Changing epidemiology of respiratory viral infections in hematopoietic cell transplant recipients and solid organ transplant recipients

Evolving Epidemiology of Pediatric Respiratory Syncytial Virus (RSV) Cases Around COVID-19 Pandemic: Impact and Clinical Insights, Retrospective Cohort Study

BACKGROUND

The burden of respiratory syncytial virus (RSV) in high-risk pediatric patients remains unclear. Therefore, this study aims to characterize pediatric RSV cases from January 2019 to December 2022 and assess the impact of the COVID-19 pandemic on RSV burden and RSV-related outcomes. In addition, examining factors influencing RSV-related hospitalization.

METHODS

This is a retrospective study that included pediatric patients (aged 14 and below) who presented at King Faisal Specialist Hospital and Research Centre (KFSHRC) in Riyadh, Saudi Arabia with RSV infection identified using real-time reverse-transcriptase polymerase chain reaction assays. Statistical analyses were performed using STATA.

RESULTS

A total of 885 RSV cases were reported; (56.05%) were males and (43.95%) were females with a median age of 24 months [interquartile range (IQR): 11-60]. 534 (60.34%) required hospitalization. As for RSV seasonality, there was a significant increase in RSV prevalence following the COVID-19 pandemic, escalating from 205 cases in 2019 to 425 cases in 2022. The increase in 2022 was evident in January and persisted from September to December, reaching its peak during the months of October (20.70% - 88 cases) and November (32.00% - 136 cases). About (27.12%) of RSV infected children were medically free patients. Symptomatic patients exhibited various clinical manifestations, with ventilation necessary in (13.11%) of cases. Further analysis revealed significant changes in RSV-related outcomes post-COVID-19, including a decrease in hospitalization rates, an increase in medically free patients, and a lower need for ventilation (p < 0.05). Notably, a significant proportion of RSV admissions occurred within the first 6 months of life, with (77.69%) in the age group of 0 to 5 months. In addition, previous RSV infection, prematurity, low birth weight, renal disease, congenital heart disease, endocrine/metabolic disease, neuro/neuromuscular diseases, and genetic disorders were positively associated with hospitalization (P < 0.05). Interestingly, asthma and bone marrow transplantation were negatively associated with hospitalization (P < 0.05). The mortality rate in this study is (2.37%) (21/885).

CONCLUSION

This study provides a comprehensive understanding of the demographic and clinical factors influencing RSV outcomes, highlighting the impact of the COVID-19 pandemic and shedding light on potential risk factors for RSV-related hospitalization. The highest prevalence of RSV during (September to January), aligning with global patterns and emphasizing the importance of timing in preventive strategies.

Epidemiological and clinical characteristics of hospitalized human metapneumovirus patients in Israel, 2015-2021: A retrospective cohort study

This study evaluated the epidemiological and clinical characteristics of human metapneumovirus (hMPV) infection among hospitalized patients with acute respiratory infections during 2015-2021 and assessed the impact of the coronavirus disease 2019 pandemic on hMPV infection. A single-center, retrospective cohort study was performed, including pediatric and adult patients with laboratory-confirmed hMPV. Of a total of 990 patients, 253 (25.6%), 105 (10.6%), 121 (12.2%), and 511 (51.6%) belonged to age groups 0-2, 3-17, 18-59, and ≥60 years, respectively. The highest percentage (23.0%) of patients were hospitalized during 2019 and the lowest (4.7%) during 2020. Patients < 18 years experienced high rates of comorbidities (immunodeficiencies: 14.4% and malignancies: 29.9%). Here, 37/39 (94.9%) of all bronchiolitis cases were diagnosed in patients < 2 years, whereas more patients in older age groups were diagnosed with pneumonia. A greater proportion of hMPV patients diagnosed with viral coinfection (mostly respiratory syncytial virus and adenovirus) were <18 years. The highest percentages of intensive care unit admissions were recorded among patients < 18 years. Our findings demonstrate that hMPV is an important cause of morbidity in young children and a possibly underestimated cause of morbidity among older adults.

Outcome of Human Parainfluenza Virus infection in allogeneic stem cell transplantation recipients: possible impact of ribavirin therapy

BACKGROUND

This retrospective study focused on analyzing community-acquired respiratory virus (CARV) infections, in particular human parainfluenza virus (hPIV) after allogeneic stem cell transplant (allo-SCT) in adults recipients. It aimed to assess the impact of ribavirin treatment, clinical characteristics, and risk factors associated with lower respiratory tract disease (LRTD) progression and all-cause mortality.

PATIENTS AND METHODS

The study included 230 allo-SCT recipients diagnosed with hPIV between December 2013 and June 2023. Risk factors for the development of LRTD, disease severity, and mortality were analyzed. Ribavirin treatment was administered at physician discretion in 61 out of 230 cases (27%).

RESULTS

Risk factors for LRTD progression in multivariate analysis were corticosteroids > 30 mg/day (Odds ratio (OR) 3.5, 95% Confidence Interval (C.I.) 1.3-9.4, p = 0.013), fever at the time of hPIV detection (OR 3.89, 95% C.I. 1.84-8.2, p < 0.001), and absolute lymphocyte count (ALC) < 0.2 × 109/L (OR 4.1, 95% C.I. 1.42-11.9, p = 0.009). In addition, the study found that ribavirin therapy significantly reduced progression to LRTD [OR 0.19, 95% C.I. 0.05-0.75, p = 0.018]. Co-infections (OR 5.7, 95% C.I. 1.4-23.5, p = 0.015) and ALC < 0.2 × 109/L (OR 17.7, 95% C.I. 3.6-87.1, p < 0.001) were independently associated with higher day + 100 after hPIV detection all-cause mortality. There were no significant differences in all-cause mortality and infectious mortality at day + 100 between the treated and untreated groups.

CONCLUSION

ALC, corticosteroids, and fever increased the risk for progression to LRTD while ribavirin decreased the risk. However, mortality was associated with ALC and co-infections. This study supports further research of ribavirin therapy for hPIV in the allo-HSCT setting.

Efficacy and safety of withholding antimicrobial therapy in children with cancer, fever, and neutropenia, with a demonstrated viral respiratory infection: a randomized clinical trial

OBJECTIVES

To validate the efficacy and safety of withholding antimicrobial therapy in a new cohort of children with cancer and febrile neutropenia (FN) having a demonstrated viral respiratory tract infection.

METHODS

Prospective, multicenter, noninferiority, randomized study, approved by the ethical committee, in children presenting with FN at seven hospitals in Chile, evaluated at admission for diagnosis of bacterial and viral pathogens. Children who were positive for a respiratory virus, negative for a bacterial pathogen, and had a favourable evolution after 48-72 hours of antimicrobial therapy were randomized to either maintain or withhold antimicrobial therapy. The primary endpoint was the percentage of episodes with an uneventful resolution, whereas the secondary endpoints were days of fever, days of hospitalization, requirement of antimicrobial treatment readministration, sepsis, paediatric intensive care unit admission, and death.

RESULTS

A total of 301 of 939 children with FN episodes recruited between March 2021 and December 2023 had a respiratory virus as a unique identified microorganism, of which 139 had a favourable evolution at 48-72 hours and were randomized, 70 to maintain and 69 to withdraw antimicrobial therapy. The median days of antimicrobial therapy was 5 (IQR 3-6) versus 3 (IQR 3-6) days (p < 0.001), with similar frequency of uneventful resolution 66/70 (94%) and 66/69 (96%); relative risk, 1.01; (95% CI, 0.93 to 1.09), absolute risk difference 0.01; (95% CI, -0.05 to 0.08) and similar number of days of fever and days of hospitalization. No cases of sepsis, paediatric intensive care unit admission, or death were reported.

DISCUSSION

We validated the strategy of withdrawal antimicrobial therapy in children with FN and viral respiratory tract infection based on clinical and microbiological/molecular diagnostic criteria. This will enable advances in antimicrobial stewardship strategies with a possible future impact on antimicrobial resistance.

Upper and/or Lower Respiratory Tract Infection Caused by Human Metapneumovirus After Allogeneic Hematopoietic Stem Cell Transplantation

BACKGROUND

Human metapneumovirus (hMPV) epidemiology, clinical characteristics and risk factors for poor outcome after allogeneic stem cell transplantation (allo-HCT) remain a poorly investigated area.

METHODS

This retrospective multicenter cohort study examined the epidemiology, clinical characteristics, and risk factors for poor outcomes associated with human metapneumovirus (hMPV) infections in recipients of allo-HCT.

