- Open Access
Human rhinoviruses: coming in from the cold
Genome Medicine volume 1, Article number: 44 (2009)
Rhinovirus infections cause at least 70% of virus-related wheezing exacerbations and cold and flu-like illnesses. Infections are also associated with otitis media, sinusitis and pneumonia. The annual impact of human rhinovirus (HRV) infections costs billions of healthcare dollars. To date, 100 serotyped HRV or 'classical' strains have been divided between two genetically distinct species based on subgenomic sequences, but many more, apparently novel strains remain un-characterized, circulating in unknown patterns and causing undefined illnesses. Until recently, the genomes of less than half the classical strains had been sequenced. In April 2009, the remaining classical HRV genome sequences were reported. These data will inform therapeutic development and phylogenetic analysis for this subset of HRV strains but should be viewed as one step in a long road leading to comprehensive HRV characterization.
Rhinoviruses: a long cold road ahead
Human rhinoviruses (HRVs) are the most common cause of acute respiratory tract illness globally , infecting both upper and lower respiratory tract tissues [2, 3]. They cause more asthma [4–6] and chronic obstructive pulmonary disease (COPD)  exacerbations than any other factor identified to date, in addition to the majority of cold and flu-like illnesses (CFLIs) . It is interesting to note that, in contrast to many of the other well-known respiratory viruses, the clinical symptoms of HRV infection are primarily caused by the host's immune response to infection rather than by viral cytopathicity [9–12]. HRVs are the most common reason for prescribing antibiotics  and are associated with pneumonia , otitis media  and sinusitis . Up to a quarter of children worldwide experience asthma symptoms, with prevalence plateauing in some countries while rising in other parts of the world . In adults, COPD exacerbations are predicted to soon become the world's third leading cause of death . The HRVs therefore create an enormous direct and indirect social and economic burden across the developed and developing world [18, 19].
Until recently, less than half the genomes from the approximately 100 serologically defined 'classical' strains (also called serotypes or types) had been sequenced. A handful of strains have had capsid structures experimentally defined and some have been subject to immunological investigations. Now, Palmenberg et al.  have completed the sequencing of all classical HRV genomes.
Rhinoviruses: more than meets the eye?
From the 1960s to the 1990s, human infection and culture-based methods of HRV detection prevailed, often augmented by strain typing using neutralizing antisera . The impracticality and insensitivity of these methods [22, 23] resulted in the misconception that compared to influenza virus and respiratory syncytial virus, for example, HRVs had straightforward and relatively minor roles in illness. This thinking limited their further characterization. Polymerase chain reaction (PCR)-based methods subsequently started to reveal the extent and complexity of HRV-induced illness  and have identified the frequent occurrence of co-detections, including some involving HRV strains, in respiratory specimens. Associations between an illness and a single respiratory virus, assumed because it was the only virus detected, now require re-examination to confirm that the association holds true. Previous concept-defining HRV-related epidemiology was conducted without knowledge of the numerous co-circulating respiratory viruses discovered since and was biased by the inability of culture to detect certain strains and species. Many of the 20th century's conclusions about HRVs will need to be revisited using modern methods. To date only one HRV strain, HRV-QPM, has been a deliberate target for intensive study using molecular tools .
In 2006 a large clade of divergent but inter-related strains was reported , and is now recognized as a proposed third species; HRV C. The HRV Cs were found entirely by molecular means from specimens collected in 2003/2004 [26–30], reflecting the unsuitability of culture for sensitive and comprehensive screening. HRV Cs have been heavily associated with wheezing illness but remain 'unculturable', perhaps reflecting their preference for different cell lines than those used routinely .
New genome sequences raise as many questions as they answer
The turn of the century has seen many significant advances in our understanding of the genetic diversity, genomic features and clinical impact of infection by the HRV group, as well as the immunological interactions of a few strains. The first classical strains were officially named in 1967 , the last in 1987 . Sequencing of the 5' untranslated (5'UTR)-VP2 region was completed for all classical strains in 2002  and the complete set of 1D regions was available in 2004 . In 2007 Kistler et al. added 28 genomes  and Tapparel et al. 12, including one common to both studies . All these data have provided tools to expand our knowledge of the phylogeny, evolution and epidemiology of HRVs and to predict their drug susceptibility, with reports indicating that subgenomic regions usefully represent the known genomes [34, 35]. Completing the sequencing of all classical strains has allowed more comprehensive in silico analyses than have been possible to date.
