Detection of human Coronavirus 229E in nasal specimens in large scale studies using an RT-PCR hybridization assay

Outbreak of acute respiratory disease caused by human adenovirus type 7 and human coronavirus-229E in Zhejiang Province, China

In 2019, an outbreak of pharyngoconjunctival fever (PCF) occurred at a swimming center in Zhejiang Province, China. A total of 97 (13.55%) of the 716 amateur swimmers had illnesses, with 24 patients (24.74%) hospitalized in the pediatric ward. Human adenovirus serotype 7 (HAdV-7) was isolated from one concentrated water from the swimming pool, and 20 of 97 positive cases without liver damage. This outbreak led to a nosocomial outbreak in the pediatric ward, in which 1 nurse had a fever and was confirmed to be adenovirus positive. The hexon, fiber, and penton genes from 20 outbreak cases, 1 water sample, and 1 nurse had 100% homology. Furthermore, 2 cases admitted to the pediatric ward, 2 parents, and 1 doctor were confirmed to be human coronaviruses (HCoV-229E) positive. Finally, all outbreak cases had fully recovered, regardless of a single infection (adenovirus or HCoV-229E) or coinfection of these two viruses simultaneously. Thus, PCF and acute respiratory disease outbreaks in Zhejiang were caused by the completely homologous type 7 adenovirus and HCoV-229E, respectively. The swimming pool water contaminated with HAdV-7 was most likely the source of the PCF outbreak, whereas nosocomial transmission might be the source of HCoV-229E outbreak.

Laboratory detection methods for the human coronaviruses

Coronaviruses are a group of envelop viruses which lead to diseases in birds and mammals as well as human. Seven coronaviruses have been discovered in humans that can cause mild to lethal respiratory tract infections. HCoV-229E, HCoV-OC43, HCoV-NL63, and HCoV-HKU1 are the low-risk members of this family and the reason for some common colds. Besides, SARS-CoV, MERS-CoV, and newly identified SARS-CoV-2, which is also known as 2019-nCoV, are the more dangerous viruses. Due to the rapid spread of this novel coronavirus and its related disease, COVID-19, a reliable, simple, fast, and low-cost detection method is necessary for patient diagnosis and tracking worldwide. Human coronaviruses detection methods were classified and presented in this article. The laboratory detection techniques include RT-PCR, RT-LAMP, electrochemical and optical biosensors for RNA detection, and whole virus or viral proteins detection assays.

Epidemiology and Control: Principles, Practice and Programs

Infectious disease epidemiology is concerned with the occurrence of both infection and disease in populations and the factors that determine their frequency, spread, expression and distribution. Viruses show characteristic infectivity, virulence and pathogenicity. The most well established host factors are age, sex and race, but other host biological and behavioral factors affect acquisition of viral infection and/or its course and manifestations. The physical, chemical and biological environment operates on the virus itself and may also alter the host biological or behavioral response. Viral infections have incubation periods lasting days or weeks, while their pathologic sequelae may not manifest for years or decades. Likewise the degree or intensity of host response and clinical expression may range from largely inapparent to highly lethal. The degree of cell, tissue and organ specificity is high. Common syndromes involve the respiratory, gastrointestinal, and central nervous systems, the liver, and mucocutaneous surfaces. Vertical transmission may produce a variety of congenital and perinatal conditions. Viruses spread by multiple modes, using nearly every bodily surface or fluid as a route of exit or entry, either by direct contact or indirectly through an animal vector or other inanimate vehicle. Different viral Infections occur nearly ubiquitously or sporadically; they may be present continuously throughout a population (endemic) or occur in seasonal rhythm or in unexpectedly explosive form (epidemic). Many viruses are refractory to all known therapeutic agents, while for a few, the increasing number of highly effective agents holds great promise. Vaccines have produced many historical successes including the ultimate goal of eradication, but many viral infections continue to elude effective vaccine development. Major government and private sector programs for treatment and prevention have raised expectations of successful control for certain widespread and serious viral diseases; however, in every case a unique set of scientific, socioeconomic, political and behavioral barriers remains to be overcome.