RESULTS

We included 428 allo-HCT recipients who developed 438 hMPV infection episodes between January 2012 and January 2019. Most recipients were adults (93%). hMPV infections were diagnosed at a median of 373 days after allo-HCT. The infections were categorized as upper respiratory tract disease (URTD) or lower respiratory tract disease (LRTD), with 60% and 40% of cases, respectively. Patients with hMPV LRTD experienced the infection earlier in the transplant course and had higher rates of lymphopenia, neutropenia, corticosteroid use, and ribavirin therapy. Multivariate analysis identified lymphopenia and corticosteroid use (>30 mg/d) as independent risk factors for LRTD occurrence. The overall mortality at day 30 after hMPV detection was 2% for URTD, 12% for possible LRTD, and 21% for proven LRTD. Lymphopenia was the only independent risk factor associated with day 30 mortality in LRTD cases.

CONCLUSIONS

These findings highlight the significance of lymphopenia and corticosteroid use in the development and severity of hMPV infections after allo-HCT, with lymphopenia being a predictor of higher mortality in LRTD cases.

Outcome of Respiratory Viral Infections in Hematopoietic Stem Cell Transplant Recipients

BACKGROUND

Respiratory viral infections (RVIs) commonly cause morbidity and mortality in hematopoietic stem cell transplant (HSCT) recipients. This study aimed at the prevalence of RVIs in adult HSCT recipients and their outcomes.

METHODS

A retrospective observational cohort study was conducted on all adult patients who underwent HSCT in the period between January 2016 and December 2020. Data were retrospectively abstracted from electronic medical records from a total of 400 patients. All cases with polymerase chain reaction-confirmed RVIs based on real-time reverse transcription polymerase chain reaction were included in the data analysis.

RESULT

A total of 79 patients had positive results. Sixty-three patients had allogeneic stem cell transplants. Women were 53% of the patients, and the mean age was 32 years (±13.5). The prevalence of documented respiratory virus infections was around 20% during the 4 years of the study. The most common virus was rhinovirus (60.76%), followed by respiratory syncytial virus (15.19%), then parainfluenza (11.39%). Among the 9 patients (11%) who required intensive care unit admission, 67% had lymphopenia (P = .03), 71% had abnormal chest computed tomography scan with pleural effusion (P = .03), 22% required renal support (P = .057), and 2 patients (22%) died (P = .057).

CONCLUSIONS

The study highlights the associated morbidity and mortality with RVIs among HSCT recipients and the need for more preventive measures and treatment studies.

Evaluation of pulmonary abnormalities in recipients of hematopoietic cell transplants and cellular therapies

Hematopoietic cell transplant (HCT) and chimeric antigen receptor T-cell (CAR-T) therapy recipients are susceptible to multiple pulmonary complications that are caused by infectious and noninfectious processes. Numerous variables can be associated with specific pulmonary diseases including time from transplantation, presence of graft versus host disease (GVHD), underlying disease, and prolonged neutropenia and lymphocytopenia. Most pulmonary complications are infectious in origin, with bacterial pneumonia remaining the most common pulmonary infection, particularly before neutrophil engraftment. Invasive fungal infections continue to affect this patient population even when antifungal prophylaxis is used. Noninfectious pulmonary complications include a wide differential of pathologies in this population, and as clinical presentations of these various pulmonary disorders often overlap, clinicians frequently will use a multidisciplinary approach in diagnosing these abnormalities. Radiography, particularly with chest computed tomography (CT) imaging, is an essential tool in identifying pulmonary pathology and potential sources. While standard microbiological cultures of respiratory specimens are still utilized, their role is limited by low sensitivity and diagnostic yield. The likelihood of obtaining a diagnosis can be improved by using other microbiological assays, including fungal antigen tests and molecular diagnostic methods, particularly if specimens are collected via bronchoscopy. This review will highlight the more common causes of pulmonary diseases encountered after HCT and CAR-T and will examine the different methods in their diagnosis.

Respiratory virus infections after allogeneic stem cell transplantation: Current understanding, knowledge gaps, and recent advances

Before the COVID-19 pandemic, common community-acquired seasonal respiratory viruses (CARVs) were a significant threat to the health and well-being of allogeneic hematopoietic cell transplant (allo-HCT) recipients, often resulting in severe illness and even death. The pandemic has further highlighted the significant risk that immunosuppressed patients, including allo-HCT recipients, face when infected with SARS-CoV-2. As preventive transmission measures are relaxed and CARVs circulate again among the community, including in allo-HSCT recipients, it is crucial to understand the current state of knowledge, gaps, and recent advances regarding CARV infection in allo-HCT recipients. Urgent research is needed to identify seasonal respiratory viruses as potential drivers for future pandemics.

In-vivo and human evidence for potential efficacy of therapeutic polyclonal RSV neutralizing antibodies for palivizumab-resistant RSV infections

BACKGROUND

Monoclonal antibody (palivizumab), intravenous immune globulin (IGIV), or respiratory syncytial virus (RSV)-polyclonal-hyperimmune-globulin (RSV-IG as Respigam®, RI-001, RI-002) are used with ribavirin in RSV-infected immunocompromised patients, with debated efficacy. Palivizumab-resistance (PR) can arise during treatment of persistent infections in this population. RSV-IG may confer benefit in PR-RSV infection.

METHODS

RSV-IG [RI-001] was provided for an immunocompromised infant with RSV-pneumonitis refractory to ribavirin and palivizumab. RSV-neutralizing antibody, respiratory RSV load (qPCR), and F-gene-sequence-detection of PR was determined. Prophylactic RSV-IG [RI-002] or palivizumab was administered in a cotton-rat model infected with wild-type and PR-RSV. Lung RSV load and neutralizing antibody were measured.

RESULTS

As protective RI-001-neutralizing antibody titers waned in the infant, a subpopulation of PR-escape mutants were detected with a fatal RSV-burden in the lungs. In PR-RSV-infected cotton rats, prophylactic RI-002 reduced RSV-load in the lungs (2.45 vs 0.28 log10 PFU/g lung-tissue reduction, respectively, p < 0.05) and provided protective RSV-neutralizing antibody.

CONCLUSIONS

RSV-IG and ribavirin use in immunocompromised patients requires further study.

Respiratory Syncytial Virus-An Update for Prenatal and Primary Health Providers

Respiratory syncytial virus (RSV) infection is a significant cause of morbidity and mortality among infants aged younger than 1 year, adults aged 65 years or older, and immunocompromised persons. Limited data exist on RSV infection in pregnancy and further research is needed. Strides are being made to develop vaccines, including vaccines for maternal immunization, as well as monoclonal antibodies for disease prevention.

Phylogenetic analysis of HA and NA genes of influenza A viruses in immunosuppressed inpatients in Beijing during the 2018-2020 influenza seasons

BACKGROUND

Influenza A viruses have undergone rapid evolution with virulent; however, complete and comprehensive data on gene evolution and amino acid variation of HA and NA in immunosuppressed patients was few. In this study, we analysed molecular epidemiology and evolution of influenza A viruses in immunosuppressed population, and immunocompetent population were used as controls.

METHODS

Full sequences of HA and NA of A(H1N1)pdm09 and A(H3N2) were acquired through reverse transcription-polymerase chain reaction (RT-PCR). HA and NA genes were sequenced using the Sanger method and phylogenetically analysed using ClustalW 2.10 and MEGA software version 11.0.

RESULTS

During the 2018-2020 influenza seasons, 54 immunosuppressed and 46 immunocompetent inpatients screened positive for influenza A viruses by using the quantitative real-time PCR (qRT-PCR) were enrolled. 27 immunosuppressed and 23 immunocompetent nasal swab or bronchoalveolar lavage fluid samples were randomly selected and sequenced using the Sanger method. A(H1N1)pdm09 were detected in 15 samples and the remaining 35 samples were A(H3N2) positive. By analyzing the HA and NA gene sequences of these virus strains, we found that all A(H1N1)pdm09 viruses shared high similarities to each other and the HA and NA genes of these viruses exclusively belonged to subclade 6B.1A.1. Some NA genes of A(H3N2) viruses were not in the same clade as those of A/Singapore/INFIMH-16-0019/2016 and A/Kansas/14/2017, which may have led to A(H3N2) being the dominant strain in the 2019-2020 influenza season. Both A(H1N1)pdm09 and A(H3N2) viruses showed similar evolutionary lineages patterns of HA and NA between immunosuppressed and immunocompetent patients. Compared with the vaccine strains, there were no statistically significant of HA and NA genes and amino acid sequences of influenza A viruses in immunosuppressed and immunocompetent patients. However, the oseltamivir resistance substitution of NA-H275Y and R292K have been observed in immunosuppressed patients.

CONCLUSIONS

A(H1N1)pdm09 and A(H3N2) viruses showed similar evolutionary lineages patterns of HA and NA between immunosuppressed and immunocompetent patients. Both immunocompetent and immunosuppressed patients have some key substitutions, which should be of note monitored, especially those with potential to affect the viral antigen.

