Molecular characterization of human rhinovirus strains detected in pediatric acute respiratory tract infections
-
V R Parvathy
,
Pryanka Thakur
,
Vikram Thakur
,
Vikrant Sharma
,
Ishani Bora
,
Radha Kanta Ratho
,
Suresh Kumar Angurana
,
Mini P Singh
Abstract
Background and Objectives: Acute respiratory tract infections (ARTI) are a leading cause of morbidity and mortality in children worldwide, accounting for approximately 18% of deaths in those <5 years of age. Viruses cause 50-90% of pediatric ARTI cases. Human rhinovirus (HRV) is increasingly associated with lower respiratory tract infections (LRTIs). This study aimed to detect HRV in pediatric ARTI cases and characterize circulating genotypes.
Materials and Methods: Nasopharyngeal swabs from 154 children (≤5 years) presenting with ARTI were screened for HRV using real-time PCR. Thirteen samples with a cycle threshold ≤30 were sequenced. Phylogenetic analysis was performed using 41 global reference sequences representing different geographical regions and HRV types.
Results: HRV was detected in 34.41% (53/154) of the samples. In children aged >1 month to 1 year, HRV positivity was significantly associated with severe acute respiratory infection (SARI) compared with influenza-like illness (ILI). Phylogenetic analysis revealed a predominance of HRV-C strains (n = 7), followed by HRV-A (n = 5) and HRV-B (n = 1).
Conclusion: HRV was detected in a significant proportion of pediatric ARTI cases, with HRV-C as the predominant strain. Infants aged >1 month to 1 year showed a higher association with severe illness, underscoring the need for closer clinical monitoring in this age group.
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26. Louie JK, Roy-Burman A, Guardia-Labar L, Boston EJ, Kiang D, Padilla T, et al. Rhinovirus associated with severe lower respiratory tract infections in children. Pediatr Infect Dis J 2009; 28: 337-339.
27. Baillie VL, Olwagen CP, Madhi SA. Review on Clinical and Molecular Epidemiology of Human Rhinovirus-Associated Lower Respiratory Tract Infections in African and Southeast Asian Children. Pediatr Infect Dis J 2018; 37(7): e185-e194.
28. Panda S, Mohakud NK, Panda S, Kumar S. Epidemiology and phylogenetic analysis of human rhinovirus/Enterovirus in Odisha, Eastern India. Indian J Med Microbiol 2019; 37: 569-573.
29. Calvo C, Casas I, García-García ML, Pozo F, Reyes N, Cruz N, et al. Role of rhinovirus C respiratory infections in sick and healthy children in Spain. Pediatr Infect Dis J 2010; 29: 717-720.
30. Mak RK, Tse LY, Lam WY, Wong GW, Chan PK, Leung TF. Clinical spectrum of human rhinovirus infections in hospitalized Hong Kong children. Pediatr Infect Dis J 2011; 30: 749-753.
31. Su YT, Lin YT, Yang CC, Tsai SS, Wang JY, Huang YL, et al. High correlation between human rhinovirus type C and children with asthma exacerbations in Taiwan. J Microbiol Immunol Infect 2020; 53: 561-568.
32. Jin Y, Yuan XH, Xie ZP, Gao HC, Song JR, Zhang RF, et al. Prevalence and clinical characterization of a newly identified human rhinovirus C species in children with acute respiratory tract infections. J Clin Microbiol 2009; 47: 2895-2900.
33. Van Piggelen RO, Van Loon AM, Krediet TG, Verboon-Maciolek MA. Human rhinovirus causes severe infection in preterm infants. Pediatr Infect Dis J 2010; 29: 364-365.
34. Ozdemir Sahan Y, Kilicoglu E, Ulger Tutar Z. Evaluation of children with congenital heart disease hospitalized with the diagnosis of lower respiratory tract infection. J Pediatr Res 2018; 5: 32-36.
35. Pretorius MA, Tempia S, Walaza S, Cohen AL, Moyes J, Variava E, et al. The role of influenza, RSV and other common respiratory viruses in severe acute respiratory infections and influenza-like illness in a population with a high HIV seroprevalence, South Africa 2012-2015. J Clin Virol 2016; 75:21-26.
2. Liu L, Chu Y, Oza S, Hogan D, Perin J, Bassani DG, et al. National, regional, and state-level all-cause and cause-specific under-5 mortality in India in 2000-15: a systematic analysis with implications for the Sustainable Development Goals. Lancet Glob Health 2019; 7(6): e721-e734.
