scholarly journals Analytical Performances of the Panther Fusion System for the Detection of Respiratory Viruses in the French National Reference Centre of Lyon, France

2020 ◽  
Vol 8 (9) ◽  
pp. 1371
Author(s):  
Maxime Pichon ◽  
Martine Valette ◽  
Isabelle Schuffenecker ◽  
Geneviève Billaud ◽  
Bruno Lina
Keyword(s):  
Respiratory Viruses ◽  
Molecular Testing ◽  
Fusion System ◽  
Viral Pathogens ◽  
Epidemic Season ◽  
National Reference ◽  
Reference Centre ◽  
System A ◽  
Syncytial Virus ◽  
Viral Target

Respiratory infection are mainly caused by viral pathogens. During the 2017–2018 epidemic season, Panther Fusion® Respiratory kits (Influenza virus A&B (FluA&B), respiratory syncytial virus (RSV), adenovirus (ADV), metapneumovirus (MPV), rhinovirus (RV), parainfluenzae virus (PIV), were compared to the Respiratory MultiWells System r-gene. Respiratory clinical specimens were tested retrospectively (n = 268) and prospectively (n = 463). Analytical performances were determined (sensitivity –Sep-, specificity –Spe- and κ) considering concordances of ≥2 molecular testing specific to each viral target (discrepant results were verified at the National Reference Centres for Enteroviruses or Respiratory viruses, Lyon, France). After retrospective (and prospective) testing, Sep, Spe, and κ were 100% (97.7%), 100% (99%) and 100% (94%) for FluA: 100% (95.5%), 100% (99.3%) and 100% (94%) for FluB, and 100% (88.5%), 100% (98.7%) and 100% (89%) for RSV; 82.1% (41.7%), 100% (99.5%) and 86% (54%) for ADV; 94.7% (73.7%), 96.1% (98.0%) and 91% (65%) for MPV; 96.1% (94.6%), 90.2% (98.5%) and 86% (91%) for HRV; and 90% (72.7%), 100% (99.3%) and 91% (72%), respectively, for PIV. Analytical performances were above 85% for all viruses except for ADV, MPV and PIV, confirming the analytical performance of the Panther Fusion system, a high throughput system with reduced turn-around-time, when compared to non-automated systems.

scholarly journals Metagenomic Sequencing To Detect Respiratory Viruses in Persons under Investigation for COVID-19

2020 ◽  
Vol 59 (1) ◽  
pp. e02142-20
Author(s):  
Ahmed Babiker ◽  
Heath L. Bradley ◽  
Victoria D. Stittleburg ◽  
Jessica M. Ingersoll ◽  
Autum Key ◽  
...  
Keyword(s):  
Influenza A ◽  
Viral Infections ◽  
Respiratory Viruses ◽  
Human Metapneumovirus ◽  
Molecular Testing ◽  
Metagenomic Sequencing ◽  
Rt Pcr ◽  
Human Coronavirus ◽  
Testing Algorithms ◽  
Syncytial Virus

ABSTRACTBroad testing for respiratory viruses among persons under investigation (PUIs) for SARS-CoV-2 has been performed inconsistently, limiting our understanding of alternative viral infections and coinfections in these patients. RNA metagenomic next-generation sequencing (mNGS) offers an agnostic tool for the detection of both SARS-CoV-2 and other RNA respiratory viruses in PUIs. Here, we used RNA mNGS to assess the frequencies of alternative viral infections in SARS-CoV-2 RT-PCR-negative PUIs (n = 30) and viral coinfections in SARS-CoV-2 RT-PCR-positive PUIs (n = 45). mNGS identified all viruses detected by routine clinical testing (influenza A [n = 3], human metapneumovirus [n = 2], and human coronavirus OC43 [n = 2], and human coronavirus HKU1 [n = 1]). mNGS also identified both coinfections (1, 2.2%) and alternative viral infections (4, 13.3%) that were not detected by routine clinical workup (respiratory syncytial virus [n = 3], human metapneumovirus [n = 1], and human coronavirus NL63 [n = 1]). Among SARS-CoV-2 RT-PCR-positive PUIs, lower cycle threshold (CT) values correlated with greater SARS-CoV-2 read recovery by mNGS (R2, 0.65; P < 0.001). Our results suggest that current broad-spectrum molecular testing algorithms identify most respiratory viral infections among SARS-CoV-2 PUIs, when available and implemented consistently.

