1887

Abstract

. Rhinoviruses (RVs) occur more frequently than other viruses and more often in people displaying symptoms than in those without. We sought to estimate the spectrum of RV diversity, RV species seasonality and to analyse RV involvement in respiratory virus co-detections.

. A convenience collection of 1179 airway sample extracts from patients with suspected respiratory infections, collected during 2001, was subjected to comprehensive molecular testing.

. RVs were the most common virus detected. We were able to genotype ~90 % of RV detections, identifying 70 distinct RVs, spanning all three species. RV-Bs were under-represented. We found RV species co-circulated at times, although one species usually dominated. Each species displayed a bimodal distribution.

. Notably, RVs and influenza A viruses (IFAV) seldom co-occurred, supporting their roles as primary pathogens of the airway among acutely ill infants. Whether RV circulation has a moderating or controlling effect on the IFAV season or is controlled by it cannot be determined from these data. Despite the frequent perception that RVs commonly co-occur with another virus, our findings indicated this was not always the case. Nearly 80 % of RV detections occurred alone. Understanding more about population-level interference between viruses may allow us to harness aspects of it to generate a non-specific antiviral intervention that mimics a putative protective effect. For routine respiratory virus screening to best serve the patient, RV testing should be a principal component of any acute respiratory illness testing algorithm throughout the year.

Loading

Article metrics loading...

/content/journal/acmi/10.1099/acmi.0.000075
2019-11-04
2019-11-13
Loading full text...

Full text loading...

/deliver/fulltext/acmi/10.1099/acmi.0.000075/acmi000075.html?itemId=/content/journal/acmi/10.1099/acmi.0.000075&mimeType=html&fmt=ahah

