Role of human polyomaviruses in respiratory tract disease in young children

Prevalence of human pathogenic viruses in wastewater: A potential transmission risk as well as an effective tool for early outbreak detection for COVID-19

Millions of human pathogenic viral particles are shed from infected individuals and introduce into wastewater, subsequently causing waterborne diseases worldwide. These viruses can be transmitted from wastewater to human beings via direct contact and/or ingestion/inhalation of aerosols. Even the advanced wastewater treatment technologies are unable to remove pathogenic viruses from wastewater completely, posing a serious health risk. Recently, coronavirus disease 2019 (COVID-19) has been urged globally due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which has resulted in >4.1 million deaths until July 2021. A rapid human-to-human transmission, uncertainties in effective vaccines, non-specific medical treatments, and unclear symptoms compelled the world into complete lockdown, social distancing, air-travel suspension, and closure of educational institutions, subsequently damaging the global economy and trade. Although, few medical treatments, rapid detection tools, and vaccines have been developed so far to curb the spread of COVID-19; however, several uncertainties exist in their applicability. Further, the acceptance of vaccines among communities is lower owing to the fear of side effects such as blood-clotting and heart inflammation. SARS-CoV-2, an etiologic agent of COVID-19, has frequently been detected in wastewater, depicting a potential transmission risk to healthy individuals. Contrarily, the occurrence of SARS-CoV-2 in wastewater can be used as an early outbreak detection tool via water-based epidemiology. Therefore, the spread of SARS-CoV-2 through fecal-oral pathway can be reduced and any possible outbreak can be evaded by proper wastewater surveillance. In this review, wastewater recycling complications, potential health risks of COVID-19 emergence, and current epidemiological measures to control COVID-19 spread have been discussed. Moreover, the viability of SARS-CoV-2 in various environments and survival in wastewater has been reviewed. Additionally, the necessary actions (vaccination, face mask, social distancing, and hand sanitization) to limit the transmission of SARS-CoV-2 have been recommended. Therefore, wastewater surveillance can serve as a feasible, efficient, and reliable epidemiological measure to lessen the spread of COVID-19.

Detection of respiratory viruses in primary cholesteatoma tissues

Cholesteatomas are frequent middle ear benign tumors of unknown etiology. Infectious agents have been considered as possible contributing factors in the pathogenesis of cholesteatomas. Aiming to investigate the presence of respiratory viruses in primary cholesteatoma tissues, 26 formalin-fixed paraffin-embedded primary cholesteatoma tissues obtained from patients seen at the of the Clinical Hospital of the University of São Paulo School of Medicine, in Ribeirão Preto, Brazil were tested by real-time polymerase chain reaction (PCR). Considering the PCR results, 35% of the tissues were positive for human rhinovirus (HRV), 15.3% for human enterovirus (EV), 3.8% for human metapneumovirus (HMPV), and 3.8% for human bocavirus (HBoV). Serial immunohistochemistry for virus antigens and cell surface markers evidenced that the viruses were associated with fibroblasts, dendritic cells, macrophages, B lymphocytes, CD4⁺ , and CD8⁺ T lymphocytes. These findings indicate for the first time the presence of active respiratory virus infection in primary cholesteatoma tissues, suggesting that persisting virus infection in the middle could play a role in the pathogenesis and evolution of cholesteatomas.

Heterogeneous associations of polyomaviruses and herpesviruses with allergy-related phenotypes in childhood

BACKGROUND

Evidence suggests a complex interplay between infections and allergic diseases.

OBJECTIVE

To explore the association of 14 common viruses with eczema, asthma, and rhinoconjunctivitis in childhood.

METHODS

We used cross-sectional (n = 686) and prospective (n = 440) data from children participating in the Rhea birth cohort. Immunoglobulin G to polyomaviruses (BK polyomavirus, JC polyomavirus, KI polyomavirus [KIPyV], WU polyomavirus [WUPyV], human polyomavirus 6, human polyomavirus 7, Trichodysplasia spinulosa polyomavirus, Merkel cell polyomavirus, human polyomavirus 9, and human polyomavirus 10) and herpesviruses (Epstein-Barr virus, Cytomegalovirus, Herpes simplex virus-1, Herpes simplex virus-2) were measured at age 4 years by fluorescent bead-based multiplex serology. Definitions of eczema, asthma, and rhinoconjunctivitis at ages 4 and 6 years were based on questionnaires. Mediation of the associations by immune biomarkers was tested.

