Respiratory virus infections of the lower respiratory tract elevate bronchoalveolar lavage eosinophil fraction: a clinical retrospective study and case review.

BACKGROUND: Eosinophilic airway inflammation caused by respiratory virus infection has been demonstrated in basic research; however, clinical investigations are lacking. To clarify the extent to which respiratory virus infection induces airway eosinophilic inflammation, we reviewed the results of bronchoalveolar lavage (BAL) and respiratory virus testing performed at our hospital. METHODS: Among the BAL procedures performed at the University of the Ryukyu Hospital from August 2012 to September 2016, we collected cases of acute respiratory disease in which multiplex polymerase chain reaction (PCR) was used to search for respiratory viruses. The effect of respiratory virus detection on BAL eosinophil fraction was analyzed using statistical analysis. A case study was conducted on respiratory virus detection, which showed an elevated BAL eosinophil fraction. RESULTS: A total of 95 cases were included in this study, of which 17 were PCR-positive. The most common respiratory virus detected was parainfluenza virus (eight cases). The PCR-positive group showed a higher BAL eosinophil fraction than the PCR-negative group (p = 0.030), and more cases had a BAL eosinophil fraction > 3% (p = 0.017). Multivariate analysis revealed that being PCR-positive was significantly associated with BAL eosinophil fraction > 1% and > 3%. There were nine PCR-positive cases with a BAL eosinophil fraction > 1%, of which two cases with parainfluenza virus infection had a marked elevation of BAL eosinophil fraction and were diagnosed with eosinophilic pneumonia. CONCLUSIONS: Cases of viral infection of the lower respiratory tract showed an elevated BAL eosinophil fraction. The increase in eosinophil fraction due to respiratory virus infection was generally mild, whereas some cases showed marked elevation and were diagnosed with eosinophilic pneumonia. Respiratory virus infection is not a rare cause of elevated BAL eosinophil fraction and should be listed as a differential disease in the practice of eosinophilic pneumonia.

Bilateral Lung Transplantation With Donor Positive for COVID-19 Infection on Bronchoalveolar Lavage: A Case Report.

Initial experience with lung transplant of COVID-19-positive donors was marked by disappointing results, including a reported case of mortality through donor to recipient transmission of infection. However, since that time a number of improvements in preventative and therapeutic measures against COVID-19 have been developed. We present the case of a 51-year-old woman with scleroderma-associated interstitial lung disease who was awaiting lung transplant. A potential donor with excellent lung physiology was located; however, initial testing on bronchoalveolar lavage (BAL) was positive for COVID-19. The donor had tested positive 2 weeks prior and had symptomatically recovered. Our patient had been fully vaccinated but not seroconverted. Given the history of a donor with recovering COVID infection and a fully immunized recipient, our multidisciplinary team elected to proceed with the transplant. The patient successfully underwent bilateral lung transplant with standard induction immunosuppression. Bebtelovimab was given post-transplant day 1 because the recipient remained seronegative to COVID-19. Serial bronchoalveolar lavages post transplant have been negative for COVID-19. The patient has done well after transplant. She was seen in the clinic 2 months post transplant and is ambulatory without supplemental oxygen requirements. To our knowledge, this represents the first reported successful case of lung transplant with a donor positive for COVID-19 on lower respiratory tract sampling.

Diagnostic value of bronchoscopy in Sars-Cov-2 infection: A systematic review.

OBJECTIVE: To investigate the diagnostic performance of bronchoscopy in patients with coronavirus disease 2019 infection. METHODS: The systematic review was conducted in April 2021 and comprised search of published articles and preprint servers for original articles assessing diagnostic performance of bronchoscopy in patients with suspected coronavirus disease 2019 infection. The primary outcome of interest was diagnostic sensitivity of bronchoalveolar lavage in the patients. The quality of each study was assessed using the Quality Assessment, Data Abstraction and Synthesis-2 tool. RESULTS: Of the 29 full-text articles assessed for eligibility, 4(13.8%) were included collectively comprising 209 patients who had undergone bronchoalveolar lavage. Mean sensitivity of bronchoalveolar lavage was 83.5% ± 10.63 (range: 68.2-940%). Overall, the 4 studies had an unclear or low risk of bias. CONCLUSIONS: Limited data suggested that bronchoscopy with bronchoalveolar lavage did not have reliably higher diagnostic sensitivity than that reported for either nasopharyngeal or oropharyngeal swabs.

