Community-acquired Respiratory Viruses Research Articles

Resurgence of common respiratory viruses in patients with community-acquired pneumonia (CAP)—A prospective multicenter study

BackgroundCommunity-acquired pneumonia (CAP) is a major global cause of death and hospitalization. Bacteria or community-acquired viruses (CARVs) cause CAP. COVID-19 associated restrictions effectively reduced the circulation of CARVs. ObjectivesThe aim of this study was to analyze the proportion of CARVs in adult patients with CAP from mid-2020 to mid-2023. Specifically, we aimed to compare the rate of influenza virus, SARS-CoV-2, and RSV detections in patients aged 18–59 years and ≥60 years. Study designWe analyze the proportion of 21 community-acquired respiratory viruses (CARVs) and three atypical bacteria (Bordetella pertussis, Legionella pneumophila, and Mycoplasma pneumoniae) in nasopharyngeal swab samples using molecular multiplex methods within the prospective, multicentre, multinational study of the German study Group CAPNETZ. We used stringent inclusion criteria throughout the study. ResultsWe identified CARVs in 364/1,388 (26.2 %) patients. In detail, we detected SARS-CoV-2 in 210/1,388 (15.1 %), rhino-/enterovirus in 64/1,388 (4.6 %), influenza virus in 23/1,388 (1.6 %) and RSV in 17/1,388 (1.2 %) of all patients. We detected RSV and influenza more frequently in patients ≥60 years, especially in 22/23 compared to the previous season. None of the atypical bacteria were detected. ConclusionsBeginning in 2023, we demonstrate a re-emergence of CARVs in CAP patients. Effective vaccines or specific antiviral therapies for more than two thirds of the detected viral infections are currently available. High detection rates of vaccine-preventable viruses in older age groups support targeted vaccination campaigns.

Are any specific respiratory viruses more severe than others in recipients of allogeneic stem cell transplantation? A focus on lower respiratory tract disease.

In the general population, influenza virus, respiratory syncytial virus, and SARS-CoV-2 are considered the most severe community-acquired respiratory viruses (CARVs). However, allogeneic stem cell transplant (allo-SCT) recipients may also face severe courses from other CARVs. This retrospective study compared outcomes of various CARV lower respiratory tract diseases (LRTD) in 235 adult allo-SCT recipients, excluding co-infection episodes. We included 235 adults allo-SCT recipients experiencing 353 CARV LRTD consecutive episodes (130 rhinovirus, 63 respiratory syncytial virus, 43 influenza, 43 human parainfluenza virus, 23 human metapneumovirus, 19 Omicron SARS-CoV-2, 17 common coronavirus, 10 adenovirus and 5 human bocavirus) between December 2013 and June 2023. Day 100 overall survival ranged from 78% to 90% without significant differences among CARV types. Multivariable analysis of day 100 all-cause mortality identified corticosteroid use of >1 to <30 mg/d [Hazard ratio (HR) 2.45, p = 0.02) and ≥30 mg/d (HR 2.20, p = 0.015) along with absolute lymphocyte count <0.2 × 109/L (HR 5.82, p < 0.001) and number of CARV episodes as a continuous variable per one episode increase (HR 0.48, p = 0.001) as independent risk factors for all-cause mortality. Degree of immunosuppression, rather than intrinsic CARV virulence, has the most significant impact on mortality in allo-SCT recipients with CARV-LRTD.

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

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. 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%). Risk factors for LRTD progression in multivariate analysis were corticosteroids > 30mg/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. 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.