RESULTS

Less likely to have eczema at age 4 years were KIPyV-seropositive (odds ratio [OR], 0.47; 95% confidence interval [CI], 0.27-0.82) and human polyomavirus 6 (OR, 0.44; 95% CI, 0.26-0.73) compared with their seronegative counterparts. Seropositivity to Epstein-Barr virus was negatively associated with eczema at age 4 years (OR, 0.39; 95% CI, 0.22-0.67) and 6 years (OR, 0.50; 95% CI, 0.25-0.99). Children with a higher burden of herpesviruses or of skin polyomaviruses had the lowest odds of eczema at age 4 years. Higher odds for asthma at age 4 years were found for WUPyV-seropositive children (OR, 3.98; 95% CI, 1.38-11.51), and for children seropositive to both respiratory polyomaviruses (KIPyV and WUPyV) (OR, 7.35; 95% CI, 1.66-32.59) compared with children seronegative to both. No associations were observed for rhinoconjunctivitis. There was no evidence of mediation by immune biomarkers.

CONCLUSION

A heterogeneous pattern of infections and allergic diseases was observed with common infections associated with a decreased eczema risk and an increased asthma risk in children.

WU polyomavirus detection in a pediatric liver transplant recipient with interstitial pneumonitis

The WU polyomavirus (WUPyV) was detected by real-time PCR in the sputum of a pediatric liver transplant recipient with interstitial pneumonitis. A lower viral load was observed seven months after the initial detection. The case provides circumstantial evidence suggesting a potential role for WUPyV as a respiratory pathogen in immunocompromised children.

The occurrence of polyomaviruses WUPyV and KIPyV among patients with severe respiratory infections

In 2007, the new polyomaviruses WUPyV and KIPyV were identified in patients with acute respiratory infections. The aim of this study was to investigate these viruses in hospitalized patients with severe acute respiratory infection (SARI). A retrospective study was conducted with 251 patients, from April 2009 to November 2010, using nasopharyngeal aspirates, naso- and oropharyngeal swab samples from hospitalized patients (children < 12 years and adults) who had SARI within 7 days of the onset of symptoms, including fever (> 38.8 °C), dyspnea, and cough. Clinical and epidemiological information was obtained through standardized questionnaire. Enrolled patients were initially suspected to have influenza A(H1N1)pdm09 infections. WUPyV and KIPyV were detected by real-time PCR. Samples were also tested for influenza A and B viruses, human respiratory syncytial virus, rhinovirus, metapneumovirus, coronavirus, adenovirus, and parainfluenza viruses. WUPyV and KIPyV were detected in 6.77% (4.78% and 1.99%, respectively) of hospitalized patients with SARI. All samples from children showed coinfections (rhinovirus was the most commonly detected). Six adults had polyomavirus infection and four (1.6%) had monoinfection. Of them, 3 reported comorbidities including immunosuppression and 1 patient had worse outcome, requiring ICU admission. These preliminary data may suggest a possible role of polyomaviruses in SARI among immunocompromised adult patients.

WU polyomavirus detected in children with severe respiratory failure

•

WU polyomavirus (WUPyV) was detected in 14 children with respiratory failure.

•

Of these children, eight had a perinatal disease and three were immunocompromised.

•

Multiplex PCR and culture were negative for other pathogens in five patients.

•

These five patients showed perihilar infiltrates after several days of symptoms.

•

WUPyV can be a pathogen in children with a history of perinatal disease.

Background

WU polyomavirus (WUPyV) is a relatively new virus associated with respiratory infections. However, its role is unclear in children with severe respiratory failure.

Objectives

We aimed to evaluate the characteristics of severe respiratory failure associated with WUPyV infection in children.

Study design

We retrospectively reviewed cases of respiratory tract infection at a tertiary children's hospital in Japan and performed real-time polymerase chain reaction (PCR) for WUPyV using residual extracted nucleic acid samples taken from respiratory tract samples of pediatric patients primarily with respiratory failure. We investigated the clinical characteristics of patients positive for WUPyV and assessed samples positive for WUPyV for other respiratory pathogens using multiplex PCR.