Massive sequencing of the V3-V4 hypervariable region of bronchoalveolar lavage from patients with COVID-19 and VAP reveals the collapse of the pulmonary microbiota.

Background. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is a predisposing factor for the development of healthcare-associated infections, of which ventilator-associated pneumonia (VAP) is one.Hypothesis. VAP is caused by ESKAPE bacteria and other pathogens not detected by microbiological culture.Aim. To elucidate the bacterial pathogens of severe coronavirus disease 2019 (COVID-19) and VAP patients by massive sequencing and to predict their degree of relationship with the age and sex of the patients.Methods. Analysis of ribosomal libraries of the V3-V4 hypervariable region obtained by Illumina sequencing of bronchoalveolar lavages from COVID-19 and VAP (first wave) patients from Hospital Juárez de México.Results. Acinetobacter and Pseudomonas were the main bacterial genera in the bronchoalveolar lavages (BALs) analysed. Other members of the ESKAPE group, such as Enterococcus and Klebsiella, were also identified. Taxonomic composition per patient showed that non-ESKAPE genera were present with significant relative abundances, such as Prevotella, Stenotrophomas, Enterococcus, Mycoplasma, Serratia and Corynebacterium. Kruskal-Wallis analysis proved that VAP acquisition is an adverse event that is not influenced by the sex and age of COVID-19 patients.Discussion. Metagenomic findings in COVID-19/VAP patients highlight the importance of implementing comprehensive microbiological diagnostics by including alternative tools for the detection of the causal agents of healthcare-associated infections (HAIs).Conclusions. Timely identification of bacteria 'not sought' in diagnostic bacteriology laboratories will allow specific and targeted treatments. Implications for the restricted diagnosis of VAP causative agents in COVID-19 patients and the presence of pathogens not detected by classical microbiology are analysed and discussed.

Pulmonary alveolar proteinosis due to heterozygous mutation in OAS1: Whole lung lavages for long-term bridging to hematopoietic stem cell transplantation.

INTRODUCTION: Pulmonary alveolar proteinosis (PAP) is defined by increased accumulation of surfactant in the alveolar space. PAP has been reported to be associated with a large number of clinical conditions and diseases. Whole lung lavages (WLLs) can be helpful to stabilize the clinical course of PAP until the underlying condition is identified, which may enable more specific treatment. Recently, heterozygous OAS1 gain-of-function variants were described as cause in patients with infantile-onset PAP combined with hypogammaglobulinemia. CASE PRESENTATION: At age 4 months, a female infant born to term was diagnosed with hypogammaglobulinemia and treated with monthly immunoglobulin injections. At age 15 months, the girl needed supplemental oxygen at night, and at age 18 months, also during the day. At age 2 years, PAP of unknown etiology was diagnosed by computed tomography scan and open lung biopsy. Subsequently, monthly WLLs were started, which stabilized the clinical course for over 2 years until a disease-causing OAS1 variant was diagnosed and the patient was successfully treated by hematopoietic stem cell transplantation (HSCT). CONCLUSION: Here, we describe the successful management of a female patient with severe PAP caused by a heterozygous OAS1 gain-of-function variant until a definitive diagnosis was made and cured by HSCT.

Cytopathological Findings in Bronchoalveolar Lavage from Patients with COVID-19.

