Epidemiology and clinical presentations of the four human coronaviruses 229E, HKU1, NL63, and OC43 detected over 3 years using a novel multiplex real-time PCR method

Abstract

Four human coronaviruses (HCoV-229E, HCoV-HKU1, HCoV-NL63, and HCoV-OC43) are associated with a range of respiratory outcomes, including bronchiolitis and pneumonia. Their epidemiologies and clinical characteristics are poorly described and are often reliant on case reports. To address these problems, we conducted a large-scale comprehensive screening for all four coronaviruses by analysis of 11,661 diagnostic respiratory samples collected in Edinburgh, United Kingdom, over 3 years between July 2006 and June 2009 using a novel four-way multiplex real-time reverse transcription-PCR (RT-PCR) assay. Coronaviruses were detected in 0.3 to 0.85% of samples in all age groups. Generally, coronaviruses displayed marked winter seasonality between the months of December and April and were not detected in summer months, which is comparable to the pattern seen with influenza viruses. HCoV-229E was the exception; detection was confined to the winter of 2008 and was sporadic in the following year. There were additional longer-term differences in detection frequencies between seasons, with HCoV-OC43 predominant in the first and third seasons and HCoV-HKU1 dominating in the second (see Results for definitions of seasons). A total of 11 to 41% of coronaviruses detected were in samples testing positive for other respiratory viruses, although clinical presentations of coronavirus monoinfections were comparable to those of viruses which have an established role in respiratory disease, such as respiratory syncytial virus, influenza virus, and parainfluenza viruses. The novel multiplex assay for real-time pan-coronavirus detection enhances respiratory virus diagnosis, overcomes potential diagnostic problems arising through seasonal variation in coronavirus frequency, and provides novel insights into the epidemiology and clinical implications of coronaviruses.

FIG. 1.

Percentages of detection frequencies of the four coronaviruses HCoV-229E, HCoV-HKU1, HCoV-NL63, and HCoV-OC43 by age group. The total number of samples within each age band is indicated at head of each column.

FIG. 2.

Coronavirus and influenza virus (A and B combined) detection frequencies by month over the 3 years of the study.

FIG. 3.

(A) Comparison of the clinical presentations of study subjects infected with coronaviruses to the clinical presentations of those infected with respiratory viruses included in diagnostic screening (adenovirus [AdV], influenza A virus, influenza B virus, PIV-1, PIV-2, PIV-3, and HRSV). Only single infections are included in the analysis. The y axis indicates proportions of subjects with symptoms or diagnoses of LRTI or URTI or symptoms not associated with respiratory infection (“None”). (B) Proportions of samples testing singly positive for each of the respiratory viruses from patients with immunosuppression. (C) Proportions of samples from patients with LRTI or URTI or with no respiratory symptoms (“None”) testing singly positive for each respiratory virus.