Results

WUPyV was detected in 14 of 318 specimens of respiratory tract infections. The median age was 34 months and males were predominant (n = 11, 64%). An underlying disease was found in 11 (79%) patients including five preterm and three immunocompromised patients. The most common clinical diagnosis was pneumonia (n = 13, 93%). The majority of the samples were endotracheal tube aspirates (n = 11, 79%). Other viruses were co-detected in nine (64%) patients, while WUPyV was the only pathogen detected in five patients with a history of admission to the neonatal intensive care unit. These five patients presented with fever and cough, and perihilar infiltrates were detected on chest radiograph in several days.

Conclusions

WUPyV was detected in children with severe respiratory failure independently or concurrently with other pathogens. WUPyV can be a pathogen for children with a history of preterm birth or an underlying disease.

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.

•

Duplex real-time PCR assay for the detection of human KIPyV and WUPyV was assessed.

•

This assay was evaluated on nasopharyngeal aspirate samples from pediatric patients.

•

KIPyV and WUPyV were detected in 3.1% and 4.9% of samples, respectively.

Prevalence of Respiratory Polyomaviruses Among Pediatric Patients With Respiratory Symptoms in Singapore

Background: Although WU polyomavirus (WU) and KI polyomavirus (KI) have been demonstrated to infect the human respiratory tract, it remains unclear if WU or KI cause human disease. We sought to further investigate the relationship between WU and KI infection and respiratory disease in a pediatric population with respiratory symptoms in Singapore. Methods: We conducted a cross-sectional study of pediatric patients with respiratory symptoms in a Singaporean pediatrics hospital. Upon consent, residual respiratory samples from pediatric inpatients, previously screened for common respiratory viruses, were collected and further screened for WU and KI using qPCR. The amplicons of positive samples were sequenced for confirmation. The severity of a patient's illness was assessed by chart review post-discharge looking for clinical markers of respiratory status such as presenting symptoms, diagnoses, and interventions. Results: From December 2016 to April 2017, 201 patients with residual respiratory samples were enrolled in the study. The average age of all participants recruited was 45 months. WU and KI were detected in 13% (26/201) and 3% (6/201) of patients, respectively. Conducting bivariate and multivariate modeling, patients with WU or KI positivity were not at increased risk of SARI, need for additional oxygen, intravenous fluids, and did not receive additional oral antibiotics or bronchodilators during admission. In contrast, patients with RSV detections were at increased risk of requiring supplemental oxygen during hospital admission. Conclusion: While limited in sample size, our pilot study data do not support the hypothesis that molecular evidence of WU or KI was associated with increased morbidity among a sample of general, pediatric patients with respiratory illness in Singapore.

Complete genome sequence of a KI polyomavirus isolated from an otherwise healthy child with severe lower respiratory tract infection

Unbiased, deep sequencing of a nasal specimen from an otherwise healthy 13-month-old boy hospitalized in intensive care revealed high gene expression and the complete genome of a novel isolate of KI polyomavirus (KIPyV). Further investigation detected minimal gene expression of additional viruses, suggesting that KIPyV was potentially the causal agent. Analysis of the complete genome of isolate NMKI001 revealed it is different from all previously reported genomes and contains two amino acid differences as compared to the closest virus isolate, Stockholm 380 (EF127908). J. Med. Virol. 89:926-930, 2017. © 2016 Wiley Periodicals, Inc.

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.

Characterization of the non-coding control region of polyomavirus KI isolated from nasopharyngeal samples from patients with respiratory symptoms or infection and from blood from healthy blood donors in Norway

Seroepidemiological studies showed that the human polyomavirus KI (KIPyV) is common in the human population, with age-specific seroprevalence ranging from 40-90 %. Genome epidemiological analyses demonstrated that KIPyV DNA is predominantly found in respiratory tract samples of immunocompromised individuals and children suffering from respiratory diseases, but viral sequences have also been detected in brain, tonsil, lymphoid tissue studies, plasma, blood and faeces. Little is known about the sequence variation in the non-coding control region of KIPyV variants residing in different sites of the human body and whether specific strains dominate in certain parts of the world. In this study, we sequenced the non-coding control region (NCCR) of naturally occurring KIPyV variants in nasopharyngeal samples from patients with respiratory symptoms or infection and in blood from healthy donors in Norway. In total 86 sequences were obtained, 44 of which were identical to the original isolated Stockholm 60 variant. The remaining NCCRs contained one or several mutations, none of them previously reported. The same mutations were detected in NCCRs amplified from blood and nasopharyngeal samples. Some patients had different variants in their specimens. Transient transfection studies in HEK293 cells with a luciferase reporter plasmid demonstrated that some single mutations had a significant effect on the relative early and late promoter strength compared with the Stockholm 60 promoter. The effect of the NCCR mutations on viral replication and possible virulence properties remains to be established.