Examination of the entire set of HRV coding and non-coding regions by Palmenberg et al. produced data that support recent reports of recombination among the HRVs , but other intensive analyses indicated that this is not a driving force behind HRV evolution [35, 38, 39]. The discrepancies may be due to the different numbers of classical strain sequences used in each study, the different origins of the viruses used for sequencing, or the way predictive algorithms were configured. The ability of HRVs to recombine in practice awaits empirical evidence. Fascinatingly, one of ten field strains (HRV-54f05) sequenced by Palmenberg et al.  was predicted to be involved in recombination events from which seven classical strains arose compared to only one event for the American Type Culture Collection (ATCC) variant of the same strain. Previously, one strain needed to vary only at a few epitopes to be considered distinct from another. Now, when comparing molecular rather than antigenic differences, two variants of the same HRV strain (HRV-54) are found to differ across the genome by almost 600 nucleotides (91% identity, equating to 46 amino acid changes resulting in 98% amino acid identity). This raises several questions. How quickly does intra-strain genetic variation occur? Can such variation accumulate in sufficient quantity to require that a clinical HRV isolate or PCR detection be reconsidered as a distinct strain? Are new HRV strains actively emerging? These questions are especially important given the obvious impact of nucleotide sequence variation on evolutionary conclusions. Future studies may address the extent and location of genetic differences between clonal yet low-passage field strains  versus culture-adapted ATCC strains. Palmenberg et al. also proposed that a previously identified (HRV A' ), small but divergent clade within the HRV A species, which was renamed clade D, may represent a new species of HRV . When aligned together, two of the three members of this clade (HRV-8 and HRV-95) differ by no more than 81 nucleotides (>98% identity) or ten amino acids (>99% identity) and should be recognized as a single strain, as has been noted [20, 34]. The International Committee on Taxonomy of Viruses (ICTV) set 70% amino acid identity in two key regions as part of the demarcation between species within the genus Enterovirus. The definition is met in the 2C+3CD genomic region for assigning clade D to a novel species, as it exhibits >89% average amino acid identity between the clade's two distinct members but only 65% identity to other HRV A strains. However, the clade remains similar enough to the other HRV A strains in the P1 region (>70% average identity), its choice of receptor (major group ) and its similar G+C content. Clade D's antiviral profile is more similar to the HRV B strains (antiviral group A). Other genetic findings from the report of Palmenberg et al.  build upon those described previously for the classical HRVs [35, 36].
These new sequence data are valuable contributions to pure knowledge, to future rational drug design and for addressing outstanding phylogeny-based issues. However, the data do not directly contribute to more clinically relevant areas of research, such as diagnostic assay design, epidemiology, immunology, viral interference and co-infection, clinical impact, differential diagnosis and infection control. To address these areas is a daunting task because to be most informative, future respiratory virus studies, whether for HRVs or other viruses, should undertake an all-inclusive approach towards virus characterization. To give statistical power to the findings, large populations should be screened regularly regardless of symptoms (addressing persistence and pathogenicity), for all viruses (addressing co-infection and interference) across multiple years (addressing recurrence and seasonality) under case-controlled conditions. Ideally, hospital and community-based settings would be sampled in parallel (addressing pathogenicity in both groups), including the collection of appropriate material to permit serology and immunology investigations. These studies will need comprehensive and reliable molecular assays capable of detecting all instances of each virus or virus group and would benefit from an internationally collaborative approach.
Have the rhinoviruses coughed up all they have to offer?
Many novel HRV A, B and C strains are found when HRV-positive respiratory specimens are typed using subgenomic regions [24, 26] (Figure 1). There are likely to be many more when sampling extends over a greater period of time, since HRV strains do not always recur every year at a single location [42, 43]. It is likely that our current PCR-based methods could identify more than 100 novel HRV strains, raising more questions. What drives the development of so many strains when compared to the small number of strains of other RNA virus species? And why are so many similar strains apparently retained as stable viral entities over time?
