Human rhinoviruses: the cold wars resume

Abstract

Background: Human rhinoviruses (HRVs) are the most common cause of viral illness worldwide but today, less than half the strains have been sequenced and only a handful examined structurally. This viral super-group, known for decades, has still to face the full force of a molecular biology onslaught. However, newly identified viruses (NIVs) including human metapneumovirus and bocavirus and emergent viruses including SARS-CoV have already been exhaustively scrutinized. The clinical impact of most respiratory NIVs is attributable to one or two major strains but there are 100+ distinct HRVs and, because we have never sought them independently, we must arbitrarily divide the literature's clinical impact findings among them. Early findings from infection studies and use of inefficient detection methods have shaped the way we think of 'common cold' viruses today.

Objectives: To review past HRV-related studies in order to put recent HRV discoveries into context.

Results: HRV infections result in undue antibiotic prescriptions, sizable healthcare-related expenditure and exacerbation of expiratory wheezing associated with hospital admission.

Conclusion: The finding of many divergent and previously unrecognized HRV strains has drawn attention and resources back to the most widespread and frequent infectious agent of humans; providing us the chance to seize the advantage in a decades-long cold war.

Fig. 1

Schematic representations of HRV components. (a) The genome structure (exemplified by HRV-QPM, GenBank accession number EF186077 including the nucleotide positions separating coding regions) is illustrated to identify the polyprotein and the subsequent precursory (P1-3) and matured proteins (named in filled boxes below the genome). The structural and non-structural regions encompass 11 proteins. Co-translational cleavage of the approximately 250 kDa polyprotein is mediated by the virus-encoded protease, 2A^PRO which catalyses its own release, freeing P1 from the P2 and P3 regions. All subsequent post-translational cleavages are performed by the 3C protease (3C^PRO), which is also likely to free itself from the polyprotein (Racaniello, 2001). The three regions commonly contributing to taxonomic placement are underlined by dashed bars. (b) A single asymmetric unit included to simplify the visualization of capsid features and symmetry. The approximate placement of the canyon (bold line; canyon faces also indicated) and the subsurface binding pocket (dashed grey oval) are indicated as are the axes of symmetry including a small filled pentagon indicating the 5-fold axis and a small oval and triangles indicating 2- and 3-fold axes of symmetry. (c) A depiction of an HRV icosahedral capsid comprising 60 of the smallest capsid units or protomers. A viral pentamer is highlighted (grey shaded panels) composed of five protomers. The HRVs assemble their capsid into an icosahedron. HRV virions are approximately 30 nm in diameter (Rotbart, 2002). (d) A pair of facing protomers (indicated on (c) by darker grey panels) depicted in cross-section using a space-filling format. Each protomer consists of a single copy of the three exposed structural proteins VP1-VP3 and the internalized structural protein, VP4 (7kDa) (Stirk and Thornton, 1994, Rossmann et al., 1985, Rotbart, 2002). The binding pocket (asterisk, ‘*’; usually filled by a ‘pocket factor’) is located beneath the ‘canyon’, a distinctive deep (2.5 nm) cleft; site of major receptor interactions. The canyon, comprised mostly of VP1 and VP3 residues, encircles the point at which five protomers come together to create the 5-fold axis (Rossmann, 1994, Rossmann et al., 1985). The canyon rim restricts entry of the 3.5 nm Fab portion of antibody molecules, evident in the conservation of the canyon floor which is sequestered away from immune pressures and provides a safe harbour for receptor contact among the majority of known HRV strains (Rossmann et al., 1985, Pevear et al., 1989). (e) Top view ribbon depiction of five protomers comprising a viral pentamer and their relative orientation. The asymmetric unit and VP2 are indicated for reference. Adapted from (Mackay et al., in press-a).

Fig. 2

A ribbon depiction of the VP1 proteins involved in the predicted HRV-QPM pentamer (constructed using Chimera (Pettersen et al., 2004); derived from (McErlean et al., 2008)) viewed (A), from above and (B), as a single VP1 molecule from the side. Significant surface-exposed loops which contain important antigenic sites are boxed. β-sheets, flat ribbons with arrowheads; α-helices, coiled ribbons.

Fig. 3

Phylogeny of the untranslated regions (UTR; 5′ 610–635 nt) of HRV and HEV sequences obtained from GenBank (accession numbers shown). For this review, the region was also divided into 100 and 200 nt fragments and trees were constructed and compared for each consecutive fragment (inset; grey bars represent 100 nt fragments; black bar represents complete UTR). The branching patterns shown were retained with only subtle changes; HRV species were always represented clearly, as shown. HEV species were muddled. Nucleotide sequences were aligned using BioEdit v7.0.5.3 (Hall, 1999) and trees were constructed from a Neighbor-Joining analysis with 500 resamplings using Mega v4.0 (Tamura et al., 2007). Nodal values were shown only until they fell below 70. HEV, human enterovirus; EV, echovirus; CV, coxsackievirus; HPV, human poliovirus.

Fig. 4

The importance of sampling time and strain typing when investigating HRV shedding. (A) The examples provided here represent different, hypothetical studies for a single individual. If sampling occurred at each time point (i–vii) and if each positive was characterized, three different HRV strains could be identified from a single subject (period of replication by each strain indicated by a grey box; strain identity is provided on the left). If typing was not performed and sampling only occurred intermittently (indicated by the shapes in Example 1 (triangles), 2 (circles) and 3 (squares)), then the laboratory data could suggest only one or two infections. If testing was only performed during a symptomatic period (usually when the study starts) and again at the conclusion of the study period (Example 1), accurate determination of HRV infection frequency or strain diversity would not be possible. Example 2 identifies a case when sampling at the cessation of a study would not identify the HRV-BB strain however symptoms could be apparent due to its soon-to-be-detectable (detection indicated by the filled circle) replication. Strain BB may be prohibited from significant replication (indicated by the brevity of the infection period) due to pre-existing immunity which results in an asymptomatic state that still yields a relevant positive detection. In Example 3, sampling is only conducted for an SRI and so HRV BB is not detected. (B) HRV-KS is a truly chronic infection by a single strain whereas HRV-TC exemplifies some culture-based studies where the same strain appeared to recur after a period of absence, in the same individual. Some of these study designs could conclude persistent shedding was occurring, confounding attempts to correlate symptomatic periods with individual HRV strains and perpetuating the belief that HRVs do not exist independently of their group.

Fig. 5

A distillation of some significant events in the history of HRV research. Antiviral milestones (downward facing arrowed boxes) recognise a significant publication but may not represent first use in humans. Hexagons-reports of untypeable/unassigned picornavirus sequences derived from PCR products; stars-complete coding sequences of HRV C strains; triangles-laboratory data suggesting a new HRV species, HRV C.

Fig. 6

Genomic features of the HRV C strains. (a) HRV genome depiction with prominent coding and polyprotein features marked, (b) plots of the average amino acid sequence identity of P1, 2C and P3 regions from all six HRV C strains compared to the same region of the other HRV species (HRV A, grey line; HRV B, black). The highest mean predicted amino acid identity is indicated by a dashed line at the specific value for the closest matching species. Constructed using SIMplot v3.2 (http://sray.med.som.jhmi.edu/SCRoftware/) using the Hamming distance model with a sliding window of 100 aa and a step of 1 aa. Adapted from (Mackay et al., in press-a).