Evidence of human coronavirus HKU1 and human bocavirus in Australian children

Abstract

Undiagnosed cases of respiratory tract disease suspected of an infectious aetiology peak during the winter months. Since studies applying molecular diagnostic assays usually report reductions in the number of undiagnosed cases of infectious disease compared to traditional techniques, we applied PCR assays to investigate the role of two recently described viruses, namely human coronavirus (HCoV) HKU1 and human bocavirus (HBoV), in a hospital-based paediatric population. Both viruses were found among Australia children with upper or lower respiratory tract disease during the autumn and winter of 2004, contributing to 21.1% of all microbial diagnoses, with individual incidences of 3.1% (HCoV-HKU1) and 5.6% (HBoV) among 324 specimens. HBoV was found to coincide with another virus in more than half of all instances and displayed a single genetic lineage, whilst HCoV-HKU1 was more likely to occur in the absence of another microbe and strains could be divided into two genetic lineages which we propose be termed HCoV-HKU1 type A and type B. Children under the age of 2 years were most at risk of infection by these viruses which contribute significantly to the microbial burden among patients with respiratory tract disease during the colder months.

Fig. 1

Phylogenetic analysis of Queensland strains of HCoV-HKU1, (QPID04), detected during 2004 presented on a topology tree prepared in MEGA 3 and compared to the type strain obtained from GenBank (HKU1) and all other human respiratory coronaviruses. A 414 bp nucleotide alignment of a portion of the polymerase (1b) gene was prepared using BioEdit V7.0.0.0. The nucleotide distance matrix was generated using the Kimura two-parameter estimation. Nodal confidence values indicate the results of boot strap resampling (n = 1000). Proposed HCoV-HKU1 genetic lineages are indicated.

Fig. 2

Phylogenetic analysis of the Queensland strains of HBoV (QPID04), detected during 2004 presented on a topology tree prepared in MEGA 3. A nucleotide alignment of a 245 bp portion of the NS1 gene was prepared using BioEdit V7.0.0.0. The nucleotide distance matrix was generated using the Kimura two-parameter estimation. Nodal confidence values indicate the results of boot strap resampling (n = 1000).