Co-circulation of four human coronaviruses (HCoVs) in Queensland children with acute respiratory tract illnesses in 2004

Acute respiratory illnesses (ARIs) with unconfirmed infectious aetiologies peak at different times of the year. Molecular diagnostic assays reduce the number of unconfirmed ARIs compared to serology- or culture-based techniques. Screening of 888 inpatient and outpatient respiratory specimens spanning late autumn through to early spring, 2004, identified the presence of a human coronavirus (HCoV) on 74 occasions (8.3% of all specimens and 26.3% of all respiratory virus detections). Prevalence peaked in August (late winter in the southern hemisphere) when they were detected in 21.9% of specimens tested. HCoV-HKU1 and HCoV-OC43 comprised 82.4% of all HCoVs detected. Positive specimens were used to develop novel reverse transcriptase real-time PCRs (RT-rtPCRs) for HCoV detection. An objective clinical severity score was assigned to each positive HCoV patient. Severity scores were similar to those from a random selection of young children who were positive for respiratory syncytial virus at a different time but from the same specimen population. During the cooler months of 2004, sensitive and specific RT-rtPCRs identified the concurrent circulation of all four HCoVs, a quarter of which co-occurred with another virus and most of which were from children under the age of two years.

Molecular diagnosis of respiratory virus infections

The appearance of eight new respiratory viruses, including the SARS coronavirus in 2003 and swine-origin influenza A/H1N1 in 2009, in the human population in the past nine years has tested the ability of virology laboratories to develop diagnostic tests to identify these viruses. Nucleic acid based amplification tests (NATs) for respiratory viruses were first introduced two decades ago and today are utilized for the detection of both conventional and emerging viruses. These tests are more sensitive than other diagnostic approaches, including virus isolation in cell culture, shell vial culture (SVC), antigen detection by direct fluorescent antibody (DFA) staining, and rapid enzyme immunoassay (EIA), and now form the backbone of clinical virology laboratory testing around the world. NATs not only provide fast, accurate and sensitive detection of respiratory viruses in clinical specimens but also have increased our understanding of the epidemiology of both new emerging viruses such as the pandemic H1N1 influenza virus of 2009, and conventional viruses such as the common cold viruses, including rhinovirus and coronavirus. Multiplex polymerase chain reaction (PCR) assays introduced in the last five years detect up to 19 different viruses in a single test. Several multiplex PCR tests are now commercially available and tests are working their way into clinical laboratories. The final chapter in the evolution of respiratory virus diagnostics has been the addition of allelic discrimination and detection of single nucleotide polymorphisms associated with antiviral resistance. These assays are now being multiplexed with primary detection and subtyping assays, especially in the case of influenza virus. These resistance assays, together with viral load assays, will enable clinical laboratories to provide physicians with new and important information for optimal treatment of respiratory virus infections.

Nucleic acid amplification-based diagnosis of respiratory virus infections

The appearance of eight new respiratory viruses in the human population in the past 9 years, including two new pandemics (SARS coronavirus in 2003 and swine-origin influenza A/H1N1 in 2009), has tested the ability of virology laboratories to develop diagnostic tests to identify these viruses. Nucleic acid amplification tests (NATs) that first appeared two decades ago have been developed for both conventional and emerging viruses and now form the backbone of the clinical laboratory. NATs provide fast, accurate and sensitive detection of respiratory viruses and have significantly increased our understanding of the epidemiology of these viruses. Multiplex PCR assays have been introduced recently and several commercial tests are now available. The final chapter in the evolution of respiratory virus diagnostics will be the addition of allelic discrimination and detection of single nucleotide polymorphisms associated with antiviral resistance to multiplex assays. These resistance assays together with new viral load tests will enable clinical laboratories to provide physicians with important information for optimal treatment of patients.

Culturing the unculturable: human coronavirus HKU1 infects, replicates, and produces progeny virions in human ciliated airway epithelial cell cultures

Culturing newly identified human lung pathogens from clinical sample isolates can represent a daunting task, with problems ranging from low levels of pathogens to the presence of growth suppressive factors in the specimens, compounded by the lack of a suitable tissue culture system. However, it is critical to develop suitable in vitro platforms to isolate and characterize the replication kinetics and pathogenesis of recently identified human pathogens. HCoV-HKU1, a human coronavirus identified in a clinical sample from a patient with severe pneumonia, has been a major challenge for successful propagation on all immortalized cells tested to date. To determine if HCoV-HKU1 could replicate in in vitro models of human ciliated airway epithelial cell cultures (HAE) that recapitulate the morphology, biochemistry, and physiology of the human airway epithelium, the apical surfaces of HAE were inoculated with a clinical sample of HCoV-HKU1 (Cean1 strain). High virus yields were found for several days postinoculation and electron micrograph, Northern blot, and immunofluorescence data confirmed that HCoV-HKU1 replicated efficiently within ciliated cells, demonstrating that this cell type is infected by all human coronaviruses identified to date. Antiserum directed against human leukocyte antigen C (HLA-C) failed to attenuate HCoV-HKU1 infection and replication in HAE, suggesting that HLA-C is not required for HCoV-HKU1 infection of the human ciliated airway epithelium. We propose that the HAE model provides a ready platform for molecular studies and characterization of HCoV-HKU1 and in general serves as a robust technology for the recovery, amplification, adaptation, and characterization of novel coronaviruses and other respiratory viruses from clinical material.