ALVR106, an Off-the-Shelf, Multivirus-Specific T-Cell Therapy, for the Treatment of Respiratory Viral Infections: Results from a Phase 1, First-in-Human, Dose-Ranging Trial

Background: Community-acquired respiratory viruses such as influenza (Flu), human metapneumovirus (hMPV), parainfluenza virus (PIV), and respiratory syncytial virus (RSV) are leading causes of morbidity and mortality after hematopoietic cell transplant (HCT) or solid organ transplant (SOT). While these viruses may begin in the upper respiratory tract, ~50% of cases progress to the lower respiratory tract, potentially leading to more severe conditions such as pneumonia, bronchiolitis, bronchiolitis obliterans, and chronic lung allograft dysfunction. ALVR106 is an allogeneic, off-the-shelf, polyclonal, multi-respiratory virus T-cell therapy specific for Flu, hMPV, PIV, and RSV. ALVR106 is generated by exposing peripheral blood mononuclear cells to peptide mixtures followed by ex vivo expansion in presence of activating cytokines. The expanded T cells are Th1-polarized, polyfunctional, and selectively able to kill viral target cells. ALVR106 cells have not shown alloreactivity, attesting to their selectivity and safety for use in HCT or SOT. Methods: In this first-in-human, placebo (PBO)-controlled, dose-ranging trial, HCT or SOT recipients 17 years or older with upper or mild lower respiratory tract infections (URTI/LRTI) caused by Flu, hMPV, PIV, or RSV were randomized in a 3:1 ratio to receive ALVR106 or PBO. Four doses of ALVR106 ranging from 1 × 10 5 cells/kg to 2 × 10 6 cells/kg were planned to be given to 4 cohorts of 4 patients each. Patients receive up to 2 infusions of ALVR106 or PBO once every 14 days and will be followed for up to 1 year. The primary objective was safety as measured by treatment emergent adverse events (AEs), AEs of special interest (acute and chronic graft vs host disease (GvHD), cytokine release syndrome (CRS), infusion related reactions (IRR), and progressive dyspnea), and clinical laboratory abnormalities from baseline (BL) through 12 weeks after the last infusion. Secondary endpoints included evaluation of antiviral activity by qualitative PCR assay by nasal swab and a composite endpoint through D28 which included change from BL in Radiation Therapy Oncology Group Lung Toxicity Scale Grade and viral detection from nasal swab. Patients with an improvement in symptoms or undetectable virus were considered partial responders (PR); those with improved symptoms and undetectable virus were complete responders (CR), and those whose condition did not improve or worsen from BL were non-responders (NR). To assess functional T-cell immune reconstitution and frequency of circulating virus-specific T cells, IFN-g virus-specific ELISpot analysis was performed on serial blood samples over time. ELISpot results will be presented. Preliminary study results presented herein will be unblinded at the time of data presentation. Results: 16 patients were dosed: four in Cohorts (C) 1 and 2, five in C3, and three in C4. Table shows BL demographics, disease characteristics, and blinded results for safety and antiviral activity by composite endpoint. Cohorts 2, 3, and 4 had at least 1 patient with mild LRTI at BL, no patients in C1 had LRTI. All patients received at least 1 infusion. No patients with Flu were enrolled. In these blinded results, no differences were seen in rate or severity of AEs among cohorts. Four patients (25%) had AEs possibly related to treatment (ALVR106 or PBO); all were Grade 1 (mild) in severity. These related events were reported in 1 patient each: diarrhea, ear pressure, neutrophil count decrease, and 1 patient had pyrexia, cGvHD oral, and aGvHD skin. Eight patients (50%) had serious AEs (SAEs), none related to treatment. One patient (6%) in C3 had G2 progressive dyspnea not related to treatment. One patient (6%) in C1 had Grade I aGVHD skin and cGVHD oral; both were considered possibly related to treatment (ALVR106 or PBO). No patients had Grade II-IV aGVHD, cGVHD, IRR, or CRS. No clinically significant changes from BL or trends over time in lab abnormalities or vital signs were seen. At Day 28, all patients in C1 and C2 had undetectable respiratory virus via nasal swab, except 1 patient in C1 who missed D28 visit due to COVID-19; 4/5 (80%) in C3 were undetectable; and 2/3 (67%) in C4 were undetectable. Conclusion: In this ongoing trial-the first-in-human, double-blind, PBO-controlled trial of virus-specific T cell therapy in transplant recipients with respiratory infection-ALVR106 was safe and well tolerated, supporting its continued evaluation in HCT and SOT recipients.

