Polyomaviruses KI and WU in children with respiratory tract infection

Duplex real-time polymerase chain reaction assay for the detection of human KIPyV and WUPyV in nasopharyngeal aspirate pediatric samples

In this study, we describe a duplex real-time PCR assay for the simultaneous detection of KIPyV and WUPyV polyomaviruses based on TaqMan probes. This assay detected 500 copies/mL both for KIPyV and WUPyV in 100% of tested positive samples. We assessed this technique on 482 nasopharyngeal aspirate specimens from hospitalized pediatric patients with respiratory symptoms, previously analyzed with commercial multiplex assay for 16 major respiratory viruses. Our assay detected KIPyV genome in 15 out of 482 samples (3.1%) and WUPyV genome in 24 out of 482 samples (4.9%), respectively, and in three samples the coinfection of the two viruses was found. Interestingly, 29 out of 36 of samples with KIPyV and/or WUPyV infection exhibited a co-infection with one or more respiratory viruses confirming that KIPyV and WUPyV were often detected in association to other viral infections. Of note, KIPyV and WUPyV were detected singularly in 4 out of 15 cases and 3 out of 24 cases, respectively, suggesting a possible direct role of these viruses in the respiratory diseases. In conclusion, this method could be taken into account as an alternative technical approach to detect KIPyV and/or WUPyV in respiratory samples for epidemiological and diagnostic analyses.

[A molecular epidemiological study of KI polyomavirus and WU polyomavirus in children with acute respiratory infection in Tianjin, China]

OBJECTIVE

To investigate the relationship of KI polyomavirus (KIPyV) and WU polyomavirus (WUPyV) with acute respiratory infection in children in Tianjin, China.

METHODS

A total of 3 730 nasopharyngeal secretions were collected from hospitalized children with acute respiratory infection in Tianjin Children's Hospital from January 2011 to December 2013. Viral nucleic acid was extracted, and virus infection (KIPyV and WUPyV) was determined by PCR. Some KIPyV-positive and WUPyV-positive PCR products were subjected to sequencing. Sequencing results were aligned with the known gene sequences of KIPyV and WUPyV to construct a phylogenetic tree. Amplified VP1 fragments of KIPyV were inserted into the cloning vector (PUCm-T) transformed into E. coli competent cells. Positive clones were identified by PCR and sequencing. The nucleotide sequences were submitted to GenBank. In addition, another seven common respiratory viruses in all samples were detected by direct immunofluorescence assay.

RESULTS

In the 3 730 specimens, the KIPyV-positive rate was 12.14% (453/3 730) and the WUPyV-positive rate was 1.69% (63/3 730). The mean infection rate of KIPyV was significantly higher in June and July, while the mean infection rate of WUPyV peaked in February and March. Most of the KIPyV-positive or WUPyV-positive children were <3 years. The co-infections with KIPyV, WUPyV, and other respiratory viruses were observed in the children. The co-infection rate was 2.31% (86/3 730) and there were nine cases of co-infections with WUPyV and KIPyV. Thirty-five KIPyV-positive and twelve WUPyV-positive PCR products were sequenced and the alignment analysis showed that they had high homology with the known sequences (94%-100% vs 95%-100%). The VP1 gene sequences obtained from two KIPyV strains in this study were recorded in GenBank with the accession numbers of KY465925 and KY465926.

CONCLUSIONS

For some children with acute respiratory infection in Tianjin, China, the acute respiratory infection may be associated with KIPyV and WUPyV infections. KIPyV infection is common in summer, and WUPyV infection in spring. The epidemic strains in Tianjin have a high homology with those in other regions.

WU and KI polyomavirus infections in Filipino children with lower respiratory tract disease

BACKGROUND

WU and KI are human polyomaviruses initially detected in the respiratory tract, whose clinical significance remains uncertain.

OBJECTIVES

To determine the epidemiology, viral load and clinical characteristics of WU and KI polyomaviruses.

STUDY DESIGN

We tested respiratory specimens collected during a randomized, placebo-controlled pneumococcal conjugate vaccine trial and related epidemiological study in the Philippines. We analyzed 1077 nasal washes from patients aged 6 weeks to 5 years who developed lower respiratory tract illness using quantitative real-time PCR for WU and KI. We collected data regarding presenting symptoms, signs, radiographic findings, laboratory data and coinfection.

RESULTS

The prevalence and co-infection rates for WU were 5.3% and 74% respectively and 4.2% and 84% respectively for KI. Higher KI viral loads were observed in patients with severe or very severe pneumonia, those presenting with chest indrawing, hypoxia without wheeze, convulsions, and with KI monoinfection compared with co-infection. There was no significant association between viral load and clinical presentation for WU.

CONCLUSIONS

These findings suggest a potential pathogenic role for KI, and that there is an association between KI viral load and illness severity.

PCR testing for paediatric acute respiratory tract infections

Acute respiratory tract infection (ARI) is a frequently occurring disease in children. It is a clinical diagnosis for which no internationally accepted diagnostic test is available. The majority of ARI is viral in origin, though diagnostic tests for viruses were rarely performed in the past. In the past 2 decades, new molecular techniques have been introduced in many hospitals. They are capable of generating a high yield of viral and bacterial diagnoses, but their impact upon clinical practices is still questionable. In this paper, we discuss the difficulties of diagnosing ARI in children, the indications for conventional and new diagnostics and their implications.

