Respiratory viruses in bronchoalveolar lavage: a hospital-based cohort study in adults

Opportunistic Infections Post-Lung Transplantation: Viral, Fungal, and Mycobacterial

Opportunistic infections are a leading cause of lung transplant recipient morbidity and mortality. Risk factors for infection include continuous exposure of the lung allograft to the external environment, high levels of immunosuppression, impaired mucociliary clearance and decreased cough reflex, and impact of the native lung microbiome in single lung transplant recipients. Infection risk is mitigated through careful pretransplant screening of recipients and donors, implementation of antimicrobial prophylaxis strategies, and routine surveillance posttransplant. This review describes common viral, fungal, and mycobacterial infectious after lung transplant and provides recommendations on prevention and treatment.

Development of Human Rhinovirus RNA Reference Material Using Digital PCR

The human rhinovirus (RV) is a positive-stranded RNA virus that causes respiratory tract diseases affecting both the upper and lower halves of the respiratory system. RV enhances its replication by concentrating RNA synthesis within a modified host membrane in an intracellular compartment. RV infections often occur alongside infections caused by other respiratory viruses, and the RV virus may remain asymptomatic for extended periods. Alongside qualitative detection, it is essential to accurately quantify RV RNA from clinical samples to explore the relationships between RV viral load, infections caused by the virus, and the resulting symptoms observed in patients. A reference material (RM) is required for quality evaluation, the performance evaluation of molecular diagnostic products, and evaluation of antiviral agents in the laboratory. The preparation process for the RM involves creating an RV RNA mixture by combining RV viral RNA with RNA storage solution and matrix. The resulting RV RNA mixture is scaled up to a volume of 25 mL, then dispensed at 100 µL per vial and stored at -80 °C. The process of measuring the stability and homogeneity of RV RMs was conducted by employing reverse transcription droplet digital polymerase chain reaction (RT-ddPCR). Digital PCR is useful for the analysis of standards and can help to improve measurement compatibility: it represents the equivalence of a series of outcomes for reference materials and samples being analyzed when a few measurement procedures are employed, enabling objective comparisons between quantitative findings obtained through various experiments. The number of copies value represents a measured result of approximately 1.6 × 105 copies/μL. The RM has about an 11% bottle-to-bottle homogeneity and shows stable results for 1 week at temperatures of 4 °C and -20 °C and for 12 months at a temperature of -80 °C. The developed RM can enhance the dependability of RV molecular tests by providing a precise reference value for the absolute copy number of a viral target gene. Additionally, it can serve as a reference for diverse studies.

Impact of SARS-CoV-2-Related Hygiene Measures on Community-Acquired Respiratory Virus Infections in Lung Transplant Recipients in Switzerland

Background and Objectives: Community-acquired respiratory virus (CARV) infections pose a serious risk for lung transplant recipients (LTR) as they are prone to severe complications. When the COVID-19 pandemic hit Switzerland in 2020, the government implemented hygiene measures for the general population. We investigated the impact of these measures on the transmission of CARV in lung transplant recipients in Switzerland. Materials and Methods: In this multicenter, retrospective study of lung transplant recipients, we investigated two time periods: the year before the COVID-19 pandemic (1 March 2019-29 February 2020) and the first year of the pandemic (1 March 2020-28 February 2021). Data were mainly collected from the Swiss Transplant Cohort Study (STCS) database. Descriptive statistics were used to analyze the results. Results: Data from 221 Swiss lung transplant cohort patients were evaluated. In the year before the COVID-19 pandemic, 157 infections were diagnosed compared to 71 infections in the first year of the pandemic (decline of 54%, p < 0.001). Influenza virus infections alone showed a remarkable decrease from 17 infections before COVID-19 to 2 infections after the beginning of the pandemic. No significant difference was found in testing behavior; 803 vs. 925 tests were obtained by two of the three centers during the respective periods. Conclusions: We observed a significant decline in CARV infections in the Swiss lung transplant cohort during the first year of the COVID-19 pandemic. These results suggest a relevant impact of hygiene measures when implemented in the population due to the COVID-19 pandemic on the incidence of CARV infections.

Viral etiology of lower respiratory tract infections in adults in the pre-COVID-19 pandemic era: A cross-sectional study in a single center experience from Cameroon

Background and Aims

Respiratory viruses are responsible for the majority of lower respiratory tract infections (LRTIs) worldwide. However, there is a gap on the epidemiology of viral LRTIs in adults in sub-Saharan African countries. In Cameroon, like in other countries, the role of viral respiratory pathogens in the etiology of LRTIs in adults is helpful for clinical management. This study aimed to determine the viral aetiologies of LRTIs among hospitalized adults in a reference center for respiratory diseases in the town of Yaounde in Cameroon and its surroundings.

Methods

A cross-sectional study was conducted from January 2017 to January 2018 at Jamot Hospital in Yaounde (Cameroon). Clinical and demographic information; BAL and sputa were collected from hospitalized patients meeting LRTI case definitions. The clinical samples were investigated for respiratory pathogens with a commercial Reverse Transcriptase Real-Time Polymerase Chain Reaction (RT-PCR) targeting 21 viruses, cultures for bacterial and fungal infections.

Results

The 77 included adult patients with LRTIs had an appropriate clinical sample for microbial investigations. A viral agent was detected in 22.1% (17/77) samples. The main viruses detected included rhinovirus (10/77), coronavirus (hCoV-OC43 and hCoV-229E), and influenza A virus (3/77 each). A concomitant viral and bacterial co-infection occurred in 7.8% of patients (6/77) while viral co-infection occurred in one patient (1.3%). No Severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) was detected in clinical samples. Most patients were under antimicrobials before getting diagnosed.

Conclusions

Respiratory viruses account for 22.1% of LRTIs in hospitalized patients in this study. Despite prior antimicrobial therapy and delay, rhinovirus, coronavirus and influenza A virus were the most detected in patients in the pre-COVID-19 pandemic era in a single center experience from Cameroon.

Opportunistic Infections Post-Lung Transplantation: Viral, Fungal, and Mycobacterial

Opportunistic infections are a leading cause of lung transplant recipient morbidity and mortality. Risk factors for infection include continuous exposure of the lung allograft to the external environment, high levels of immunosuppression, impaired mucociliary clearance and decreased cough reflex, and impact of the native lung microbiome in single lung transplant recipients. Infection risk is mitigated through careful pretransplant screening of recipients and donors, implementation of antimicrobial prophylaxis strategies, and routine surveillance posttransplant. This review describes common viral, fungal, and mycobacterial infectious after lung transplant and provides recommendations on prevention and treatment.

Epidemiologic Characteristics and Clinical Significance of Respiratory Viral Infections Among Adult Patients Admitted to the Intensive Care Unit

Background

The diagnosis of respiratory viral infections (RVIs) in critically ill patients is important for determining treatment options and adhering to infection-control protocols. However, data on the incidence and occurrence patterns of RVIs are scarce. We investigated the epidemiology and clinical impact of RVIs in critically ill patients.

Methods

This retrospective observational study was conducted in a tertiary hospital in South Korea between November 2014 and September 2020. Adult patients (≥ 18 years of age) who tested positive for an RVI by multiplex polymerase chain reaction (mPCR) and were admitted to the intensive care unit (ICU) were included in the study. Clinical characteristics and outcomes were obtained by reviewing electronic medical records. Pearson's χ2 test and Fisher's exact test, Mann-Whitney U test was used to compare between groups of patients. Trend analysis and the χ2-based Q test was used to analyze test behavior of physicians performing mPCR test.