Detection of respiratory viruses by molecular methods

SUMMARY

Clinical laboratories historically diagnose seven or eight respiratory virus infections using a combination of techniques including enzyme immunoassay, direct fluorescent antibody staining, cell culture, and nucleic acid amplification tests. With the discovery of six new respiratory viruses since 2000, laboratories are faced with the challenge of detecting up to 19 different viruses that cause acute respiratory disease of both the upper and lower respiratory tracts. The application of nucleic acid amplification technology, particularly multiplex PCR coupled with fluidic or fixed microarrays, provides an important new approach for the detection of multiple respiratory viruses in a single test. These multiplex amplification tests provide a sensitive and comprehensive approach for the diagnosis of respiratory tract infections in individual hospitalized patients and the identification of the etiological agent in outbreaks of respiratory tract infection in the community. This review describes the molecular methods used to detect respiratory viruses and discusses the contribution that molecular testing, especially multiplex PCR, has made to our ability to detect respiratory viruses and to increase our understanding of the roles of various viral agents in acute respiratory disease.

Nucleic acid amplification tests for detection of respiratory viruses

Nucleic acid amplification tests (NATs) are increasingly being used for diagnosis of respiratory virus infections. The most familiar formats use DNA or RNA target amplification methods for enhanced sensitivity above culture and antigen-based procedures. Although gel and plate-hybridisation methods are still utilised for analysis of amplified products, detection using "real-time" methods which do not require handling of amplified products are favoured in many laboratories. Assays based on nucleic acid amplification and detection can be designed against a broad range of respiratory viruses and have been particularly useful for detection of recently identified viruses such as human metapneumovirus and coronaviruses NL63 and HKU1. However, the wide range of potential pathogens which can cause similar respiratory symptomology and disease makes application of individual diagnostic assays based on detection of DNA and RNA both complex and expensive. One way to resolve this potential problem is to undertake multiplexed nucleic acid amplification reactions with analysis of amplified products by suspension microarray. The Respiratory Virus Panel (RVP) from Luminex Molecular Diagnostics is one example of such an approach which could be made available to diagnostic and public health laboratories for broad spectrum respiratory virus detection.

Respiratory virus surveillance and outbreak investigation

Sensitive, rapid detection of respiratory viruses is needed for surveillance and for investigation of epidemiologically linked cases. The utility of rapid antigen-based methods for detection of common respiratory viruses and to confirm the cause of outbreaks is well established. However, nucleic acid amplification tests (NATs) offer some benefits above antigen or culture-based procedures, with the main advantages being sensitivity and range of pathogens detectable. It is important to understand how changes in our testing methodology alter respiratory virus detection and information for epidemiological studies. For viruses such as influenza A, influenza B and respiratory syncytial virus, NATs offer enhanced sensitivity above antigen assays but still identify the seasonal peaks important for predicting disease and managing time-sensitive prophylaxis. For other viruses, such as rhinoviruses, coronaviruses, human bocavirus and parainfluenza virus type 4, culture and antigen-based procedures are not available and/or lack sensitivity. Thus such targets would be missed if NATs were not included in testing for surveillance and outbreak investigation. As more respiratory viruses are identified there is a need to expand surveillance and further evaluate new technologies and automation beyond currently-available diagnostics to address detection of a broad range of potential pathogens.

Materno-fetal transmission of human coronaviruses: a prospective pilot study

This prospective pilot study investigates the possibility of materno-fetal transmission of human coronaviruses (HCoV) responsible for cases of neonatal infection. This vertical transmission was studied with 159 samples from mother-child couples: maternal vaginal (MV) and respiratory (MR) samples during labor; and newborn gastric sample (NG) with detection of HCoV (229E, OC-43, NL-63, HKU1) via real time RT PCR. HCoV was detected in 12 samples (229E: 11; HKU1: 1) from seven mother-child couples. For three couples, only MR tested positive (cases 1–3). For two other couples all three samples (MV, MR and NG) tested positive (cases 4 and 5). For case 6, only MV and NG tested positive. In case 7, only MV was positive. Possible vertical transmission of HCoV was hypothesized in this pilot study and requires further investigation on a larger scale.