WU and KI polyomavirus prevalence in invasive respiratory samples from transplant recipients in Cantabria, Spain

Background

WU and KI polyomaviruses were discovered in 2007 in samples of respiratory secretions of children with acute respiratory symptoms. Seroepidemiologic studies have shown that these viruses are widely distributed throughout the world, but their incidence in Spain has not been determined. In transplant patients, early detection and treatment of viral infections may influence prognosis and survival, because they are associated with increased morbidity and mortality, including graft failure.

Methods

We aimed to determine the prevalence and clinical characteristics of WU and KI polyomaviruses among patients undergoing hematologic or solid organ transplant in the Hospital Marqués de Valdecilla (Santander, Spain). An in-house polymerase chain reaction with the use of specific primers was carried out in invasive lower respiratory samples from hospitalized patients with suspected respiratory infection and/or graft dysfunction and compared with asymptomatic transplant patients.

Results

Overall, we obtained 5.5% KI-positive samples and 1.4% WU-positive samples, with a higher prevalence of WU and KI polyomaviruses in the symptomatic population compared with the control group. Although the data suggest that their detection in respiratory samples is sporadic and often associated with other microorganisms, we should pay special attention to their association with cases of graft failure. Studies are needed with a larger number of samples to explore the potential clinical impact of these emerging polyomaviruses in transplant recipients.

Detection of KI WU and Merkel cell polyomavirus in respiratory tract of cystic fibrosis patients

In the last few years, many reports have confirmed the presence of WU, KI and Merkel cell (MC) polyomaviruses (PyV) in respiratory samples wordwide, but their pathogenic role in patients with underlying conditions such as cystic fibrosis is still debated. To determine the prevalence of MCPyV, WUPyV and KIPyV, we conducted a 1-year-long microbiological testing of respiratory specimens from 93 patients with cystic fibrosis in Brescia, Italy. We detected PyV DNA in 94 out of 337 analysed specimens. KIPyV was the most common virus detected (12.1%), followed by WUPyV (8.9%) and MCPyV (6.8%). We found an intriguing association between the presence of MCPyV and the concurrent isolation of Pseudomonas aeruginosa, as well as with the patient status, classified as chronically colonized with P. aeruginosa. Our study adds perspective on the prevalence and the potential pathogenic role of PyV infections.

Infectious pathogens and bronchiolitis outcomes

Bronchiolitis is a common early childhood illness and an important cause of morbidity, it is the number one cause of hospitalization among US infants. Bronchiolitis is also an active area of research, and recent studies have advanced our understanding of this illness. Although it has long been the conventional wisdom that the infectious etiology of bronchiolitis does not affect outcomes, a growing number of studies have linked specific pathogens of bronchiolitis (e.g., rhinovirus) to short- and long-term outcomes, such as future risk of developing asthma. The authors review the advent of molecular diagnostic techniques that have demonstrated diverse pathogens in bronchiolitis, and they review recent studies on the complex link between infectious pathogens of bronchiolitis and the development of childhood asthma.

WU polyomavirus detected in respiratory tract specimens from young children in Japan

Polyomaviruses (PyV) WU and KI are reportedly associated with respiratory tract disease (RTD) worldwide but their incidence is unclear in Japan. In a 2 year prospective study, WU/KIPyV were detected in 48 (13.9%) and in five (1.4%) of 345 children hospitalized with lower RTD, respectively. The seasonal distribution was observed in spring and early summer. Other respiratory viruses were co-detected in 51% of PyV-positive patients, but eight (2.3%) of the WUPyV-positive patients were negative for other known pathogens.

A cornucopia of human polyomaviruses

During the past 6 years, focused virus hunting has led to the discovery of nine new human polyomaviruses, including Merkel cell polyomavirus, which has been linked to Merkel cell carcinoma, a lethal skin cell cancer. The discovery of so many new and highly divergent human polyomaviruses raises key questions regarding their evolution, tropism, latency, reactivation, immune evasion and contribution to disease. This Review describes the similarities and differences among the new human polyomaviruses and discusses how these viruses might interact with their human host.