Results

Among 22,517 patients admitted to the ICU during the study period, 2,222 (9.9%) underwent mPCR testing for an RVI. The median timing of mPCR testing after ICU admission was 1 day (IQR, 0-2). A total of 335 (15.1%) non-duplicative RVI-positive cases were included in the analysis. The incidence rate of RVIs in ICU patients was 30.45 per 10,000 patient-days. The most frequently detected RVI was influenza A (27.8%), followed by rhinovirus (25.4%). Thirty-two (9.6%) RVI-positive patients were diagnosed with upper respiratory infections, 193 (64.1%) with community-acquired, and 108 (35.9%) with hospital-acquired pneumonia. All-cause mortality and mortality related to respiratory tract infection (RTI) were 30.7% and 22.1%, respectively. The initial presentation of septic shock, requirement for mechanical ventilation, and lymphocytopenia were significant predictors of RTI-related mortality. Of the RVI-positive patients, 151 (45.1%) had nonviral coinfections and presented with higher clinical severity and longer hospital stays than patients infected solely with viral pathogens.

Conclusion

The incidence of RVIs in ICU patients is common. ICU patients with RVIs had high mortality and frequently presented with coinfections with nonviral pathogens, which were associated with a higher clinical severity than sole RVI. Increased testing for RVIs will enhance infection-control efforts and improve patient care.

NMR spectroscopy spotlighting immunogenicity induced by COVID-19 vaccination to mitigate future health concerns

In this review, the disease and immunogenicity affected by COVID-19 vaccination at the metabolic level are described considering the use of nuclear magnetic resonance (NMR) spectroscopy for the analysis of different biological samples. Consistently, we explain how different biomarkers can be examined in the saliva, blood plasma/serum, bronchoalveolar-lavage fluid (BALF), semen, feces, urine, cerebrospinal fluid (CSF) and breast milk. For example, the proposed approach for the given samples can allow one to detect molecular biomarkers that can be relevant to disease and/or vaccine interference in a system metabolome. The analysis of the given biomaterials by NMR often produces complex chemical data which can be elucidated by multivariate statistical tools, such as PCA and PLS-DA/OPLS-DA methods. Moreover, this approach may aid to improve strategies that can be helpful in disease control and treatment management in the future.

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NMR analysis of various bio-samples can explore disease course and vaccine interaction.

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Immunogenicity and reactogenicity caused by COVID-19 vaccination can be studied by NMR.

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Vaccine interaction alters metabolic pathway(s) at a certain stage, and this mechanism can be probed at the metabolic level.

Human bocavirus 1 respiratory tract reactivations or reinfections in two adults, contributing to neurological deficits and death

Human bocavirus 1 (HBoV1) of the family Parvoviridae causes mild to life-threatening respiratory tract infections in young children, but, due to widespread immunity, it is uncommon in adults. HBoV1 reinfections or reactivations leading to casualties are rare, but might be underdiagnosed. We report two young adults, one previously healthy and one immunosuppressed, with rare diagnostic patterns of HBoV1 respiratory tract infection. Both patients exhibited very high loads of HBoV1 DNA in respiratory samples. The immunosuppressed patient was also HBoV1 DNA-positive in blood, stool and a colon biopsy, but exhibited prior HBoV1-specific high-avidity IgG and weak IgM positivity 9 months before the respiratory symptoms. Likewise, the previously healthy patient exhibited HBoV1 IgG of high avidity and very weak IgM in serum, pointing to prior immunity, but with a seroconversion in cerebrospinal fluid. This patient also showed strong HBoV2 cross-reactivity. The molecular and serological results, together with their ages, suggest that both patients exhibited unusual reinfection or reactivation of HBoV1, contributing to neurological deficits and death.

Bronchoalveolar lavage in suspected COVID-19 cases with a negative nasopharyngeal swab: a retrospective cross-sectional study in a high-impact Northern Italy area

COVID-19 diagnosis relies on molecular testing for SARS-CoV-2 via nasopharyngeal swab in the presence of suggestive clinical, radiological and laboratory findings. Since bronchoalveolar lavage liquid (BAL) collected during fibrobronchoscopy may increase test sensitivity compared to nasopharyngeal swabs, it was performed during the 2020 pandemic in clinically or radiologically suspected cases. Our aim was to determine whether clinical features, chest computed tomography (CT) findings or laboratory tests may predict patients testing positive for SARS-CoV-2 at BAL after a negative nasopharyngeal swab. We performed a retrospective cross-sectional study with multivariable analysis of suspected patients who were tested for SARS-CoV-2 at BAL after at least one negative nasopharyngeal swab. Univariable logistic regression for odds ratio and multivariate models was calculated to determine clinical, radiological and laboratory predictors. 32/198 (16%) patients had BAL positive for SARS-CoV-2, while 65/198 tested positive for other pathogens at BAL. Of the 32 patients positive for COVID, 4 had a coinfection at BAL, being thus positive both for COVID as well as for another pathogen while the remaining 105 patients were negative for COVID and other pathogens at BAL. COVID-19 patients had more often highly suggestive CT findings, higher number of involved lobes, more often ground glass opacity of more than 50% of lung parenchyma, and less frequently other radiologically suspected infections. At multivariate model, temperature also predicted BAL positivity. The procedure was well tolerated-with only one desaturation episode-while no healthcare worker was infected. In conclusion, when nasopharyngeal swabs are negative but there is clinical or imaging suspicion of COVID-19, BAL represents a complementary diagnostic tool, particularly in conjunction with suggestive/more extensive lung involvement at CT scan. The procedure did not carry increased risks for patients nor for operators, while allowing to free hospital resources, avoiding unnecessary isolations.

Lack of clinical significance for molecular detection of respiratory viruses in bronchoalveolar lavage samples

The clinical significance of molecular detection of respiratory viruses in bronchoalveolar lavage (BAL) samples is poorly defined. We performed an observational retrospective study including all patients who underwent a BAL procedure in our institution, regardless of the reason for bronchoscopy, from January 2015 to December 2018. Respiratory viruses were detected by real-time polymerase chain reaction with a commercial multiplex panel, and a cell culture was performed to detect cytomegalovirus and herpes simplex virus. Positive results were correlated with clinical symptoms and patients' characteristics. Of 540 BAL samples analyzed, 113 (20.9%) were positive for any respiratory virus. Viral detection was significantly associated with respiratory symptoms (83.2% vs. 68.9%, p = .004) and radiological infiltrates (67.3% vs. 52.2%, p = .006). The most frequent viruses detected were rhinovirus (42/113, 37.2%), influenza virus (20/113, 17.7%), and parainfluenza virus (PIV) (16/113, 14.2%). Respiratory pathogens codetections were found in 51/113 (45.1%) BAL samples, including more than one virus (16/51, 31.4%), fungi (8/51, 15.7%), and bacteria (9/51, 17.6%). Viral detection was significantly higher in immunocompromised patients (26.5% vs. 16.9%; p = .022). PIV and human metapneumovirus were mostly observed in lung (50.0%, 8/16) and hemopoietic transplant recipients (25%, 2/8), respectively, with clinical repercussions. Our data underline that molecular diagnosis allows identification of viral agents as the etiology of respiratory infections; however, the high frequency of codetections hinders identification of the agent responsible for the current respiratory symptomatology. Immunocompromised patients are the target population in whom to investigate the presence of respiratory viruses in their BAL samples.

SARS-CoV-2 Detection on Bronchoalveolar Lavage: An Italian Multicenter experience

Background

Bronchoscopy with bronchoalveolar lavage (BAL) during the SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) pandemic should be reserved to a limited number of clinical indications. The yield of BAL for the diagnosis of suspected or confirmed pulmonary SARS-CoV-2 infection is still unknown.

Objectives

We aimed to evaluate the diagnostic ratio of BAL in detecting SARS-CoV-2 pulmonary infection in patients undergoing bronchoscopy for different indications as well as describe the clinical, radiological, and endoscopic characteristics of patients with SARS-CoV-2 on BAL.

