Prevalence and molecular epidemiology of human coronavirus HKU1 in patients with acute respiratory illness

Abstract

In 2005, human coronavirus HKU1 (HCoV-HKU1) was isolated and identified from a 71-year-old man with pneumonia in Hong Kong. To identify and classify genotypes of HCoV-HKU1 in Korea, a sensitive, specific, and quantitative real-time polymerase chain reaction (PCR) assay was developed and analyzed the sequences of HCoV-HKU1 isolated in Korea. A total of 1,985 respiratory specimens taken from patients with acute respiratory illness were tested for HCoV-HKU1 from January 2007 to May 2008. The major clinical symptoms associated with HCoV-HKU1 infection were examined statistically and sequence variations of the RNA-dependent RNA polymerase (RdRp), spike, and nucleocapsid genes were also analyzed. Fifty cases (2.5%) HCoV-HKU1 were identified by real-time PCR and viral loads ranged from 6.7 × 10(4) to 1.6 × 10(9) copies/ml. The clinical symptoms of HCoV-HKU1 infection included rhinorrhea (72%), cough (64%), nasal congestion (56%), fever (32%), sputum (30%), sore throat (18%), chills (16%), postnasal discharge (14%), and tonsillar hypertrophy (10%). There was a seasonal distribution of HCoV-HKU1 infection, peaking in winter and spring. Both genotypes A and B were detected but no recombination between them was found. This is the first report on the identification and genotyping of HCoV-HKU1 as a causative agent of acute respiratory illness in Korea. The data suggest that at least two genotypes, A and B, of HCoV-HKU1 with scattered silent mutations were circulating in Korea from 2007 to 2008.

Figure 1

Comparison of the sensitivity of the real‐time polymerase chain reaction (PCR) assay for the human coronavirus HKU1 (HCoV‐HKU1) ORF 1b gene with conventional PCR. The RT‐PCR assay detected up to 10 copies/µl of standard DNA, whereas the detection limit of conventional PCR was 1 × 10⁶ copies/µl.

Figure 2

Seasonal distribution of HCoV‐HKU1 infection from January 2007 to May 2008. The HCoV‐HKU1 prevailed from early winter to late spring in Korea. Bars indicate the monthly number of clinical specimens. The line represents the monthly proportion of positive cases as a whole.

Figure 3

Phylogenetic analysis of the RdRp, S, and N genes of HCoV‐HKU1. Eleven positive cases were classed as genotype A (n = 3) or B (n = 8). There was no HCoV‐HKU1 genotype C detected in Korea during the study period. Each shadowed number indicates the specimen identification number, and reference sequences are marked as GenBank accession numbers. Phylogenetic trees are shown of (A) the RdRp gene (897 neucleotide (nt)), (B) the S gene (309 nt), and (C) the N gene (425 nt). Primer sequences were excluded from phylogenetic analysis.