WU and KI polyomaviruses in respiratory samples from allogeneic hematopoietic cell transplant recipients

Routine testing for these viruses in immunocompromised patients is not recommended.

Data are limited regarding 2 new human polyomaviruses, KI polyomavirus (KIPyV) and WU polyomavirus (WUPyV), in immunocompromised patients. We used real-time PCR to test for these and 12 respiratory viruses in 2,732 nasal wash samples collected during the first year after allogeneic hematopoietic cell transplantation from 222 patients. Specimens were collected weekly until day 100; then at least every 3 months. One year after hematopoietic cell transplantation, the cumulative incidence estimate was 26% for KIPyV and 8% for WUPyV. Age <20 years predicted detection of KIPyV (hazard ratio [HR] 4.6) and WUPyV (HR 4.4), and detection of a respiratory virus in the previous 2 weeks predicted KIPyV detection (HR 3.4). Sputum production and wheezing were associated with detection of KIPyV in the past week and WUPyV in the past month. There were no associations with polyomavirus detection and acute graft versus host disease, cytomegalovirus reactivation, neutropenia, lymphopenia, hospitalization, or death.

Common WU polyomavirus infection in a Beijing population indicated by surveillance for serum IgG antibody against capsid protein VP2

BACKGROUND

WU polyomavirus (WU virus) was identified as a novel polyomavirus in 2007 from specimens of pediatric patients with acute respiratory infection (ARI). A lack of permissive cell lines has limited investigations into WU virus pathogenesis and prevalence.

METHODS

The encoding region of the capsid protein VP2 gene was amplified from a WU virus DNA-positive clinical specimen and expressed as a recombinant Histagged protein in Escherichia coli BL21 (DE3). The expressed VP2 was identified by expected molecular weight and immunoreactivity with anti-His monoclonal antibody in Western blotting assay. Serum samples collected from 455 individuals of all ages in Beijing without symptoms of ARI were tested for IgG antibodies against the affinity-purified recombinant VP2 protein by Western blotting to investigate the prevalence of natural WU virus infection. In addition, serum samples from four ARI pediatric patients, whose nasopharyngeal aspirates were positive for WU virus DNA and negative for all other respiratory-related viruses, were tested for IgM antibody against the recombinant VP2.

RESULTS

Of the 455 serum samples, 238 reacted with the recombinant VP2, yielding an overall positive rate of 52.3% for IgG against VP2 of WU virus. The positive rate was the highest in serum samples from infants and children between 1 to 4 years of age. One of four ARI pediatric patients was positive for IgM against WU virus VP2, implicating WU virus as the causative disease agent.

CONCLUSIONS

The high prevalence of IgG against WU polyomavirus in Beijing-based study population indicates that WU virus infection is common in Beijing. WU virus may be responsible for some pediatric ARI cases, and primary infection of this virus may occur mostly in childhood.

Discovery of a novel polyomavirus in acute diarrheal samples from children

Polyomaviruses are small circular DNA viruses associated with chronic infections and tumors in both human and animal hosts. Using an unbiased deep sequencing approach, we identified a novel, highly divergent polyomavirus, provisionally named MX polyomavirus (MXPyV), in stool samples from children. The ∼5.0 kB viral genome exhibits little overall homology (<46% amino acid identity) to known polyomaviruses, and, due to phylogenetic variation among its individual proteins, cannot be placed in any existing taxonomic group. PCR-based screening detected MXPyV in 28 of 834 (3.4%) fecal samples collected from California, Mexico, and Chile, and 1 of 136 (0.74%) of respiratory samples from Mexico, but not in blood or urine samples from immunocompromised patients. By quantitative PCR, the measured titers of MXPyV in human stool at 10% (weight/volume) were as high as 15,075 copies. No association was found between the presence of MXPyV and diarrhea, although girls were more likely to shed MXPyV in the stool than boys (p=0.012). In one child, viral shedding was observed in two stools obtained 91 days apart, raising the possibility of chronic infection by MXPyV. A multiple sequence alignment revealed that MXPyV is a closely related variant of the recently reported MWPyV and HPyV10 polyomaviruses. Further studies will be important to determine the association, if any, of MXPyV with disease in humans.