Method

We conducted a multicenter retrospective study including all patients who underwent bronchoscopy for the detection of SARS-CoV-2 on BAL. Clinical, computed tomography (CT), endoscopic, and microbiologic data were gathered from March 16th to May 27th, 2020.

Results

131 patients were included. Bronchoscopy was performed for suspected SARS-CoV-2 infection (65.5%), alternative diagnosis (12.9%), suspected superinfections (19.8%), and lung atelectasis (1.5%). SARS-CoV-2 was isolated on BAL 43 times (32.8%) and the highest isolation rate was in patients with suspected SARS-CoV-2 infection (74.4%); 76% of positive patients had a double-negative nasopharyngeal swab. Peripheral, posterior and multilobar CT opacities were more frequent in SARS-CoV-2 patients, and the number of CT findings was higher in positive patients, particularly those with suspected SARS-CoV-2 infection. We recorded a progressive reduction of SARS-CoV-2 isolation during the observation period.

Conclusions

In our centers, the rate of detection of SARS-CoV-2 on BAL in patients with suspected infection was 37.2%. The agreement of BAL with nasopharyngeal swabs was high; CT alterations could predict the pretest probability of SARS-CoV-2 infection, but suspicion of viral infection should be always considered.

Total alveolar lavage with oxygen fine bubble dispersion directly improves lipopolysaccharide-induced acute respiratory distress syndrome of rats

Severe respiratory disorder induced by pulmonary inflammation is one of the causes of acute respiratory distress syndrome, which still has high mortality. It is crucial to remove causative substances and inflammatory mediators early in order to inhibit the progression of pulmonary inflammation. Total alveolar lavage (TAL) may avert the inflammatory response by eliminating causative substances in certain inflammatory lung diseases. We developed an efficient TAL system and examined the efficacy of short-term TAL treatment performed for acute lung injury models of rats. In the first experiment with a severe lung injury model, 15 rats were divided into 3 groups: sham group, mechanical gas ventilation (MGV) treatment group, and TAL treatment group. The treatments were conducted for 5 min, 20 min after the provocation of inflammation. Two days after treatment, the TAL and MGV treatment groups exhibited significant differences in blood oxygen levels, mean arterial pressure, weight-loss ratio, and inflammatory cytokine levels in the lungs. In contrast, almost no differences were observed between the TAL treatment and sham groups. In the second experiment with a lethal lung injury model, the TAL treatment dramatically improved the survival rate of the rats compared to the MGV treatment groups (p = 0.0079). Histopathological analysis confirmed pronounced differences in neutrophil accumulation and thickening of the interstitial membrane between the TAL and MGV treatment groups in both experiments. These results indicate that as little as 5 min of TAL treatment can protect rats from acute lung injury by removing causative substances from the lungs.

Human Bocavirus Infection in Adults: Clinical Features and Radiological Findings

OBJECTIVE

Human bocavirus (HBoV) is a newly identified pathogen that can cause upper and lower respiratory infections usually in children; however, its clinical characteristics and significance in respiratory infections in adults have not been well known. Our objective was to evaluate the clinical features of respiratory HBoV infection and to describe the CT findings of HBoV pneumonia in adults.

MATERIALS AND METHODS

A total of 185 adult patients diagnosed with HBoV infection at a tertiary referral center between January 2010 and December 2017 were retrospectively evaluated with respect to the clinical characteristics of HBoV infection and its risk factors for pneumonia. Chest CT findings for 34 patients with HBoV pneumonia without co-infection were analyzed and compared between immunocompetent (n = 18) and immunocompromised (n = 16) patients.

RESULTS

HBoV infections were predominantly noted between February and June. Among the 185 patients with HBoV infection, 119 (64.3%) had community-acquired infections and 110 (59.5%) had pneumonia. In multivariable analysis, older age (odds ratio [OR], 1.02; 95% confidence interval [CI], 1.00-1.04; p = 0.045) and nosocomial infection (OR, 2.07; 95% CI, 1.05-4.10; p = 0.037) were associated with HBoV pneumonia. The main CT findings were bilateral consolidation (70.6%) and/or ground-glass opacities (64.7%); centrilobular nodules (14.7%) were found less frequently. The pattern of CT findings were not significantly different between immunocompetent and immunocompromised patients (all, p > 0.05).

CONCLUSION

HBoV infection can be a potential respiratory tract infection in adults. The most frequent CT findings of HBoV pneumonia were bilateral consolidation and/or ground-glass opacities.

The evolving burden of viruses in pneumonia

PURPOSE OF REVIEW

To describe the evolving microbiology of various forms of pneumonia and the importance of viruses as etiologic causes of pneumonia.

RECENT FINDINGS

Multiple studies utilizing novel diagnostic modalities demonstrate that the prevalence of viruses as causes for pneumonia varies from approximately 10-30% depending on the specific pneumonia type evaluated. Viral pneumonias appear similar in presentation and severity of illness to bacterial causes of pulmonary infection. Clinical criteria do not reliably allow the differentiation of viral from bacterial causes in pneumonia.

SUMMARY

Viruses represent a pool of important culprit organisms in pneumonia and identification of a viral pathogen may facilitate attempts at antibiotic stewardship.

Infection prophylaxis and management of viral infection

Viral infections are associated with significant morbidity and mortality in lung transplant recipients. Importantly, several viral infections have been associated with the development of chronic lung allograft dysfunction (CLAD). Community-acquired respiratory viruses (CARV) such as influenza and respiratory syncytial virus (RSV), are frequently associated with acute and chronic rejection. Cytomegalovirus (CMV) remains a significant burden in regards to morbidity and mortality in lung transplant recipients. Epstein-Barr virus (EBV) is mostly involved with the development of post-transplant lymphoproliferative disorder (PTLD), a lymphoid proliferation that occurs in the setting of immunosuppression. On the other hand, the development of direct acting antivirals for hepatitis C virus (HCV) is changing the use of HCV-positive organs in transplantation. In this article we will focus on reviewing common viral infections that have a significant impact on lung transplant recipients looking at epidemiology, prevention and potential treatment.

MERS-CoV infection is associated with downregulation of genes encoding Th1 and Th2 cytokines/chemokines and elevated inflammatory innate immune response in the lower respiratory tract

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MERS-CoV infection downregulates Th1 and Th2 cytokines and chemokines.

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MERS-CoV infection provokes high levels of IL-1α, IL-1β and IL-8 (CXCL8).

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Inflammatory cytokines/chemokines correlate with MERS-CoV case fatality rate.

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Th1/Th2 downregulation may contribute to severe infection and evolution of ARDS.

MERS-CoV, a highly pathogenic virus in humans, is associated with high morbidity and case fatality. Inflammatory responses have a significant impact on MERS-CoV pathogenesis and disease outcome. However, CD4⁺ T-cell induced immune responses during acute MERS-CoV infection are barely detectable, with potent inhibition of effector T cells and downregulation of antigen presentation. The local pulmonary immune response, particularly the Th1 and Th2-related immune response during acute severe MERS-CoV infection is not fully understood. In this study, we offer the first insights into the pulmonary gene expression profile of Th1 and Th2-related cytokines/chemokines (Th1 & Th2 responses) during acute MERS-CoV infection using RT² Profiler PCR Arrays. We also quantified the expression level of primary inflammatory cytokines/chemokines. Our results showed a downregulation of Th2, inadequate (partial) Th1 immune response and high expression levels of inflammatory cytokines IL-1α and IL-1β and the neutrophil chemoattractant chemokine IL-8 (CXCL8) in the lower respiratory tract of MERS-CoV infected patients. Moreover, we identified a high viral load in all included patients. We also observed a correlation between inflammatory cytokines, Th1, and Th2 downregulation and the case fatality rate. Th1 and Th2 response downregulation, high expression of inflammatory cytokines, and high viral load may contribute to lung inflammation, severe infection, the evolution of pneumonia and ARDS, and a higher case fatality rate. Further study of the molecular mechanisms underlying the Th1 and Th2 regulatory pathways will be vital for active vaccine development and the identification of novel therapeutic strategies.

