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Volume 15, Number 5—May 2009
Research

New Respiratory Enterovirus and Recombinant Rhinoviruses among Circulating Picornaviruses

Caroline Tapparel1Comments to Author , Thomas Junier1, Daniel Gerlach, Sandra Van Belle, Lara Turin, Samuel Cordey, Kathrin Mühlemann, Nicolas Regamey, John-David Aubert, Paola M. Soccal, Philippe Eigenmann, Evgeny M. Zdobnov1, and Laurent Kaiser1
Author affiliations: University of Geneva Hospitals, Geneva, Switzerland (C. Tapparel, S. Van Belle, L. Turin, S. Cordey, P. M. Soccal, P. Eigenmann, L. Kaiser); University of Geneva Medical School, Geneva (C. Tapparel, T. Junier, D. Gerlach, S. Van Belle, L. Turin, S. Cordey, E. Zdobnov, L. Kaiser); Swiss Institute of Bioinformatics, Geneva (T. Junier, D. Gerlach, E. Zdobnov); University Hospital of Bern, Bern, Switzerland (K. Mühlemann, N. Regamey); University Hospital of Lausanne, Lausanne, Switzerland (J.-D. Aubert); Imperial College London, London, UK (E. Zdobnov); 1These authors contributed equally to this article.

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Table

Characteristics of screened study populations and respiratory samples, Switzerland*

Type of study (no. enrolled) Age group Patient characteristics Years of study Type of specimens PCR No. (%) positive Reference
Respiratory infection in newborns (243) <1 y Nonhospitalized children with initial respiratory episode with cough 1999–2005 NPS HRV-A and HRV-B specific real time for the first 203 and panenterhino for 40 36 (15) (20)
Lower respiratory tract infection in hospitalized patients (147) Adults Mainly immunocompromised patients with lower respiratory tract complications and comorbidities 2001–2003 BAL, NPS HRV-A and HRV-B specific real time 16 (11) (21)
Acute respiratory tract infection in children (653) <17 y Nonhospitalized children with AOM or pneumonia 2004–2007 NPS Panenterhino 121 (18) (22) and ongoing study
Lower respiratory tract infection in hospitalized patients (485) Adults Mainly immunocompromised patients with lower respiratory tract complications and concurrent illnesses 2003–2006 BAL, NPS Panenterhino 52 (11) (21) and ongoing study
Acute respiratory tract infection in children (64) <12 y Children at an emergency department with fever and acute respiratory symptoms treated with antimicrobial drugs 2006–2007 NPS Panenterhino 23 (36) NP
Isolation in routine procedures (NA) Children and adults Hospitalized patients 1999–2008 BAL, NPS HE culture isolation NA NP

*NPS, nasopharyngeal samples; HRV, human rhinovirus; BAL, bronchoalveolar lavage; AOM, acute otitis media; NP, not published; NA, not available; HE, human embryonic primary fibroblast cell line.