Information on cellular analysis of bronchoalveolar lavage (BAL) in patients with COVID-19 is limited. Some studies have described an increase in lymphocyte percentage or exuberant plasmacytosis. Some reports addressed the importance of molecular testing on BAL samples to confirm COVID-19 pneumonia, in clinically highly suspected patients with consecutive negative nasopharyngeal swab results. In addition to atypical lymphocytes in the peripheral blood, morphologic findings of atypical lymphocytes in BAL were also reported in a few patients. The objective of this study was to describe the cytopathic characteristics identified, any data presented here are descriptives and intended to trigger further research. Three general aspects have been evaluated in each sample: reactive changes, virus-related pathological changes, and differential leukocyte count. Seventeen samples were collected. All samples were negative for malignancy, with an inflammatory background, predominantly lymphohistiocytic in 5 samples, histiocytic in 9, and 3 with predominantly neutrophilic. Hemosiderin-laden macrophages were observed in 12/17. Nonspecific reactive cell changes were identified in 4 samples, including bronchial, alveolar, and reserve cell hyperplasia. Virus-related pathological changes were observed in 14 samples, such as loss of nuclear chromatin pattern, lymphocytes with atypical nuclei, nuclear and cytoplasmic inclusions, multinucleations in bronchial cells and macrophages, or multinucleated giant cells. The identification of multinucleated giant cells could represent a cytopathic effect induced by the virus, at the same time the nuclear clearance of pneumocytes as a possible direct effect. BAL is a procedure aimed at obtaining cells from the respiratory tract that can provide valuable and rapid information. It is important to collect and describe as many cytopathological findings as possible, which can provide relevant information for future studies.

Tracheal Aspirate and Bronchoalveolar Lavage as Potential Specimen Types for COVID-19 Testing Using the Cepheid Xpert Xpress SARS-CoV-2/Flu/RSV.

Xpert Xpress SARS-CoV-2/Flu/RSV is a rapid diagnostic test currently approved for the detection of SARS-CoV-2 using upper respiratory tract specimens. This study attempts to assess the performance of this assay using upper and lower respiratory tract specimens by comparing its results to the lab-developed PCR test. We assessed the performance of GeneXpert for the detection of SARS-CoV-2, influenza A, influenza B, and respiratory syncytial virus for upper respiratory tract specimens. In addition, the SARS-CoV-2 detection was evaluated for lower respiratory tract specimens (bronchoalveolar lavage and tracheal aspirate). Precision and reproducibility of the test were also assessed using samples with varying cycle threshold values. Xpert Xpress SARS-CoV-2/Flu/RSV shows 100% positive and negative agreements for all four targets when tested using upper respiratory tract specimens. For lower respiratory tract specimens, tracheal aspirate and bronchoalveolar lavage samples respectively show 96% and 100% positive percent agreement for SARS-Cov-2 target only. No positive flu/RSV samples were included for lower respiratory tract specimens. Both samples show 100% negative percent agreement. The precision and reproducibility assay also showed 100% correspondence. Xpert Xpress SARS-CoV-2/Flu/RSV can be potentially used for SARS-Cov-2 detection in lower respiratory tract specimens. Performance passed our study acceptance criteria and shows promising implications as a point of care detection assay. IMPORTANCE Cepheid's Xpert Xpress SARS-CoV-2/Flu/RSV provides a means of rapid diagnosis that can help in hospital bed management and patient flow. It is also important for each microbiology lab to increase its capacity and most importantly have a different platform to overcome the anticipated reagent shortage at times of peak community transmission. There is limited evidence on using it for lower respiratory tract specimens. Here we present our validation for upper respiratory tract specimens as well as a potential use for lower respiratory specimens (BAL and TA), and we discuss some of the applications we have been using in our organization.

Aspergillus-PCR in bronchoalveolar lavage - diagnostic accuracy for invasive pulmonary aspergillosis in critically ill patients.

