Characterisation of a newly identified human rhinovirus, HRV-QPM, discovered in infants with bronchiolitis

Abstract

Background: Human rhinoviruses (HRVs) are some of the earliest identified and most commonly detected viruses associated with acute respiratory tract infections (ARTIs) and yet the molecular epidemiology and genomic variation of individual serotypes remains undefined.

Objectives: To molecularly characterise a novel HRV and determine its prevalence and clinical impact on a predominantly paediatric population.

Study design: Nucleotide sequencing was employed to determine the complete HRV-QPM coding sequence. Two novel real-time RT-PCR diagnostic assays were designed and employed to retrospectively screen a well-defined population of 1244 specimen extracts to identify the prevalence of HRV-QPM during 2003.

Results: Phylogenetic studies of complete coding sequences defined HRV-QPM as a novel member the genus Rhinovirus residing within the previously described HRV-A2 sub-lineage. Investigation of the relatively short VP1 sequence suggest that the virus is resistant to Pleconaril, setting it apart from the HRV A species. Sixteen additional HRV-QPM strains were detected (1.4% of specimens) often as the sole micro-organism present among infants with suspected bronchiolitis. HRV-QPM was also detected in Europe during 2006, and a closely related virus circulated in the United States during 2004.

Conclusions: We present the molecular characterisation and preliminary clinical impact of a newly identified HRV along with sequences representing additional new HRVs.

Fig. 1

The monthly distribution of tested respiratory specimens (open bars). The HRV-QPM detections (filled bars) are presented as a percentage of the specimens tested each month. Seasons are indicated.

Fig. 2

Nucleotide-based maximum likelihood phylogenies of the complete HRV structural genes 1A, 1B, and 1D (Genbank #EF512632–EF512682). The trees depict relationships among HRV-QPM strains, HRV species B serotype 14, and HRV species A serotypes 89, 39, 16, 1B, and 2 (accession numbers NC_001490, NC_001617, AY751783, L24917, D00239, X02316). The trees are rooted with human echovirus 1 (E1), a distantly related cluster B HEV, and branch lengths are drawn to scale. The two HRV species are indicated.

Fig. 3

Unrooted neighbour-joining trees of the complete VP1 amino acid sequences from representatives of (A), all four HEV clusters (includes examples from each HRV species; PV: poliovirus; CAV: coxsackievirus A; CBV: coxsackievirus B; EV: enterovirus; E: echovirus; Oberste et al., 1999) and (B), known HRV serotypes (includes examples from each HEV cluster). HRV-QPM is included in both trees.

Fig. 4

Alignment of predicted VP1 amino acid sequences HRV-QPM and HRV-A (HRV-1A, 16, 82 and 98) and HRV-B (HRV-5, 14,2 and 42) species. Numbering based on the HRV-QPM sequence (EF186077). The 25 residues of the pleconaril binding pocket are arrowed (majority HRV-B amino acid sequence listed below each arrow, Ledford et al., 2005). Two regions, indicated by overhead lines, appeared to be absent in HRV-QPM when compared with all other HRV VP1 sequences on GenBank (representative data shown here). Two residues predicted by Ledford to convey complete antiviral resistance to natural HRV-B strains (e.g. in HRV-5 and 14) are indicated by stars. Residues identical to HRV-QPM are indicated by dots. The absence of a residue is indicated by a dash.

Fig. 5

Relationships among HRV-A2 strains, as depicted by a maximum likelihood phylogeny of VP4/VP2 nucleotide sequences. Sequences described here (QPID strains and HRV-QPM prototype are compared to similar strains detected in the state of New York (as reported by Lamson et al., 2006) and HRV-A1 and B serotypes virus. HRV-87 is included as an outgroup. Accession numbers: HRV-2, AB079139; HRV-14, K02121; HRV-16, L24917; HRV-23, AF343597; HRV-25, AF343617; HRV-62, AF343618; HRV-86, AF343648; HRV-92, AY040238; HRV-87/HEV-68, AY040243; NY-074, DQ875932; NY-028, DQ875931; NY-003, DQ875929; NY-060, DQ875928; NY-042, DQ875926; NY-1085, DQ875925; NY-063, DQ875924; NY-041, DQ875921; HRV-QPM, EF186077. Previously identified but uncharacterised strains of the HRV-A2 sublineage (*; Arden et al., 2006) are indicated.