Human Metapneumovirus (hMPV) Infection and MPV467 Treatment in Immunocompromised Cotton Rats Sigmodon hispidus

Human metapneumovirus (hMPV) is an important cause of respiratory disease in immunocompromised individuals, yet hMPV infection has not been modeled before in immunocompromised animals. In this work, cotton rats S. hispidus immunosuppressed by cyclophosphamide were infected with hMPV, and viral replication and pulmonary inflammation in these animals were compared to those in normal hMPV-infected S. hispidus. The efficacy of prophylactic and therapeutic administration of the anti-hMPV antibody MPV467 was also evaluated. Immunosuppressed animals had higher pulmonary and nasal titers of hMPV on day 5 post-infection compared to normal animals, and large amounts of hMPV were still present in the respiratory tract of immunosuppressed animals on days 7 and 9 post-infection, indicating prolonged viral replication. Immunosuppression was accompanied by reduced pulmonary histopathology in hMPV-infected cotton rats compared to normal animals; however, a delayed increase in pathology and pulmonary chemokine expression was seen in immunosuppressed cotton rats. Prophylactic and therapeutic MPV467 treatments protected both upper and lower respiratory tracts against hMPV infection. The lung pathology and pulmonary expression of IP-10 and MIP-1α mRNA were reduced by therapeutic MPV467 administration. These results indicate that immunosuppressed cotton rats represent a useful model for studying hMPV pathogenesis and for evaluating therapeutics that could alleviate hMPV-induced disease in immunocompromised subjects.

Clinical value of metagenomic next-generation sequencing by Illumina and Nanopore for the detection of pathogens in bronchoalveolar lavage fluid in suspected community-acquired pneumonia patients

At present, metagenomic next-generation sequencing (mNGS) based on Illumina platform has been widely reported for pathogen detection. There are few studies on the diagnosis of major pathogens and treatment regulation using mNGS based on Illumina versus Nanopore. We aim to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) by Illumina and Nanopore for the detection of pathogens in bronchoalveolar lavage fluid (BALF) in suspected community-acquired pneumonia (CAP) patients. BALF samples collected from 66 suspected CAP patients within 48 hours of hospitalization were divided into two parts, one for conventional culture and the other for mNGS by two platforms (Illumina and Nanopore). The clinical value based on infection diagnosis, diagnostic performance for main pathogens and treatment guidance were assessed. More types of species were detected by Nanopore than Illumina, especially in viruses, fungus and mycobacterium. Illumina and Nanopore showed similar detectability in bacterium except for mycobacterium tuberculosis complex/nontuberculosis mycobacteria. Pathogenic infection was established or excluded in 53 of 66 patients. There was little difference in the coincidence rate between Illumina and Nanopore with the clinical diagnosis, but both were superior to the culture (57.81%, 59.38%, 25%, respectively). Compared with Illumina, the diagnostic area under the curve of Nanopore was higher in fungi, but lower in bacteria and Chlamydia psittaci. There was no statistically significant difference between Illumina and Nanopore in guiding drug treatment (56.1% vs. 50%, p=0.43), but both were superior to the culture (56.1% vs. 28.8%, p=0.01; 50% vs. 28.8%, p=0.01). Single inflammatory indicators could not be used to determine whether the patients with culture-negative BALF were established or excluded from infection. The species detected at 1 h and 4 h by Nanopore were consistent to some extent, and its turn-around time (TAT) was significantly shorter than Illumina (p<0.01). Illumina and Nanopore both have its own advantages in pathogenic diagnosis and play similar roles in infection diagnosis and guiding clinical treatment. Nanopore has a relatively short TAT, which may be promising in rapid etiological diagnosis of acute and critically ill patients.

Metagenomic Next-Generation Sequencing Successfully Detects Pulmonary Infectious Pathogens in Children With Hematologic Malignancy

Background

Pulmonary infection is a leading cause of mortality in pediatric patients with hematologic malignancy (HM). In clinical settings, pulmonary pathogens are frequently undetectable, and empiric therapies may be costly, ineffective and lead to poor outcomes in this vulnerable population. Metagenomic next-generation sequencing (mNGS) enhances pathogen detection, but data on its application in pediatric patients with HM and pulmonary infections are scarce.

Methods

We retrospectively reviewed 55 pediatric patients with HM and pulmonary infection who were performed mNGS on bronchoalveolar lavage fluid from January 2020 to October 2021. The performances of mNGS methods and conventional microbiological methods in pathogenic diagnosis and subsequently antibiotic adjustment were investigated.

Results

A definite or probable microbial etiology of pulmonary infection was established for 50 of the 55 patients (90.9%) when mNGS was combined with conventional microbiological tests. The positive rate was 87.3% (48 of 55 patients) for mNGS versus 34.5% (19 of 55 patients) with conventional microbiological methods (P < 0.001). Bacteria, viruses and fungi were detected in 17/55 (30.9%), 25/55 (45.5%) and 19/55 (34.5%) cases using mNGS, respectively. Furthermore, 17 patients (30.9%) were identified as pulmonary mixed infections. Among the 50 pathogen-positive cases, 38% (19/50) were not completely pathogen-covered by empirical antibiotics and all of them were accordingly made an antibiotic adjustment. In the present study, the 30-day mortality rate was 7.3%.

Conclusion

mNGS is a valuable diagnostic tool to determine the etiology and appropriate treatment in pediatric patients with HM and pulmonary infection. In these vulnerable children with HM, pulmonary infections are life-threatening, so we recommend that mNGS should be considered as a front-line diagnostic test.

Economic and clinical burden associated with respiratory viral infections after allogeneic hematopoietic cell transplant in the United States

Background

Methods

Results

Conclusion

When Viruses Meet Fungi: Tackling the Enemies in Hematology

The association of invasive fungal infections (IFI) and viral infections has been described in patients with hematologic malignancies (HM), in particular in hematopoietic stem cell transplant recipients. Regrettably, the diagnosis is often challenging, making the treatment inappropriate in some circumstances. The present review takes into consideration the viral infections commonly associated with IFI. Clinical presentation of IFI and viral infections, risk factors, and impact on the outcome of HM patients are discussed throughout the paper.

Clinical characteristics, risk factors and antiviral treatments of influenza in immunosuppressed inpatients in Beijing during the 2015-2020 influenza seasons

BACKGROUND

Compared with immunocompetent patients, immunosuppressed patients have higher morbidity and mortality, a longer duration of viral shedding, more frequent complications, and more antiviral resistance during influenza infections. However, few data on this population in China have been reported. We analysed the clinical characteristics, effects of antiviral therapy, and risk factors for admission to the intensive care unit (ICU) and death in this population after influenza infections and explored the influenza vaccination situation for this population.

METHODS

We analysed 111 immunosuppressed inpatients who were infected with influenza virus during the 2015-2020 influenza seasons. Medical data were collected through the electronic medical record system and analysed. Univariate analysis and multivariate logistics analysis were used to identify risk factors.

RESULTS

The most common cause of immunosuppression was malignancies being treated with chemotherapy (64.0%, 71/111), followed by haematopoietic stem cell transplantation (HSCT) (23.4%, 26/111). The most common presenting symptoms were fever and cough. Dyspnoea, gastrointestinal symptoms and altered mental status were more common in HSCT patients than in patients with immunosuppression due to other causes. Approximately 14.4% (16/111) of patients were admitted to the ICU, and 9.9% (11/111) of patients died. Combined and double doses of neuraminidase inhibitors did not significantly reduce the risk of admission to the ICU or death. Risk factors for admission to the ICU were dyspnoea, coinfection with other pathogens and no antiviral treatment within 48 h. The presence of dyspnoea and altered mental status were independently associated with death. Only 2.7% (3/111) of patients less than 12 months old had received a seasonal influenza vaccine.

CONCLUSION

Fever and other classic symptoms of influenza may be absent in immunosuppressed recipients, especially in HSCT patients. Conducting influenza virus detection at the first presentation seems to be a good choice for early diagnosis. Clinicians should pay extra attention to immunosuppressed patients with dyspnoea, altered mental status, coinfection with other pathogens and no antiviral treatment within 48 h because these patients have a high risk of severe illness. Inactivated influenza vaccines are recommended for immunosuppressed patients.

Short-term experiences of a liver transplant centre before and after the COVID-19 pandemic

BACKGROUND/AIM

With the COVID-19 pandemic, managing the process of solid organ transplantation has become a significant matter for transplant centres. In this study, we report our experiences on evaluating the effects of COVID-19 in patients with recent liver transplants.

MATERIALS AND METHODS

We evaluated patients who received liver transplants during three close consecutive periods of time. For transplants conducted between October 1 and December 31, 2019, January 1 and March 10, 2020 and March 11 and June 22, 2020, the lung tomographies of patients were inspected for radiological signs of viral pneumonia. For patients after March 11, 2020, the hospital's electronic database system was scanned for preoperative and postoperative SARS-CoV-2 testing from Real-time Polymerase Chain Reaction (RT-PCR) of the respiratory tract samples.

