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

Abstract

Although human rhinoviruses (HRVs) are common causes of respiratory illness, their molecular epidemiology has been poorly investigated. Despite the recent findings of new HRV genotypes, their clinical disease spectrum and phylogenetic positions were not fully understood. In this study, 203 prospectively collected nasopharyngeal aspirates (NPAs), negative for common respiratory viruses (83 were human bocavirus [HBoV] positive and 120 HBoV negative), from hospitalized children during a 1-year period were subjected to reverse transcription-PCR for HRV. HRV was detected in 14 NPAs positive and 12 NPAs negative for HBoV. Upon VP4 gene analysis, 5 of these 26 HRV strains were found to belong to HRV-A while 21 belonged to a genetic clade probably representing a previously undetected HRV species, HRV-C, that is phylogenetically distinct from the two known HRV species, HRV-A and HRV-B. The VP4 sequences of these HRV-C strains were closely related to the newly identified HRV strains from the United States and Australia. Febrile wheeze or asthma was the most common presentation (76%) of HRV-C infection, which peaked in fall and winter. Complete genome sequencing of three HRV-C strains revealed that HRV-C represents an additional HRV species, with features distinct from HRV-A and HRV-B. Analysis of VP1 of HRV-C revealed major deletions in regions important for neutralization in other HRVs, which may be signs of a distinct species, while within-clade amino acid variation in potentially antigenic regions may indicate the existence of different serotypes among HRV-C strains. A newly identified HRV species, HRV-C, is circulating worldwide and is an important cause of febrile wheeze and asthmatic exacerbations in children requiring hospitalization.

FIG. 1.

(A) Phylogenetic tree of the VP4 region of the 26 HRV strains from NPAs. (A) Two hundred nine nucleotide positions in each VP4 region were included in the analysis. The scale bar indicates the estimated number of substitutions per 50 bases. HRV NY strains were from New York, and strain HRV-QPM was from Queensland. The GenBank accession numbers of the previously published sequences are as follows: 003-HRV NY, DQ875929; 1085-HRV NY, DQ875925; HRV-QPM, EF186077; HRV1B, D00239; HRV2, X02316; HRV16, L24917; HRV39, AY751783; HRV89, A10937; HRV3, AY016403; HRV14, NC_001490; HRV42, AY016404; HRV84, AY040240; CAV16 (coxsackievirus A16), NC_001612; CAV21 (coxsackievirus A21), NC_001428; CAV24 (coxsackievirus A24), D90457; Echo1 (echovirus 1), AF029859; Echo2 (echovirus 2), AF465518; EV70, NC_001430; EV71, DQ452074; EV73, AF241359; and PV1 (poliovirus 1), V01150. (B) Seasonality of HRV and distribution of HBoV codetections.

FIG. 2.

Phylogenetic trees of the 5′-NCR, VP1, 3C, and 3D regions of three HRV-C strains. The analysis included 793, 1,004, 549, and 1,394 nucleotide positions in each 5′-NCR, VP1, 3C, and 3D region, respectively. The scale bars indicate the estimated number of substitutions per 50 bases. PV, poliovirus.

FIG. 3.

Comparison of the deduced amino acid sequences of VP1 in the three strains of HRV-C and HRV-QPM to those of HRV-A and HRV-B strains. The 10 motifs conserved between HRV-A and HRV-B, based on X-ray crystallographic analysis described previously, are shaded. Amino acid substitutions within the corresponding motifs in HRV-C are in bold. The putative secondary structures are marked above the sequence alignment. *, amino acid residues fully conserved across the RVs; :, strongly conserved residues; ., weakly conserved residues.