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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 complete G gene of 22 hMPV Kolkata strains. Phylogenetic analysis of nt. sequences of hMPV group A and B strains from Kolkata (named with the prefix KOL followed by sample number and the year of collection) with that of other hMPV strains from different subgroups. Trees were built using neighbor-joining algorithm through MEGA 4 program. The tree was rooted with cognate stretch of G gene of strain AMPV-C (GenBank accession number AY198394).
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Figure 1: Phylogenetic analysis of the complete G gene of 22 hMPV Kolkata strains. Phylogenetic analysis of nt. sequences of hMPV group A and B strains from Kolkata (named with the prefix KOL followed by sample number and the year of collection) with that of other hMPV strains from different subgroups. Trees were built using neighbor-joining algorithm through MEGA 4 program. The tree was rooted with cognate stretch of G gene of strain AMPV-C (GenBank accession number AY198394).

Mentions: Phylogenetic analysis of 22 Kolkata strains (five representative strains from each year), confirmed two main genetic lineages A and B. Each lineage A and B was further divided into 2 sub-lineage A1 & A2 and B1 & B2 respectively (Figure 1). Interestingly, all the Kolkata strains clustered with A2 and B1 sub-lineage only (Figure 1). During 2006 and 2007, both sub group A2 and B1 co-circulated, with 77% (n = 59) of the circulating strains belonging to A2 subgroup. Of 32 hMPV positive samples in 2006, 26 were as subgroup A2 and 6 as subgroup B1, whereas in 2007, 27 were A2-positive and 8 were B1 positive strains. Interestingly no B1 strains were found in 2008 and 2009 and subgroup A2 remained as dominant strain throughout the study.


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 complete G gene of 22 hMPV Kolkata strains. Phylogenetic analysis of nt. sequences of hMPV group A and B strains from Kolkata (named with the prefix KOL followed by sample number and the year of collection) with that of other hMPV strains from different subgroups. Trees were built using neighbor-joining algorithm through MEGA 4 program. The tree was rooted with cognate stretch of G gene of strain AMPV-C (GenBank accession number AY198394).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Phylogenetic analysis of the complete G gene of 22 hMPV Kolkata strains. Phylogenetic analysis of nt. sequences of hMPV group A and B strains from Kolkata (named with the prefix KOL followed by sample number and the year of collection) with that of other hMPV strains from different subgroups. Trees were built using neighbor-joining algorithm through MEGA 4 program. The tree was rooted with cognate stretch of G gene of strain AMPV-C (GenBank accession number AY198394).
Mentions: Phylogenetic analysis of 22 Kolkata strains (five representative strains from each year), confirmed two main genetic lineages A and B. Each lineage A and B was further divided into 2 sub-lineage A1 & A2 and B1 & B2 respectively (Figure 1). Interestingly, all the Kolkata strains clustered with A2 and B1 sub-lineage only (Figure 1). During 2006 and 2007, both sub group A2 and B1 co-circulated, with 77% (n = 59) of the circulating strains belonging to A2 subgroup. Of 32 hMPV positive samples in 2006, 26 were as subgroup A2 and 6 as subgroup B1, whereas in 2007, 27 were A2-positive and 8 were B1 positive strains. Interestingly no B1 strains were found in 2008 and 2009 and subgroup A2 remained as dominant strain throughout the study.

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