Seroepidemiology of WU polyomavirus among children exposed perinatally to HIV-1

WU polyomavirus (WUPyV), a new member of the genus wukipolyomavirus in the family Polyomaviridae, has been detected in serum and tissues of individuals infected with HIV. However, the epidemiology of WUPyV among children exposed perinatally to HIV-1 is unknown. To investigate the epidemiology of WUPyV in children exposed to and infected perinatally with HIV, serum samples from 150 children exposed to HIV and 114 children infected with HIV were screened for IgG antibodies to WUPyV. A subset was screened for IgM antibodies to WUPyV. Both antibody detection assays were performed using a recombinant WUPyV VP1-based ELISA. The overall seroprevalence of WUPyV IgG was 76.3% in children infected with HIV and 62% in children exposed perinatally to HIV. In the group of children infected with HIV, the prevalence of WUPyV IgG antibody reached its peak in 2-3 year olds (90.9%). In children 0-5 months of age, IgG seroprevalence was lower in those children exposed to HIV compared to children infected with HIV (43.1% vs.75%, P = 0.047). However, the seroprevalence of WUPyV IgM antibody was higher in children exposed to HIV compared to infants infected with HIV (27.4% vs. 8.3%, P = 0.044). WUPyV infection is acquired in early childhood in the majority of children born to mothers infected with HIV. The implication of this infection and the specific clinical syndrome that it produces, if any, remain to be defined.

Viral infections of the lower respiratory tract

Lower respiratory tract infections (LRTIs) are a global burden to public health and are frequently caused by respiratory viruses. Advances in molecular diagnostic techniques have allowed the identification of previously undetected viral pathogens and have improved our understanding of respiratory virus infections. Here we review the epidemiological and clinical characteristics of recently identified viruses including human metapneumovirus, human coronaviruses NL63 and HKU1, human rhinovirus C, bocavirus, WU and KI polyomaviruses, and parechovirus. The roles of these viruses in LRTIs in children and adults are discussed.

Respiratory viral pathogens associated with lower respiratory tract disease among young children in the highlands of Papua New Guinea

Background

Acute lower respiratory tract infections (ALRI) commonly result in fatal outcomes in the young children of Papua New Guinea (PNG). However, comprehensive studies of the viral aetiology of ALRI have not been conducted in PNG for almost 30 years.

Objectives

To determine the viruses associated with ALRI among children living in the PNG highlands using sensitive molecular detection techniques.

Study design

Pernasal swabs were collected routinely between 1 week and 18 months of age and also during episodes of ALRI, as part of a neonatal pneumococcal conjugate vaccine trial. A tandem multiplex real-time PCR assay was used to test for a comprehensive range of respiratory viruses in samples collected from 221 young children. Picornavirus typing was supported by DNA sequence analysis.

Results

Recognized pathogenic respiratory viruses were detected in 198/273 (73%) samples collected from children with no evidence of ALRI and 69/80 (86%) samples collected during ALRI episodes. Human rhinoviruses (HRV) species A, B and C were detected in 152 (56%) samples from non-ALRI children and 50 (63%) samples collected during ALRI episodes. Partial structural region sequences for two new species C rhinoviruses were added to the GenBank database. ALRI was associated with detection of adenovirus species B (p < 0.01) or C (p < 0.05), influenza A (p < 0.0001) or respiratory syncytial virus (p < 0.0001). Multiple viruses were detected more often during ALRI episodes (49%) than when children displayed no symptoms of ALRI (18%) (p < 0.0001).

Conclusions

The burden of infection with respiratory viruses remains significant in young children living in the PNG highlands.

Management of viral infections in solid organ transplant recipients

Management of viral infections after transplantation involves antiviral drug therapy (if available) and reduction in immunosuppression, which allows for development of pathogen-specific immunity to the offending virus. Prevention of viral infections is of the utmost importance, and this may be accomplished through vaccination, antiviral strategies and infection control measures. This article discusses the current management of selected viral pathogens that cause clinical illness in solid organ transplant recipients. The benefits and toxicities of antiviral therapies are discussed in the context of prevention and treatment of various viral diseases. The emerging issue of antiviral resistance is emphasized for cytomegalovirus, recurrent hepatitis B and influenza, while the importance of immunominimization is discussed in the management of BK nephropathy and virus-associated malignancies.