RESULTS

A total of 149 patients over the age of 18 who received liver transplants at our centre between October 1, 2019 and June 22, 2020 were evaluated. During this time span, our centre conducted liver transplants on patients from 34 different provinces and also abroad. Within this time period, a total of nine patients had respiratory samples with a positive SARS-CoV-2 RT-PCR test. PCR of respiratory tract samples was performed in 21 (14%) patients to identify the other potential infective agents in the respiratory tracts; Rhinovirus and Influenza A were detected in two and respiratory syncytial virus (RSV) was detected in one patient. During the transplant periods, 99 (67.1%) patients were evaluated with computed tomography (CT). The CT findings of 18 (12%) patients were consistent with viral pneumonia. There was a statistically significant difference between the groups only in terms of air bronchogram findings (P = .012).

CONCLUSION

The clinical status of our short-term liver transplant patients was far better than we originally anticipated, but it remains obvious that the necessary precautions should continue to be taken.

Impact of Influenza Infection Among Adult and Pediatric Populations With Hematologic Malignancy and Hematopoietic Stem Cell Transplant: A Systematic Review and Meta-Analysis

PURPOSE

Influenza is increasingly recognized as a leading cause of morbidity and mortality in patients with hematologic malignancies and recipients of hematopoietic stem cell transplantation (HSCT). However, the impact of influenza on this population has not been previously evaluated in a systematic review. This study systematically reviewed and summarized the outcomes of influenza infection as to in-hospital influenza-related mortality, development of lower respiratory tract infection and acute respiratory distress syndrome, need for hospitalization, intensive care unit admission, and mechanical ventilation.

METHODS

We conducted a systematic search of literature using the PubMed and EMBASE databases for articles published from January 1989 through January 19, 2020, reporting laboratory-confirmed influenza in patients of any age with hematologic malignancies and HSCT. Time from transplantation was not included in the search criteria. The impact of antiviral therapy on influenza outcomes was not assessed due to heterogeneity in antiviral treatment provision across the studies. Patients with influenza-like illness, solid-tumor cancers, or nonmalignant hematologic diseases were excluded from the study. A random-effects meta-analysis was performed to estimate the prevalences and 95% CIs of each outcome of interest. A subgroup analysis was carried out to assess possible sources of heterogeneity and to evaluate the potential impact of age on the influenza infection outcomes. Heterogeneity was assessed using the I² statistic.

FINDINGS

Data from 52 studies providing data on 1787 patients were included in this analysis. During seasonal epidemics, influenza-related in-hospital mortality was 16.60% (95% CI, 7.49%-27.7%), with a significantly higher death rate in adults compared to pediatric patients (19.55% [95% CI, 10.59%-29.97%] vs 0.96% [95% CI, 0%-6.77%]; P < 0.001). Complications from influenza, such as lower respiratory tract infection, developed in 35.44% of patients with hematologic malignancies and HSCT recipients, with a statistically significant difference between adults and children (46.14% vs 19.92%; P < 0.001). However, infection resulted in a higher hospital admission rate in pediatric patients compared to adults (61.62% vs 22.48%; P < 0.001). For the 2009 H1N1 pandemic, no statistically significant differences were found between adult and pediatric patients when comparing the rates of influenza-related in-hospital mortality, lower respiratory tract infection, and hospital admission. Similarly, no significant differences were noted in any of the outcomes of interest when comparing H1N1 pandemic with seasonal epidemics.

IMPLICATIONS

Regardless of influenza season, patients, and especially adults, with underlying hematologic malignancies and HSCT recipients with influenza are at risk for severe outcomes including lower respiratory tract infection and in-hospital mortality.

Design and evaluation of Taqman low density array for monitoring post-transplant viral infections

BACKGROUND

The majority of transplant recipients undergo immunosuppressive treatment to prevent organ or tissue rejection. Consequently, they are more susceptible to infection agents including a number of viruses causing a significant morbidity and mortality. Only a limited number of viruses are currently tested for in transplant donors and recipients due to the cost and complexity. Taqman low density array (TLDA) may provide a suitable format to address more systematic testing approach.

METHODS

One hundred and one liver transplant recipient samples were retrospectively tested for 48 viral targets including two controls (bovine viral diarrhea virus and MS2) and two common viruses (TTV and HPgV), using a custom designed TLDA. Eight samples were analysed simultaneously on 384-well TLDA. Samples giving a signal considered positive/indeterminant were re-tested by different individual confirmatory assays.

RESULTS

Infections with six previously untested for viruses-EBV, HPIV3, HuPuV9, KIV, HMPV and HPV-were detected in fourteen patients. Previously detected HCV infections were also confirmed. These infections did not seem have an effect on 5 year post-transplant outcome. 55 of 79 and 17 of 87 samples available for confirmatory assays were positive for TTV and HPgV, included for the evaluation of the TLDA performance.

CONCLUSIONS

The custom viral TLDA can be successfully used for simultaneous detection of a range of post-transplant viral infections. To fully exploit its potential for monitoring and intervention, a whole blood testing should be applied in a prospective setting.

Nasal Wash Cytokines during Respiratory Viral Infection in Pediatric Allogeneic Hematopoietic Cell-Transplant Recipients

Allogeneic hematopoietic cell-transplant (alloHCT) recipients are at increased risk of complications from viral respiratory-tract infections (vRTIs). We measured cytokine concentrations in nasal washes (NWs) from pediatric alloHCT recipients to better understand their local response to vRTI. Forty-one immunologic analytes were measured in 70 NWs, collected during and after vRTI, from 15 alloHCT recipients (median age, 11 yr) with 19 episodes of vRTI. These were compared with NW cytokine concentrations from an independent group of otherwise healthy patients. AlloHCT recipients are able to produce a local response to vRTI and produce IFN-α2 and IL-12p40 in significant quantities above an uninfected baseline early in infection. Compared with otherwise healthy comparator-group patients, alloHCT recipients have higher NW concentrations of IL-4 when challenged with vRTI. Further study of these immunologic analytes as well as of type 1 versus type 2 balance in the respiratory mucosa in the context of vRTI during immune reconstitution may be of future research interest in this vulnerable patient population.

The COVID-19 pandemic: A community approach

An unprecedented global pandemic caused by a novel coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS‐CoV‐2) has quickly overwhelmed the health care systems worldwide. While there is an absence of consensus among the community in how to manage solid organ transplant recipients and donors, a platform provided by the American Society of Transplantation online community “Outstanding Questions in Transplantation,” hosted a collaborative multicenter, multinational discussions to share knowledge in a rapidly evolving global situation. Here, we present a summary of the discussion in addition to the latest published literature.

Antigenic Fingerprinting of Respiratory Syncytial Virus (RSV)-A-Infected Hematopoietic Cell Transplant Recipients Reveals Importance of Mucosal Anti-RSV G Antibodies in Control of RSV Infection in Humans

BACKGROUND

Respiratory syncytial virus (RSV) infection causes significant morbidity in hematopoietic cell transplant (HCT) recipients. However, antibody responses that correlate with recovery from RSV disease are not fully understood.

METHODS

In this study, antibody repertoire in paired serum and nasal wash samples from acutely RSV-A-infected HCT recipients who recovered early (<14 days of RSV shedding) were compared with late-recovered patients (≥14 days of shedding) using gene fragment phage display libraries and surface plasmon resonance.

RESULTS

Anti-F serum responses were similar between these 2 groups for antibody repertoires, neutralization titers, anti-F binding antibodies (prefusion and postfusion proteins), antibody avidity, and binding to specific antigenic sites. In contrast, nasal washes from early-recovered individuals demonstrated higher binding to F peptide containing p27. While the serum RSV G antibody repertoires in the 2 groups were similar, the strongest difference between early-recovered and late-recovered patients was observed in the titers of nasal wash antibodies, especially binding to the central conserved domain. Most importantly, a significantly higher antibody affinity to RSV G was observed in nasal washes from early-recovered individuals compared with late-recovered HCT recipients.

CONCLUSIONS

These findings highlight the importance of mucosal antibodies in resolution of RSV-A infection in the upper respiratory tract.

Viral Respiratory Infections in Hematological Patients

Viral infections of the respiratory system represent one of the most important complications in hematological patients in terms of both the severity of the clinical picture and its related impact on the duration of hospitalization, and of mortality. The most implicated viruses are those that commonly cause community-based respiratory diseases: respiratory syncytial virus, Influenza virus and rhinovirus. However, in some cases the clinical picture may be triggered by first infection with or reactivation of pathogens normally not responsible for clinically relevant diseases in immunocompetent subjects. This issue is currently being taken into greater consideration within the scientific community. However, the strong heterogeneity in the epidemiology and clinical expression of these infections and the lack of adequate therapeutic options imply that there is currently no uniform consensus on the best management of these patients. The main purpose of this review is to highlight which viruses are currently most implicated in the onset of these infections, what is their incidence in so heterogeneous and fragile patients and the factors that lead to disease's onset and evolution. Possible or available clinical management options, diagnostic and therapeutic tools, and preventive and prophylaxis measures are also discussed.