BACKGROUND: The diagnosis of invasive pulmonary aspergillosis (IPA) in intensive care unit (ICU) patients is challenging, and the role of Aspergillus-PCR in bronchoalveolar lavage (BAL) is unknown. OBJECTIVES: This study evaluated diagnostic accuracy of Aspergillus-PCR in BAL in IPA in three different cohorts: ICU-admitted patients with COVID-19, ICU-admitted patients without COVID-19 and immunocompromised patients. METHODS: All stored available BAL samples collected from three patient groups were tested with Aspergillus-PCR (AsperGenius® ). IPA was diagnosed according to appropriate criteria for each patient group. RESULTS: We included 111 BAL samples from 101 patients: 52 (51%) patients admitted to ICU for COVID-19, 24 (24%) admitted to ICU for other reasons and 25 (25%) immunocompromised. There were 31 cases of IPA (28%). Aspergillus-PCR sensitivity was 64% (95% CI 47-79) and specificity 99% (95% CI 93-100). Aspergillus-PCR sensitivity was 40% (95%CI 19-64) in ICU COVID-19, 67% (95% CI 21-93) in non-COVID-19 ICU patients and 92% (95%CI 67-98) in the immunocompromised. The concordance between positive BAL-GM and BAL-PCR in patients with and without IPA was significantly lower in ICU patients (32%; 43% in COVID-19, 18% in non-COVID-19) than in the immunocompromised (92%), p < .001. CONCLUSIONS: Aspergillus-PCR in BAL improves the diagnostic accuracy of BAL-GM in ICU patients.

Myeloid cell interferon responses correlate with clearance of SARS-CoV-2.

Emergence of mutant SARS-CoV-2 strains associated with an increased risk of COVID-19-related death necessitates better understanding of the early viral dynamics, host responses and immunopathology. Single cell RNAseq (scRNAseq) allows for the study of individual cells, uncovering heterogeneous and variable responses to environment, infection and inflammation. While studies have reported immune profiling using scRNAseq in terminal human COVID-19 patients, performing longitudinal immune cell dynamics in humans is challenging. Macaques are a suitable model of SARS-CoV-2 infection. Our longitudinal scRNAseq of bronchoalveolar lavage (BAL) cell suspensions from young rhesus macaques infected with SARS-CoV-2 (n = 6) demonstrates dynamic changes in transcriptional landscape 3 days post- SARS-CoV-2-infection (3dpi; peak viremia), relative to 14-17dpi (recovery phase) and pre-infection (baseline) showing accumulation of distinct populations of both macrophages and T-lymphocytes expressing strong interferon-driven inflammatory gene signature at 3dpi. Type I interferon response is induced in the plasmacytoid dendritic cells with appearance of a distinct HLADR+CD68+CD163+SIGLEC1+ macrophage population exhibiting higher angiotensin-converting enzyme 2 (ACE2) expression. These macrophages are significantly enriched in the lungs of macaques at 3dpi and harbor SARS-CoV-2 while expressing a strong interferon-driven innate anti-viral gene signature. The accumulation of these responses correlated with decline in viremia and recovery.

Acute Dyspnea and Hemoptysis in an 84-Year-Old Man With Multiple Comorbidities.

CASE PRESENTATION: An 84-year-old man with an active smoking habit presented to the ED with dyspnea, hemoptysis, and thick phlegm that was difficult to clear. He reported no weight loss, no fever, and no chest pain or dysphonia. He denied both international travel and previous contact with confirmed cases of TB or SARS-CoV-2. He had no known occupational exposures. The patient's personal history included a resolved complete atrioventricular block that required a permanent pacemaker, moderate-to-severe COPD, rheumatoid arthritis (treated with oral prednisone, 2.5 mg/d) and B-chronic lymphocytic leukemia (treated with methotrexate and prophylactic oral supplements of ferrous sulfate). Moreover, he was in medical follow up because of a peptic ulcer, atrophic gastritis, and colonic diverticulosis. The patient also had a history of thoracic surgery after an episode of acute mediastinitis from an odontogenic infection, which required ICU management and temporal tracheostomy.

Targeting RNA with Next- and Third-Generation Sequencing Improves Pathogen Identification in Clinical Samples.