Community-Acquired Respiratory Viruses in Transplant Patients: Diversity, Impact, Unmet Clinical Needs

Patients undergoing solid-organ transplantation (SOT) or allogeneic hematopoietic cell transplantation (HCT) are at increased risk for infectious complications. Community-acquired respiratory viruses (CARVs) pose a particular challenge due to the frequent exposure pre-, peri-, and posttransplantation. Although influenza A and B viruses have a top priority regarding prevention and treatment, recent molecular diagnostic tests detecting an array of other CARVs in real time have dramatically expanded our knowledge about the epidemiology, diversity, and impact of CARV infections in the general population and in allogeneic HCT and SOT patients. These data have demonstrated that non-influenza CARVs independently contribute to morbidity and mortality of transplant patients. However, effective vaccination and antiviral treatment is only emerging for non-influenza CARVs, placing emphasis on infection control and supportive measures. Here, we review the current knowledge about CARVs in SOT and allogeneic HCT patients to better define the magnitude of this unmet clinical need and to discuss some of the lessons learned from human influenza virus, respiratory syncytial virus, parainfluenzavirus, rhinovirus, coronavirus, adenovirus, and bocavirus regarding diagnosis, prevention, and treatment.

Epidemiology and clinical impact of viral, atypical, and fungal respiratory pathogens in symptomatic immunocompromised patients: a two-center study using a multi-parameter customized respiratory Taqman® array card

The prevalence of respiratory viruses in immunocompromised adult patients and the association with clinical outcomes is still underexplored. Our goal was to assess the epidemiology and the potential clinical impact of respiratory viral infections in a high-risk patient population. Two large hospitals performed a respiratory Taqman array card (TAC), targeting 24 viruses, 8 bacteria, and 2 fungi simultaneously, on 435 samples from 397 symptomatic immunocompromised patients. Clinical details were collected retrospectively using a structured case report form. An overall positivity rate of 68% was found (51% mono- and 17% co-infections). Pathogen distribution was as follows: influenza A (20.7%), rhinoviruses (15.2%), coronaviruses (7.8%), Pneumocystis jirovecii (7.4%), RSV (7.1%), and CMV (6.0%) were the most frequently encountered, followed by HSV (5.5%), hMPV (4.4%), parainfluenza viruses (3.9%), influenza B (3.7%), and Aspergillus species (3.7%). Other pathogens were not detected or detected only in ≤ 1% of samples. Hospital and ICU admission rates were 84% and 11%, respectively. The presence of a pathogen was strongly associated with higher need for supplemental oxygen (p = 0.001), but it had no impact on ICU admission, mechanical ventilation requirement, antibacterial therapy, or mortality. In conclusion, our study described the epidemiology of respiratory pathogens in a large group of symptomatic immunocompromised patients and provides evidence of a relationship between pathogen detection and the need for supplemental oxygen. This association was still found after the exclusion of the results positive for influenza viruses, suggesting that non-influenza viruses contribute to severe respiratory illness in patients with compromised immunity.

Use of an innovative and non-invasive device for virologic sampling of cough aerosols in patients with community and hospital acquired pneumonia: a pilot study

BACKGROUND

The aetiology of lower respiratory tract infections is challenging to investigate. Despite the wide array of diagnostic tools, invasive techniques, such as bronchoalveolar lavage (BAL), are often required to obtain adequate specimens. PneumoniaCheckTM is a new device that collects aerosol particles from cough, allowing microbiological analyses. Up to now it has been tested only for bacteria detection, but no study has investigated its usefulness for virus identification.

METHODS

In this pilot study we included 12 consecutive patients with pneumonia. After testing cough adequacy via a peak flow meter, a sampling with PneumoniaCheckTM was collected and a BAL was performed in each patient. Microbiological analyses for virus identification were performed on each sample and concordance between the two techniques was tested (sensitivity, specificity and positive/negative predictive values), taking BAL results as reference.

RESULTS

BAL was considered adequate in 10 patients. Among them, a viral pathogen was identified by PneumoniaCheckTM 6 times, each on different samples, whereas BAL allowed to detect the presence of a virus on 7 patients (14 positivities). Overall, the specificity for PneumoniaCheckTM to detect a virus was 100%, whereas the sensitivity was 66%. When considering only herpes viruses, PneumoniaCheckTM showed a lower sensitivity, detecting a virus in 1/4 of infected patients (25%).

CONCLUSIONS

In this pilot study PneumoniaCheckTM showed a good correlation with BAL for non-herpes virologic identification in pneumonia patients, providing excellent specificity. Further studies on larger population are needed to confirm these results and define its place in the panorama of rapid diagnostic tests for lower respiratory tract infections.

Viral Pneumonia Requiring Differentiation from Acute and Progressive Diffuse Interstitial Lung Diseases

Objective The clinical characteristics and chest imaging findings of viral pneumonia and several interstitial lung diseases (ILDs) overlap, and viral pneumonia may be underrecognized and misdiagnosed as certain ILDs. To clarify the frequency of viral pneumonia among patients with acute progressive clinical courses that required a differential diagnosis between ILDs and pneumonia, and to determine the most frequent ILDs misdiagnosed in cases of viral pneumonia. Patients and Methods We retrospectively analyzed patients hospitalized from 2010 to 2017 with an acute clinical course (≤30 days) who underwent bronchoalveolar lavage (BAL) for the differential diagnosis of infection and ILDs. We performed a multiplex PCR for respiratory viruses using the patients' preserved BAL fluid. The final diagnosis was made by a multidisciplinary approach and after considering the PCR results. The diagnosis at discharge was compared to the final diagnosis. Results Among the 109 patients, 53 were diagnosed with viral pneumonia. Viral pneumonia and other diseases showed some differences in symptoms and laboratory data; however, the differences were small or overlapped. Viral pneumonia was misdiagnosed on discharge as acute fibrinous organizing pneumonia, cryptogenic organizing pneumonia, or chronic eosinophilic pneumonia (AFOP/COP/CEP) (n=22), acute interstitial pneumonia (n=5), connective tissue disease-related ILDs (n=3), unclassifiable interstitial pneumonia (n=2), drug-induced ILD (n=1), and pneumonia (n=20). Conclusion Approximately half of the patients who underwent BAL had viral pneumonia. The most common ILD-related misdiagnoses were AFOP/COP/CEP. Differences in symptoms and laboratory findings between viral pneumonia and other diseases were small, and viral pneumonia should be included in the differential diagnosis when physicians encounter cases in which the abovementioned ILDs are suspected.

Rare and Emerging Viral Infections in the Transplant Population

Viral infections account for a large proportion of emerging infectious diseases, and the agents included in this group consist of recently identified viruses as well as previously identified viruses with an apparent increase in disease incidence. In transplant recipients, this group can include viruses with no recognized pathogenicity in immunocompetent patients and those that result in atypical or more severe disease presentations in the immunocompromised host. In this chapter, we begin by discussing viral diagnostics and techniques used for viral discovery, specifically as they apply to emerging and rare infections in this patient population. Focus then shifts to specific emerging and re-emerging viruses in the transplant population, including human T-cell leukemia virus 1, rabies, lymphocytic choriomeningitis virus, human bocavirus, parvovirus 4, measles, mumps, orf, and dengue. We have also included a brief discussion on emerging viruses and virus families with few or no reported cases in transplant recipients: monkeypox, nipah and hendra, chikungunya and other alphaviruses, hantavirus and the Bunyaviridae, and filoviruses. Finally, concerns regarding infectious disease complications in xenotransplantation and the reporting of rare viral infections are addressed. With the marked increase in the number of solid organ and hematopoietic stem cell transplants performed worldwide, we expect a corresponding rise in the reports of emerging viral infections in transplant hosts, both from known viruses and those yet to be identified.

