Skip to main content

Advertisement

SpringerLink
Log in

Molecular investigation of human metapneumovirus in children with acute respiratory infections in Chennai, South India, from 2016–2018

  • Bacterial, Fungal and Virus Molecular Biology - Short Communication
  • Published:
Brazilian Journal of Microbiology Aims and scope Submit manuscript

Abstract

Human metapneumovirus (hMPV) has emerged as a frequent cause of acute respiratory infections (ARI) among young children. The prevalence and genetic diversity of hMPV circulating in Chennai, Southern India, has not been studied yet. Hence, this study was aimed to investigate the prevalence, co-infection with other respiratory viruses like HRSV A and B, influenza A and B, hRV and HPIV 1–4 viruses, socio-demographic associations, and genotypes of hMPV among children in Chennai. A total of 350 nasal swab specimens were collected from children with ARI during April 2016 to August 2018 and tested for hMPV by real time PCR method. In this study, hMPV was detected in 4% (14/350) of the samples. One hMPV positive sample was found to be co-infected with influenza B virus. The mean and median ages of the children with hMPV infection were 61.5 months (5.1 years) and 83 months (6.9 years), respectively. Phylogenetic analysis of the partial F gene revealed the presence of A2c subcluster among the study strains as well as with B1 and B2 lineages. The prevalence data obtained in this study is important in evaluating the role of hMPV in childhood ARI and emphasizes the importance of routine viral diagnosis in hospitals. To the best of our knowledge, this is the first study to report the prevalence, seasonality, and genetic diversity of hMPV in Chennai as well as the first study to report A2c subcluster of hMPV among children in India.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

References

  1. Afonso CL, Amarasinghe GK, Bányai K, Bào Y, Basler CF, Bavari S, Bejerman N, Blasdell KR, Briand FX, Briese T, Bukreyev A (2016) Taxonomy of the order Mononegavirales: update. Arch Virol 161:2351–2360

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Van den Hoogen BG, de Jong JC, Groen J, Kuiken T, de Groot R, Fouchier RA, Osterhaus AD (2001) A newly discovered human pneumovirus isolated from young children with respiratory tract disease. Nat Med 7:719–724

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  3. Boivin G, Abed Y, Pelletier G, Ruel L, Moisan D, Côté S, Peret TC, Erdman DD, Anderson LJ (2002) Virological features and clinical manifestations associated with human metapneumovirus: a new paramyxovirus responsible for acute respiratory-tract infections in all age groups. J Infect Dis 186:1330–1334

    Article  PubMed  Google Scholar 

  4. Falsey AR, Walsh EE (2006) Viral pneumonia in older adults. Clin Infect Dis 42:518–524

    Article  PubMed  Google Scholar 

  5. Kahn JS (2006) Epidemiology of human metapneumovirus. Clin Microbiol Rev 19:546–557

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Rao BL, Gandhe SS, Pawar SD, Arankalle VA, Shah SC, Kinikar AA (2004) First detection of human metapneumovirus in children with acute respiratory infection in India: a preliminary report. J Clin Microbiol 42:5961–5962

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Singh AK, Jain B, Verma AK, Kumar A, Dangi T, Dwivedi M, Singh KP, Jain A (2015) Hospital outbreak of human respiratory syncytial virus (HRSV) illness in immunocompromised hospitalized children during summer. Clin Respir J 9:180–184

    Article  PubMed  Google Scholar 

  8. Banerjee S, Bharaj P, Sullender W, Kabra SK, Broor S (2007) Human metapneumovirus infections among children with acute respiratory infections seen in a large referral hospital in India. J Clin Virol 38:70–72

    Article  PubMed  Google Scholar 

  9. Narayanan H, Sankar S, Simoes EA, Nandagopal B, Sridharan G (2013) Molecular detection of human metapneumovirus and human bocavirus on oropharyngeal swabs collected from young children with acute respiratory tract infections from rural and peri-urban communities in South India. Mol Diagn Ther 17:107–115

    Article  PubMed  PubMed Central  Google Scholar 

  10. Principi N, Esposito S (2014) Paediatric human metapneumovirus infection: epidemiology, prevention and therapy. J Clin Virol 59(3):141–147

    Article  PubMed  Google Scholar 

  11. Van den Hoogen BG, Bestebroer TM, Osterhaus AD, Fouchier RA (2002) Analysis of the genomic sequence of a human metapneumovirus. Virol 295:119–132

    Article  CAS  Google Scholar 

  12. Huck B, Scharf G, Neumann-Haefelin D, Puppe W, Weigl J, Falcone V (2006) Novel human metapneumovirus sublineage. Emerg Infect Dis 12:147–150