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.

Reduced Community-acquired Respiratory Virus Infection, but Not Non-virus Infection, in Lung Transplant Recipients During Government-mandated Public Health Measures to Reduce COVID-19 Transmission.

A single-center, retrospective cohort analysis comparing CARV infection before a statewide stay-at-home order, during the stay-at-home order and subsequent statewide mask mandate, and during 5 mo following the elimination of NPI was performed. All LTx recipients followed by and tested at our center were included. Data (multiplex respiratory viral panels; SARS-CoV-2 reverse transcription polymerase chain reaction; blood cytomegalovirus and Epstein Barr virus polymerase chain reaction; blood and bronchoalveolar lavage bacterial and fungal cultures) were collected from the medical record. Chi-square or Fisher exact tests were utilized for categorical variables. A mixed-effect model was used for continuous variables. Incidence of non-COVID CARV infection was significantly lower during the MASK period than during the PRE period. No difference was noted in airway or bloodstream bacterial or fungal infections, but cytomegalovirus bloodborne viral infections increased. Reductions in respiratory viral infections, but not bloodborne viral infections nor nonviral respiratory, bloodborne, or urinary infections, were observed in the setting of public health COVID-19 mitigation strategies, suggesting the effectiveness of NPI in preventing general respiratory virus transmission.

Impact of the COVID-19 pandemic on antiviral drug development for other community-acquired respiratory viruses’ infections

The coronavirus disease 2019 (COVID-19) pandemic indirectly resulted in missed therapeutic opportunities for many diseases. Here we focus on community-acquired respiratory viruses other than severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) [respiratory syncytial virus, parainfluenza and influenza A], and highlight the pandemics impact on clinical trials to develop novel therapies for other severe respiratory viral infections. We retrospectively reviewed inclusion rates within respiratory antiviral clinical trials in comparison with all other clinical trials in our clinical investigations center, before and during the COVID-19 pandemic. As opposed to the remaining clinical trials developed within our unit, respiratory antiviral trials inclusion rates did not recover after the initial recruitment decrease observed across all trials during the first pandemic wave. These results were discussed in the context of non-COVID-19 respiratory viral infection rates within our center, showing a general decline in seasonal respiratory viruses spread since the COVID-19 pandemic onset. Virus epidemiology changes upon the wide SARS-CoV-2 expansion as well as the lifestyle changes globally adopted to prevent SARS-CoV-2 transmission could have therefore contributed to the negative impact of the COVID-19 pandemic on antiviral drug development. Our study highlights the peculiarity of respiratory antiviral drug development during the COVID-19 pandemic era and describes potential explanations for such drug development halting.

Epidemiology of Lower Respiratory Tract Infections and Community-Acquired Respiratory Viruses in Patients with Bronchiolitis Obliterans Syndrome after Hematopoietic Cell Transplantation: A Retrospective Cohort Study