Clinical course and risk factors for mortality from COVID-19 in patients with haematological malignancies

BACKGROUND

The impact of coronavirus disease 2019 (COVID-19) in haematological patients (HP) has not been comprehensively reported.

METHODS

We analysed 39 patients with SARS-CoV-2 infection and haematological malignancies. Clinical characteristics and outcomes were compared to a matched control group of 53 non-cancer patients with COVID-19. Univariate and multivariate analyses were carried out to assess the risk factors associated with poor outcome.

RESULTS

The most frequent haematological diseases were lymphoma (30%) and multiple myeloma (30%). Eighty-seven % HP developed moderate or severe disease. Patients with haematological malignancies had a significantly higher mortality rate compared to non-cancer patients (35.9% vs 13.2%; P = .003 (odds ratio 6.652). The worst outcome was observed in chronic lymphocytic leukaemia patients. Only age >70 years and C reactive protein >10 mg/dl at admission were associated with higher risk of death (odds ratio 34.86, P = .003 and 13.56,P = .03). Persistent viral sheddind was detected in 5 HP. Active chemotherapy, viral load at diagnosis and COVID-19 therapy were not predictors of outcome.

CONCLUSION

Mortality of COVID-19 is significantly higher in patients with haematological malignancies compared to non-cancer patients. The impact of persistent viral shedding must be considered in order to re-start therapies and maintain infectious control measures.

Community acquired respiratory virus infections in adult patients undergoing umbilical cord blood transplantation

Characteristics and risk factors (RFs) of community-acquired respiratory virus (CARV) infections after umbilical cord blood transplantation (UCBT) are lacking. We retrospectively analyzed CARV infections in 216 single-unit myeloablative UCBT recipients. One-hundred and fourteen episodes of CARV infections were diagnosed in 62 (29%) patients. Upper respiratory tract disease (URTD) occurred in 61 (54%) whereas lower respiratory tract disease (LRTD) in 53 (46%). The 5-year cumulative incidence of CARV infection was 29%. RFs for developing CARV infections were: prednisone-based graft-versus-host disease (GVHD) prophylaxis and grade II–IV acute GVHD. RFs analysis of CARV progression to LRTD identified 2007–2009 period and absolute lymphocyte count (ALC) < 0.5 × 10⁹/L. ALC < 0.5 × 10⁹/L had a negative impact on day 60 mortality in both overall CARV and those with LRTD, whereas proven LRTD was associated with higher day 60 mortality. CARV infections had a negative effect on non-relapse mortality. Overall survival at day 60 after CARV detection was significantly lower in recipients with LRTD compared with URTD (74% vs. 93%, respectively). In conclusion, CARV infections after UCBT are frequent and may have a negative effect in the outcomes, in particular in the context of lymphocytopenia.

The Value of Combined Radial Endobronchial Ultrasound-Guided Transbronchial Lung Biopsy and Metagenomic Next-Generation Sequencing for Peripheral Pulmonary Infectious Lesions

Background

Metagenomic next-generation sequencing (mNGS) is a new technology that allows for unbiased detection of pathogens. However, there are few reports on mNGS of lung biopsy tissues for pulmonary infection diagnosis. In addition, radial endobronchial ultrasound (R-EBUS) is widely used to detect peripheral pulmonary lesions (PPLs), but it is rarely used in the diagnosis of peripheral lung infection.

Objective

The present study aims to evaluate the combined application of R-EBUS-guided transbronchial lung biopsy (TBLB) and mNGS for the diagnosis of peripheral pulmonary infectious lesions.

Methods

From July 2018 to April 2019, 121 patients from Tianjin Medical University General Hospital diagnosed with PPLs and lung infection were enrolled in this prospective randomized study . Once the lesion was located, either TBLB or R-EBUS-guided-TBLB was performed in randomly selected patients, and mNGS was applied for pathogen detection in lung biopsy tissues. The results of mNGS were compared between the TBLB group and R-EBUS-guided TBLB group. In addition, the clinical characteristics and EBUS images from 61 patients receiving bronchoscopy for peripheral lung infectious detection were analyzed and compared with the results of mNGS.

Results

The positivity rate of mNGS in R-EBUS-guided TBLB was (78.7%, 48/61) that was significantly higher than (60.0%, 36/60) in the TBLB group. Difference in the position of R-EBUS probe and image characteristics of peripheral lung infectious lesions affected the positivity rate of mNGS. Tissue collected by R-EBUS within the lesion produced higher positivity rate than samples collected adjacent to the lesion (P=0.030, odds ratio 17.742; 95% confidence interval, from 1.325 to 237.645). Anechoic areas and luminant areas of ultrasonic image characteristics were correlated with lower positivity rate of mNGS (respectively, P=0.019, odds ratio 17.878; 95% confidence interval, from 1.595 to 200.399; P=0.042, odds ratio 16.745; 95% confidence interval, from 1.106 to 253.479).

Conclusions

R-EBUS-guided TBLB is a safe and effective technique in the diagnosis of peripheral lung infectious lesions. R-EBUS significantly facilitates the accurate insertion of bronchoscope into the lesions, which improves positivity rate of mNGS analysis in pathogen detection. The R-EBUS probe position within lesion produced a higher positivity rate of mNGS analysis. Nevertheless, the presence of anechoic and luminant areas on ultrasonic image was correlated with poor mNGS positivity rate.

Metagenomic Next-Generation Sequencing versus Traditional Pathogen Detection in the Diagnosis of Peripheral Pulmonary Infectious Lesions

Purpose

The aim of this study was to evaluate the value of metagenomic next-generation sequencing (mNGS) in peripheral pulmonary infection management by comparing the diagnostic yield of mNGS and traditional pathogen detection methods on interventional specimens obtained by bronchoscopy.

Patients and Methods

This study enrolled patients suspected with pulmonary infection who were admitted to Tianjin Medical University General Hospital from June 2018 to August 2019. Specimens were obtained from bronchoscopy for mNGS analysis and traditional pathogen detection (including bronchoalveolar lavage fluid microbial culture, smear microscopy, and lung biopsy histopathology), and the diagnostic yields were compared between mNGS and traditional methods to evaluate the diagnostic value of mNGS in peripheral pulmonary infection diagnosis.

Results

In this study, by comparing mNGS with traditional pathogen detection, the results indicated that, first, mNGS identified at least one microbial species in almost 89% of the patients with pulmonary infection; second, mNGS detected microbes related to human diseases in 94.49% of samples from pulmonary infection patients who had received negative results from traditional pathogen detection; third, the accuracy and sensitivity of mNGS are higher than those of traditional pathogen detection; and, finally, mNGS could simultaneously detect and identify a large variety of pathogens.

Conclusion

Metagenomic NGS analysis provided fast and precise pathogen detection and identification, contributing to prompt and accurate treatment of peripheral pulmonary infection.

Respiratory Viruses Cause Late Morbidity in Recipients of Hematopoietic Stem Cell Transplantation

Common respiratory viral infections (CRVIs) frequently complicate hematopoietic stem cell transplantation (HSCT). We conducted a retrospective, single-center, observational cohort study to determine the incidence of CRVI in patients who received an allogeneic (allo) or autologous (auto) HSCT at the Royal Adelaide Hospital between 2009 and 2017. The median follow-up was 8.9 and 4.5 years for auto- and allo-HSCT recipients, respectively. There were 149 CRVI episodes in 74 patients, with rhinovirus being the most commonly isolated virus (n = 81, 47%). The majority of CRVIs (113/149, 75.8%) occurred more than 100 days post-HSCT and 67% were diagnosed in the outpatient setting. There was evidence of lower respiratory tract infection (LRTI) in 45.6% (68/149) of CRVIs. On multivariate logistic regression analysis, coviral infections and cytomegalovirus viremia were independent risk factors for progression of CRVI to LRTI. Ten (6.7%) CRVI episodes resulted in admission to intensive care for ventilatory support and 8 (5.4%) patients died within 30 days of CRVI diagnosis. In our study, 10.4% of HSCT recipients experienced a CRVI post-transplant, primarily causing late morbidity and potentially mortality. Prevention with strict infection control practices, vaccination, and patient education is essential.