Infections after lung transplantation

The good clinical result of lung transplantation is constantly undermined by the high incidence of infection, which negatively impacts on function and survival. Moreover, infections may also have immunological interactions that play a role in the acute rejection and in the development of chronic lung allograft dysfunction. There is a temporal sequence in the types of infection that affects lung allograft: in the first postoperative month bacteria are the most frequent cause of infection; following this phase, cytomegalovirus and Pneumocystis carinii are common. Fungal infections are particularly feared due to their association with bronchial complication and high mortality. Scrupulous postoperative surveillance is mandatory for the successful management of lung transplantation patients with respect to early detection and treatment of infections. This paper is aimed to address clinicians in the management of the major infectious complications that affect the lung transplant population.

Post-transplant Viral Respiratory Infections in the Older Patient: Epidemiology, Diagnosis, and Management

Organ and stem cell transplantation has been one of the greatest advances in modern medicine, and is the primary treatment modality for many end-stage diseases. As our population ages, so do the transplant recipients, and with that comes many new challenges. Respiratory viruses have been a large contributor to the mortality and morbidity of solid organ transplant (SOT) and hematopoietic stem cell transplant (HSCT) recipients. Respiratory viruses are generally a long-term complication of transplantation and primarily acquired in the community. With the emergence of molecular methods, newer respiratory viruses are being detected. Respiratory viruses appear to cause severe disease in the older transplant population. Influenza vaccine remains the mainstay of prevention in transplant recipients, although immunogenicity of current vaccines is suboptimal. Limited therapies are available for other respiratory viruses. The next decade will likely bring newer antivirals and vaccines to the forefront. Our goal is to provide the most up to date knowledge of respiratory viral infections in our aging transplant population.

Mahfouz M, Zytouni DM. Detection of human bocavirus in Saudi healthy blood donors

Human bocavirus is associated with respiratory disease worldwide, mainly in children. There are conflicting results, however, regarding the existence of the HBoV in blood donors. Three hundred whole blood samples from non-immunodeficient healthy blood donors were screened for the presence of HBoV by polymerase chain reaction. The HBoV genotype of positive samples was determined using direct gene sequencing. Twenty-one out of the three hundred blood samples were found to be positive for HBoV. Sequence analysis of the positive samples revealed that all the strains were related to the HBoV-1 type with a low rate of variation among the detected sequences. It was concluded that there is a considerable risk of contracting HBoV from a blood transfusion from normal healthy individuals.

The Burden of Viruses in Pneumonia Associated With Acute Respiratory Failure: An Underappreciated Issue

BACKGROUND

Pneumonia associated with mechanical ventilation (MV) results in substantial mortality and represents a leading reason for the use of antibiotics. The role of viruses in this setting is unclear. Identifying a viral cause in such instances could facilitate antibiotic stewardship.

METHODS

We performed a secondary analysis of a prospective cohort with pneumonia requiring MV. We included both cases occurring in the community and hospital-onset cases and classified patients according to the cause of the pneumonia. The prevalence of viral pathogens represented the primary end point. We identified variables independently associated with isolation of a viral organism as the sole pathogen.

RESULTS

The cohort included 364 patients, and a virus was the sole pathogen in 79 cases (21.7%). The most common viruses included rhinovirus/enterovirus (n = 20), influenza A (n = 12), and respiratory syncytial virus (n = 11). The rate of in-hospital death was high (37.2%) and did not differ from that seen in other patients (36.5%). The duration of MV, hospital length of stay, and 30-day readmission rates also did not differ based on the cause of pneumonia. Two variables were independently associated with recovery of a virus: an Acute Physiology and Health Evaluation II score of < 26 (adjusted odds ratio [AOR], 0.51; 95% CI, 0.28-0.93; P = .027) and stem cell transplantation (SCT) (AOR, 4.39; 95% CI, 2.03-9.50; P = .001). A sensitivity analysis excluding patients who underwent SCT did not substantially alter our observations.

CONCLUSIONS

Viruses represent a major cause of pneumonia in critically ill patients requiring MV. Identifying such subjects presents an opportunity for discontinuing antibiotics. Clinicians should consider systematically evaluating patients with pneumonia requiring MV for viral pathogens.

Severe Respiratory Viral Infections: New Evidence and Changing Paradigms

Lower respiratory tract infection is a leading cause of death in the United States. Advances in diagnostic testing have improved our ability to detect pathogens. Viral pathogens are important causal pathogens in immunocompetent patients. As the number of elderly adults and those with chronic medical conditions increases, the burden of viral respiratory infections will increase. Clinicians must be familiar with the characteristics of rhinovirus, human adenoviruses, respiratory syncytial virus, and human metapneumovirus. Major challenges include distinguishing true infection from asymptomatic carriage and characterizing patients admitted with severe lower respiratory tract infection who do not have a causative pathogen identified.

Parallel pathogens in the upper and lower respiratory tracts in children with a respiratory tract infection, as revealed by the Filmarray assay

Background

Respiratory tract infection (RTI) is a common disease among children of all ages that causes high hospitalization and mortality rates. Infection with more than one pathogen has been reported in RTI; however, the association of the pathogen spectrum in upper and lower respiratory tract infections remains unclear.

Methods

A prospective study was conducted during February to October 2016. Fifty-five nasopharyngeal swabs (NPS) and 30 bronchoalveolar lavage fluid (BALF) samples from 55 hospitalized children aged less than 14 years (mean age 40 months) and diagnosed with an RTI were collected. All samples were detected for 18 respiratory pathogens using the Filmarray assay, real-time PCR, or nested PCR methods. Detection results and clinical characteristics of all cases were analyzed using chi-square and t tests.

Results

Forty-one of 55 (74.5%) NPS obtained from children were positive for at least one pathogen by the Filmarray assay. Of these cases, 53.7% (22/41) were co-infected. The most commonly detected pathogen was rhinovirus (RV), followed by Mycoplasma pneumoniae (MP) and respiratory syncytial virus (RSV). Infection by both RV and MP was the most frequently observed pattern of co-infection. Similar results were observed using real-time PCR. The pathogens in the NPS from 76.6% of cases detected by Filmarray and 80.0% of cases by real-time PCR included all the pathogens detected in the BALF sample from the same individual. The Filmarray assay showed an 80% concordance rate with real-time PCR and had a turnaround time of less than 1.2 h. No significant differences were observed between the association of single-infection and co-infection with clinical characteristics, neither by Filmarray nor real-time PCR.

Conclusion

The spectrum of pathogens is mostly concordant in the upper and lower respiratory tract. Collecting NPS for detection can be a non-invasive and more convenient option compared with BALF. Although co-infection is common in children with an RTI, the clinical significance of co-infection remains unclear and warrants further analysis.

Human Parvoviruses

Parvovirus B19 (B19V) and human bocavirus 1 (HBoV1), members of the large Parvoviridae family, are human pathogens responsible for a variety of diseases. For B19V in particular, host features determine disease manifestations. These viruses are prevalent worldwide and are culturable in vitro, and serological and molecular assays are available but require careful interpretation of results. Additional human parvoviruses, including HBoV2 to -4, human parvovirus 4 (PARV4), and human bufavirus (BuV) are also reviewed. The full spectrum of parvovirus disease in humans has yet to be established. Candidate recombinant B19V vaccines have been developed but may not be commercially feasible. We review relevant features of the molecular and cellular biology of these viruses, and the human immune response that they elicit, which have allowed a deep understanding of pathophysiology.