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References
  1. Tapparel  C, Junier  T, Gerlach  D, Cordey  S, Van Belle  S, Perrin  L, New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features. BMC Genomics. 2007;8:224. DOIPubMed
  2. Newcombe  NG, Andersson  P, Johansson  ES, Au  GG, Lindberg  AM, Barry  RD, Cellular receptor interactions of C-cluster human group A coxsackieviruses. J Gen Virol. 2003;84:304150. DOIPubMed
  3. Pulli  T, Koskimies  P, Hyypia  T. Molecular comparison of coxsackie A virus serotypes. Virology. 1995;212:308. DOIPubMed
  4. Dufresne  AT, Gromeier  M. A nonpolio enterovirus with respiratory tropism causes poliomyelitis in intercellular adhesion molecule 1 transgenic mice. Proc Natl Acad Sci U S A. 2004;101:1363641. DOIPubMed
  5. Oberste  MS, Maher  K, Schnurr  D, Flemister  MR, Lovchik  JC, Peters  H, Enterovirus 68 is associated with respiratory illness and shares biological features with both the enteroviruses and the rhinoviruses. J Gen Virol. 2004;85:257784. DOIPubMed
  6. Ledford  RM, Patel  NR, Demenczuk  TM, Watanyar  A, Herbertz  T, Collett  MS, VP1 sequencing of all human rhinovirus serotypes: insights into genus phylogeny and susceptibility to antiviral capsid-binding compounds. J Virol. 2004;78:366374. DOIPubMed
  7. Laine  P, Blomqvist  S, Savolainen  C, Andries  K, Hovi  T. Alignment of capsid protein VP1 sequences of all human rhinovirus prototype strains: conserved motifs and functional domains. J Gen Virol. 2006;87:12938. DOIPubMed
  8. Savolainen  C, Blomqvist  S, Mulders  MN, Hovi  T. Genetic clustering of all 102 human rhinovirus prototype strains: serotype 87 is close to human enterovirus 70. J Gen Virol. 2002;83:33340.PubMed
  9. Arden  KE, McErlean  P, Nissen  MD, Sloots  TP, Mackay  IM. Frequent detection of human rhinoviruses, paramyxoviruses, coronaviruses, and bocavirus during acute respiratory tract infections. J Med Virol. 2006;78:123240. DOIPubMed
  10. Kistler  A, Avila  PC, Rouskin  S, Wang  D, Ward  T, Yagi  S, Pan-viral screening of respiratory tract infections in adults with and without asthma reveals unexpected human coronavirus and human rhinovirus diversity. J Infect Dis. 2007;196:81725. DOIPubMed
  11. Lamson  D, Renwick  N, Kapoor  V, Liu  Z, Palacios  G, Ju  J, MassTag polymerase-chain-reaction detection of respiratory pathogens, including a new rhinovirus genotype, that caused influenza-like illness in New York State during 2004–2005. J Infect Dis. 2006;194:1398402. DOIPubMed
  12. Lau  SK, Yip  CC, Tsoi  HW, Lee  RA, So  LY, Lau  YL, 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;45:365564. DOIPubMed
  13. Lee  WM, Kiesner  C, Pappas  T, Lee  I, Grindle  K, Jartti  T, A diverse group of previously unrecognized human rhinoviruses are common causes of respiratory illnesses in infants. PLoS One. 2007;2:e966. DOIPubMed
  14. McErlean  P, Shackelton  LA, Lambert  SB, Nissen  MD, Sloots  TP, Mackay  IM. Characterisation of a newly identified human rhinovirus, HRV-QPM, discovered in infants with bronchiolitis. J Clin Virol. 2007;39:6775. DOIPubMed
  15. McErlean  P, Shackelton  LA, Andrews  E, Webster  DR, Lambert  SB, Nissen  MD, Distinguishing molecular features and clinical characteristics of a putative new rhinovirus species, human rhinovirus C (HRV C). PLoS One. 2008;3:e1847.
  16. Renwick  N, Schweiger  B, Kapoor  V, Liu  Z, Villari  J, Bullmann  R, A recently identified rhinovirus genotype is associated with severe respiratory-tract infection in children in Germany. J Infect Dis. 2007;196:175460. DOIPubMed
  17. Cordey  S, Gerlach  D, Junier  T, Zdobnov  EM, Kaiser  L, Tapparel  C. The cis-acting replication elements define human enterovirus and rhinovirus species. RNA. 2008;14:156878. DOIPubMed
  18. Savolainen  C, Laine  P, Mulders  MN, Hovi  T. Sequence analysis of human rhinoviruses in the RNA-dependent RNA polymerase coding region reveals large within-species variation. J Gen Virol. 2004;85:22717. DOIPubMed
  19. Deffernez  C, Wunderli  W, Thomas  Y, Yerly  S, Perrin  L, Kaiser  L. Amplicon sequencing and improved detection of human rhinovirus in respiratory samples. J Clin Microbiol. 2004;42:32128. DOIPubMed
