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Molecular Genotyping of Human Rhinovirus by Using PCR and Sanger Sequencing

  • Wei Wang
  • Jing He
  • Yi Liu
  • Lei Xu
  • Wencai Guan
  • Yunwen HuEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1221)

Abstract

Human rhinovirus (HRV) is the virus most often associated with acute upper respiratory tract infections. Advances in molecular detection have shown that HRV is also the major viral cause of asthma exacerbations. Genotypic assignment and identification of HRV types are of significant value in the investigation of type-associated differences in disease outcomes, transmission, and epidemiology. Here, we describe a genotyping process involving two separate RT-PCR assays, targeted to VP4/VP2 and 5′ UTR regions of HRV genome, respectively. Together with the reference sequences of each HRV species, the generated sequences are used to construct phylogenetic tree for genotyping.

Key words

Human rhinovirus Genotyping VP4/VP2 5′ UTR 

References

  1. 1.
    Gavala ML, Bertics PJ, Gern JE (2011) Rhinoviruses, allergic inflammation, and asthma. Immunol Rev 242(1):69–90, PMCID: 3119863PubMedCrossRefPubMedCentralGoogle Scholar
  2. 2.
    Mackay AJ, Hurst JR (2013) COPD exacerbations: causes, prevention, and treatment. Immunol Allergy Clin North Am 33(1):95–115PubMedCrossRefGoogle Scholar
  3. 3.
    Mak RK, Tse LY, Lam WY, Wong GW, Chan PK, Leung TF (2011) Clinical spectrum of human rhinovirus infections in hospitalized Hong Kong children. Pediatr Infect Dis J 30(9):749–753PubMedCrossRefGoogle Scholar
  4. 4.
    Ko FW, Ip M, Chan PK, Chan MC, To KW, Ng SS et al (2007) Viral etiology of acute exacerbations of COPD in Hong Kong. Chest 132(3):900–908PubMedCrossRefGoogle Scholar
  5. 5.
    Lau SK, Yip CC, Tsoi HW, Lee RA, So LY, Lau YL et al (2007) 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 45(11):3655–3664, PMCID: 2168475PubMedCrossRefPubMedCentralGoogle Scholar
  6. 6.
    McErlean P, Shackelton LA, Andrews E, Webster DR, Lambert SB, Nissen MD et al (2008) Distinguishing molecular features and clinical characteristics of a putative new rhinovirus species, human rhinovirus C (HRV C). PLoS One 3(4):e1847, PMCID: 2268738PubMedCrossRefPubMedCentralGoogle Scholar
  7. 7.
    Palmenberg AC, Spiro D, Kuzmickas R, Wang S, Djikeng A, Rathe JA et al (2009) Sequencing and analyses of all known human rhinovirus genomes reveal structure and evolution. Science 324(5923):55–59PubMedCrossRefPubMedCentralGoogle Scholar
  8. 8.
    Wisdom A, Leitch EC, Gaunt E, Harvala H, Simmonds P (2009) 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 47(12):3958–3967, PMCID: 2786677PubMedCrossRefPubMedCentralGoogle Scholar
  9. 9.
    Lee WM, Kiesner C, Pappas T, Lee I, Grindle K, Jartti T et al (2007) A diverse group of previously unrecognized human rhinoviruses are common causes of respiratory illnesses in infants. PLoS One 2(10):e966, PMCID: 1989136PubMedCrossRefPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Wei Wang
    • 1
  • Jing He
    • 1
  • Yi Liu
    • 1
  • Lei Xu
    • 1
  • Wencai Guan
    • 1
  • Yunwen Hu
    • 1
    Email author
  1. 1.Pathogen Diagnosis and Biosafety Department, Shanghai Public Health Clinical CenterFudan UniversityShanghaiPeople’s Republic of China

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