New respiratory viral infections

PURPOSE OF REVIEW

The first era in the discoveries of respiratory viruses occured between 1933 and 1965 when influenza virus, enteroviruses, adenovirus, respiratory syncytial virus, rhinovirus, parainfluenza virus and coronavirus (CoV) were found by virus culture. In the 1990s, the development of high throughput viral detection and diagnostics instruments increased diagnostic sensitivity and enabled the search for new viruses. This article briefly reviews the clinical significance of newly discovered respiratory viruses.

RECENT FINDINGS

In 2001, the second era in the discoveries of respiratory viruses began, and several new respiratory viruses and their subgroups have been found: human metapneumovirus, CoVs NL63 and HKU1, human bocavirus and human rhinovirus C and D groups.

SUMMARY

Currently, a viral cause of pediatric respiratory illness is identifiable in up to 95% of cases, but the detection rates decrease steadily by age, to 30-40% in the elderly. The new viruses cause respiratory illnesses such as common cold, bronchitis, bronchiolitis, exacerbations of asthma and chronic obstructive pulmonary disease and pneumonia. Rarely, acute respiratory failure may occur. The clinical role of other new viruses, KI and WU polyomaviruses and the torque teno virus, as respiratory pathogens is not clear.

The polyomaviruses WUPyV and KIPyV: a retrospective quantitative analysis in patients undergoing hematopoietic stem cell transplantation

BACKGROUND

The polyomaviruses WUPyV and KIPyV have been detected in various sample types including feces indicating pathogenicity in the gastrointestinal (GI) system. However, quantitative viral load data from other simultaneously collected sample types are missing. As a consequence, primary replication in the GI system cannot be differentiated from swallowed virus from the respiratory tract. Here we present a retrospective quantitative longitudinal analysis in simultaneously harvested specimens from different organ sites of patients undergoing hematopoietic stem cell transplantation (HSCT). This allows the definition of sample types where deoxyribonucleic acid (DNA) detection can be expected and, as a consequence, the identification of their primary replication site.

FINDINGS

Viral DNA loads from 37 patients undergoing HSCT were quantified in respiratory tract secretions (RTS), stool and urine samples as well as in leukocytes (n = 449). Leukocyte-associated virus could not be found. WUPyV was found in feces, RTS and urine samples of an infant, while KIPyV was repeatedly detected in RTS and stool samples of 4 adult patients.RTS and stool samples were matched to determine the viral load difference showing a mean difference of 2.3 log copies/ml (p < 0.001).

CONCLUSIONS

The data collected in this study suggest that virus detection in the GI tract results from swallowed virus from the respiratory tract (RT). We conclude that shedding from the RT should be ruled out before viral DNA detection in the feces can be correlated to GI symptoms.

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.

PCR for detection of respiratory viruses: seasonal variations of virus infections

Real-time PCR and related methods have revolutionized the laboratory diagnosis of viral respiratory infections because of their high detection sensitivity, rapidness and potential for simultaneous detection of 15 or more respiratory agents. Results from studies with this diagnostic modality have significantly expanded our knowledge about the seasonality of viral respiratory diseases, pinpointed the difficulties to make a reliable etiologic diagnosis without the aid of an unbiased multiplex molecular assay for respiratory viruses, and revealed previously unknown details as to possible infections with multiple agents as aggravating factors. The scope of this article is to review and discuss this new knowledge and its implications for diagnostic strategies and other measures essential for the clinical management of respiratory viral infections and for epidemiological surveillance of seasonal respiratory infections.

WU polyomavirus infection among children in South China

This study aimed at investigating the prevalence and clinical characteristics of children with respiratory infection by WU polyomavirus (WUPyV) in Southern China. Nasopharyngeal aspirate samples were collected from 771 children with acute respiratory tract infection admitted to hospital and 82 samples from healthy subjects for routine examination at the outpatient service at the Second Affiliated Hospital of Shantou University, Medical College from July 2008 to June 2009. WUPyV was detected by the polymerase chain reaction (PCR) and DNA sequencing. All WUPyV-positive specimens were characterized further for nine viruses causing common respiratory infections, including influenza A and B, respiratory syncytial virus (RSV), parainfluenza virus (PIV) 1 and 3, human metapneumovirus, human bocavirus, adenovirus, and rhinovirus by PCR or real time (RT)-PCR. Fifteen out of 771 specimens from patients with acute respiratory tract infection, but none from healthy subjects, were positive for WUPyV and the positivity rate was 2%. Patients with WUPyV infection were between 2 and 48 months of age, and nine of the patients were male while six female. Four out of 15 patients were co-infected with RSV, one with adenovirus or rhinovirus, respectively. Patients with WUPyV infection displayed predominantly cough, moderate fever, and wheezing, and were diagnosed with pneumonia (n = 8), bronchiolitis (n = 4), upper respiratory tract infections (n = 2) and bronchitis (n = 1). One patient developed encephalitis. Therefore, WUPyV infection can cause acute respiratory tract infection with atypical symptoms, including severe complications, in children.

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.