Spirometry filters can be used to detect exhaled respiratory viruses

Respiratory viruses are very common in the community and contribute to the burden of illness for patients with chronic respiratory diseases, including acute exacerbations. Traditional sampling methods are invasive and problematic to repeat. Accordingly, we explored whether respiratory viruses could be isolated from disposable spirometry filters and whether detection of viruses in this context represented presence in the upper or lower respiratory tract. Discovery (n  =  53) and validation (n  =  49) cohorts were recruited from a hospital outpatient department during two different time periods. Spirometry mouthpiece filters were collected from all participants. Respiratory secretions were sampled from the upper and lower respiratory tract by nasal washing (NW), sputum, and bronchoalveolar lavage (BAL). All samples were examined using RT-PCR to identify a panel of respiratory viruses (rhinovirus, respiratory syncytial virus, influenza A, influenza B, parainfluenza virus 1, 2 & 3, and human metapneumovirus). Rhinovirus was quantified using qPCR. Paired filter-NW samples (n  =  29), filter-sputum samples (n  =  24), filter-BAL samples (n  =  39) and filter-NW-BAL samples (n  =  10) provided a range of comparisons. At least one virus was detected in any sample in 85% of participants in the discovery cohort versus 45% in the validation cohort. Overall, 72% of viruses identified in the paired comparator method matched those detected in spirometry filters. There was a high correlation between viruses identified in spirometry filters compared with viruses identified in both the upper and lower respiratory tract using traditional sampling methods. Our results suggest that examination of spirometry filters may be a novel and inexpensive sampling method for the presence of respiratory viruses in exhaled breath.

Respiratory Syncytial Virus and Human Metapneumovirus Infection in Transplant Recipients

Respiratory viral infections due to respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) cause infections in immunocompromised transplant patients ranging from mild upper respiratory infections to severe lower respiratory tract disease with respiratory failure. These viruses are more readily diagnosed due to improvements in sensitive molecular diagnostic methods. The epidemiology of RSV and hMPV is similarly becoming more readily appreciated in hematopoietic stem cell transplant (HSCT) patients of all ages as well as solid organ transplant (SOT) patients, with lung transplant recipients having evidence of more frequent and severe complications related to these viruses. RSV and hMPV infection typically but not always present with upper respiratory signs and symptoms that progress to lower respiratory tract disease. Treatment options for RSV are limited, with aerosolized, intravenous, and oral ribavirin all studied in HSCT and lung transplant patients. No antiviral therapy for the treatment of hMPV is available, although ribavirin has shown some effectiveness in vitro. New antiviral agents including RSV fusion inhibitors and nucleoside analogs are being developed, with some under clinical evaluation.

Benefits and drawbacks of molecular techniques for diagnosis of viral respiratory infections. Experience with two multiplex PCR assays

Molecular techniques have represented a major step forward in the diagnosis of viral respiratory infections. They are considered highly sensitive and specific compared to conventional techniques. In this study two nucleic acid amplification tests (NAATs) were compared to conventional methods (immunofluorescence and viral culture). The aim of this work was to discuss the clinical interpretation of the results obtained by NAATs on the basis of the two-decade experience of our group and the literature. Eighty nasopharyngeal aspirates were collected from children under six years attended for acute respiratory illness at the pediatric emergency room of a third level Hospital. Both NAATs tested (Seeplex(®) and Clart(®)) showed an overall higher performance regarding sensitivity (76% and 90%, respectively). Compared to Seeplex(®), the Clart(®) system tripled the number of multiple detections (8 by Seeplex(®) vs. 25 by Clart(®)). In some specimens both NAATs detected different viruses. Given these discrepancies and the fact that detection of viral nucleic acids is not necessarily related to the current clinical syndrome, the interpretation of molecular results may not always be so straightforward. The pros and cons of NAATs should always be taken into account when giving a result.

Infections and Asthma

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Wheezing viral respiratory illnesses are the most common initial presentation of childhood asthma.

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Once asthma is established, viral infections, most notably rhinovirus (RV), are the most frequent trigger of severe asthma exacerbations. RV-C appears to be a particularly pathogenic virus in children with asthma.

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Evidence has recently emerged to suggest that bacterial pathogens in the lower airway may contribute to the expression of asthma. Ongoing studies are critical to our understanding of the role of the airway microbiome in asthma inception and exacerbation.

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Synergistic interactions between underlying allergy and virus infections play an important mechanistic role in asthma inception and exacerbation, and are an important therapeutic target.

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Novel therapies are needed to prevent and treat virus-induced wheezing and asthma exacerbations.

Co-infections with respiratory viruses in dogs with bacterial pneumonia

Background

Bacterial pneumonia (BP) is an inflammation of the lower airways and lung parenchyma secondary to bacterial infection. The pathogenesis of BP in dogs is complex and the role of canine respiratory viruses has not been fully evaluated.

Objectives

The aim of this study was to investigate the occurrence of viral co‐infections in dogs with BP and to assess demographic or clinical variables as well as disease severity associated with viral co‐infections.

Animals

Twenty household dogs with BP caused by opportunistic bacteria and 13 dogs with chronic (>30 days) tracheobronchitis caused by Bordetella bronchiseptica (BBTB).

Methods

Prospective cross‐sectional observational study. Diagnosis was confirmed by clinical and laboratory findings, diagnostic imaging, and cytologic and microbiologic analysis of bronchoalveolar lavage or transtracheal wash fluid. Canine parainfluenza virus (CPIV), canine adenovirus, canine herpes virus, canine influenzavirus, canine distemper virus, canine respiratory coronavirus (CRCoV) and canine pneumovirus, as well as B. bronchiseptica and Mycoplasma spp. were analyzed in respiratory samples using PCR assays.

Results

CPIV was detected in 7/20 and CRCoV in 1/20 dogs with BP. Respiratory viruses were not detected in dogs with BBTB. There were no significant differences in clinical variables between BP dogs with and without a viral co‐infection.

Conclusion and Clinical Importance

Respiratory viruses were found frequently in dogs with BP and may therefore play an important role in the etiology and pathogenesis of BP. Clinical variables and disease severity did not differ between BP dogs with and without viral co‐infection.

A novel primer set for improved direct gene sequencing of human bocavirus genotype-1 from clinical samples

Human bocavirus genotype (HBoV-1) is a parvovirus associated with respiratory tract infections in children with different degrees of severity. The current study intended to improve the direct gene sequencing of the HBoV-1 using a newly developed primer set. Screening the presence of human bocavirus infection among in-patients children suffering from lower respiratory tract infections was another aim of the current study. Nasopharyngeal swab samples from in-patients children suffering from lower respiratory tract infections were examined. The real-time polymerase chain reaction was used for the initial screening as a highly sensitive method to detect the HBoV. Genotyping of real-time positive samples was attempted by direct sequencing of PCR amplicons using NP, VP1/2 and the newly developed VP/NC primers. HBoV-1 was present in 56.8% of the examined children. The newly developed primer set successfully amplified all real-time PCR positive samples, however, the other primer pairs did not reliably detect real-time PCR positive samples. The gene sequences of the detected HBoV-1 showed conserved sequences to each other with a low rate of discrepancies. The high rate of infection and the similarity between the detected strains strongly suggest nosocomial infections.

Acute human bocavirus infection in MDS patient, Cologne, Germany

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A clinical case of persisting and reactivated HBoV infection is described.

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HBoV can be detected in iliac crest in MDS patients.

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The current episode appears to be a reactivation of the HBoV-1 strain that was detected 5 years ago in a colorectal biopsy of the patient.

Persistent rhinovirus infection in pediatric hematopoietic stem cell transplant recipients with impaired cellular immunity

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Persistent rhinovirus infections are associated with impaired cellular immunity.