Paramyxovirus infections in hematopoietic cell transplant recipients

PURPOSE OF REVIEW

In hematopoietic cell transplant (HCT) recipients, paramyxovirus infections are major viral respiratory tract infections that, if they progress to lower respiratory tract infections, are associated with reduced survival rates in this population. There are important knowledge gaps regarding treatment decisions for HCT recipients with these infections and in the identification of risk factors that predict infection severity. Here, we review recent data on paramyxovirus infections in HCT recipients focusing on risk factors, new diagnostic and prognostic tools, and management including new drugs and vaccines under development.

RECENT FINDINGS

Multiplexed molecular assays associated with immunodeficiency scoring index for respiratory syncytial virus (RSV) have improved our understanding of the epidemiology of RSV and other paramyxovirus infections and the risk factors for worse outcomes. Novel antiviral drugs, monoclonal antibodies, and vaccines are under evaluation with mixed preliminary results.

SUMMARY

Advances in our knowledge of paramyxovirus infections in HCT recipients in the last two decades contributed to better strategies for management and prevention of these infections. A widespread understanding of how to stratify HCT recipients with paramyxovirus infections who would benefit most from antiviral therapy remains to be ascertained. Vaccines and new drugs under development may mitigate the burden of paramyxovirus infections.

Leukopenia and lack of ribavirin predict poor outcomes in patients with haematological malignancies and respiratory syncytial virus infection

Objectives

Respiratory syncytial virus (RSV) infection causes morbidity and mortality in cancer patients. However, studies describing this infection in patients with haematological malignancies are scarce. We sought to evaluate the clinical impact of RSV infection on this patient population.

Methods

We reviewed the records of patients with haematological malignancies and RSV infections cared for at our institution between January 2000 and March 2013.

Results

Of the 181 patients, 71 (39%) had AML, ALL or myelodysplastic syndrome, 12 (7%) had CML or CLL, 4 (2%) had Hodgkin lymphoma, 35 (19%) had non-Hodgkin lymphoma and 59 (33%) had multiple myeloma. Most patients [117 (65%)] presented with an upper respiratory tract infection (URTI) and 15 (13%) had a subsequent lower respiratory tract infection (LRTI). The overall LRTI rate was 44% and the 90 day mortality rate was 15%. Multivariable regression analysis showed that having both neutropenia and lymphocytopenia (adjusted OR = 7.17, 95% CI = 1.94-26.53, P < 0.01) and not receiving ribavirin-based therapy during RSV URTI (adjusted OR = 0.03; 95% CI = 0.01-0.11, P < 0.001) were independent risk factors for LRTI. Having both neutropenia and lymphocytopenia at RSV diagnosis was also a risk factor for death at 90 days after RSV diagnosis (adjusted OR = 4.32, 95% CI = 1.24-15.0, P = 0.021).

Conclusions

Patients with haematological malignancies and RSV infections, especially those with immunodeficiency, may be at risk of LRTI and death; treatment with ribavirin during RSV URTI may prevent these outcomes.

Clinical and Radiologic Characteristics of Human Metapneumovirus Infections in Adults, South Korea

Clinical features of human metapneumovirus (HMPV) infection have not been well documented for adults. We investigated clinical and radiologic features of HMPV infection in 849 adults in a tertiary hospital in South Korea. We classified patients into groups on the basis of underlying diseases: immunocompetent patients, solid tumor patients, solid organ transplantation recipients, hematopoietic stem cell transplant recipients, hematologic malignancy patients, and patients receiving long-term steroid treatment. Of 849 HMPV-infected patients, 756 had community-acquired infections, 579 had pneumonia, and 203 had infections with other pathogens. Mortality rates were highest in hematopoietic stem cell transplantation recipients (22% at 30 days). Older age, current smoking, and underlying disease were associated with HMPV pneumonia. Body mass index and an immunocompromised state were associated with 30-day mortality rates in HMPV-infected patients. Bronchial wall thickening, ground-glass opacity, and ill-defined centrilobular nodules were common computed tomography findings for HMPV pneumonia. Macronodules and consolidation were observed in <50% of patients.

Respiratory Virus Infections of the Stem Cell Transplant Recipient and the Hematologic Malignancy Patient

Respiratory virus infections in hematologic stem cell transplant recipients and patients with hematologic malignancies are increasingly recognized as a cause of significant morbidity and mortality. The often overlapping clinical presentation makes molecular diagnostic strategies imperative for rapid diagnosis and to inform understanding of the changing epidemiology of each of the respiratory viruses. Most respiratory virus infections are managed with supportive therapy, although there is effective antiviral therapy for influenza. The primary focus should remain on primary prevention infection control procedures and isolation precautions, avoidance of ill contacts, and vaccination for influenza.

A prospective study on the epidemiology and clinical significance of viral respiratory infections among pediatric oncology patients

Respiratory infections in oncology are both common and potentially severe. However, there is still a gap in the literature, regarding the epidemiology of viral respiratory infections in children with cancer. We prospectively enrolled 224 patients, from September 2012 to August 2015. The cohort included children with hematologic or solid malignancies receiving chemotherapy, or undergoing hemopoietic stem cell transplantation, outpatients/inpatients exhibiting signs/symptoms of febrile/afebrile upper/lower respiratory infection. Viral infection was diagnosed by detection of ≥1 viruses from a sample at time of enrollment, using the CLART^® PneumoVir kit (GENOMICA, Spain). Α detailed questionnaire including demographics and medical history was also completed. Samples were processed in batches, results were communicated as soon as they became available. Children recruited in whom no virus was detected composed the no virus detected group. Viral prevalence was 38.4% in children presenting with respiratory illness. A single virus was found in 30.4%, with RSV being the most frequent. Viral coinfections were detected in 8%. Children with viral infection were more likely to be febrile upon enrollment and to present with lower respiratory signs/symptoms. They had longer duration of illness and they were more likely to receive antibiotics/antifungals. Only 22% of children with influenza received oseltamivir. Mortality was low (2.7%), however, pediatric intensive care unit (PICU) admission and death were correlated with virus detection. In our study mortality was low and PICU admission was related to virus identification. Further research is needed to clarify whether antibiotics in virus-proven infection are of value and underline the importance of oseltamivir's timely administration in influenza.

Respiratory Virus Infections in Hematopoietic Cell Transplant Recipients

Highly immunocompromised pediatric and adult hematopoietic cell transplant (HCT) recipients frequently experience respiratory infections caused by viruses that are less virulent in immunocompetent individuals. Most of these infections, with the exception of rhinovirus as well as adenovirus and parainfluenza virus in tropical areas, are seasonal variable and occur before and after HCT. Infectious disease management includes sampling of respiratory specimens from nasopharyngeal washes or swabs as well as sputum and tracheal or tracheobronchial lavages. These are subjected to improved diagnostic tools including multiplex PCR assays that are routinely used allowing for expedient detection of all respiratory viruses. Disease progression along with high mortality is frequently associated with respiratory syncytial virus, parainfluenza virus, influenza virus, and metapneumovirus infections. In this review, we discuss clinical findings and the appropriate use of diagnostic measures. Additionally, we also discuss treatment options and suggest new drug formulations that might prove useful in treating respiratory viral infections. Finally, we shed light on the role of the state of immune reconstitution and on the use of immunosuppressive drugs on the outcome of infection.

Risk Factors for Parainfluenza Virus Lower Respiratory Tract Disease after Hematopoietic Cell Transplantation

Parainfluenza virus (PIV) infection can progress from upper respiratory tract infection (URTI) to lower respiratory tract disease (LRTD) in immunocompromised hosts. Risk factors for progression to LRTD and presentation with LRTD without prior URTI are poorly defined. Hematopoietic cell transplant (HCT) recipients with PIV infection were retrospectively analyzed using standardized definitions of LRTD. PIV was detected in 540 HCT recipients; 343 had URTI alone and 197 (36%) had LRTD (possible, 76; probable, 19; proven, 102). Among 476 patients with positive nasopharyngeal samples, the cumulative incidence of progression to probable/proven LRTD by day 40 was 12%, with a median time to progression of 7 days (range, 2 to 40). In multivariable analysis monocytopenia (hazard ratio, 2.22; P = .011), steroid use ≥1mg/kg prior to diagnosis (hazard ratio, 1.89; P = .018), co-pathogen detection in blood (hazard ratio, 3.21; P = .027), and PIV type 3 (hazard ratio, 3.57; P = .032) were associated with increased progression risk. In the absence of all 4 risk factors no patients progressed to LRTD, whereas progression risk increased to >30% if 3 or more risk factors were present. Viral load or ribavirin use appeared to have no effect on progression. Among 121 patients with probable/proven LRTD, 64 (53%) presented LRTD without prior URTI, and decreased lung function before infection and lower respiratory co-pathogens were risk factors for this presentation. Mortality was unaffected by the absence of prior URTI. We conclude that the risk of progression to probable/proven LRTD exceeded 30% with ≥3 risk factors. To detect all cases of LRTD, virologic testing of lower respiratory samples is required regardless of URTI symptoms.