scholarly journals Respiratory Viral Pathogens in Children Evaluated at Military Treatment Facilities in Oahu, Hawaii From 2014 to 2018: Seasonality and Climatic Factors

2020 ◽  
Author(s):  
Agnes S Montgomery ◽  
Michael B Lustik ◽  
Milissa U Jones ◽  
Timothy S Horseman
Keyword(s):  
Respiratory Syncytial Virus ◽  
Influenza A ◽  
Climatic Factors ◽  
Medical Center ◽  
Respiratory Viruses ◽  
Preventive Strategies ◽  
Viral Pathogens ◽  
Treatment Facilities ◽  
Syncytial Virus ◽  
Military Treatment Facilities

Abstract Five-year retrospective analysis of respiratory viruses in children less than 18 years old at Tripler Army Medical Center and outlying clinics in Oahu. Respiratory syncytial virus and influenza A showed pronounced seasonality with peaks from September to December and December to March, respectively. Results provide a better understanding of the timing of viral preventive strategies in Oahu.

The Immune Response to Respiratory Viruses: From Start to Memory

2021 ◽  
Vol 42 (06) ◽  
pp. 759-770
Author(s):  
Tom D.Y. Reijnders ◽  
Alex R. Schuurman ◽  
Tom van der Poll
Keyword(s):  
Immune Response ◽  
Viral Infections ◽  
Respiratory Viruses ◽  
Viral Pathogens ◽  
Adaptive Immune ◽  
Adaptive Immune Cells ◽  
Respiratory Viral Infections ◽  
Syncytial Virus ◽  
Destructive Inflammation ◽  
Systemic Memory

AbstractBiomedical research has long strived to improve our understanding of the immune response to respiratory viral infections, an effort that has become all the more important as we live through the consequences of a pandemic. The disease course of these infections is shaped in large part by the actions of various cells of the innate and adaptive immune systems. While these cells are crucial in clearing viral pathogens and establishing long-term immunity, their effector mechanisms may also escalate into excessive, tissue-destructive inflammation detrimental to the host. In this review, we describe the breadth of the immune response to infection with respiratory viruses such as influenza and respiratory syncytial virus. Throughout, we focus on the host rather than the pathogen and try to describe shared patterns in the host response to different viruses. We start with the local cells of the airways, onto the recruitment and activation of innate and adaptive immune cells, followed by the establishment of local and systemic memory cells key in protection against reinfection. We end by exploring how respiratory viral infections can predispose to bacterial superinfection.

scholarly journals Acute respiratory viral infections in children in Rio de Janeiro and Teresópolis, Brazil

2012 ◽  
Vol 54 (5) ◽  
pp. 249-255 ◽  
Author(s):  
Maria Carolina M. Albuquerque ◽  
Rafael B. Varella ◽  
Norma Santos
Keyword(s):  
Rio De Janeiro ◽  
Influenza A ◽  
Viral Infections ◽  
Respiratory Infections ◽  
Respiratory Viruses ◽  
Respiratory Pathogens ◽  
Viral Pathogens ◽  
Nasal Swabs ◽  
Syncytial Virus ◽  
Viral Respiratory Infections