Fast and accurate identification of microbial pathogens is critical for the proper treatment of infections. Traditional culture-based diagnosis in clinics is increasingly supplemented by metagenomic next-generation-sequencing (mNGS). Here, RNA/cDNA-targeted sequencing (meta-transcriptomics using NGS (mtNGS)) is established to reduce the host nucleotide percentage in clinic samples and by combining with Oxford Nanopore Technology (ONT) platforms (meta-transcriptomics using third-generation sequencing, mtTGS) to improve the sequencing time. It shows that mtNGS improves the ratio of microbial reads, facilitates bacterial identification using multiple-strategies, and discovers fungi, viruses, and antibiotic resistance genes, and displaying agreement with clinical findings. Furthermore, longer reads in mtTGS lead to additional improvement in pathogen identification and also accelerate the clinical diagnosis. Additionally, primary tests utilizing direct-RNA sequencing and targeted sequencing of ONT show that ONT displays important potential but must be further developed. This study presents the potential of RNA-targeted pathogen identification in clinical samples, especially when combined with the newest developments in ONT.

A systematic review and metanalysis of diagnostic yield of BAL for detection of SARS-CoV-2.

BACKGROUND: The gold standard for diagnosing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is microbiological confirmation by reverse transcriptase-polymerase chain reaction (RT-PCR)1 most commonly done using oropharyngeal (OP) and nasopharyngeal swabs (NP). But in suspected cases, where these samples are false-negative, bronchoalveolar lavage (BAL) may prove diagnostic. OBJECTIVES: Hence, the diagnostic yield of BAL for detection of SARS-CoV-2 in cases of non-diagnostic upper respiratory tract samples is reviewed. METHODS: Databases such as MEDLINE, Scopus, and Google Scholar were searched using a systematic search strategy. The current study has been in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines and has been registered with the International Prospective Registry of Systematic Reviews (CRD42020224088). RESULTS: 911 records were identified at initial database extraction, of which 317 duplicates were removed and, 596 records were screened for inclusion eligibility. We included total 19 studies in the systematic review, and 17 were included in metanalysis. The pooled estimate of SARS-CoV-2 positivity in BAL was 11% (95%CI: 0.01-0.24). A sensitivity analysis also showed that the results appear to be robust and minimal risk of bias amongst the studies. CONCLUSION: The current study demonstrates that BAL can be used to diagnose additional cases primary disease and superadded infections in patients with severe COVID-19 lower respiratory tract infection.

Safety and harms of bronchoalveolar lavage for acute respiratory failure: A systematic review and meta-analysis.

BACKGROUND: This review aimed to investigate whether bronchoalveolar lavage (BAL) is safe in patients with severe acute respiratory failure (ARF). METHODS: We searched the MEDLINE, CENTRAL, and other databases up to June 2, 2021 for studies that examined BAL for severe ARF. We included all cohort studies and randomized or non-randomized trials, while we excluded case-control studies, case reports, and case series. We evaluated the quality of the evidence using the Grading of Recommendations, Assessment, Development, and Evaluation approach. RESULTS: We included 17 studies (1085 patients) in the meta-analysis. The integrated frequency of death was 0.000% (95% confidence interval [CI]: 0.000-0.045%, I2 = 0.0%). The pooled risk of severe complications of respiratory system, cardiovascular system, and major bleeding was 1.32% (95% CI: 0.000-4.41%, I2 = 84.8%), 0.040% (95% CI: 0.000-0.71%, I2 = 9.3%), and 0.000% (95% CI: 0.000-0.27%, I2 = 0.0%), respectively. In the subgroup analysis with mechanical ventilation during BAL, there were few severe complications of the respiratory system (3/717 patients in 13 studies) and almost no heterogeneity (I2 = 0.0%). CONCLUSIONS: Our study suggests that severe complications of BAL for severe ARF are probably rare, particularly in patients receiving mechanical ventilation. After considering the risks and benefits, it would be worthwhile to consider performing BAL in patients with severe ARF of unknown etiology to pursue its cause. TRIAL REGISTRATION: The protocol was registered with the University Hospital Medical Information Network Clinical Trials Registry (UMIN000040600).

