Limits...
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.

Show MeSH

Related in: MedlinePlus

Multiple alignment of aa sequences of G protein gene of hMPV group B strains. Deduced aa sequence of complete G ORF of 5 hMPV subgroup B1 strains from Kolkata. The prototype strain NL/1/99 (GenBank accession number AY525843) were considered as representative for group B. Identical residues are indicated by dots and dashes represent gaps. Cysteine residues are marked with asterisks. Potential N-glycosylation sites are underlined.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3045894&req=5

Figure 3: Multiple alignment of aa sequences of G protein gene of hMPV group B strains. Deduced aa sequence of complete G ORF of 5 hMPV subgroup B1 strains from Kolkata. The prototype strain NL/1/99 (GenBank accession number AY525843) were considered as representative for group B. Identical residues are indicated by dots and dashes represent gaps. Cysteine residues are marked with asterisks. Potential N-glycosylation sites are underlined.

Mentions: The alignment of deduced aa sequence of G protein of Kolkata strains with their prototype strains revealed that intracellular and transmembrane regions were highly conserved across the strains (Figure 2 and Figure 3). Most of the aa changes were observed in extracellular domain due to nt substitution and insertion. Changes in position of stop codon have been observed among strains of different subgroups {nt 658 (UAG); nt 652 (UAA), nt 685 (UAG), nt 694 (UGA)}, which correspond to variable lengths in polypeptides. Strains from subgroup A2 used two different stop codons resulting in G proteins of 217aa (UAA), 219aa (UAG) and 228aa (UAG) (Figure 2), whereas subgroup B1 strains terminated at UGA stop codon and exhibited protein of 231 aa in length (Figure 3). For both the subgroup A2 and B1, a cysteine residue at position 27 is strictly conserved among all isolates in the intracellular domain except in one strain Kol/1446/08 which did not contain any cysteine residue. The G ectodomain also has a high content of proline residues, ranging from 7.8% for group B to 10% for group A, which could contribute to an extended, unfolded secondary structure.


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)

Multiple alignment of aa sequences of G protein gene of hMPV group B strains. Deduced aa sequence of complete G ORF of 5 hMPV subgroup B1 strains from Kolkata. The prototype strain NL/1/99 (GenBank accession number AY525843) were considered as representative for group B. Identical residues are indicated by dots and dashes represent gaps. Cysteine residues are marked with asterisks. Potential N-glycosylation sites are underlined.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Multiple alignment of aa sequences of G protein gene of hMPV group B strains. Deduced aa sequence of complete G ORF of 5 hMPV subgroup B1 strains from Kolkata. The prototype strain NL/1/99 (GenBank accession number AY525843) were considered as representative for group B. Identical residues are indicated by dots and dashes represent gaps. Cysteine residues are marked with asterisks. Potential N-glycosylation sites are underlined.
Mentions: The alignment of deduced aa sequence of G protein of Kolkata strains with their prototype strains revealed that intracellular and transmembrane regions were highly conserved across the strains (Figure 2 and Figure 3). Most of the aa changes were observed in extracellular domain due to nt substitution and insertion. Changes in position of stop codon have been observed among strains of different subgroups {nt 658 (UAG); nt 652 (UAA), nt 685 (UAG), nt 694 (UGA)}, which correspond to variable lengths in polypeptides. Strains from subgroup A2 used two different stop codons resulting in G proteins of 217aa (UAA), 219aa (UAG) and 228aa (UAG) (Figure 2), whereas subgroup B1 strains terminated at UGA stop codon and exhibited protein of 231 aa in length (Figure 3). For both the subgroup A2 and B1, a cysteine residue at position 27 is strictly conserved among all isolates in the intracellular domain except in one strain Kol/1446/08 which did not contain any cysteine residue. The G ectodomain also has a high content of proline residues, ranging from 7.8% for group B to 10% for group A, which could contribute to an extended, unfolded secondary structure.

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