3. Xiang S, Chen Z, Dai Z, Wang F. Global burden of lower respiratory infections attributable to secondhand smoke among children under 5 years of age, 2010-2019: a systematic analysis of the global burden of disease study 2019. BMC Public Health 2023; 23: 1920.
4. Smith KR, Samet JM, Romieu I, Bruce N. Indoor air pollution in developing countries and acute lower respiratory infections in children. Thorax 2000; 55: 518-532.
5. Williams BG, Gouws E, Boschi-Pinto C, Bryce J, Dye C. Estimates of world-wide distribution of child deaths from acute respiratory infections. Lancet Infect Dis 2002; 2:25-32.
6. Palmenberg AC, Gern JE. Classification and evolution of human rhinoviruses. Methods Mol Biol 2015; 1221:1-10.
7. Jacobs SE, Lamson DM, St George K, Walsh TJ. Human rhinoviruses. Clin Microbiol Rev 2013; 26 :135-162.
8. McIntyre CL, Knowles NJ, Simmonds P. Proposals for the classification of human rhinovirus species A, B and C into genotypically assigned types. J Gen Virol 2013; 94: 1791-1806.
9. Sonawane AA, Shastri J, Bavdekar SB. Respiratory Pathogens in Infants Diagnosed with Acute Lower Respiratory Tract Infection in a Tertiary Care Hospital of Western India Using Multiplex Real Time PCR. Indian J Pediatr 2019; 86: 433-438.
10. Ali SA, Gern JE, Hartert TV, Edwards KM, Griffin MR, Miller EK, et al. Real-world comparison of two molecular methods for detection of respiratory viruses. Virol J 2011; 8:332.
11. Wisdom A, Leitch EC, Gaunt E, Harvala H, Simmonds P. Screening respiratory samples for detection of human rhinoviruses (HRVs) and enteroviruses: comprehensive VP4-VP2 typing reveals high incidence and genetic diversity of HRV species C. J Clin Microbiol 2009; 47: 3958-3967.
12. Mishra P, Nayak L, Das RR, Dwibedi B, Singh A. Viral Agents Causing Acute Respiratory Infections in Children under Five: A Study from Eastern India. Int J Pediatr 2016; 2016: 7235482.
13. Nair H, Simões EA, Rudan I, Gessner BD, Azziz-Baumgartner E, Zhang JSF, et al. Severe Acute Lower Respiratory Infections Working Group. Global and regional burden of hospital admissions for severe acute lower respiratory infections in young children in 2010: a systematic analysis. Lancet 2013; 381: 1380-1390.
14. Lauinger IL, Bible JM, Halligan EP, Bangalore H, Tosas O, Aarons EJ, et al. Patient characteristics and severity of human rhinovirus infections in children. J Clin Virol 2013; 58: 216-220.
15. Sung CC, Chi H, Chiu NC, Huang DT, Weng LC, Wang NY, et al. Viral etiology of acute lower respiratory tract infections in hospitalized young children in Northern Taiwan. J Microbiol Immunol Infect 2011; 44: 184-190.
16. Yeolekar LR, Damle RG, Kamat AN, Khude MR, Simha V, Pandit AN. Respiratory viruses in acute respiratory tract infections in Western India. Indian J Pediatr 2008; 75: 341-345.
17. Maitreyi RS, Broor S, Kabra SK, Ghosh M, Seth P, Dar L, et al. Rapid detection of respiratory viruses by centrifugation enhanced cultures from children with acute lower respiratory tract infections. J Clin Virol 2000; 16: 41-47.
18. Singh AK, Jain A, Jain B, Singh KP, Dangi T, Mohan M, et al. Viral aetiology of acute lower respiratory tract illness in hospitalised paediatric patients of a tertiary hospital: one year prospective study. Indian J Med Microbiol 2014; 32:13-18.
19. Taylor S, Lopez P, Weckx L, Borja-Tabora C, Ulloa-Gutierrez R, Lazcano-Ponce E, et al. Respiratory viruses and influenza-like illness: Epidemiology and outcomes in children aged 6 months to 10 years in a multi-country population sample. J Infect 2017; 74: 29-41.
20. Xiao Q, Zheng S, Zhou L, Ren L, Xie X, Deng Y, et al. Impact of Human Rhinovirus Types and Viral Load on the Severity of Illness in Hospitalized Children With Lower Respiratory Tract Infections. Pediatr Infect Dis J 2015; 34: 1187-1192.