References

  1. Miller EK, Khuri-Bulos N, Williams JV, Shehabi AA, Faouri S et al. Human rhinovirus C associated with wheezing in hospitalised children in the middle East. J Clin Virol 2009;46: 85– 89 [CrossRef]
    [Google Scholar]
  2. Piotrowska Z, Vázquez M, Shapiro ED, Weibel C, Ferguson D et al. Rhinoviruses are a major cause of wheezing and hospitalization in children less than 2 years of age. Pediatr Infect Dis J 2009;28: 25– 29 [CrossRef]
    [Google Scholar]
  3. Sarna M, Ware RS, Lambert SB, Sloots TP, Nissen MD et al. Timing of first respiratory virus detections in infants: a community-based birth cohort study. J Infect Dis 2018;217: 418– 427 [CrossRef]
    [Google Scholar]
  4. Lambert SB, Allen KM, Druce JD, Birch CJ, Mackay IM et al. Community epidemiology of human metapneumovirus, human coronavirus NL63, and other respiratory viruses in healthy preschool-aged children using parent-collected specimens. Pediatrics 2007;120: e929– e937 [CrossRef]
    [Google Scholar]
  5. 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: 1232– 1240 [CrossRef]
    [Google Scholar]
  6. Simmonds P, McIntyre C, Savolainen-Kopra C, Tapparel C, Mackay IM et al. Proposals for the classification of human rhinovirus species C into genotypically assigned types. J Gen Virol 2010;91: 2409– 2419 [CrossRef]
    [Google Scholar]
  7. Royston L, Tapparel C, Rhinoviruses TC. Rhinoviruses and respiratory enteroviruses: not as simple as ABC. Viruses 2016;8: 16 [CrossRef]
    [Google Scholar]
  8. Mackay IM, Bialasiewicz S, Jacob KC, McQueen E, Arden KE et al. Genetic diversity of human metapneumovirus over 4 consecutive years in Australia. J Infect Dis 2006;193: 1630– 1633 [CrossRef]
    [Google Scholar]
  9. Syrmis MW, Whiley DM, Thomas M, Mackay IM, Williamson J et al. A sensitive, specific, and cost-effective multiplex reverse transcriptase-PCR assay for the detection of seven common respiratory viruses in respiratory samples. J Mol Diagn 2004;6: 125– 131 [CrossRef]
    [Google Scholar]
  10. Maertzdorf J, Wang CK, Brown JB, Quinto JD, Chu M et al. Real-Time reverse transcriptase PCR assay for detection of human metapneumoviruses from all known genetic lineages. J Clin Microbiol 2004;42: 981– 986 [CrossRef]
    [Google Scholar]
  11. Mackay IM, Arden KE, Speicher DJ, O'Neil NT, McErlean PK et al. Co-circulation of four human coronaviruses (HCoVs) in Queensland children with acute respiratory tract illnesses in 2004. Viruses 2012;4: 637– 653 [CrossRef]
    [Google Scholar]
  12. Lu X, Holloway B, Dare RK, Kuypers J, Yagi S et al. Real-Time reverse transcription-PCR assay for comprehensive detection of human rhinoviruses. J Clin Microbiol 2008;46: 533– 539 [CrossRef]
    [Google Scholar]
  13. Arden KE, Mackay IM. Newly identified human rhinoviruses: molecular methods heat up the cold viruses. Rev Med Virol 2010;20: 156– 176 [CrossRef]
    [Google Scholar]
  14. 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: 333– 340 [CrossRef]
    [Google Scholar]
  15. Wisdom A, McWilliam Leitch EC, Gaunt E, Harvala H, Simmonds P. Screening and comprehensive VP4/2-typing of human rhinoviruses (HRVs) and enteroviruses: comprehensive VP4-VP2 typing reveals high incidence and genetic diversity HRV species C. J Clin Microbiol 2009;47: 3958– 3967
    [Google Scholar]
  16. Gama RE, Horsnell PR, Hughes PJ, North C, Bruce CB et al. Amplification of rhinovirus specific nucleic acids from clinical samples using the polymerase chain reaction. J Med Virol 1989;28: 73– 77 [CrossRef]
    [Google Scholar]
  17. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M et al. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 2012;28: 1647– 1649 [CrossRef]
    [Google Scholar]
  18. Mackay IM. 2018; Human rhinovirus screening conventional RT-PCR ("Gama assay") protocols.io. https://www.protocols.io/view/human-rhinovirus-screening-conventional-rt-pcr-gam-n7gdhjw
  19. Mackay IMR, Wang CYT, Arden KE. 2018; Respiratory picornavirus genotyping conventional nested RT-PCR ("Wisdom VP42 assay") [Protocol]. protocols.io2018. https://www.protocols.io/view/respiratory-picornavirus-genotyping-conventional-n-nz7df9n
  20. Mackay IM. 2018; Human rhinovirus screening real-time RT-PCR ("modified Lu assay") protocols.io2018. https://www.protocols.io/view/human-rhinovirus-screening-real-time-rt-pcr-modifi-nz4df8w
  21. Greer RM, McErlean P, Arden KE, Faux CE, Nitsche A et al. Do rhinoviruses reduce the probability of viral co-detection during acute respiratory tract infections?. J Clin Virol 2009;45: 10– 15 [CrossRef]
    [Google Scholar]
  22. Australian Bureau of S Population by age and sex, Australia, states and territories: Australian Bureau of statistics. 2013
  23. Lee WM, Lemanske RF, Evans MD, Vang F, Pappas T et al. Human rhinovirus species and season of infection determine illness severity. Am J Respir Crit Care Med 2012;186: 886– 891 [CrossRef]
    [Google Scholar]
  24. Marcone DN, Culasso A, Carballal G, Campos R, Echavarría M. Genetic diversity and clinical impact of human rhinoviruses in hospitalized and outpatient children with acute respiratory infection, Argentina. J Clin Virol 2014;61: 558– 564 [CrossRef]
    [Google Scholar]