The frequency of viral pathogens causing respiratory infections in children in the cities of Rio de Janeiro and Teresópolis was investigated. Nasal swabs from children with acute respiratory illnesses were collected between March 2006 and October 2007. Specimens were tested for viral detection by conventional (RT)-PCR and/or real time PCR. Of the 205 nasal swabs tested, 64 (31.2%) were positive for at least one of the viral pathogens. Single infections were detected in 56 samples, 50 of those were caused by RNA viruses: 33 samples tested positive for rhinovirus, five for influenza A, five for metapneumovirus, four for coronavirus and, three for respiratory syncytial virus. For the DNA viruses, five samples were positive for bocavirus and one for adenovirus. Co-infections with these viruses were detected in eight samples. Our data demonstrate a high frequency of viral respiratory infections, emphasizing the need for a more accurate diagnosis particularly for the emerging respiratory viruses. The fact that the emerging respiratory viruses were present in 9.2% of the tested samples suggests that these viruses could be important respiratory pathogens in the country.

Other Respiratory Viruses as a Cause of Community-Acquired Pneumonia

2020 ◽  
Vol 41 (04) ◽  
pp. 579-591
Author(s):  
James M. Walter
Keyword(s):  
Pneumococcal Vaccination ◽  
Respiratory Viruses ◽  
Community Acquired Pneumonia ◽  
Nucleic Acid Amplification ◽  
Respiratory Pathogens ◽  
Viral Pathogens ◽  
Vaccination Programs ◽  
Syncytial Virus ◽  
Human Parainfluenza Virus ◽  
Immunocompetent Patients

AbstractCommunity-acquired pneumonia (CAP) is a major cause of morbidity and mortality worldwide. There is growing appreciation of the burden of noninfluenza viral pathogens in CAP. Due to multiple factors including pneumococcal vaccination programs, declining rates of cigarette smoking, an aging population, and increasingly sensitive diagnostic tests, respiratory viruses are now the most common pathogens detected in CAP, outpacing Streptococcus pneumoniae. Noninfluenza respiratory pathogens are widely accepted as causal pathogens in CAP including in immunocompetent patients. This review provides an overview of five noninfluenza respiratory viral pathogens commonly implicated in CAP pathogenesis: rhinovirus, human metapneumovirus, respiratory syncytial virus, human parainfluenza virus, and human adenoviruses. Nucleic acid amplification testing platforms and their impact on antimicrobial stewardship efforts are also considered.

Respiratory viral testing and antibacterial treatment in patients hospitalized with community-acquired pneumonia

2020 ◽  
pp. 1-9
Author(s):  
Michael Klompas ◽  
Peter B. Imrey ◽  
Pei-Chun Yu ◽  
Chanu Rhee ◽  
Abhishek Deshpande ◽  
...  
Keyword(s):  
Retrospective Cohort ◽  
Respiratory Virus ◽  
Respiratory Viruses ◽  
Community Acquired Pneumonia ◽  
Blood Cultures ◽  
Antibacterial Treatment ◽  
Viral Pathogens ◽  
Antimicrobial Utilization ◽  
Viral Testing ◽  
Virus Testing

Abstract Objective: Viruses are more common than bacteria in patients hospitalized with community-acquired pneumonia. Little is known, however, about the frequency of respiratory viral testing and its associations with antimicrobial utilization. Design: Retrospective cohort study. Setting: The study included 179 US hospitals. Patients: Adults admitted with pneumonia between July 2010 and June 2015. Methods: We assessed the frequency of respiratory virus testing and compared antimicrobial utilization, mortality, length of stay, and costs between tested versus untested patients, and between virus-positive versus virus-negative patients. Results: Among 166,273 patients with pneumonia on admission, 40,787 patients (24.5%) were tested for respiratory viruses, 94.8% were tested for influenza, and 20.7% were tested for other viruses. Viral assays were positive in 5,133 of 40,787 tested patients (12.6%), typically for influenza and rhinovirus. Tested patients were younger and had fewer comorbidities than untested patients, but patients with positive viral assays were older and had more comorbidities than those with negative assays. Blood cultures were positive for bacterial pathogens in 2.7% of patients with positive viral assays versus 5.3% of patients with negative viral tests (P < .001). Antibacterial courses were shorter for virus-positive versus -negative patients overall (mean 5.5 vs 6.4 days; P < .001) but varied by bacterial testing: 8.1 versus 8.0 days (P = .60) if bacterial tests were positive; 5.3 versus 6.1 days (P < .001) if bacterial tests were negative; and 3.3 versus 5.2 days (P < .001) if bacterial tests were not obtained (interaction P < .001). Conclusions: A minority of patients hospitalized with pneumonia were tested for respiratory viruses; only a fraction of potential viral pathogens were assayed; and patients with positive viral tests often received long antibacterial courses.