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The persistence of HRV infection is due to unrestricted replication of single virus strains rather than reinfections by different strains.

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The reconstitution of cell-mediated immunity might be crucial for complete virus clearance.

Background

HRV infections are generally self-limiting in healthy subjects, whereas in immunocompromised hosts HRV infections can lead to severe complications and persistent infections. The persistence of HRV shedding could be due to the inefficient immunological control of a single infectious episode.

Objectives

To investigate the clinical, virologic and immunologic characteristics of pediatric HSCT recipients with HRV-PI infection.

Study design

During the period 2006–2012, eight hematopoietic stem cell transplant (HSCT) recipients presented with persistent rhinovirus infection (HRV-PI, ≥30 days). Viral load and T-CD4⁺, T-CD8⁺, B and NK lymphocyte counts at the onset of infection were compared with those of fourteen HSCT recipients with acute HRV infection (HRV-AI, ≤15 days).

Results

The median duration of HRV positivity in patients with HRV-PI was 61 days (range 30–174 days) and phylogenetic analysis showed the persistence of a single HRV type in all patients (100%). In HSCT recipients with HRV-PI, T-CD4⁺, T-CD8⁺ and NK cell counts at the onset of infection were significantly lower than those observed in recipients with HRV-AI (p < 0.01), while B cell counts were similar in the two groups (p =  0.25). A decrease in HRV load was associated with a significant increase in T-CD4⁺, T-CD8⁺and NK lymphocyte counts in HRV-PI patients (p < 0.01).

Conclusions

This study suggests a role for cellular immunity in HRV clearance and highlights the importance of its recovery for the control of HRV infection in HSCT recipients.

Role of rhinovirus load in the upper respiratory tract and severity of symptoms in lung transplant recipients

BACKGROUND

Rhinovirus is the most common cause of respiratory viral infections and leads to frequent respiratory symptoms in lung transplant recipients. However, it remains unknown whether the rhinovirus load correlates with the severity of symptoms.

OBJECTIVES

This study aimed to better characterize the pathogenesis of rhinoviral infection and the way in which viral load correlates with symptoms.

STUDY DESIGN

We assessed rhinovirus load in positive upper respiratory specimens of patients enrolled prospectively in a cohort of 116 lung transplant recipients. Rhinovirus load was quantified according to a validated in-house, real-time, reverse transcription polymerase chain reaction in pooled nasopharyngeal and pharyngeal swabs. Symptoms were recorded in a standardised case report form completed at each screening/routine follow-up visit, or during any emergency visit occurring during the 3-year study.

RESULTS

Rhinovirus infections were very frequent, including in asymptomatic patients not seeking a specific medical consultation. Rhinovirus load ranged between 4.1 and 8.3 log copies/ml according to the type of visit and clinical presentation. Patients with highest symptom scores tended to have higher viral loads, particularly those presenting systemic symptoms. When considering symptoms individually, rhinovirus load was significantly higher in the presence of symptoms such as sore throat, fever, sputum production, cough, and fatigue. There was no association between tacrolimus levels and rhinovirus load.

CONCLUSIONS

Rhinovirus infections are very frequent in lung transplant recipients and rhinoviral load in the upper respiratory tract is relatively high even in asymptomatic patients. Patients with the highest symptom scores tend to have a higher rhinovirus load.

Utilization of the respiratory virus multiplex reverse transcription-polymerase chain reaction test for adult patients at a Korean tertiary care center

BACKGROUND/AIMS

Respiratory viruses (RVs) are considered to be important respiratory pathogens in adult patients, and the multiplex reverse transcription-polymerase chain reaction (RT-PCR) test is used frequently in adult patients with respiratory infections. However, clinical data regarding utilization of the multiplex RT-PCR test for RVs are lacking.

METHODS

We investigated the utilization of the multiplex RT-PCR test for RVs at Chung-Ang University Hospital in Seoul, Korea, between January 2012 and April 2013.

RESULTS

During the study period, the multiplex RT-PCR test was performed for 291 adult patients. The test frequency was 4.9% of rapid influenza antigen detection tests and 0.8% of respiratory bacterial culture studies. A turnaround time of < 48 hours was observed in 25.9% of positive tests. Most of the tests were performed for admitted patients (97.9%) with a community-acquired infection (84.2%) during the flu season (82.5%). RVs were detected in 81 of 291 cases (27.8%). The RV positivity rates for community- and hospital-acquired infections did not differ (28.6% vs. 23.9%, p = 0.52). Of 166 patients with pneumonia, 44 (26.5%) had a viral infection. Among the patients with RV-associated pneumonia, an RV other than influenza was detected in 20 patients (45.4%).

CONCLUSIONS

The multiplex RT-PCR test for RVs was infrequently performed at a tertiary care center, and the test results were often reported late. The test was most often performed for admitted adult patients with community-acquired infections during the flu season. The utilization of multiplex RT-PCR testing for RVs in current clinical practice should be improved.

Frequency of viral etiology in symptomatic adult upper respiratory tract infections

Aims

To determine the frequency of viral pathogens causing upper respiratory tract infections in non-hospitalized, symptomatic adults in the city of Rio de Janeiro.

Methods

Respiratory samples (nasal/throat swabs) were collected between August 2010 and November 2012 and real time PCR was used to detect different viral pathogens.

Results

Viruses were detected in 32.1% (43/134) of samples from 101 patients. Specifically, 9% (12/134) were positive for HBoV, 8.2% (11/134) were positive for HAdV, 5.2% (7/134) were positive for HRV, and 1.5% (2/134) were positive for FLUBV or HMPV, as single infections. HRSV-A, HPIV-3, and HCoV-HKU1 were detected in one (0.75%) sample each. Co-infections were detected in 4.8% (6/134) of the samples. Peaks of viral infections were observed in March, April, May, August, and October. However, positive samples were detected all year round. Only 23.3% (10/43) of the positive samples were collected from patients with febrile illness.

Conclusion

Results presented in this report suggest that respiratory viral infections are largely under diagnosed in immunocompetent adults. Although the majority of young adult infections are not life-threatening they may impose a significant burden, especially in developing countries since these individuals represent a large fraction of the working force.

Other respiratory viruses are important contributors to adult respiratory hospitalizations and mortality even during peak weeks of the influenza season

BACKGROUND

During peak weeks of seasonal influenza epidemics, severe respiratory infections without laboratory confirmation are typically attributed to influenza.

METHODS

In this prospective study, specimens and demographic and clinical data were collected from adults admitted with respiratory symptoms to 4 hospitals during the 8-10 peak weeks of 2 influenza seasons. Specimens were systematically tested for influenza and 13 other respiratory viruses (ORVs) by using the Luminex RVP FAST assay.

RESULTS

At least 1 respiratory virus was identified in 46% (21% influenza, 25% noninfluenza; 2% coinfection) of the 286 enrolled patients in 2011-2012 and in 62% (46% influenza, 16% noninfluenza; 3% coinfection) of the 396 enrolled patients in 2012-2013. Among patients aged ≥75 years, twice as many ORVs (32%) as influenza viruses (14%) were detected in 2011-2012. During both seasons, the most frequently detected ORVs were enteroviruses/rhinoviruses (7%), respiratory syncytial virus (6%), human metapneumovirus (5%), coronaviruses (4%), and parainfluenza viruses (2%). Disease severity was similar for influenza and ORVs during both seasons.

CONCLUSIONS

Although ORV contribution relative to influenza varies by age and season, during the peak weeks of certain influenza seasons, ORVs may be a more frequent cause of elderly hospitalization than influenza.