Bronchiolitis obliterans syndrome (BOS)-chronic graft-versus-host disease (cGVHD) affecting the lungs-is an uncommon complication of allogeneic hematopoietic cell transplant (HCT). The epidemiology and complications of lower respiratory tract infections (LRTIs) and community-acquired respiratory viruses (CARVs) in these patients are poorly understood. We aim to characterize the epidemiology of LRTIs in patients with BOS complicating HCT. We also aim to explore the association of LRTIs and CARV detection on lung function in BOS patients. Adult patients with BOS at Stanford Health Care between January 2010 and December 2019 were included in this retrospective cohort study. LRTI diagnosis was based on combined clinical, microbiologic, and radiographic criteria, using consensus criteria where available. Fifty-five patients with BOS were included. BOS was diagnosed at a median of 19.2 (IQR 12.5-24.7) months after HCT, and patients were followed for a median of 29.3 (IQR 9.9-53.2) months from BOS diagnosis. Twenty-two (40%) patients died after BOS diagnosis; 17 patients died from complications of cGVHD (including respiratory failure and infection) and 5 died from relapsed disease. Thirty-four (61.8%) patients developed at least one LRTI. Viral LRTIs were most common, occurring in 29 (52.7%) patients, primarily due to rhinovirus. Bacterial LRTIs-excluding Nocardia and non-tuberculous mycobacteria (NTM)-were the second most common, occurring in 21 (38.2%) patients, mostly due to Pseudomonas aeruginosa. Fungal LRTIs, NTM, and nocardiosis occurred in 14 (25.5%), 10 (18.2%), and 4 (7.3%) patients, respectively. Median time to development of the first LRTI after BOS diagnosis was 15.3 (4.7-44.7) months. Twenty-six (76.5%) of the 34 patients who developed LRTIs had infections due to more than one type of organism-fungi, viruses, Nocardia, NTM, and other bacteria-over the observation period. Patients with at least one LRTI had significantly lower forced expiratory volume in one second percent predicted (FEV1%) (37% vs. 53%, p = 0.0096) and diffusing capacity of carbon monoxide (DLCO) (45.5% predicted vs. 69% predicted, p = 0.0001). Patients with at least one LRTI trended toward lower overall survival (OS) (p = 0.0899) and higher non-relapse mortality (NRM) (p = 0.2707). Patients with a CARV detected or LRTI diagnosed after BOS-compared to those without any CARV detected or LRTI diagnosed-were more likely to have a sustained drop in FEV1% from baseline of at least 10% (21 [61.8%] versus 7 [33.3%]) and a sustained drop in FEV1% of at least 30% (12 [36.4%] versus 2 [9.5%]). LRTIs are common in BOS and associated with lower FEV1%, lower DLCO, and a trend toward decreased OS and higher NRM. Patients with LRTIs or CARVs (even absent lower respiratory tract involvement) were more likely to have substantial declines in FEV1% over time than those without. The array of organisms-including P. aeruginosa, mold, Nocardia, NTM, and CARVs-seen in BOS reflects the unique pathophysiology of this form of cGVHD, involving both systemic immunodeficiency and structural lung disease. These patterns of LRTIs and their outcomes can be used to guide clinical decisions and inform future research.

Insights Into the Role of the Lung Virome During Respiratory Viral Infections.

The virome constitutes the viral component of the microbiome and it consists of the genomes of all the viruses that inhabit a particular region of the human body, including those that cause acute, persistent or latent infection, and retroviral elements integrated to host chromosomes. The human virome is composed by eukaryotic viruses, bacteriophages and archaeal viruses. The understanding of the virome composition and role on human health has been delayed by the absence of specific tools and techniques to accurately characterize viruses. However, more recently, advanced methods for viral diagnostics, such as deep sequencing and metagenomics, have allowed a better understanding of the diverse viral species present in the human body. Previous studies have shown that the respiratory virome modulates the host immunity and that, since childhood, the human lung is populated by viruses for whom there is no disease association. Whether these viruses are potentially pathogenic and the reason for their persistence remain elusive. Increased respiratory viral load can cause exacerbation of chronic pulmonary diseases, including COPD, cystic fibrosis, and asthma. Moreover, the presence of resident viral populations may contribute to the pathogenesis of community-acquired respiratory virus infections. In this mini review, I will discuss the recent progress on our understanding of the human lung virome and summarize the up-to-date knowledge on the relationships among community-acquired respiratory viruses, the lung virome and the immune response to better understand disease pathophysiology and the factors that may lead to viral persistence.

Evaluation of healthcare-associated infection rates in patients with hematologic malignancies and stem cell transplantation during the coronavirus disease 2019 (COVID-19) pandemic.