scholarly journals Extracellular amoebal-vesicles: potential transmission vehicles for respiratory viruses

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Rafik Dey ◽  
Melanie A. Folkins ◽  
Nicholas J. Ashbolt
Keyword(s):  
Respiratory Syncytial Virus ◽  
Respiratory Tract ◽  
Respiratory Tract Infections ◽  
Respiratory Viruses ◽  
Environmental Persistence ◽  
Viral Dissemination ◽  
Acute Respiratory Tract Infections ◽  
High Concentrations ◽  
Syncytial Virus ◽  
Tract Infections

AbstractHuman respiratory syncytial virus (RSV) is a major cause of acute respiratory tract infections in children and immunocompromised adults worldwide. Here we report that amoebae-release respirable-sized vesicles containing high concentrations of infectious RSV that persisted for the duration of the experiment. Given the ubiquity of amoebae in moist environments, our results suggest that extracellular amoebal-vesicles could contribute to the environmental persistence of respiratory viruses, including potential resistance to disinfection processes and thereby offering novel pathways for viral dissemination and transmission.

scholarly journals Thapsigargin Is a Broad-Spectrum Inhibitor of Major Human Respiratory Viruses: Coronavirus, Respiratory Syncytial Virus and Influenza A Virus

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 234
Author(s):  
Sarah Al-Beltagi ◽  
Cristian Alexandru Preda ◽  
Leah V. Goulding ◽  
Joe James ◽  
Juan Pu ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Respiratory Syncytial Virus ◽  
Influenza A Virus ◽  
Broad Spectrum ◽  
Influenza A ◽  
Respiratory Viruses ◽  
Influenza Viruses ◽  
Virus Challenge ◽  
2009 H1n1 ◽  
Syncytial Virus

The long-term control strategy of SARS-CoV-2 and other major respiratory viruses needs to include antivirals to treat acute infections, in addition to the judicious use of effective vaccines. Whilst COVID-19 vaccines are being rolled out for mass vaccination, the modest number of antivirals in use or development for any disease bears testament to the challenges of antiviral development. We recently showed that non-cytotoxic levels of thapsigargin (TG), an inhibitor of the sarcoplasmic/endoplasmic reticulum (ER) Ca2+ ATPase pump, induces a potent host innate immune antiviral response that blocks influenza A virus replication. Here we show that TG is also highly effective in blocking the replication of respiratory syncytial virus (RSV), common cold coronavirus OC43, SARS-CoV-2 and influenza A virus in immortalized or primary human cells. TG’s antiviral performance was significantly better than remdesivir and ribavirin in their respective inhibition of OC43 and RSV. Notably, TG was just as inhibitory to coronaviruses (OC43 and SARS-CoV-2) and influenza viruses (USSR H1N1 and pdm 2009 H1N1) in separate infections as in co-infections. Post-infection oral gavage of acid-stable TG protected mice against a lethal influenza virus challenge. Together with its ability to inhibit the different viruses before or during active infection, and with an antiviral duration of at least 48 h post-TG exposure, we propose that TG (or its derivatives) is a promising broad-spectrum inhibitor against SARS-CoV-2, OC43, RSV and influenza virus.

