPV. This is the first report on the genetic variability of G and F gene of hMPV strains from India which clearly shows that the G protein of hMPV is continuously evolving. Though the study partially fulfills lacunae of information, further studies from other regions are necessary for better understanding of prevalence, epidemiology and virus evolution in Indian subcontinent.

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Related in: MedlinePlus

Phylogenetic analysis of the partial F gene of 8 hMPV Kolkata strains. Phylogenetic analysis of nt. sequences of hMPV group A and B strains from with that of other hMPV strains. Trees were built using neighbor-joining algorithm through MEGA 4 program. Strains from different subgroups were included in analysis.
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Figure 4: Phylogenetic analysis of the partial F gene of 8 hMPV Kolkata strains. Phylogenetic analysis of nt. sequences of hMPV group A and B strains from with that of other hMPV strains. Trees were built using neighbor-joining algorithm through MEGA 4 program. Strains from different subgroups were included in analysis.

Mentions: Out of 118 hMPV positive Kolkata strains, F-gene was partially sequenced from positive patients covering throughout the study period. Blast analysis and sequence alignment revealed very little difference (≥98% homology) among the strains. Thus the phylogenetic analysis of the F-gene fragment was done with only 8 representative Kolkata strains (two strains per year). The Kolkata strains clustered with A2 (six strains) and B1 (two strains) sub-lineage strains NL/17/00 and NL/1/99 respectively (Figure 4). At the nt level, Kolkata strains shared higher percentage of homology with subgroup B1 prototype strain NL/1/99 (98.1%) than the A2 subgroup strain CAN97-83 (96.05−96.8%). Amino acid alignment of eight partial hMPV F gene (295 aa long) was compared with the prototype strains from Canada and the Netherland (see Additional file 1). For both the subgroup cysteine residues were conserved at position 28, 60, 182, 283 and 292 which could be involved in proper folding of F monomer, as been suggested for hRSV [30]. Some of the important aa changes were subgroup specific which differentiated group A from group B (Table 2).


Genetic variability of attachment (G) and Fusion (F) protein genes of human metapneumovirus strains circulating during 2006-2009 in Kolkata, Eastern India.

Agrawal AS, Roy T, Ghosh S, Chawla-Sarkar M - Virol. J. (2011)

Phylogenetic analysis of the partial F gene of 8 hMPV Kolkata strains. Phylogenetic analysis of nt. sequences of hMPV group A and B strains from with that of other hMPV strains. Trees were built using neighbor-joining algorithm through MEGA 4 program. Strains from different subgroups were included in analysis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3045894&req=5

Figure 4: Phylogenetic analysis of the partial F gene of 8 hMPV Kolkata strains. Phylogenetic analysis of nt. sequences of hMPV group A and B strains from with that of other hMPV strains. Trees were built using neighbor-joining algorithm through MEGA 4 program. Strains from different subgroups were included in analysis.
Mentions: Out of 118 hMPV positive Kolkata strains, F-gene was partially sequenced from positive patients covering throughout the study period. Blast analysis and sequence alignment revealed very little difference (≥98% homology) among the strains. Thus the phylogenetic analysis of the F-gene fragment was done with only 8 representative Kolkata strains (two strains per year). The Kolkata strains clustered with A2 (six strains) and B1 (two strains) sub-lineage strains NL/17/00 and NL/1/99 respectively (Figure 4). At the nt level, Kolkata strains shared higher percentage of homology with subgroup B1 prototype strain NL/1/99 (98.1%) than the A2 subgroup strain CAN97-83 (96.05−96.8%). Amino acid alignment of eight partial hMPV F gene (295 aa long) was compared with the prototype strains from Canada and the Netherland (see Additional file 1). For both the subgroup cysteine residues were conserved at position 28, 60, 182, 283 and 292 which could be involved in proper folding of F monomer, as been suggested for hRSV [30]. Some of the important aa changes were subgroup specific which differentiated group A from group B (Table 2).

Bottom Line: Sequence analysis also revealed changes in the position of stop codon in G protein, which resulted in variable length (217-231 aa) polypeptides.The study suggests that approximately 5% of ARTI in the region were caused by hMPV.Though the study partially fulfills lacunae of information, further studies from other regions are necessary for better understanding of prevalence, epidemiology and virus evolution in Indian subcontinent.

View Article: PubMed Central - HTML - PubMed

Affiliation: Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road Scheme XM, Beliaghata, Kolkata-700010, India.

ABSTRACT

Background: Human metapneumovirus (hMPV) is associated with the acute respiratory tract infection (ARTI) in all the age groups. However, there is limited information on prevalence and genetic diversity of human metapneumovirus (hMPV) strains circulating in India.

Objective: To study prevalence and genomic diversity of hMPV strains among ARTI patients reporting in outpatient departments of hospitals in Kolkata, Eastern India.

Methods: Nasal and/or throat swabs from 2309 patients during January 2006 to December 2009, were screened for the presence of hMPV by RT-PCR of nucleocapsid (N) gene. The G and F genes of representative hMPV positive samples were sequenced.

Results: 118 of 2309 (5.11%) clinical samples were positive for hMPV. The majority (≈80%) of the positive cases were detected during July-November all through the study period. Genetic analysis revealed that 77% strains belong to A2 subgroup whereas rest clustered in B1 subgroup. G sequences showed higher diversity at the nucleotide and amino acid level. In contrast, less than 10% variation was observed in F gene of representative strains of all four years. Sequence analysis also revealed changes in the position of stop codon in G protein, which resulted in variable length (217-231 aa) polypeptides.

Conclusion: The study suggests that approximately 5% of ARTI in the region were caused by hMPV. This is the first report on the genetic variability of G and F gene of hMPV strains from India which clearly shows that the G protein of hMPV is continuously evolving. Though the study partially fulfills lacunae of information, further studies from other regions are necessary for better understanding of prevalence, epidemiology and virus evolution in Indian subcontinent.

Show MeSH
Related in: MedlinePlus