Outbreaks of human coronavirus in a pediatric and neonatal intensive care unit

Human coronavirus 229E (HCoV) has been recently recognized as a potential agent of nosocomial viral respiratory infections (NRVI) in high-risk infants. We have confirmed this as fact through the study of a 1-year period of HCoV outbreaks occurring during a prospective survey of NRVI in a paediatric and neonatal intensive care unit (PNICU) using new molecular techniques for HCoV detection. Nasal samples obtained at admission and weekly thereafter for all hospitalised children, as well as monthly nasal samples from staff, were analysed using immunofluorescence for respiratory syncytial virus (RSV), influenza viruses A and B, paramyxoviruses 1, 2, 3 and adenoviruses. RT-PCR was used for HCoV detection. During the year 1998, 43 HCoV-related NRVI were detected in 152 neonates (incidence 28.3%), and 7 HCoV-related NRVI were found in 92 children (incidence 7.6%). Three HCoV-related outbreaks were observed (February, August and December), associated with a high prevalence of HCoV infection in the staff. During the August outbreak, 50% to 78% of hospitalised neonates and children were infected. Seventy-five percent of hospitalised preterm neonates with a gestational age less than 32 weeks and 52.4% of staff members were infected. Risk factors for NRVI in neonates were birth weight, gestational age, ventilation, oxygenation and hospitalisation length. Ninety-two percent of infected preterm neonates were symptomatic, mainly with bradycardia and respiratory worsening. These data provide additional evidence for a possibly significant role of HCoV in NRVI in a PNICU. The role of staff or hospitalised children in spreading HCoV is hypothesised.

[Vertical transmission of human coronavirus. Prospective pilot study]

Les coronavirus humains (HCoV) ont été impliqués dans la survenue d'infections respiratoires nosocomiales chez les nouveau-nés. Plusieurs cas d'infections néonatales ont été mis en évidence. Cette étude pilote recherche l'existence d'une éventuelle transmission maternofœtale des HCoV pouvant expliquer les cas infections néonatales observées dans les premières 24 heures de vie.

Matériel et méthode

Étude monocentrique prospective pilote. Étude des couples mère–enfant par la réalisation de trois prélèvements : vaginal et respiratoire chez la mère (VM et RM) lors du travail, gastrique chez le nouveau-né (GNN). Suivi clinique des nouveau-nés et des mères jusqu'à j3. Analyse virologique des échantillons par reverse transcription-polymerase chain reaction (RT-PCR) en temps réel pour la recherche des HCoV 229-E et OC43.

Résultats

Cent cinquante-neuf couples mère–enfant ont été inclus de juillet 2003 à août 2005. Seul HCoV 229-E a été détecté dans 11 échantillons chez six couples mère–enfant. Pour deux couples, les trois prélèvements (VM, RM et GNN) étaient positifs (cas 1 et 2). Pour le cas 3, seuls le VM et GNN étaient positifs. Pour deux couples, seuls les RM étaient positifs (cas 4 et 5). Pour le cas 6, seul le VM était positif. Pour les trois GNN positifs, aucun enfant n'était symptomatique.

Conclusion

Une possible transmission verticale des HCoV est mise en évidence dans cette étude pilote qui nécessite désormais d'être poursuivie à plus large échelle. Il convient également d'inclure la recherche des coronavirus humains identifiés récemment, HCoV NL63 et HKU1, et d'analyser le profil génomique des HCoV détectés chez les trois couples mère–enfant positifs.