To evaluate whether rates of healthcare-associated infections (HAIs) changed during the coronavirus disease 2019 (COVID-19) pandemic in malignant hematology and stem cell transplant patients. A retrospective, cohort study. The study included malignant hematology and stem cell transplant patients admitted between March 1, 2019, through July 31, 2019, and March 1, 2020, through July 31, 2020. Rates of catheter-associated urinary tract infections (CAUTIs), central-line-associated bloodstream infections (CLABSIs), central-line-associated mucosal barrier injury infections (CLAMBIs), and Clostridioides difficile infections (CDIs) during the pandemic were compared to those in a control cohort. Secondary outcomes included the rate of non-COVID-19 respiratory viruses. The rate of CAUTIs per 1,000 hospital days was 0.435 before the pandemic and 0.532 during the pandemic (incidence rate ratio [IRR], 1.224; 95% confidence interval [CI], 0.0314-47.72; P = .899). The rate of CLABSIs was 0.435 before the pandemic and 1.064 during the pandemic (IRR, 2.447; 95% CI, 0.186-72.18; P = .516). The rate of CLAMBIs was 2.61 before the pandemic and 1.064 during the pandemic (IRR 0.408, 95% CI 0.057-1.927; P = .284). The rate of CDIs was 2.61 before the pandemic and 1.579 during the pandemic (IRR, 0.612; 95% CI, 0.125-2.457; P = .512). Non-COVID-19 respiratory virus cases decreased significantly from 12 (30.8%) to 2 cases (8.3%) (P = 0.014). There was no significant difference in HAIs among inpatient malignant hematology and stem cell transplant patients during the COVID-19 pandemic compared to those of a control cohort. Rates of infection were low among both cohorts. Rates of community-acquired respiratory viruses decreased significantly during the pandemic among this population.

Community-acquired Respiratory Virus Cases Mimic COVID-19 on Lung Computed Tomography.

We herein report four patients with community-acquired respiratory virus (CRV) infection. Although they had no history of contact with any individual with coronavirus disease 2019 (COVID-19), they were suspected of having COVID-19 based on findings of high-resolution computed tomography (CT) of the lungs. Among the four patients, two were infected with rhinovirus, one with metapneumovirus, and one with influenza A. Their chest CT findings were similar to those of COVID-19 patients reported in previous studies. Both CRV infection and COVID-19 can show various patterns on chest CT. CRV infection is thus indistinguishable from COVID-19 based on CT findings alone.

Epi-P-05 - COVID-19 infection in patients with Sézary syndrome: report of three cases

Introduction:A severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread worldwide during 2020, was declared as a public health emergency and potentially life-threatening. Patients with hematologic malignancies may have an increased risk of severe COVID-19, due to immunosuppression related to the underlying disease and its treatment. In the absence of specific data, potential risk factors for severe events of COVID-19 should be considered as for other community acquired respiratory virus (CARV) infections: >60 years, severe immunodeficiency, chemotherapy treatment. We present three patients with Sézary syndrome (SS) and COVID-19 infection.Objective:We aim to report the outcome of COVID-19 in patients with SS treated at the department of Dermatology of the Hospital Italiano de Buenos Aires.Methods and material:Patients with SS who were diagnosed positive for COVID19 infection, during worldwide pandemic in 2020. We collected retrospectively clinical data, SS evolution and treatment response.Case 1:A 58-year-old male with hypertension was diagnosed with SS stage IVA1 in July 2014, he received multiple systemic treatments such as extracorporeal photopheresis (ECP), IFN 2b, bexarotene, with partial response (PR) and eventually stable disease. In August 2020, he was hospitalized due to fever, dry cough and progressive cutaneous disease. SARS-CoV2 was confirmed, requiring invasive mechanical ventilatory (IMV) in the ICU and systemic corticosteroids. The clinical course improved with complete response (CR) of cutaneous disease and persistence of hematologic involvement. He was discharged 3 months later with no SARS-CoV-2 sequels.Case 2:A 66-year-old female with breast cancer in 2002 treated with RT and tamoxifeno was diagnosed with SS stage IVA1 in March 2012. She was treated with IFN 2b, TSEB, vorinostat and ECP with CR, relapse and then PR. In November 2020 she started chemotherapy due to cutaneous and nodal progression. A month later, she required hospitalisation and IMV due to dry cough and respiratory distress, SARS-CoV-2 was confirmed. She died 7 days later due to progression of respiratory distress.Case 3:An 86-year-old male with arterial hypertension was diagnosed with SS stage IVA1 in March 2017. He received ECP, methotrexate, with PR. In February 2021 he was hospitalized due to dry cough, headache with cutaneous disease relapse. Laboratory parameters showed pre-existing lymphopenia. SARS CoV-2 was confirmed. He was admitted to the ICU requiring IMV due to respiratory distress, and died 15 days after.Conclusions:Among our patients, two had several associated comorbidities and risk factors for a severe event of COVID-19, besides case 3 presented pre-existing lymphopenia at presentation. Case 1, despite his comorbidities and IMV, developed a favorable clinical course. To our knowledge there are many unknown factors and limited published studies, describing COVID-19 outcomes in patients with SS, most of them based on case reports.