Respiratory Viral Infections in Transplant Recipients

Respiratory viral infections (RVIs) are common among the general population; however, these often mild viral illnesses can lead to serious morbidity and mortality among recipients of hematopoietic stem cell and solid organ transplantation. The disease spectrum ranges from asymptomatic or mild infections to life-threatening lower respiratory tract infection or long-term airflow obstruction syndromes. Progression to lower respiratory tract infection or to respiratory failure is determined by the intrinsic virulence of the specific viral pathogen as well as various host factors, including the type of transplantation, status of the host’s immune dysfunction, the underlying disease, and other comorbidities. This chapter focuses on the epidemiology, clinical manifestations, diagnosis, and management of RVIs in this susceptible population and includes respiratory syncytial virus, parainfluenza virus, human metapneumovirus, influenza virus, human coronavirus, and human rhinovirus. The optimal management of these infections is limited by the overall paucity of available treatment, highlighting the need for new antiviral drug or immunotherapies.

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.

Respiratory Tract Infections: Sinusitis, Bronchitis, and Pneumonia

Solid organ and hematopoietic stem cell transplant recipients are at increased risk of upper and lower respiratory tract infections. While these infections are frequently encountered in the general population, the spectrum of their clinical presentation including morbidity and mortality is increased in patients undergoing transplantation procedures. Impaired innate and adaptive immunity, potential anatomical abnormalities resulting from extensive surgical procedures, presences of indwelling medical devices, and increased healthcare exposure put transplant recipients at particularly high risk for respiratory tract disease. Infections of the respiratory tract can be divided into those affecting the paranasal sinuses, the upper airways such as bronchitis and tracheobronchitis, and the lower airways like pneumonia. Each of these clinical syndromes can further be classified based on their chronicity, acute vs. chronic; their setting, community vs. nosocomial; and the etiology such as bacteria, viruses, fungi, and rarely parasites. It is also important to realize that such immunologically vulnerable patients are at risk for polymicrobial infection that may present concurrently or in a sequential, consecutive fashion. This chapter reviews the common respiratory tract infections affecting transplant recipients with particular attention directed toward epidemiological risk factors, clinical presentations, diagnostic strategies, and common pathogens. Specific causes of opportunistic pneumonias are also reviewed.

Respiratory Viral Infections in Patients With Cancer or Undergoing Hematopoietic Cell Transplant

Survival rates for pediatric cancer have steadily improved over time but it remains a significant cause of morbidity and mortality among children. Infections are a major complication of cancer and its treatment. Community acquired respiratory viral infections (CRV) in these patients increase morbidity, mortality and can lead to delay in chemotherapy. These are the result of infections with a heterogeneous group of viruses including RNA viruses, such as respiratory syncytial virus (RSV), influenza virus (IV), parainfluenza virus (PIV), metapneumovirus (HMPV), rhinovirus (RhV), and coronavirus (CoV). These infections maintain a similar seasonal pattern to those of immunocompetent patients. Clinical manifestations vary significantly depending on the type of virus and the type and degree of immunosuppression, ranging from asymptomatic or mild disease to rapidly progressive fatal pneumonia Infections in this population are characterized by a high rate of progression from upper to lower respiratory tract infection and prolonged viral shedding. Use of corticosteroids and immunosuppressive therapy are risk factors for severe disease. The clinical course is often difficult to predict, and clinical signs are unreliable. Accurate prognostic viral and immune markers, which have become part of the standard of care for systemic viral infections, are currently lacking; and management of CRV infections remains controversial. Defining effective prophylactic and therapeutic strategies is challenging, especially considering, the spectrum of immunocompromised patients, the variety of respiratory viruses, and the presence of other opportunistic infections and medical problems. Prevention remains one of the most important strategies against these viruses. Early diagnosis, supportive care and antivirals at an early stage, when available and indicated, have proven beneficial. However, with the exception of neuraminidase inhibitors for influenza infection, there are no accepted treatments. In high-risk patients, pre-emptive treatment with antivirals for upper respiratory tract infection (URTI) to decrease progression to LRTI is a common strategy. In the future, viral load and immune markers may prove beneficial in predicting severe disease, supporting decision making and monitor treatment in this population.

Human Metapneumovirus Infection: Pneumonia Risk Factors in Patients With Solid Organ Transplantation and Computed Tomography Findings

BACKGROUND

Human metapneumovirus (HMPV) is a newly detected pathogen that can cause lower respiratory tract disease. Clinical characteristics, computed tomography (CT) findings, and outcomes of HMPV pneumonia in patients with solid organ transplantation (SOT) have not been well demonstrated.

METHODS

Between January 2010 and February 2016, clinical and imaging findings of 59 patients with SOT (types of organ: kidney, 37; liver, 16; heart, 4; and pancreas and kidney, 2) who had HMPV infection detected in nasopharyngeal or bronchoalveolar lavage by reverse transcription polymerase chain reaction were retrospectively evaluated.

RESULTS

Most (90%) of the patients were detected between March and June. In the 59 patients with SOT with upper respiratory tract infection (URI), 29 (49%) progressed to lower respiratory tract disease after a median of 7 days (range, 2-31 days). Coinfection was noted in 39% of the patients. In Cox proportional hazards analysis, low lymphocyte count (≤0.7 × 10/μL; hazard ratio, 2.24; 95% confidence interval, 1.04-4.85; P = 0.04) and high C-reactive protein (>10 mg/dL; hazard ratio, 2.93; 95% confidence interval, 1.19-7.21; P = 0.02) at URI diagnosis were associated with HMPV pneumonia. On CT, HMPV pneumonia presented as bilateral ill-defined centrilobular nodules, consolidation and ground-glass opacities, whereas lymphadenopathy or effusion is not common. There were no significantly different imaging CT findings between patients with HMPV infection alone and those with coinfection.

CONCLUSIONS

Human metapneumovirus pneumonias were detected in nearly half of patients with SOT showing URI symptoms with positive HMPV, and low lymphocyte count and high C-reactive protein at URI diagnosis were significant factors associated with HMPV pneumonia.

Incidence, significance, and persistence of human coronavirus infection in hematopoietic stem cell transplant recipients

Hematopoietic stem cell transplant (HSCT) recipients are at increased risk of respiratory viral infections and their associated complications. Unlike other respiratory viruses, little is known about the clinical significance of human coronavirus infection (HCoV) in this population. We retrospectively identified all HSCT recipients who were transplanted between May 2013 and June 2017 at our institution and characterized the cumulative incidence of post-transplant HCoV infection. Of 678 patients who underwent HSCT during the study period, 112 (17%) developed HCoV infection, making HCoV the fourth most common respiratory viral infection. Thirty-four (30%) HCoV-infected patients progressed to proven or probable lower respiratory tract infection (LRTI). Age ≥50, graft-versus-host disease, corticosteroids, hypoalbuminemia, and inpatient status at the time of infection were independently associated with progression to LRTI. Twenty-seven (59%) patients who underwent repeat NP swab had persistent viral shedding for ≥21 days, with a median duration of 4 weeks of viral shedding. We conclude that HCoV is common and clinically significant in HSCT recipients, with nearly one-third of patients progressing to proven or probable LRTI. Evaluating for LRTI risk factors found in this study may identify patients who require closer surveillance and aggressive supportive care when infected with HCoV.

Clinical characteristics and treatment outcomes among respiratory syncytial virus (RSV)-infected hematologic malignancy and hematopoietic stem cell transplant recipients receiving palivizumab

Palivizumab has been used to treat respiratory syncytial virus (RSV)-infected hematologic malignancy patients at our institution based on limited published data. We conducted this retrospective study to evaluate clinical outcomes and mortality rates of RSV-infected hematologic malignancy patients from 2007 to 2016. A total of 67 patients (19 received palivizumab and 47 received supportive care) were identified. Palivizumab-treated patients had a significantly higher proportion of underlying ischemic heart disease, graft-versus-host-disease, hypogammaglobulinemia, and concomitant pulmonary infections. There were no significant differences in mortality rates or readmission rates between the two groups. The estimated odds ratio for death in patients receiving palivizumab after adjusting for propensity scores and covariates were 0.12 ([0.01, 1.32], p = .08) and 0.09 ([0.01, 1.03], p = .05) respectively. After adjustment for factors associated with severity of illness, there was no difference in mortality among patients treated with palivizumab.