Palmenberg et al.  conclude that future HRV epidemiology should make use of full genome sequencing rather than serotyping. Clearly, serotyping is no longer best or even most frequent practice, but it is to be hoped that future studies can determine sequence regions that suitably replicate these subdivisions, avoiding costly, time-consuming and technically demanding complete genome sequencing. Currently, it is impractical for most diagnostic and many clinical research laboratories to routinely sequence the full genome of every HRV detected, a task made especially daunting by the high prevalence of these viruses. The 1D region is the best subgenomic target for enterotyping  and has previously proven suitable for rhinotyping. However, the extent to which intra-species recombination will render subgenomic regions unreliable indicators of strain identity is a new source of uncertainty. The use of capsid-derived subgenomic regions for speciation remains reliable. Regions with high inter-strain sequence homology, such as the 5'UTR, are understandably risky targets for strain or species typing. An agreed upon definition of what constitutes a distinct HRV strain would be helpful for future studies and may become available from the Picornaviridae Study Group  in due course. Once all HRVs are identified, we may reliably define associations between strains, clades or species and clinical illnesses and syndromes. Characterizing the full spectrum of HRVs, including full genome sequencing, will better inform our efforts to create reliable therapeutics, such as antivirals that reduce viral replication and the symptoms of illness. The scope of HRV antigenic diversity and the possible importance of frequent, mild HRV infections for the development of a robust antiviral immunity during the early years of life may mean that a sterilizing vaccine, if feasible, is not desirable.
Although HRVs have increasingly become thought of as a single viral supergroup, now residing alongside their cousins in the genus Enterovirus, there may be important, discriminating antigenic, immunogenic, epidemic, clinical [20, 46] and now genomic features that support the treatment of some strains, clades or species as discrete viral entities, deserving targeted antiviral interventions and virological, clinical and epidemiological characterization . The rhinoviruses, known for decades, but often considered less of a public health and research priority than other viruses, may at last be facing the modern molecular, epidemiological and clinical research onslaught due such an intriguing group of pathogens.
IMM leads a research team, including KEA, that focuses on the identification of novel respiratory viruses followed by characterization of their virological and immunobiological features, epidemiology, and clinical impact among pediatric populations.
American Type Culture Collection
cold and flu-like illness
chronic obstructive pulmonary disease
International Committee on Taxonomy of Viruses
polymerase chain reaction
5' untranslated region.
Rotbart HA, Hayden FG: Picornavirus infections: a primer for the practitioner. Arch Fam Med. 2000, 9: 913-920. 10.1001/archfami.9.9.913
Arruda E, Boyle TR, Winther B, Pevear DC, Gwaltney JM, Hayden FG: Localization of human rhinovirus replication in the upper respiratory tract by in situ hybridization. J Infect Dis. 1995, 171: 1329-1333.
Jakiela B, Brockman-Schneider R, Amineva S, Lee W-M, Gern JE: Basal cells of differentiated bronchial epithelium are more susceptible to rhinovirus infection. Am J Respir Cell Mol Biol. 2008, 38: 517-523. 10.1165/rcmb.2007-0050OC
Chauhan AJ, Inskip HM, Linaker CH, Smith S, Schreiber J, Johnston SL, Holgate ST: Personal exposure to nitrogen dioxide (NO2) and the severity of virus-induced asthma in children. Lancet. 2003, 361: 1939-1944. 10.1016/S0140-6736(03)13582-9
Johnston SL, Pattemore PK, Sanderson G, Smith S, Lampe F, Josephs L, Symington P, O'Toole S, Myint SH, Tyrrell DAJ, Holgate ST: Community study of role of viral infections in exacerbations of asthma in 9-11 year old children. BMJ. 1995, 310: 1225-1229.
Rakes GP, Arruda E, Ingram JM, Hoover GE, Zambrano JC, Hayden FG, Platts-Mills TAE, Heymann PW: Rhinovirus and respiratory syncytial virus in wheezing children requiring emergency care. Am J Respir Crit Care Med. 1999, 159: 785-790.
Johnston SL: Overview of virus-induced airway disease. Proc Am Thorac Soc. 2005, 2: 150-156. 10.1513/pats.200502-018AW
Ruohola A, Waris M, Allander T, Ziegler T, Heikkinen T, Ruuskanen O: Viral etiology of common cold in children, Finland. Emerg Infect Dis. 2009, 15: 344-346. 10.3201/eid1502.081468
Winther B, Brofeldt S, Gronborg H, Mygind N: Pathology of naturally occurring colds. Eur J Respir Dis Suppl. 1983, 128: 345-347.
Dreschers S, Dumitru CA, Adams C, Gulbins E: The cold case: are rhinoviruses perfectly adapted pathogens?. Cell Mol Life Sci. 2007, 64: 181-191. 10.1007/s00018-006-6266-5
Hendley JO: The host response, not the virus, causes the symptoms of the common cold. Clin Infect Dis. 1998, 26: 847-848.
