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Analysis of Sequence Diversity of Human Metapneumovirus Collected from Young Children with Acute Respiratory Tract Infections in South India

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Abstract

Background

Human metapneumovirus (hMPV), which has a global distribution, is an important cause of acute respiratory tract infections, especially in children and immunocompromised patients.

Methods

We investigated the genetic variability of partial nucleoprotein (N) gene sequences of hMPV strains identified among young children in South India. The sequences of the N gene were compared with previously reported sequences available in the GenBank repository.

Results

The results showed that strains are localized in a geographically circumscribed area (topotype). The results also demonstrates that viruses from the same genetic lineage can circulate concurrently within a given location during a given season. The close clustering of the majority of our hMPV isolates indicates that the N gene sequences in the virus population are relatively homogeneous, and suggests temporal rather than geographic variations in the evolutionary pattern. In our study, the majority of the strains belonged to genetic lineage B2 (71.1 %), followed by A2b (18.4 %), A2a (7.9 %), and B1 (2.6 %), demonstrating the presence of 4 of the 5 known genotypes of hMPV. Global alignment of the nucleotide sequences showed that the strains are closely related to sequences from Canada, The Netherlands, and Australasia. Differences at the nucleotide level and the amino acid level were identified. The results provide evidence for the diversity of the N gene of hMPV in samples collected from South India compared with global strains. When investigated for selective pressure, the sequences showed 1 positively selected site and 19 negatively selected sites.

Conclusion

These data should prove useful in further investigations of the evolutionary dynamics of hMPV infection.

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Acknowledgments

This research work was funded by the Indian Council of Medical Research (ICMR, grant no. 5/8/7/15/2009/ECD-I). The authors have no conflicts of interest that are directly relevant to the content of this article.

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Authors and Affiliations

  1. Sri Sakthi Amma Institute of Biomedical Research, Sri Narayani Hospital and Research Centre, Sripuram, Vellore, 632 055, Tamil Nadu, India

    Harikrishnan Narayanan, Sathish Sankar, Balaji Nandagopal & Gopalan Sridharan

  2. Division of Infectious Diseases, Department of Pediatrics, The Children’s Hospital, Aurora, CO, USA

    Eric A. F. Simoes

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  1. Harikrishnan Narayanan
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  2. Sathish Sankar
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  3. Eric A. F. Simoes
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  5. Gopalan Sridharan
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Correspondence to Sathish Sankar.

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Narayanan, H., Sankar, S., Simoes, E.A.F. et al. Analysis of Sequence Diversity of Human Metapneumovirus Collected from Young Children with Acute Respiratory Tract Infections in South India. Mol Diagn Ther 17, 247–255 (2013). https://doi.org/10.1007/s40291-013-0032-9

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