Delayed positive COVID19 nasopharyngeal test, a case study with clinical and pathological correlation.

BACKGROUND: There are various reasons for delayed positive nasopharyngeal PCR tests for coronavirus disease 2019 (COVID19) in not only asymptomatic but also severely diseased patients. The pathophysiological attributes are not known. We explore this possibility through a case report. CASE PRESENTATION: A 64-year-old male with history of pulmonary fungal infection, asthma and chronic pulmonary obstructive disease (COPD), diabetes, coronary artery disease presented with shortness of breath, fever and chest image of ground opacity, reticular interstitial thickening, highly suspicious for COVID19. However, nasopharyngeal swab tests were discordantly negative for four times in two weeks, and IgG antibody for COVID19 was also negative. However, serum IgE level was elevated. No other pathogens are identified. His symptoms deteriorated despite corticosteroid, antibiotics and bronchodilator treatment. Bronchoalveolar lavage (BAL) and open lung wedge biopsy were performed for etiology diagnosis. They demonstrated COVID19 viral RNA positive fibrosing organizing pneumonia with respiratory tract damage characterized by suspicious viral cytopathic effect, mixed neutrophilic, lymphoplasmacytic, histiocytic and eosinophilic inflammation and fibrosis besides expected asthma and COPD change. One week later, repeated COVID19 nasopharyngeal tests on day 40 and day 49 became positive. CONCLUSION: Our case and literature review indicate that allergic asthma and associated high IgE level together with corticosteroid inhalation might contribute to the delayed positive nasopharyngeal swab in upper airway; COPD related chronic airways obstruction and the addition of fibrosis induced ventilator dependence and poor prognosis in COVID19 pneumonia, and should be therapeutically targeted besides antiviral therapy.

Mycotic infection prevalence among patients undergoing bronchoalveolar lavage with search of SARS-CoV-2 after two negative nasopharyngeal swabs.

The evidence that severe coronavirus disease 2019 (COVID-19) is a risk factor for development of mycotic respiratory infection with an increased mortality is rising. Immunosuppressed are among the most susceptible patients andAspergillusspecies is the most feared superinfection. In this study we evaluated mycotic isolation prevalence on bronchoalveolar lavage (BAL) of patients who underwent bronchoscopy in search of severe acute respiratory coronavirus 2 (SARS-CoV-2) RNA. Moreover, we described the clinical characteristics and main outcomes of these patients. We included 118 patients, 35.9% of them were immunosuppressed for different reasons: in 23.7% we isolated SARS-CoV-2 RNA, in 33.1% we identified at least one mycotic agent and both in 15.4%. On BAL we observed in three casesAspergillusspp, in six casesPneumocystisand in 32Candidaspp. The prevalence of significant mold infection was 29.3% and 70.7% of cases were false positive or clinically irrelevant infections. In-hospital mortality of patients with fungal infection was 15.3%. The most frequent computed tomography (CT) pattern, evaluated with the Radiological Society of North America consensus statement, among patients with a mycotic pulmonary infection was the atypical one (p< 0.0001). Mycotic isolation on BAL may be interpreted as an innocent bystander, but its identification could influence the prognosis of patients, especially in those who need invasive investigations during the COVID-19 pandemic; BAL plays a fundamental role in resolving clinical complex cases, especially in immunosuppressed patients independently from radiological features, without limiting its role in ruling out SARS-CoV-2 infection.

Diffuse alveolar haemorrhage: a rare complication of clopidogrel use.