Genetic variability of human coronavirus OC43-, 229E-, and NL63-like strains and their association with lower respiratory tract infections of hospitalized infants and immunocompromised patients

In the winter-spring seasons 2003-2004 and 2004-2005, 47 (5.7%) patients with acute respiratory infection associated with human coronavirus (hCoV) 229E-, NL63-, and OC43-like strains were identified among 823 (597 immunocompetent and 226 immunocompromised) patients admitted to hospital with acute respiratory syndromes. Viral infections were diagnosed by either immunological (monoclonal antibodies) or molecular (RT-PCR) methods. Each of two sets of primer pairs developed for detection of all CoVs (panCoV) failed to detect 15 of the 53 (28.3%) hCoV strains identified. On the other hand, all hCoV strains could be detected by using type-specific primers targeting genes 1ab and N. The HuH-7 cell line was found to be susceptible to isolation and identification of OC43- and 229E-like strains. Overall, hCoV infection was caused by OC43-like, 229E-like, and NL63-like strains in 25 (53.2%), 10 (21.3%), and 9 (19.1%) patients, respectively. In addition, three patients (6.4%) were infected by untypeable hCoV strains. NL63-like strains were not found to circulate in 2003-2004, and 229E-like strains did not circulate in 2004-2005, while OC43-like strains were detected in both seasons. The monthly distribution reached a peak during January through March. Lower predominated over upper respiratory tract infections in each age group. In addition, hCoV infections interested only immunocompetent infants and young children during the first year of life, while all adults were immunocompromised patients. Coinfections of hCoVs and other respiratory viruses (mostly interesting the first year of life) were observed in 14 of the 47 (29.8%) patients and were associated with severe respiratory syndromes more frequently than hCoV single infections (P = 0.002). In conclusion, the use of multiple primer sets targeting different genes is recommended for diagnosis of all types of hCoV infection. In addition, the detection of still untypeable hCoV strains suggests that the number of hCoVs involved in human pathology might further increase. Finally, hCoVs should be screened routinely for in both infants and immunocompromised patients with acute respiratory infection.

Infections by human coronavirus-NL in hospitalized children

BACKGROUND

A new human coronavirus (HCoV), HCoV-NL, was recently reported for Dutch patients with acute respiratory tract infections (ARTI). Little information is available on the incidence, clinical manifestations and epidemiologic features of HCoV-NL infections.

METHODS

We performed a prospective study of symptomatic (case subjects with ARTI) and asymptomatic (control subjects undergoing elective surgery) children, <or=3 years of age, hospitalized in Canada during 2 winter seasons (2001-2003), to look at the prevalence of respiratory viruses. Reverse transcription-PCR assays were used to retrospectively detect HCoV-NL and to correlate its presence with clinical symptoms.

RESULTS

HCoV-NL was detected in nasopharyngeal aspirates from 3.0% of young children (12 of 396 children) hospitalized for treatment of ARTI (case subjects), compared with 1.7% of asymptomatic control subjects (3 of 177 children) (P = 0.6). Nine (75.0%) of the symptomatic children had mixed viral infections. The mean age and mean duration of hospitalization of case subjects were 10.1 months and 4.9 days, respectively. Final diagnoses consisted of bronchiolitis or bronchitis (9 of 12 cases), pneumonitis (1 of 12 cases) and upper respiratory tract infections (2 of 12 cases), although 2 of 3 subjects with single HCoV-NL infections had upper respiratory tract infections only. Sequence analysis of the 1a and spike genes revealed that multiple HCoV-NL strains circulated in the same geographical area in each of the 2 winter seasons. Variability was more pronounced for the spike gene, with 2 clusters of strains.

CONCLUSIONS

HCoV-NL was not a major respiratory pathogen in Canada during our study, as shown by its low detection rate in hospitalized children with ARTI, coupled with the high frequency of additional pathogens and its occasional detection in healthy children.

Molecular diagnosis of severe acute respiratory syndrome: the state of the art

Severe acute respiratory syndrome (SARS) first appeared in Guangdong Province, China, in November 2002. Although virus isolation and serology were useful early in the SARS outbreak for diagnosing new cases, these tests are not generally useful because virus culture requires a BSL-3 laboratory and seroconversion is often delayed until 2 to 3 weeks after infection. The first qualitative reverse transcriptase-polymerase chain reaction tests for SARS-coronavirus (CoV) were sensitive and capable of detecting 1 to 10 genome equivalents. These assays were quickly supplemented with quantitative real-time assays that helped elucidate the natural history of SARS, particularly the initial presence of low viral loads in the upper respiratory tract and high viral loads in the lower respiratory tract. The unique natural history of SARS-CoV infection dictates the testing of both respiratory and nonrespiratory specimens, the testing of multiple specimens from the same patient, and sending out positives to be confirmed by a reference laboratory. Commercially available reverse transcriptase-polymerase chain reaction tests for SARS have recently appeared; however, meaningful evaluations of these assays have not yet been performed and their true performance has not been determined. These and other issues related to diagnosis of SARS-CoV infection are discussed in this review.