Therapeutic approach to respiratory infections in lung transplantation

Lung transplant recipients (LTRs) are at life-long risk for infections and disseminated diseases owing to their immunocompromised state. Besides organ failure and sepsis, infection can trigger acute and chronic graft rejection which increases mortality. Medical prophylaxis and treatment are based on comprehensive diagnostic work-up including previous history of infection and airway colonisation to reduce long-term complications and mortality. Common bacterial pathogens include Pseudomonas and Staphylococcus, whilst Aspergillus and Cytomegalovirus (CMV) are respectively the commonest fungal and viral pathogens. Clinical symptoms can be various in lung transplant recipients presenting an asymptomatic to severe progress. Regular control of infection parameters, daily lung function testing and lifelong follow-up in a specialist transplant centre are mandatory for early detection of bacterial, viral and fungal infections.

After transplantation each patient receives intensive training with rules of conduct concerning preventive behaviour and to recognize early signs of post transplant complications. Early detection of infection and complications are important goals to reduce major complications after lung transplantation.

Etiology and clinical outcomes of acute respiratory virus infection in hospitalized adults

BACKGROUND

Etiologies and clinical profiles of acute respiratory viral infections need to be clarified to improve preventive and therapeutic strategies.

MATERIALS AND METHODS

A retrospective observational study at a single, university-affiliated center was performed to evaluate the respiratory viral infection etiologies in children compared to that in adults and to document the clinical features of common viral infections for adults from July 2009 to April 2012.

RESULTS

The common viruses detected from children (2,800 total patients) were human rhinovirus (hRV) (31.8%), adenovirus (AdV) (19.2%), respiratory syncytial virus (RSV) A (17.4%), RSV B (11.7%), and human metapneumovirus (hMPV) (9.8%). In comparison, influenza virus A (IFA) had the highest isolation rate (28.5%), followed by hRV (15.5%), influenza virus B (IFB) (15.0%), and hMPV (14.0%), in adults (763 total patients). Multiple viruses were detected in single specimens from 22.4% of children and 2.0% of adults. IFA/IFB, RSV A/B, and hMPV exhibited strong seasonal detection and similar circulating patterns in children and adults. Adult patients showed different clinical manifestations according to causative viruses; nasal congestion and rhinorrhea were more common in hRV and human coronavirus (hCoV) infection. Patients with RSV B, hRV, or AdV tended to be younger, and those infected with RSV A and hMPV were likely to be older. Those with RSV A infection tended to stay longer in hospital, enter the intensive care unit more frequently, and have a fatal outcome more often. The bacterial co-detection rate was 26.5%, and those cases were more likely to have lower respiratory tract involvement (P = 0.001), longer hospital stay (P = 0.001), and higher mortality (P = 0.001).

CONCLUSIONS

The etiologic virus of an acute respiratory infection can be cautiously inferred based on a patient's age and clinical features and concurrent epidemic data. Large-scale prospective surveillance studies are required to provide more accurate information about respiratory viral infection etiology, which could favorably influence clinical outcomes.

Immunogenicity of recombinant human bocavirus-1,2 VP2 gene virus-like particles in mice

Human bocavirus (HBoV), a recently identified pathogen with a worldwide distribution is closely related to paediatric acute respiratory infection and gastroenteritis. The present study was performed to evaluate the immunogenicity of HBoV1 and HBoV2 virus-like particles (VLPs) as vaccine candidates in mice. Both HBoV1 and HBoV2 VLPs were expressed in the bacmid virus–SF9 cell system. Mice were inoculated three times at 3-week intervals with HBoV VLPs at one dose intramuscular (i.m.) or intradermal (i.d.) with or without the addition of the alum adjuvant. ELISA was used to detected antibody, and ELISPOT was used to test cellular immune responses. HBoV-specific IgG antibodies were induced and alum adjuvant improved the antibody titres and avidity, while the inoculation pathway had no influence. T helper type 1/ type 2 immune responses were balanced induced by HBoV1 VLPs but not HBoV2 VLPs. Serum IgG antibody cross-reactivity rates of the two subtypes were similar, but cross-reactions of HBoV1 immunization groups were higher. The single i.m. group had more interferon-γ-secreting splenocytes. These data indicate that HBoV VP2 VLPs have good immunogenicity with induction of strong humoral and cellular immune responses, and they may be potential candidate vaccines for HBoV infection.

Epidemiology of viral respiratory infections in a tertiary care centre in the era of molecular diagnosis, Geneva, Switzerland, 2011-2012

Few studies have examined the epidemiology of respiratory viral infections in large tertiary centres over more than one season in the era of molecular diagnosis. Respiratory clinical specimens received between 1 January 2011 and 31 December 2012 were analysed. Respiratory virus testing was performed using a large panel of real‐time PCR or RT‐PCR. Results were analysed according to sample type (upper versus lower respiratory tract) and age group. In all, 2996 (2469 (82.4%) upper; 527 (17.6%) lower) specimens were analysed. Overall positivity rate was 47.4% and 23.7% for upper and lower respiratory samples, respectively. The highest positivity rate was observed in patients under 18 years old (p <0.001); picornaviruses were the most frequent viruses detected over the year. Influenza virus, respiratory syncytial virus, human metapneumovirus and coronaviruses showed a seasonal peak during the winter season, while picornaviruses and adenoviruses were less frequently detected in these periods. Multiple viral infections were identified in 12% of positive cases and were significantly more frequent in children (p <0.001). In conclusion, we observed significant differences in viral infection rates and virus types among age groups, clinical sample types and seasons. Follow‐up of viral detection over several seasons allows a better understanding of respiratory viral epidemiology.

Epidemiology of respiratory viruses in bronchoalveolar lavage samples in a tertiary hospital

Background

The prevalence of respiratory viruses in adults is largely underexplored, as most studies focus on children. Additionally, in severely ill or immunocompromised adults, where respiratory infections are mostly attributed to bacteria and fungi; respiratory viruses can lead to severe complications.

Objectives

To evaluate the epidemiology of respiratory viruses in bronchoalveolar lavage fluid (BAL) specimens from patients with lower respiratory tract disease. The study population consisted of different groups including immunocompetent patients (control patients), solid organ transplant recipients, patients with haematological malignancies and other immunocompromised adults.

Study design

A total of 134 BAL fluid specimens collected during 2009–2011 were retrospectively assessed with the new commercial multiplex real-time PCR FTD Respiratory 21 Plus^®, targeting 18 different viruses and 2 atypical bacterial pathogens.

Results

Viral or atypical bacterial pathogens were detected in 29.1% of BAL fluid specimens. Coronaviruses were most prevalent (13.4%), followed by rhinoviruses (5.2%), RSV (4.5%) and bocaviruses (3.7%). Comparing the total number of viruses detected, a statistically significant difference was observed between the control group and patients with haematological malignancies (27.5% vs. 57.1%, p < 0.05).

Conclusion

In conclusion, our study highlights the high prevalence of respiratory viruses in BAL fluid specimens from adult patients with lower respiratory tract disease. The methods to be used should be sensitive and cover a wide range of potential pathogens. The specific patient population can also influence the detection rates of respiratory viruses.

Prolonged respiratory viral shedding in transplant patients

Respiratory viral infections are frequent causes of morbidity in transplant patients. We screened symptomatic adult transplant recipients for respiratory viruses in a cohort of patients attending a referral medical center in Brazil. The duration of viral shedding and the prevalence of viral codetections were also determined. During a 1‐year period (2011–2012), swabs were obtained from 50 patients. An in‐house polymerase chain reaction panel designed to detect 10 viruses was used. Viruses were identified in 19 (38%) patients, particularly parainfluenza III (32%) and the respiratory syncytial virus (20%); multiple viruses were identified in 26% of patients. Prolonged viral shedding was observed with 60% of individuals excreting viruses for >10 days. The clinical and epidemiologic relevance of prolonged viral shedding remains to be determined.