Diffuse alveolar haemorrhage (DAH) has been reported as a rare complication of clopidogrel use and is usually a diagnosis of exclusion. We describe the case of an 88-year-old Native American woman who presented with acute hypoxic respiratory failure with CT scan of the chest showing diffuse bilateral ground-glass opacities. She had been on clopidogrel for 6 months for a carotid artery stent. Bronchoscopy with bronchoalveolar lavage and transbronchial biopsies revealed DAH. Infectious and autoimmune work-up were all negative. Clopidogrel was stopped and high-dose steroids were started. Her symptoms gradually improved until she was discharged from the hospital. The differential DAH is broad. Anticoagulant-induced DAH should be part of the differential diagnosis, and is usually a diagnosis of exclusion.

Concentrated Secretome of Adipose Stromal Cells Limits Influenza A Virus-Induced Lung Injury in Mice.

Despite vaccination and antivirals, influenza remains a communicable disease of high burden, with limited therapeutic options available to patients that develop complications. Here, we report the development and preclinical characterization of Adipose Stromal Cell (ASC) concentrated secretome (CS), generated by process adaptable to current Good Manufacturing Practices (cGMP) standards. We demonstrate that ASC-CS limits pulmonary histopathological changes, infiltration of inflammatory cells, protein leak, water accumulation, and arterial oxygen saturation (spO2) reduction in murine model of lung infection with influenza A virus (IAV) when first administered six days post-infection. The ability to limit lung injury is sustained in ASC-CS preparations stored at -80 °C for three years. Priming of the ASC with inflammatory factors TNFα and IFNγ enhances ASC-CS ability to suppress lung injury. IAV infection is associated with dramatic increases in programmed cell death ligand (PDL1) and angiopoietin 2 (Angpt2) levels. ASC-CS application significantly reduces both PDL1 and Angpt2 levels. Neutralization of PDL1 with anti-mouse PDL1 antibody starting Day6 onward effectively ablates lung PDL1, but only non-significantly reduces Angpt2 release. Most importantly, late-phase PDL1 neutralization results in negligible suppression of protein leakage and inflammatory cell infiltration, suggesting that suppression of PDL1 does not play a critical role in ASC-CS therapeutic effects.

Epidemiology and precision of SARS-CoV-2 detection following lockdown and relaxation measures.

OBJECTIVES: Detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is key to the clinical and epidemiological assessment of CoVID-19. We cross-validated manual and automated high-throughput testing for SARS-CoV-2-RNA, evaluated SARS-CoV-2 loads in nasopharyngeal-oropharyngeal swabs (NOPS), lower respiratory fluids, and plasma, and analyzed detection rates after lockdown and relaxation measures. METHODS: Basel-S-gene, Roche-E-gene, and Roche-cobas®6800-Target1 and Target2 were prospectively validated in 1344 NOPS submitted during the first pandemic peak (Week 13). Follow-up cohort (FUP) 1, 2, and 3 comprised 10,999, 10,147, and 19,389 NOPS submitted during a 10-week period until Weeks 23, 33, and 43, respectively. RESULTS: Concordant results were obtained in 1308 cases (97%), including 97 (9%) SARS-CoV-2-positives showing high quantitative correlations (Spearman's r > .95; p < .001) for all assays and high precision by Bland-Altman analysis. Discordant samples (N = 36, 3%) had significantly lower SARS-CoV-2 loads (p < .001). Following lockdown, detection rates declined to <1% in FUP-1, reducing single-test positive predictive values from 99.3% to 85.1%. Following relaxation, rates flared up to 4% and 12% in FUP-2 and -3, but infected patients were younger than during lockdown (34 vs. 52 years, p < .001). In 261 patients providing 936 NOPS, SARS-CoV-2 loads declined by three orders of magnitude within 10 days postdiagnosis (p < .001). SARS-CoV-2 loads in NOPS correlated with those in time-matched lower respiratory fluids or in plasma but remained detectable in some cases with negative follow-up NOPS, respectively. CONCLUSION: Manual and automated assays significantly correlated qualitatively and quantitatively. Following a successful lockdown, declining positive predictive values require independent dual-target confirmation for reliable assessment. Confirmatory and quantitative follow-up testing should be obtained within <5 days and consider lower respiratory fluids in symptomatic patients with SARS-CoV-2-negative NOPS.