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Biacchesi S, Skiadopoulos MH, Boivin G, Hanson CT, Murphy BR, Collins PL, Buchholz UJ (2003) Genetic diversity between human metapneumovirus subgroups. Virol 315:1–9

    Article  CAS  Google Scholar 

  14. Regev L, Meningher T, Hindiyeh M, Mendelson E, Mandelboim M (2012) Increase human metapneumovirus mediated morbidity following pandemic influenza infection. PLoS ONE 7:e34750

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Carr MJ, Waters A, Fenwick F, Toms GL, Hall WW, O’Kelly E (2008) Molecular epidemiology of human metapneumovirus in Ireland. J Med Virol 80:510–516

    Article  CAS  PubMed  Google Scholar 

  16. Nidaira M, Taira K, Hamabata H, Kawaki T, Gushi K, Mahoe Y, Maeshiro N, Azama Y, Okano S, Kyan H, Kudaka J (2012) Molecular epidemiology of human metapneumovirus from 2009 to 2011 in Okinawa, Japan. Jpn J Infect Dis 65:337–340

    Article  PubMed  Google Scholar 

  17. Chow WZ, Chan YF, Oong XY, Ng LJ, Nor’E SS, Ng KT, Chan KG, Hanafi NS, Pang YK, Kamarulzaman A, Tee KK (2016) Genetic diversity, seasonality and transmission network of human metapneumovirus: identification of a unique sub-lineage of the fusion and attachment genes. Sci Rep 6:27730–27739

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Jagušić M, Slović A, Ljubin-Sternak S, Mlinarić-Galinović G, Forčić D (2017) Genetic diversity of human metapneumovirus in hospitalized children with acute respiratory infections in Croatia. J Med Virol 89:1885–1893

    Article  PubMed  Google Scholar 

  19. Gauthier P, Cardot JM (2011) Developing drugs for children and the adjustment of medication—is it a new challenge or an adaptation of past ideas? J Pers Med 1(1):5–16

    Article  PubMed  PubMed Central  Google Scholar 

  20. Bonroy C, Vankeerberghen A, Boel A, De Beenhouwer H (2007) Use of a multiplex real-time PCR to study the incidence of human metapneumovirus and human respiratory syncytial virus infections during two winter seasons in a Belgian paediatric hospital. Clin Microbiol Infect 13:504–509

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Hindupur A, Dhandapani P, Menon T (2019) Influenza virus among children with acute respiratory infections in Chennai. India Indian Pediatr 56(1):74–75

    PubMed  Google Scholar 

  22. Hindupur A, Menon T, Dhandapani P (2019) Genetic diversity of human respiratory syncytial virus in children with acute respiratory infections in Chennai. South India Indian J Med Microbiol 37(2):248–254

    Article  PubMed  Google Scholar 

  23. Kaida A, Iritani N, Kubo H, Shiomi M, Kohdera U, Murakami T (2006) Seasonal distribution and phylogenetic analysis of human metapneumovirus among children in Osaka City, Japan. J Clin Virol 35:394–399

    Article  PubMed  Google Scholar 

  24. Ishiguro N, Ebihara T, Endo R, Ma X, Kikuta H, Ishiko H, Kobayashi K (2004) High genetic diversity of the attachment (G) protein of human metapneumovirus. J Clin Microbiol 42(8):3406–3414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Van den Hoogen BG, Herfst S, Sprong L, Cane PA, Forleo-Neto E, De Swart RL, Osterhaus AD, Fouchier RA (2004) Antigenic and genetic variability of human metapneumoviruses. Emerg Infect Dis 10(4):658

    Article  PubMed  PubMed Central  Google Scholar 

  26. de Graaf M, Osterhaus AD, Fouchier RA, Holmes EC (2008) Evolutionary dynamics of human and avian metapneumoviruses. J Gen Virol 89(12):2933–2942

    Article  PubMed  CAS  Google Scholar 

  27. Bastien N, Normand S, Taylor T, Ward D, Peret TC, Boivin G, Anderson LJ, Li Y (2003) Sequence analysis of the N, P, M and F genes of Canadian human metapneumovirus strains. Virus Res 93(1):51–62

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Pybus OG, Tatem AJ, Lemey P (2015) Virus evolution and transmission in an ever more connected world. Proc R Soc B: Biol Sci 282(1821):20142878

