Characterization of Human Coronavirus Etiology in Chinese Adults with Acute Upper Respiratory Tract Infection by Real-Time RT-PCR Assays

Abstract

Background In addition to SARS associated coronaviruses, 4 non-SARS related human coronaviruses (HCoVs) are recognized as common respiratory pathogens. The etiology and clinical impact of HCoVs in Chinese adults with acute upper respiratory tract infection (URTI) needs to be characterized systematically by molecular detection with excellent sensitivity. Methodology/Principal Findings In this study, we detected 4 non-SARS related HCoV species by real-time RT-PCR in 981 nasopharyngeal swabs collected from March 2009 to February 2011. All specimens were also tested for the presence of other common respiratory viruses and newly identified viruses, human metapneumovirus (hMPV) and human bocavirus (HBoV). 157 of the 981 (16.0%) nasopharyngeal swabs were positive for HCoVs. The species detected were 229E (96 cases, 9.8%), OC43 (42 cases, 4.3%), HKU1 (16 cases, 1.6%) and NL63 (11 cases, 1.1%). HCoV-229E was circulated in 21 of the 24 months of surveillance. The detection rates for both OC43 and NL63 were showed significantly year-to-year variation between 2009/10 and 2010/11, respectively (P<0.001 and P = 0.003), and there was a higher detection frequency of HKU1 in patients aged over 60 years (P = 0.03). 48 of 157(30.57%) HCoV positive patients were co-infected. Undifferentiated human rhinoviruses and influenza (Flu) A were the most common viruses detected (more than 35%) in HCoV co-infections. Respiratory syncytial virus (RSV), human parainfluenza virus (PIV) and HBoV were detected in very low rate (less than 1%) among adult patients with URTI. Conclusions/Significance All 4 non-SARS-associated HCoVs were more frequently detected by real-time RT-PCR assay in adults with URTI in Beijing and HCoV-229E led to the most prevalent infection. Our study also suggested that all non-SARS-associated HCoVs contribute significantly to URTI in adult patients in China.

Detection of the Human Coronavirus 229E, HKU1, NL63, and OC43 between 2010 and 2013 in Yamagata, Japan

“…Our result and those of previous reports (3)(4)(5)(6)(7)(8)(9)(10)12,(14)(15)(16)19,20) suggest that HCoVs peak mainly in winter, although they can be detected throughout the year. Table 1 shows respiratory specimens with coinfection of HCoVs and other viruses, which were identified by virus isolation using a microplate method between 2010 and 2013 in Yamagata, Japan.…”

“…Our results also indicated that the frequency of HCoV detection per year ranged from 3.5z in 2013 to 9.7z in 2012. The detection frequencies of HCoVs in respiratory samples reported in the literature are highly variable, ranging from 1.6z to 16.0z, depending on the country, study period, study population, and detection modality (2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20). The most commonly observed HCoV in our survey was HCoV-NL63, whereas many previous studies reported a predominance of HCoV-OC43 (2,5-15).…”

“…Four HCoVs (HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1) are associated with a wide range of respiratory illness, including common colds, and with high morbidity outcomes, such as pneumonia and bronchiolitis (1)(2)(3). These four HCoVs are found globally, although the frequency of detection of these HCoVs varies with geographical location (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20). Poor growth and a lack of cytopathic effects on cell cultures have been major deterrents to HCoV research in the past (1).…”

“…The respiratory viruses most frequently detected with HCoVs were enterovirus (4.2z), parainfluenza virus (3.6z), adenovirus (3.3z), and rhinovirus (3.0z). The coinfection rates of HCoVs in respiratory samples reported in the literature vary, ranging from 30.5z to 70.0z (2,3,(12)(13)(14)(15)(16)(17)(18)(19)(20). Previous studies have demonstrated a high rate of HCoV coinfection with respiratory syncytial virus, influenza virus, and rhinovirus (2,3,(13)(14)(15)(16)(17)(18)(19).…”

Coronavirus Infections in Pediatric Outpatients with Febrile Respiratory Tract Infections in Hiroshima, Japan, over a 3-Year Period

“…RSV was detected in 138 children, HMPV in 66, PIV1-3 in 73, AdV in 124, rhinovirus in 23, enterovirus in 38, and Flu-C in 11 based on viral culture and real-time PCR assays; patients with multi-virus infections were counted multiple times, once independently for each type of virus. QIAamp Viral RNA Mini Kits (Qiagen, Hilden, Germany) were used to extract RNA and DNA from the 495 archival NPA specimens, which had been kept at -759 C. QuantiTect Virus Kits (Qiagen) were used to perform real-time reverse transcription-PCR (RT-PCR) for multiplex detection of HCoV-NL63, HKU1, OC43, and 229E (14). We used Student's t-test to compare between patient groups infected with HCoVs with respect to duration of fever, peak temperature, and clinical diagnosis.…”