Turner RB, Weingand KW, Yeh C-H, Leedy DW: Association between interleukin-8 concentration in nasal secretions and severity of experimental rhinovirus colds. Clin Infect Dis. 1998, 26: 840-846. 10.1086/513922
Abzug MJ, Bam AC, Gyorkos EA, Levin MJ: Viral pneumonia in the first month of life. Pediatr Infect Dis J. 1990, 9: 881-885.
Arola M, Ziegler T, Puhakka H, Lehtonen OP, Ruuskanen O: Rhinovirus in otitis media with effusion. Ann Otol Rhinol Laryngol. 1990, 99: 451-453.
Gwaltney JM, Phillips CD, Miller RD, Riker DK: Computed tomographic study of the common cold. N Engl J Med. 1994, 330: 25-30. 10.1056/NEJM199401063300105
Asher MI, Montefort S, Bjorksten B, Lai CK, Strachan DP, Weiland SK, Williams H: Worldwide time trends in the prevalence of symptoms of asthma, allergic rhinoconjunctivitis, and eczema in childhood: ISAAC Phases One and Three repeat multicountry cross-sectional surveys. Lancet. 2006, 368: 733-743. 10.1016/S0140-6736(06)69283-0
Murray CJL, Lopez AD: Alternative projections of mortality and disability by cause 1990-2020: Global Burden of Disease Study. Lancet. 1997, 349: 1498-1504. 10.1016/S0140-6736(96)07492-2
Fendrick AM, Monto AS, Nightengale B: The economic burden of non-influenza-related viral respiratory tract infection in the United States. Arch Intern Med. 2003, 163: 487-494.
Bertino JS: Cost burden of viral respiratory infections: issues for formulary decision makers. Am J Med. 2002, 112: 42S-49S. 10.1016/S0002-9343(01)01063-4
Palmenberg AC, Spiro D, Kuzmickas R, Wang S, Djikeng A, Rathe JA, Fraser-Liggett CM, Liggett SB: Sequencing and analyses of all known human rhinovirus genomes reveals structure and evolution. Science. 2009, 324: 55-59. 10.1126/science.1165557
Mackay IM: Human rhinoviruses: the cold wars resume. J Clin Virol. 2008, 42: 297-320. 10.1016/j.jcv.2008.04.002
Johnston SL, Bardin PG, Pattemore PK: Viruses as precipitants of asthma symptoms III. Rhinoviruses: molecular biology and prospects for future intervention. Clin Exp Allergy. 1993, 23: 237-246. 10.1111/j.1365-2222.1993.tb00316.x
Gwaltney JM: Micro-neutralization test for identification of rhinovirus serotypes. Proc Soc Exp Biol Med. 1966, 122: 1137-1141.
Lee W-M, Kiesner C, Pappas T, Lee I, Grindle K, Jartti T, Jakiela B, Lemanske RF, Shult PA, Gern JE: A diverse group of previously unrecognized human rhinoviruses are common causes of respiratory illness in infants. PLoS One. 2007, 2: e966. 10.1371/journal.pone.0000966
McErlean P, Shackleton LA, Andrewes E, Webster DR, Lambert SB, Nissen MD, Sloots TP, Mackay IM: Distinguishing molecular features and clinical characteristics of a putative new rhinovirus species, human rhinovirus C (HRV C). PLoS ONE. 2008, 3: e1847-. 10.1371/journal.pone.0001847
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. 10.1002/jmv.20689
Lamson D, Renwick N, Kapoor V, Liu Z, Palacios G, Ju J, Dean A, St GK, Briese T, Lipkin WI: 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: 1398-1402. 10.1086/508551
Kistler A, Avila PC, Rouskin S, Wang D, Ward T, Yagi S, Schnurr D, Ganem D, DeRisi JL, Boushey HA: 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: 817-825. 10.1086/520816
Lau SKP, Yip CCY, Tsoi H-W, Lee RA, So L-Y, Lau Y-L, Chan K-H, Woo PCY, Yuen K-Y: Clinical features and complete genome characterization of a distinct human rhinovirus 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. 10.1128/JCM.01254-07
Guex N, Peitsch MC: SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modelling. Electrophoresis. 1997, 18: 2714-2723. 10.1002/elps.1150181505
Kapikian AZ, Conant RM, Chanock RM, Chapple PJ, Dick EC, Fenters JD, Gwaltney JM, Hamre D, Holper JC, Jordan WS, Lennette EH, Melnick JL, Mogabgab WJ, Mufson MA, Phillips CA, Schieble JH, Tyrrell DAJ: Rhinoviruses: a numbering system. Nature. 1967, 213: 761-762. 10.1038/213761a0
Hamparian VV, Colonno RJ, Cooney MK, Dick EC, Gwaltney JM, Hughes JH, Jordan WS, Kapikian AZ, Mogabgab WJ, Monto A, Phillips CA, Rueckert RR, Schieble JH, Stott EJ, Tyrrell DAJ: A collaborative report: rhinoviruses - extension of the numbering system from 89 to 100. Virology. 1987, 159: 191-192. 10.1016/0042-6822(87)90367-9
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.