    Article  CAS  Google Scholar 

  30. Nandhini G, Sujatha S, Jain N, Dhodapkar R, Tamilarasu K, Krishnamurthy S, Biswal N (2016) Prevalence of human metapneumovirus infection among patients with influenza-like illness: report from a tertiary care centre, Southern India. Indian J Med Microbiol 34:27–32

    Article  CAS  PubMed  Google Scholar 

  31. Roy Mukherjee T, Chanda S, Mullick S, De P, Dey-Sarkar M, Chawla-Sarkar M (2013) Spectrum of respiratory viruses circulating in eastern India: prospective surveillance among patients with influenza-like illness during 2010–2011. J Med Virol 85:1459–1465

    Article  PubMed  PubMed Central  Google Scholar 

  32. Jain B, Singh AK, Dangi T, Agarwal A, Verma AK, Dwivedi M, Singh KP, Jain A (2014) High prevalence of human metapneumovirus subtype B in cases presenting as severe acute respiratory illness: an experience at tertiary care hospital. Clin Respir J 8:225–233

    Article  PubMed  Google Scholar 

  33. Arnott A, Vong S, Sek M, Naughtin M, Beauté J, Rith S, Guillard B, Deubel V, Buchy P (2013) Genetic variability of Human metapneumovirus amongst an all ages population in Cambodia between 2007 and 2009. Infect Genet Evol 15:43–52

    Article  CAS  PubMed  Google Scholar 

  34. Sung CC, Chi H, Chiu NC, Huang DT, Weng LC, Wang NY, Huang FY (2011) Viral etiology of acute lower respiratory tract infections in hospitalized young children in Northern Taiwan. J Microbiol Immunol Infect 44:184–219

    Article  PubMed  PubMed Central  Google Scholar 

  35. Panda S, Mohakud NK, Pena L, Kumar S (2014) Human metapneumovirus: review of an important respiratory pathogen. Int J Infect Dis 25:45–52

    Article  PubMed  PubMed Central  Google Scholar 

  36. Sarkar S, Ratho RK, Singh M, Singh MP, Singh A, Sharma M (2022) Comparative analysis of epidemiology, clinical features, and cytokine response of respiratory syncytial and human metapneumovirus infected children with acute lower respiratory infections. Jpn J Infect Dis 75:56–62

  37. Foulongne V, Guyon G, Rodière M, Segondy M (2006) Human metapneumovirus infection in young children hospitalized with respiratory tract disease. Pediatr Infect Dis J 25:354–359

    Article  PubMed  Google Scholar 

  38. König B, König W, Arnold R, Werchau H, Ihorst G, Forster J (2004) Prospective study of human metapneumovirus infection in children less than 3 years of age. J Clin Microbiol 42:4632–4635

    Article  PubMed  PubMed Central  Google Scholar 

  39. van Woensel JB, Bos AP, Lutter R, Rossen JW, Schuurman R (2006) Absence of human metapneumovirus co-infection in cases of severe respiratory syncytial virus infection. Pediatr Pulmonol 41:872–874

    Article  PubMed  Google Scholar 

  40. Zhang C, Zhu N, Xie Z, Lu R, He B, Liu C et al (2013) Viral etiology and clinical profiles of children with severe acute respiratory infections in China. PLoS One 8:e72606

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Moe N, Krokstad S, Stenseng IH, Christensen A, Skanke LH, Risnes KR, Nordbø SA, Døllner H (2017) Comparing human metapneumovirus and respiratory syncytial virus: viral co-detections, genotypes and risk factors for severe disease. PLoS One 12(1):e0170200

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  42. Zhu R, Guo C, Zhao L, Deng J, Wang F, Sun Y, Qian Y (2020) Epidemiological and genetic characteristics of human metapneumovirus in pediatric patients across six consecutive seasons in Beijing, China. Int J Infect Dis 91:137–142

    Article  PubMed  Google Scholar 

  43. Choudhary ML, Anand SP, Sonawane NS, Chadha MS (2014) Development of real-time RT-PCR for detection of human metapneumovirus and genetic analysis of circulating strains (2009–2011) in Pune, India. Arch Virol 159:217–225

    Article  CAS  PubMed  Google Scholar 

  44. Rueda AJV, Mistchenko AS, Viegas M (2013) Phylogenetic and phylodynamic analyses of human metapneumovirus in Buenos Aires (Argentina) for a three-year period (2009–2011). PloS One 8:e63070

    Article  CAS  Google Scholar 

  45. Ljubin-Sternak S, Mlinaric-Galinovic G, Buntic AM, Tabain I, Vilibic-Cavlek T, Cepin-Bogovic J, Tesovic G (2014) Seasonal occurrence of human metapneumovirus infections in Croatia. Pediatr Infect Dis J33:165–167