Secondary lymphoid tissue as an important site for WU polyomavirus infection in immunocompetent children

The polyomaviruses KI and WU (KIPyV and WUPyV) have been identified in respiratory specimens from children with acute respiratory infections, which suggests the respiratory tract as a possible site of infection. However, the persistence of infection in the lymphoid system is unknown. Fresh samples (n = 211) of tonsils, adenoids, and peripheral blood mononuclear cells (PBMCs) from 83 immunocompetent children (mean age 4.8 years) were tested for amplification of the KIPyV VP1 and WUPyV VP2 genes. The known BK and JC polyomaviruses and the lymphotropic human herpesvirus (HHV)-6 were also investigated by quantitative real-time PCR and direct sequencing. In addition, 98 nasopharyngeal swabs collected from children (mean age 6.2 years) affected by seasonal influenza-like illness were tested. Of the lymphoid tissues, 34.9% were positive for WUPyV, 4.8% for BK virus, and 33.8% for HHV-6. KIPyV and JC virus were not detected in these specimens. None of the polyomaviruses were detected in PBMCs. Among the nasopharyngeal samples, the prevalence of WUPyV was 27.5%, although 70% of the positive samples were co-infected with at least one of the following respiratory viruses: influenza virus, adenovirus, and respiratory syncytial virus. Phylogenetic analysis revealed high sequence homology (99%) between lymphoid- and nasopharynx-derived WUPyV strains. These results suggest that the tonsils and adenoids of immunocompetent children are a reservoir for WUPyV infection; probably due to the respiratory route of transmission. In addition, the prevalence of WUPyV was high among the children, and the virus was identified more frequently in older children than during the first years of life.

The airway epithelium: soldier in the fight against respiratory viruses

The airway epithelium acts as a frontline defense against respiratory viruses, not only as a physical barrier and through the mucociliary apparatus but also through its immunological functions. It initiates multiple innate and adaptive immune mechanisms which are crucial for efficient antiviral responses. The interaction between respiratory viruses and airway epithelial cells results in production of antiviral substances, including type I and III interferons, lactoferrin, β-defensins, and nitric oxide, and also in production of cytokines and chemokines, which recruit inflammatory cells and influence adaptive immunity. These defense mechanisms usually result in rapid virus clearance. However, respiratory viruses elaborate strategies to evade antiviral mechanisms and immune responses. They may disrupt epithelial integrity through cytotoxic effects, increasing paracellular permeability and damaging epithelial repair mechanisms. In addition, they can interfere with immune responses by blocking interferon pathways and by subverting protective inflammatory responses toward detrimental ones. Finally, by inducing overt mucus secretion and mucostasis and by paving the way for bacterial infections, they favor lung damage and further impair host antiviral mechanisms.

Molecular diagnosis of viral respiratory infections

In clinical practice, a rapid and accurate identification of pathogens causing viral respiratory tract infections can be problematic because of nonspecific clinical presentations, lack of rapid and sensitive tests, and the emergence of new and mutating viral pathogens. Nucleic acid-targeted molecular techniques are increasingly being used to provide high sensitivity and specificity, short test turnaround time, and automatic and high-throughput processing. In-house and commercially available molecular methods have been developed to qualitatively and quantitatively detect and identify a single or a panel of clinically encountered respiratory tract viruses in a single reaction. Molecular techniques are being gradually introduced in routine laboratory diagnosis of viral respiratory tract infections. However, their performance characteristics and limitations must be clearly understood by both laboratory personnel and clinicians to ensure proper utilization and interpretation.

Newly discovered KI, WU, and Merkel cell polyomaviruses: no evidence of mother-to-fetus transmission

Background

Three* human polyomaviruses have been discovered recently, KIPyV, WUPyV and MCPyV. These viruses appear to circulate ubiquitously; however, their clinical significance beyond Merkel cell carcinoma is almost completely unknown. In particular, nothing is known about their preponderance in vertical transmission. The aim of this study was to investigate the frequency of fetal infections by these viruses. We sought the three by PCR, and MCPyV also by real-time quantitative PCR (qPCR), from 535 fetal autopsy samples (heart, liver, placenta) from intrauterine fetal deaths (IUFDs) (N = 169), miscarriages (120) or induced abortions (246). We also measured the MCPyV IgG antibodies in the corresponding maternal sera (N = 462) mostly from the first trimester.