Detection of Pulmonary Infectious Pathogens From Lung Biopsy Tissues by Metagenomic Next-Generation Sequencing

Metagenomic next-generation sequencing (mNGS) is a comprehensive approach for sequence-based identification of pathogenic microbes. However, reports on the use of mNGS in pulmonary infection applied to lung biopsy tissues remain scarce. In this study, we applied mNGS to detect the presence of pathogenic microbes in lung biopsy tissues from 20 patients with pulmonary disorders indicating possible infection. We applied a new data management for identifying pathogen species based on mNGS data. We determined the thresholds for the unique reads and relative abundance required to identify the infectious pathogens. Potential pathogens of pulmonary infections in 15 patients were identified by mNGS. The comparison between mNGS and culture method resulted that the sensitivity and specificity were 100.0% (95% CI: 31.0–100.0%) and 76.5% (95% CI: 49.8–92.2%) for bacteria, 57.1% (95% CI: 20.2–88.2%) and 61.5% (95% CI: 32.2–84.9%) for fungi. The positive predictive value (PPV) (42.9% for bacteria, 44.4% for fungi) was much lower than negative predictive value (NPV) (100% for bacteria, 72.7% for fungi) in mNGS vs. culture method. The mNGS showed the highest specificity (100.0 and 94.1%) and PPV (100.0 and 75.0%) in the evaluation of fungi and MTBC respectively, when compared with histopathology method. The study indicated that mNGS of lung biopsy tissues can be used to detect the presence (or absence) of pulmonary pathogens in patients, with potential benefits in speed and sensitivity. However, accurate data management and interpretation of mNGS are required, and should be combined with observations of clinical manifestations and conventional laboratory-based diagnostic methods.

Community-acquired respiratory virus lower respiratory tract disease in allogeneic stem cell transplantation recipient: Risk factors and mortality from pulmonary virus-bacterial mixed infections

Risk factors (RFs) and mortality data of community‐acquired respiratory virus (CARVs) lower respiratory tract disease (LRTD) with concurrent pulmonary co‐infections in the setting of allogeneic hematopoietic stem cell transplantation (allo‐HSCT) is scarce. From January 2011 to December 2017, we retrospectively compared the outcome of allo‐HSCT recipients diagnosed of CARVs LRTD mono‐infection (n = 52, group 1), to those with viral, bacterial, or fungal pulmonary CARVs LRTD co‐infections (n = 15, group 2; n = 20, group 3, and n = 11, group 4, respectively), and with those having bacterial pneumonia mono‐infection (n = 19, group 5). Overall survival (OS) at day 60 after bronchoalveolar lavage (BAL) was significantly higher in group 1, 2, and 4 compared to group 3 (77%, 67%, and 73% vs 35%, respectively, P = .012). Recipients of group 5 showed a trend to better OS compared to those of group 3 (62% vs 35%, P = .1). Multivariate analyses showed bacterial co‐infection as a RF for mortality (hazard ratio[HR] 2.65, 95% C.I. 1.2‐6.9, P = .017). We identified other 3 RFs for mortality: lymphocyte count <0.5 × 10⁹/L (HR 2.6, 95% 1.1‐6.2, P = .026), the occurrence of and CMV DNAemia requiring antiviral therapy (CMV‐DNAemia‐RAT) at the time of BAL (HR 2.32, 95% C.I. 1.1‐4.9, P = .03), and the need of oxygen support (HR 8.3, 95% C.I. 2.9‐35.3, P = .004). CARV LRTD co‐infections are frequent and may have a negative effect in the outcome, in particular in the context of bacterial co‐infections.

Respiratory Viruses and Other Relevant Viral Infections in the Lung Transplant Recipient

As advances occur in surgical technique, postoperative care, and immunosuppressive therapy, the rate of mortality in the early postoperative period following lung transplantation continues to decline. With the improvements in immediate and early posttransplant mortality, infections and their sequel as well as rejection and chronic allograft dysfunction are increasingly a major cause of posttransplant mortality. This chapter will focus on infections by respiratory viruses and other viral infections relevant to lung transplantation, including data regarding the link between viral infections and allograft dysfunction.

Viral pneumonia: etiologies and treatment

Viral pathogens are increasingly recognized as a cause of pneumonia, in immunocompetent patients and more commonly among immunocompromised. Viral pneumonia in adults could present as community-acquired pneumonia (CAP), ranging from mild disease to severe disease requiring hospital admission and mechanical ventilation. Moreover, the role of viruses in hospital-acquired pneumonia and ventilator-associated pneumonia as causative agents or as co-pathogens and the effect of virus detection on clinical outcome are being investigated.More than 20 viruses have been linked to CAP. Clinical presentation, laboratory findings, biomarkers, and radiographic patterns are not characteristic to specific viral etiology. Currently, laboratory confirmation is most commonly done by detection of viral nucleic acid by reverse transcription-PCR of respiratory secretions.Apart from the US Food and Drug Administration-approved medications for treatment of influenza pneumonia, the treatment of non-influenza respiratory viruses is limited. Moreover, the evidence supporting the use of available antivirals to treat immunocompromised patients is modest at best. With the widespread use of molecular diagnostics, an aging population, and advancement in cancer therapy, physicians will face a bigger challenge in managing viral respiratory tract infections. Emphasis on infection control measures to prevent the spread of respiratory viruses especially in healthcare settings is extremely important.

Community-Acquired Respiratory Paramyxovirus Infection After Allogeneic Hematopoietic Cell Transplantation: A Single-Center Experience

Background

Paramyxoviruses include respiratory syncytial virus (RSV), parainfluenza virus (PIV), and human metapneumovirus (MPV), which may cause significant respiratory tract infectious disease (RTID) and mortality after allogeneic hematopoietic cell transplantation (HCT). However, clinical data regarding frequency and outcome are scarce.

Methods

We identified all paramyxovirus RTIDs in allogeneic HCT recipients diagnosed by multiplex polymerase chain reaction between 2010 and 2014. Baseline characteristics of patients, treatment, and outcome of each episode were analyzed; ie, moderate, severe, and very severe immunodeficiency (verySID) according to HCT ≤6 months, T- or B-cell depletion ≤3 months, graft-versus-host disease, neutropenia, lymphopenia, or hypo-gammaglobulinemia.

Results

One hundred three RTID episodes in 66 patients were identified (PIV 47% [48 of 103], RSV 32% [33 of 103], MPV 21% [22 of 103]). Episodes occurred in 85% (87 of 103) at >100 days post-HCT. Lower RTID accounted for 36% (37 of 103). Thirty-nine percent (40 of 103) of RTID episodes required hospitalization and more frequently affected patients with lower RTID. Six percent progressed from upper to lower RTID. Overall mortality was 6% and did not differ between paramyxoviruses. Sixty-one percent (63 of 103) of episodes occurred in patients with SID, and 20.2% (19 of 63) of episodes occurred in patients with verySID. Oral ribavirin plus intravenous immunoglobulin was administered in 38% (39 of 103) of RTIDs, preferably for RSV or MPV (P ≤ .001) and for SID patients (P = .001). Patients with verySID frequently progressed to lower RTID (P = .075), required intensive care unit transfer, and showed higher mortality.

Conclusion

Paramyxovirus RTID remains a major concern in allogeneic HCT patients fulfilling SID and verySID, emphasizing that efficacious and safe antiviral treatments are urgently needed.

Characteristics and Outcomes of Coronavirus Infection in Children: The Role of Viral Factors and an Immunocompromised State

BACKGROUND

Immunocompromised children might be predisposed to serious infections from human coronaviruses (HCoVs), including strains OC43, NL63, HKU1, and 229E; however, the virologic and clinical features of HCoV infection in immunocompromised children have not been compared to those in nonimmunocompromised children.

METHODS

We retrospectively analyzed a cohort of children who presented to Seattle Children's Hospital and in whom HCoV was detected by a multiplex respiratory polymerase chain reaction assay of a nasal sample between October 2012 and March 2016. Lower respiratory tract disease (LRTD) was defined as possible or definite infiltrate seen in chest imaging, need for oxygen, or abnormal lung examination in conjunction with a physician diagnosis of LRTD. We used logistic regression modeling to evaluate risk factors for LRTD and LRTD that necessitated oxygen use (severe LRTD), including an immunocompromised state, in children with HCoV infection.

RESULTS

The median ages of 85 immunocompromised and 1152 nonimmunocompromised children with HCoV infection were 6.3 and 1.6 years, respectively. The prevalence of LRTD and of severe LRTD did not differ greatly between the immunocompromised and nonimmunocompromised patients (22% vs 26% [LRTD] and 15% vs 11% [severe LRTD], respectively); however, in a multivariable model, an immunocompromised state was associated with an increased likelihood of severe LRTD (adjusted odds ratio, 2.5 [95% confidence interval, 1.2-4.9]; P = .01). Younger age, having an underlying pulmonary disorder, and the presence of respiratory syncytial virus were also associated with LRTD or severe LRTD in multivariable models. The risks of LRTD or severe LRTD did not differ among the children with different HCoV strains.

CONCLUSIONS

The presence of a copathogen and host factors, including an immunocompromised state, were associated with increased risk for severe LRTD. Recognizing risk factors for severe respiratory illness might assist in risk stratification.