  20. Regamey  N, Kaiser  L, Roiha  HL, Deffernez  C, Kuehni  CE, Latzin  P, Viral etiology of acute respiratory infections with cough in infancy: a community-based birth cohort study. Pediatr Infect Dis J. 2008;27:1005.PubMed
  21. Garbino  J, Gerbase  MW, Wunderli  W, Deffernez  C, Thomas  Y, Rochat  T, Lower respiratory viral illnesses: improved diagnosis by molecular methods and clinical impact. Am J Respir Crit Care Med. 2004;170:1197203. DOIPubMed
  22. Kronenberg  A, Zucs  P, Droz  S, Muhlemann  K. Distribution and invasiveness of Streptococcus pneumoniae serotypes in Switzerland, a country with low antibiotic selection pressure, from 2001 to 2004. J Clin Microbiol. 2006;44:20328. DOIPubMed
  23. Allander  T, Tammi  MT, Eriksson  M, Bjerkner  A, Tiveljung-Lindell  A, Andersson  B. Cloning of a human parvovirus by molecular screening of respiratory tract samples. Proc Natl Acad Sci U S A. 2005;102:128916. DOIPubMed
  24. Edgar  RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:17927. DOIPubMed
  25. Rice  P, Longden  I, Bleasby  A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000;16:2767. DOIPubMed
  26. Guindon  S, Gascuel  O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003;52:696704. DOIPubMed
  27. Salminen  MO, Carr  JK, Burke  DS, McCutchan  FE. Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning. AIDS Res Hum Retroviruses. 1995;11:14235. DOIPubMed
  28. Garbino  J, Soccal  PM, Aubert  JD, Rochat  T, Meylan  P, Thomas  Y, Respiratory viruses in bronchoalveolar lavage: a hospital-based cohort study in adults. Thorax. 2009; [Epub ahead of print].
  29. Brown  B, Oberste  MS, Maher  K, Pallansch  MA. Complete genomic sequencing shows that polioviruses and members of human enterovirus species C are closely related in the noncapsid coding region. J Virol. 2003;77:897384. DOIPubMed
  30. Nix  WA, Oberste  MS, Pallansch  MA. Sensitive, seminested PCR amplification of VP1 sequences for direct identification of all enterovirus serotypes from original clinical specimens. J Clin Microbiol. 2006;44:2698704. DOIPubMed
  31. Kistler  AL, Webster  DR, Rouskin  S, Magrini  V, Credle  JJ, Schnurr  DP, Genome-wide diversity and selective pressure in the human rhinovirus. Virol J. 2007;4:40. DOIPubMed
  32. Simmonds  P. Recombination and selection in the evolution of picornaviruses and other mammalian positive-stranded RNA viruses. J Virol. 2006;80:1112440. DOIPubMed
  33. Smura  T, Blomqvist  S, Paananen  A, Vuorinen  T, Sobotova  Z, Bubovica  V, Enterovirus surveillance reveals proposed new serotypes and provides new insight into enterovirus 5′-untranslated region evolution. J Gen Virol. 2007;88:25206. DOIPubMed
  34. Oberste  MS, Maher  K, Michele  SM, Belliot  G, Uddin  M, Pallansch  MA. Enteroviruses 76, 89, 90 and 91 represent a novel group within the species Human enterovirus A. J Gen Virol. 2005;86:44551. DOIPubMed
  35. Junttila  N, Leveque  N, Kabue  JP, Cartet  G, Mushiya  F, Muyembe-Tamfum  JJ, New enteroviruses, EV-93 and EV-94, associated with acute flaccid paralysis in the Democratic Republic of the Congo. J Med Virol. 2007;79:393400. DOIPubMed
  36. Norder  H, Bjerregaard  L, Magnius  L, Lina  B, Aymard  M, Chomel  JJ. Sequencing of ‘untypable’ enteroviruses reveals two new types, EV-77 and EV-78, within human enterovirus type B and substitutions in the BC loop of the VP1 protein for known types. J Gen Virol. 2003;84:82736. DOIPubMed
  37. Witso  E, Palacios  G, Cinek  O, Stene  LC, Grinde  B, Janowitz  D, High prevalence of human enterovirus a infections in natural circulation of human enteroviruses. J Clin Microbiol. 2006;44:4095100. DOIPubMed
  38. Jiang  P, Faase  JA, Toyoda  H, Paul  A, Wimmer  E, Gorbalenya  AE. Evidence for emergence of diverse polioviruses from C-cluster coxsackie A viruses and implications for global poliovirus eradication. Proc Natl Acad Sci U S A. 2007;104:945762. DOIPubMed
  39. Domingo  E, Martin  V, Perales  C, Escarmis  C. Coxsackieviruses and quasispecies theory: evolution of enteroviruses. Curr Top Microbiol Immunol. 2008;323:332. DOIPubMed
  40. Lukashev  AN. Role of recombination in evolution of enteroviruses. Rev Med Virol. 2005;15:15767. DOIPubMed

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Page created: December 16, 2010
Page updated: December 16, 2010
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