Results

No sample showed KIPyV or WUPyV DNA. Interestingly, one placenta was reproducibly PCR positive for MCPyV. Among the 462 corresponding pregnant women, 212 (45.9%) were MCPyV IgG seropositive.

Conclusions

Our data suggest that none of the three emerging polyomaviruses often cause miscarriages or IUFDs, nor are they transmitted to fetuses. Yet, more than half the expectant mothers were susceptible to infection by the MCPyV.

Merkel cell polyomavirus: a specific marker for Merkel cell carcinoma in histologically similar tumors

The recently described Merkel cell polyomavirus (MCPyV) is reportedly present in 50% to 80% of Merkel cell carcinomas (MCC). Although the virus has been shown to be absent from other cutaneous neoplasms, its association with malignancies that are histologically similar to MCC, specifically small cell carcinoma of the lung and other high-grade neuroendocrine tumors, has yet to be thoroughly investigated. To address this issue, we identified a set of 74 cases of visceral high-grade neuroendocrine tumors from a variety of anatomic sites, including 32 cases from the lung, 16 cases from the gastrointestinal tract, 20 cases from the female reproductive system, 3 cases from soft tissue, 2 cases from the head and neck region, and 1 case from the bladder. Using a set of primers optimized to detect MCPyV in formalin-fixed tissue, polymerase chain reaction (PCR)-based testing showed evidence of MCPyV DNA in only 1 of the 74 tumors; however, clinicopathologic review of the positive case (a neuroendocrine tumor of the small intestine) disclosed that the patient had a history of primary MCC of the buttock. PCR-based testing also showed no evidence of the related WU and KI polyomaviruses in the set of 74 cases. We conclude that, when evaluated by PCR-based testing, MCPyV is a specific marker for MCC that can be helpful in distinguishing cases of metastatic MCC from other high-grade neuroendocrine tumors. Our results also suggest that MCPyV does not have a role in the oncogenesis of visceral high-grade neuroendocrine tumors.

Serologic evidence of frequent human infection with WU and KI polyomaviruses

WU polyomavirus (WUPyV) and KI polyomavirus (KIPyV) are novel human polyomaviruses. They were originally identified in human respiratory secretions, but the extent of human infection caused by these viruses has not been described to date. To determine the seroepidemiology of WUPyV and KIpyIV, we used an ELISA to screen serum samples from 419 patients at the St. Louis Children's Hospital and Barnes-Jewish Hospital during 2007-2008. The age-stratified deidentified samples were examined for antibodies to the major capsid proteins of WUPyV and KIPyV. Seropositivity for each virus was similar; antibody levels were high in the youngest age group (<6 months), decreased to a nadir in the next age group (6 to <12 months), and then steadily increased with subsequent age groups, eventually reaching a plateau of approximate, equals 80% for WUPyV and approximate, equals 70% for KIPyV. These results demonstrate that both KIPyV and WUPyV cause widespread infection in the human population.

WU Polyomavirus (WUPyV): A Recently Detected Virus Causing Respiratory Disease?

The WU polyomavirus (WUPyV) is a novel member of the family Polyomaviridae recently detected in respiratory tract specimens by shotgun sequencing. Intriguingly, viral genome has been detected in 0.4% to 11.5% of respiratory tract specimens from children with respiratory disease. The levels of co-infection with established respiratory viruses were in the range between 30.8% and 91.7%. Moreover, some studies report detection of WUPyV in stool or serum. So far, WUPyV infections can not be distinguished from other viral infections by means of clinical symptoms. Respiratory tract disease like pneumonia or bronchitis is frequently observed in patients harbouring WUPyV. Detection of viremia suggests systemic infections. However, the available data do not prove WUPyV to be a human pathogen. Further investigations are necessary.

WU polyomavirus in patients infected with HIV or hepatitis C virus, Connecticut, USA, 2007

WU polyomavirus (WUPyV) was detected in 10 (8.3%) of 121 HIV-positive plasma specimens, 0 (0%) of 120 HIV-negative serum specimens, and 2 (2.5%) of 79 hepatitis C virus (HCV)–positive serum specimens. KI polyomavirus was not detected in HIV-positive plasma or HCV-positive serum specimens. HIV-infected persons may be susceptible to systemic WUPyV infection.