COVID-19 AND ITS IMPACT ON RADIATION ONCOLOGY PRACTICE IN INDIA.

Patients with cancer are known to be at an increased risk for community-acquired respiratory viruses, because of their frequently observed systemic immunosuppressive state caused by the malignancy and anticancer treatments, such as chemotherapy, targeted therapy and immunotherapy. In this study different challenges of radiation oncology department and their infection control practices are given such as Pt screening, temperature monitoring and pt staff education, hygiene and departmental cleaning, zoning,work load management etc.There must be national and departmental measures to be taken in response to covid 19 pandemic.Some of risk adapted triage strategies for radiotherapy patients during covid 19 is discussed further. Comparison between covishield, covaxin and sputnik V covid 19 vaccines and lack of vaccine prioritisation for cancer patients in India have been elaborated.

Community-Acquired Respiratory Viruses Post–Lung Transplant

Survival in lung transplant recipients (LTRs) lags behind heart, liver, and kidney transplant, in part due to the direct and indirect effects of infection. LTRs have increased susceptibility to infection due to the combination of a graft continually exposed to the outside world, multiple mechanisms for impaired mucus clearance, and immunosuppression. Community-acquired respiratory viral infections (CARVs) are common in LTRs. Picornaviruses have roughly 40% cumulative incidence followed by respiratory syncytial virus and coronaviruses. Although single-center retrospective and prospective series implicate CARV in rejection and mortality, conclusive evidence for and well-defined mechanistic links to long-term outcome are lacking. Treatment of viral infections can be challenging except for influenza. Future studies are needed to develop better treatments and clarify the links between CARV and long-term outcomes.

The respiratory microbiome after lung transplantation: Reflection or driver of respiratory disease?

With the introduction of high-throughput sequencing methods, our understanding of the human lower respiratory tract's inhabitants has expanded significantly in recent years. What is now termed the "lung microbiome" has been described for healthy patients, as well as people with chronic lung diseases and lung transplants. The lung microbiome of lung transplant recipients (LTRs) has proven to be unique compared with nontransplant patients, with characteristic findings associated with disease states, such as pneumonia, acute rejection, and graft failure. In this review, we summarize the current understanding of the lung microbiome in LTRs, not only focusing on bacteria but also highlighting key findings of the viral and the fungal community. Based on our knowledge of the lung microbiome in LTRs, we propose multiple opportunities for clinical use of the microbiome to improve outcomes in this population.

The epidemiology of community-acquired respiratory viruses during the SARS-CoV-2 pandemic.