21. Guerrier G, Goyet S, Chheng ET, Rammaert B, Borand L, Te V, et al. Acute viral lower respiratory tract infections in Cambodian children: clinical and epidemiologic characteristics. Pediatr Infect Dis J 2013; 32(1): e8-13.
22. Fujitsuka A, Tsukagoshi H, Arakawa M, Goto-Sugai K, Ryo A, Okayama Y, et al. A molecular epidemiological study of respiratory viruses detected in Japanese children with acute wheezing illness. BMC Infect Dis 2011; 11: 168.
23. Yan Y, Huang L, Wang M, Wang Y, Ji W, Zhu C, et al. Clinical and epidemiological profiles including meteorological factors of low respiratory tract infection due to human rhinovirus in hospitalized children. Ital J Pediatr 2017; 43: 23.
24. Lau SK, Yip CC, Tsoi HW, Lee RA, So LY, Lau YL, et al. Clinical features and complete genome characterization of a distinct human rhinovirus (HRV) genetic cluster, probably representing a previously undetected HRV species, HRV-C, associated with acute respiratory illness in children. J Clin Microbiol 2007; 45: 3655-3664.
25. Daleno C, Piralla A, Scala A, Senatore L, Principi N, Esposito S. Phylogenetic analysis of human rhinovirus isolates collected from otherwise healthy children with community-acquired pneumonia during five successive years. PLoS One 2013; 8(11): e80614.
26. Louie JK, Roy-Burman A, Guardia-Labar L, Boston EJ, Kiang D, Padilla T, et al. Rhinovirus associated with severe lower respiratory tract infections in children. Pediatr Infect Dis J 2009; 28: 337-339.
27. Baillie VL, Olwagen CP, Madhi SA. Review on Clinical and Molecular Epidemiology of Human Rhinovirus-Associated Lower Respiratory Tract Infections in African and Southeast Asian Children. Pediatr Infect Dis J 2018; 37(7): e185-e194.
28. Panda S, Mohakud NK, Panda S, Kumar S. Epidemiology and phylogenetic analysis of human rhinovirus/Enterovirus in Odisha, Eastern India. Indian J Med Microbiol 2019; 37: 569-573.
29. Calvo C, Casas I, García-García ML, Pozo F, Reyes N, Cruz N, et al. Role of rhinovirus C respiratory infections in sick and healthy children in Spain. Pediatr Infect Dis J 2010; 29: 717-720.
30. Mak RK, Tse LY, Lam WY, Wong GW, Chan PK, Leung TF. Clinical spectrum of human rhinovirus infections in hospitalized Hong Kong children. Pediatr Infect Dis J 2011; 30: 749-753.
31. Su YT, Lin YT, Yang CC, Tsai SS, Wang JY, Huang YL, et al. High correlation between human rhinovirus type C and children with asthma exacerbations in Taiwan. J Microbiol Immunol Infect 2020; 53: 561-568.
32. Jin Y, Yuan XH, Xie ZP, Gao HC, Song JR, Zhang RF, et al. Prevalence and clinical characterization of a newly identified human rhinovirus C species in children with acute respiratory tract infections. J Clin Microbiol 2009; 47: 2895-2900.
33. Van Piggelen RO, Van Loon AM, Krediet TG, Verboon-Maciolek MA. Human rhinovirus causes severe infection in preterm infants. Pediatr Infect Dis J 2010; 29: 364-365.
34. Ozdemir Sahan Y, Kilicoglu E, Ulger Tutar Z. Evaluation of children with congenital heart disease hospitalized with the diagnosis of lower respiratory tract infection. J Pediatr Res 2018; 5: 32-36.
35. Pretorius MA, Tempia S, Walaza S, Cohen AL, Moyes J, Variava E, et al. The role of influenza, RSV and other common respiratory viruses in severe acute respiratory infections and influenza-like illness in a population with a high HIV seroprevalence, South Africa 2012-2015. J Clin Virol 2016; 75:21-26.
| Files | ||
| Issue | Vol 18 No 1 (2026) | |
| Section | Original Article(s) | |
| DOI | https://doi.org/10.18502/ijm.v18i1.21031 | |
| Keywords | ||
| Rhinovirus Respiratory tract infections Molecular characterization Phylogeny Acute disease Real-time polymerase chain reaction | ||
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How to Cite
1.
Parvathy V, Thakur P, Thakur V, Sharma V, Bora I, Ratho R, Angurana S, Singh M. Molecular characterization of human rhinovirus strains detected in pediatric acute respiratory tract infections. Iran J Microbiol. 2026;18(1):122-130.