Ledford RM, Patel NR, Demenczuk TM, Watanyar A, Herbertz T, Collett MS, Pevear DC: VP1 sequencing of all human rhinovirus serotypes: insights into genus phylogeny and susceptibility to antiviral capsid-binding compounds. J Virol. 2004, 78: 3663-3674. 10.1128/JVI.78.7.3663-3674.2004
Kistler A, Webster DR, Rouskin S, Magrini V, Credle J, Schnurr D, Boushey HA, Mardis ER, Li H, DeRisi JL: Genome-wide diversity and selective pressure in the human rhinovirus. Virol J. 2007, 4: 40. 10.1186/1743-422X-4-40
Tapparel C, Junier T, Gerlach D, Cordey S, van Belle S, Perrin L, Zdobnoy EM, Kaiser L: New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features. BMC Genomics. 2007, 8: 224. 10.1186/1471-2164-8-224
Tapparel C, Junier T, Germann D, van Belle S, Turin L, Cordey S, Mühlemann K, Regamey N, Aubert J-D, Soccal PM, Eigenmann P, Zdobnoy E, Kaiser L: New respiratory enterovirus and recombinant rhinoviruses among circulating strains. Emerg Infect Dis. 2009
Lewis-Rogers N, Bendall ML, Crandall KA: Phylogenetic relationships and molecular adaptation dynamics of human rhinoviruses. Mol Biol Evol. 2009, 26: 969-981. 10.1093/molbev/msp009
Simmonds P: Recombination and selection in the evolution of picornaviruses and other mammalian positive-stranded RNA viruses. J Virol. 2006, 80: 11124-11140. 10.1128/JVI.01076-06
Savolainen C, Mulders MN, Hovi T: Phylogenetic analysis of rhinovirus isolates collected during successive epidemic seasons. Virus Res. 2002, 85: 41-46. 10.1016/S0168-1702(02)00016-3
Uncapher CR, DeWitt CM, Colonno RJ: The major and minor group receptor families contain all but one human rhinovirus serotype. Virology. 1991, 180: 814-817. 10.1016/0042-6822(91)90098-V
McErlean P, Shackleton 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: 67-75. 10.1016/j.jcv.2007.03.012
Andrewes CH: Rhinoviruses and common colds. Annu Rev Med. 1966, 17: 361-370. 10.1146/annurev.me.17.020166.002045
Oberste MS, Maher K, Williams AJ, Dybdahl-Sissoko N, Brown BA, Gookin MS, Peñaranda S, Mishrik N, Uddin M, Pallansch MA: Species-specific RT-PCR amplification of human enteroviruses: a tool for rapid species identification of uncharacterized enteroviruses. J Gen Virol. 2006, 87: 119-128. 10.1099/vir.0.81179-0
The Picornaviridae Study Group.http://www.picornastudygroup.com
Wark PA, Grissell T, Davies B, See H, Gibson PG: Diversity in the bronchial epithelial cell response to infection with different rhinovirus strains. Respirology. 2009, 14: 180-186. 10.1111/j.1440-1843.2009.01480.x
We thank Laura Shackelton, Laurent Kaiser, Peter McErlean, Caroline Tapparel and Daniel Gerlach for helpful discussions and advice. The authors' research is funded by the National Health and Medical Research Council (grant number 455905) and Royal Children's Hospital Foundation (grant number 10281).
The authors declare that they have no competing interests.
Both authors contributed to the writing of the manuscript and have approved the final version.
Authors’ original submitted files for images
Below are the links to the authors’ original submitted files for images.
About this article
Cite this article
Arden, K.E., Mackay, I.M. Human rhinoviruses: coming in from the cold. Genome Med 1, 44 (2009). https://doi.org/10.1186/gm44
- Chronic Obstructive Pulmonary Disease
- Respiratory Virus
- Chronic Obstructive Pulmonary Disease Exacerbation
- Viral Entity
- Full Genome Sequencing