In regions of high COVID‐19 endemicity, the incidence of other respiratory viral illnesses is depressed, which may reflect biologic displacement of other pathogens or the impact of preventive strategies to reduce transmission of SARS‐CoV‐2.

Corrigendum to: Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2 Emergence Amidst Community-Acquired Respiratory Viruses.

Corrigendum to: Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2 Emergence Amidst Community-Acquired Respiratory Viruses.

COVID-19 in lung transplant recipients: A multicenter study.

This study describes the clinical presentation, treatment, and outcomes of SARS-CoV-2 infection in lung transplant recipients (LTRs). This is a multicenter, retrospective study of all adult LTRs with confirmed SARS-CoV-2 infection from March 4 until April 28, 2020 in six Spanish reference hospitals for lung transplantation. Clinical and radiological data, treatment characteristics, and outcomes were reviewed. Forty-four cases were identified in that period. The median time from transplantation was 4.2 (interquartile range: 1.11-7.3) years. Chest radiography showed acute parenchymal abnormalities in 32 (73%) cases. Hydroxychloroquine was prescribed in 41 (93%), lopinavir/ritonavir (LPV/r) in 14 (32%), and tocilizumab in 19 (43%) patients. There was a strong interaction between tacrolimus and LPV/r in all cases. Thirty-seven (84%) patients required some degree of respiratory support and/or oxygen therapy, and 13 (30%) were admitted to intermediate or intensive critical care units. Seventeen (39%) patients had died and 20 (45%) had been discharged at the time of the last follow-up. Deceased patients had a worse respiratory status and chest X-ray on admission and presented with higher D-dimer, interleukin-6, and lactate dehydrogenase levels. In this multicenter LTR cohort, SARS-CoV-2 presented with high mortality. Additionally, the severity of disease on presentation predicted subsequent mortality.

Coronavirus Disease 2019 in Recipient of Allogeneic Hematopoietic Stem Cell Transplantation: Life-threating Features Within the Early Post-engraftment Phase.

Coronavirus Disease 2019 in Recipient of Allogeneic Hematopoietic Stem Cell Transplantation: Life-threating Features Within the Early Post-engraftment Phase.

Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2 Emergence Amidst Community-Acquired Respiratory Viruses.

BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in China as the cause of coronavirus disease 2019 in December 2019 and reached Europe by late January 2020, when community-acquired respiratory viruses (CARVs) are at their annual peak. We validated the World Health Organization (WHO)–recommended SARS-CoV-2 assay and analyzed the epidemiology of SARS-CoV-2 and CARVs.MethodsNasopharyngeal/oropharyngeal swabs (NOPS) from 7663 patients were prospectively tested by the Basel S-gene and WHO-based E-gene (Roche) assays in parallel using the Basel N-gene assay for confirmation. CARVs were prospectively tested in 2394 NOPS by multiplex nucleic acid testing, including 1816 (75%) simultaneously for SARS-CoV-2.ResultsThe Basel S-gene and Roche E-gene assays were concordant in 7475 cases (97.5%) including 825 (11%) SARS-CoV-2 positives. In 188 (2.5%) discordant cases, SARS-CoV-2 loads were significantly lower than in concordant positive ones and confirmed in 105 (1.4%). Adults were more frequently SARS-CoV-2 positive, whereas children tested more frequently CARV positive. CARV coinfections with SARS-CoV-2 occurred in 1.8%. SARS-CoV-2 replaced CARVs within 3 weeks, reaching 48% of all detected respiratory viruses followed by rhinovirus/enterovirus (13%), influenza virus (12%), coronavirus (9%), respiratory syncytial virus (6%), and metapneumovirus (6%).ConclusionsWinter CARVs were dominant during the early SARS-CoV-2 pandemic, impacting infection control and treatment decisions, but were rapidly replaced, suggesting competitive infection. We hypothesize that preexisting immune memory and innate immune interference contribute to the different SARS-CoV-2 epidemiology among adults and children.