  25. Stelzer-Braid S, Tovey ER, Willenborg CM, Toelle BG, Ampon R et al. Absence of back to school peaks in human rhinovirus detections and respiratory symptoms in a cohort of children with asthma. J Med Virol 2016;88: 578– 587 [CrossRef]
    [Google Scholar]
  26. Tran DN, Trinh QD, Pham NTK, Pham TMH, Ha MT et al. Human rhinovirus infections in hospitalized children: clinical, epidemiological and virological features. Epidemiol Infect 2016;144: 346– 354 [CrossRef]
    [Google Scholar]
  27. Byington CL, Ampofo K, Stockmann C, Adler FR, Herbener A et al. Community surveillance of respiratory viruses among families in the Utah better identification of Germs-Longitudinal viral epidemiology (BIG-LoVE) study. Clin Infect Dis 2015;61: 1217– 1224 [CrossRef]
    [Google Scholar]
  28. Sarna M, Alsaleh A, Lambert SB, Ware RS, Mhango LP et al. Respiratory viruses in neonates: a prospective, community-based birth cohort study. Pediatr Infect Dis J 2016;35: 1355– 1357 [CrossRef]
    [Google Scholar]
  29. Mackay IM, Lambert SB, Faux CE, Arden KE, Nissen MD et al. Community-Wide, contemporaneous circulation of a broad spectrum of human rhinoviruses in healthy Australian preschool-aged children during a 12-month period. J Infect Dis 2013;207: 1433– 1441 [CrossRef]
    [Google Scholar]
  30. Smuts HE, Workman LJ, Zar HJ. Human rhinovirus infection in young African children with acute wheezing. BMC Infect Dis 2011;11: 65 [CrossRef]
    [Google Scholar]
  31. Miller EK, Williams JV, Gebretsadik T, Carroll KN, Dupont WD et al. Host and viral factors associated with severity of human rhinovirus-associated infant respiratory tract illness. J Allergy Clin Immunol 2011;127: 883– 891 [CrossRef]
    [Google Scholar]
  32. Principi N, Zampiero A, Gambino M, Scala A, Senatore L et al. Prospective evaluation of rhinovirus infection in healthy young children. J Clin Virol 2015;66: 83– 89 [CrossRef]
    [Google Scholar]
  33. Miller EK, Edwards KM, Weinberg GA, Iwane MK, Griffin MR et al. A novel group of rhinoviruses is associated with asthma hospitalizations. J Allergy Clin Immunol 2009;123: 98– 104 [CrossRef]
    [Google Scholar]
  34. Arden KE, Chang AB, Lambert SB, Nissen MD, Sloots TP et al. Newly identified respiratory viruses in children with non-hospitalised asthma exacerbation. J Med Virol 2010;82: 1458– 1461
    [Google Scholar]
  35. Müller L, Mack I, Tapparel C, Kaiser L, Alves MP et al. Human rhinovirus types and association with respiratory symptoms during the first year of life. Pediatr Infect Dis J 2015;34: 907– 909 [CrossRef]
    [Google Scholar]
  36. Xiang Z, Gonzalez R, Wang Z, Xiao Y, Chen L et al. Human rhinoviruses in Chinese adults with acute respiratory tract infection. J Infect 2010;61: 289– 298 [CrossRef]
    [Google Scholar]
  37. Xiang Z, Gonzalez R, Xie Z, Xiao Y, Liu J et al. Human rhinovirus C infections mirror those of human rhinovirus A in children with community-acquired pneumonia. J Clin Virol 2010;49: 94– 99 [CrossRef]
    [Google Scholar]
  38. Lau SKP, Yip CCY, Lin AWC, Lee RA, So LY et al. Clinical and molecular epidemiology of human rhinovirus C in children and adults in Hong Kong reveals a possible distinct human rhinovirus C subgroup. J Infect Dis 2009;200: 1096– 1103 [CrossRef]
    [Google Scholar]
  39. van der Zalm MM, Wilbrink B, van Ewijk BE, Overduin P, Wolfs TFW et al. Highly frequent infections with human rhinovirus in healthy young children: a longitudinal cohort study. J Clin Virol 2011;52: 317– 320 [CrossRef]
    [Google Scholar]
  40. Yang Y, Wang Z, Ren L, Wang W, Vernet G et al. Influenza A/H1N1 2009 pandemic and respiratory virus infections, Beijing, 2009-2010. PLoS One 2012;7: e45807 [CrossRef]
    [Google Scholar]
  41. Ånestad G, Vainio K, Hungnes O. Interference between outbreaks of epidemic viruses. Scand J Infect Dis 2007;39: 653– 654 [CrossRef]
    [Google Scholar]
  42. Casalegno JS, Ottmann M, Duchamp MB, Escuret V, Billaud G et al. Rhinoviruses delayed the circulation of the pandemic influenza A (H1N1) 2009 virus in France. Clin Microbiol Infect 2010;16: 326– 329 [CrossRef]
    [Google Scholar]
  43. Linde A, Rotzen-Ostlund M, Zweygberg-Wirgart B, Rubinova S, Brytting M. Does viral interference affect spread of influenza?. EuroSurveill 2009;14:
    [Google Scholar]
  44. Furuse Y, Oshitani H. Mechanisms of replacement of circulating viruses by seasonal and pandemic influenza A viruses. Int J Infect Dis 2016;51: 6– 14 [CrossRef]
    [Google Scholar]
  45. Bedford T, Riley S, Barr IG, Broor S, Chadha M et al. Global circulation patterns of seasonal influenza viruses vary with antigenic drift. Nature 2015;523: 217– 220 [CrossRef]
    [Google Scholar]
  46. Buchan SA, Chung H, Campitelli MA, Crowcroft NS, Gubbay JB et al. Vaccine effectiveness against laboratory-confirmed influenza hospitalizations among young children during the 2010-11 to 2013-14 influenza seasons in Ontario, Canada. PLoS One 2017;12: e0187834 [CrossRef]
    [Google Scholar]
  47. Lambert SB, Ware RS, Cook AL, Maguire FA, Whiley DM et al. Observational research in childhood infectious diseases (orchid): a dynamic birth cohort study. BMJ Open 2012;2: e002134 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/acmi/10.1099/acmi.0.000075
Loading
/content/journal/acmi/10.1099/acmi.0.000075
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error