    Article  Google Scholar 

  46. Malhotra B, Swamy MA, Reddy PJ, Gupta ML (2016) Viruses causing severe acute respiratory infections (SARI) in children ≤ 5 years of age at a tertiary care hospital in Rajasthan, India. Indian J Med Res 144:877–885

    Article  PubMed  PubMed Central  Google Scholar 

  47. Agrawal AS, Roy T, Ghosh S, Chawla-Sarkar M (2011) Genetic variability of attachment (G) and fusion (F) protein genes of human metapneumovirus strains circulating during 2006–2009 in Kolkata, Eastern India. Virol J 8:1–8

    Article  CAS  Google Scholar 

  48. Banerjee S, Sullender WM, Choudekar A, John C, Tyagi V, Fowler K, Lefkowitz EJ, Broor S (2011) Detection and genetic diversity of human metapneumovirus in hospitalized children with acute respiratory infections in India. J Med Virol 83:1799–1810

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Narayanan H, Sankar S, Simoes EA, Nandagopal B, Sridharan G (2013) 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

    Article  PubMed  Google Scholar 

  50. Rahman MZ, Sumiya M, Sahabuddin M, Pell LG, Gubbay JB, Rahman R, Momtaz F, Azmuda N, Shanta SS, Jahan I, Rahman M (2019) Genetic characterization of human metapneumovirus identified through community and facility-based surveillance of infants in Dhaka, Bangladesh. J Med Virol 91:549–554

    Article  PubMed  Google Scholar 

  51. Yang CF, Wang CK, Tollefson SJ, Piyaratna R, Lintao LD, Chu M, Liem A, Mark M, Spaete RR, Crowe JE, Williams JV (2009) Genetic diversity and evolution of human metapneumovirus fusion protein over twenty years. Virol J 6:138–147

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  52. Hansen JE, Lund O, Tolstrup N, Gooley AA, Williams KL, Brunak S (1998) NetOglyc: prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility. Glycoconj J 15:115–130

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank Dr. Elilarasi, Dr. Kalpana, and Dr. Sarathbalaji — Department of Pulmonology, Institute of Child Health, Egmore, Chennai; Dr. Indumathi — Pediatric Clinic, Triplicane, Chennai; and Dr. Rohit Bharadwaj — Rabindran’s Health Care Centre, Ambattur, Chennai for providing the clinical samples used in this study.

Funding

This work was supported by the Intramural Research funds, University of Madras, Chennai, India.

Author information

Authors and Affiliations

  1. Department of Microbiology, Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras, Chennai, Tamil Nadu, India

    Anusha Hindupur & Prabu Dhandapani

  2. Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India

    Thangam Menon

Authors
  1. Anusha Hindupur
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Thangam Menon
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Prabu Dhandapani
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Thangam Menon.

Ethics declarations

Ethics approval

The study was approved by the Institutional Human Ethics Committee of Dr. ALM Post Graduate Institute of Basic Medical Sciences, University of Madras (Approval No: UM/IHEC/12–2014-II and UM/IHEC/07–2017-I).

Conflict of interest

The authors declare no competing interests.

Additional information

Publisher's note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Responsible Editor: Mauricio Nogueira

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOC 39 kb)

Supplementary file2 (DOCX 17 kb)

42770_2022_689_MOESM3_ESM.jpg

Supplementary file3 (jpg 418 kb) Supplement Fig. 1 Maximum Likelihood fits of 24 different nucleotide substitution models

42770_2022_689_MOESM4_ESM.jpeg

Supplementary file4 (jpeg 365 kb) Supplement Fig. 2 Deduced amino acid alignment of partial F gene of hMPV strains belonging to the A2c subcluster obtained in this study

42770_2022_689_MOESM5_ESM.jpg

Supplementary file5 (jpg 370 kb) Supplement Fig. 3 Deduced amino acid alignment of partial F gene of hMPV strains belonging to the B1 lineage obtained in this study

42770_2022_689_MOESM6_ESM.jpg

Supplementary file6 (jpg 393 kb) Supplement Fig. 4 Deduced amino acid alignment of partial F gene of hMPV strains belonging to the B2 lineage obtained in this study

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Hindupur, A., Menon, T. & Dhandapani, P. Molecular investigation of human metapneumovirus in children with acute respiratory infections in Chennai, South India, from 2016–2018. Braz J Microbiol 53, 655–661 (2022). https://doi.org/10.1007/s42770-022-00689-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s42770-022-00689-2

Keywords

Search

Navigation