scholarly journals 913. Distribution of Respiratory Viral Pathogens in Infants Across Different Clinical Settings from December 2019 to April 2020

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S491-S492
Author(s):  
Zaid Haddadin ◽  
Danielle A Rankin ◽  
loren lipworth ◽  
Jon Fryzek ◽  
Mina Suh ◽  
...  
Keyword(s):  
Clinical Setting ◽  
Respiratory Viruses ◽  
Clinical Settings ◽  
Research Support ◽  
Viral Pathogens ◽  
Abrupt Decrease ◽  
Nasal Swabs ◽  
Viral Testing ◽  
Support Research ◽  
Research Grant

Abstract Background Acute respiratory infections (ARI) are a major cause of morbidity and mortality in young children, with viral pathogens being the most common etiologies. However, due to limited and inconsistent clinical diagnostic viral testing in the outpatient (OP) setting compared to the inpatient (IP) setting, the actual burden and distribution of viral pathogens across these clinical settings remain largely underreported. We aimed to evaluate the frequency of common respiratory viruses in medically attended ARI in infants. Methods We conducted a prospective viral surveillance study in Davidson County, TN. Eligible infants under one year presenting with fever and/or respiratory symptoms were enrolled from OP, emergency department (ED), or IP settings. Nasal swabs were collected and tested for common viral pathogens using Luminex® NxTAG Respiratory Pathogen Panel and for SARS-CoV-2 using Luminex® NxTAG CoV extended panel. Results From 12/16/2019 to 4/30/2020, 364 infants were enrolled, and 361 (99%) had nasal swabs collected and tested. Of those, 295 (82%) had at least one virus detected; rhinovirus/enterovirus (RV/EV) [124 (42%)], respiratory syncytial virus (RSV) [101 (32%)], and influenza (flu) [44 (15%)] were the three most common pathogens detected. No samples tested positive for SARS-CoV-2. Overall, the mean age was 6.1 months, 50% were male, 45% White and 27% Hispanic. Figure 1 shows the total number of PCR viral testing results by month. RSV was the most frequent virus detected in the IP (63%) and ED (37%) settings, while RV/EV was the most common in the OP setting (Figure 2). Figure 3 displays viral seasonality by clinical setting, showing an abrupt decrease in virus-positive cases following the implementation of a stay-at-home order on March 23, 2020 in Nashville, TN. Distribution of Respiratory Viruses in Different Settings Distribution of Respiratory Viruses in Different Settings by Season Conclusion Most medical encounters in infants are due to viral pathogens, with RSV, RV/EV, and flu being the most common. However, distributions differed by clinical setting, with RSV being the most frequently detected in the IP and ED settings, and second to RV/EV in the OP setting. Continued active viral ARI surveillance in various clinical settings is warranted. Preventative measures such as vaccines and infection control measures deserve study to reduce viral ARI burden. Disclosures Zaid Haddadin, MD, CDC (Grant/Research Support, Research Grant or Support)Quidel Corporation (Grant/Research Support, Research Grant or Support)sanofi pasteur (Grant/Research Support, Research Grant or Support) Danielle A. Rankin, MPH, CIC, Sanofi Pasteur (Grant/Research Support, Research Grant or Support) Jon Fryzek, PhD, MPH, EpidStrategies (Employee) Mina Suh, MPH, International Health, EpidStrategies (Employee) Donald S. Shepard, PhD, Sanofi Pasteur (Grant/Research Support) Natasha B. Halasa, MD, MPH, Genentech (Other Financial or Material Support, I receive an honorarium for lectures - it’s a education grant, supported by genetech)Karius (Consultant)Moderna (Consultant)Quidel (Grant/Research Support, Research Grant or Support)Sanofi (Grant/Research Support, Research Grant or Support)

scholarly journals Assay System for Simultaneous Detection of SARS-CoV-2 and Other Respiratory Viruses

Diagnostics ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1084
Author(s):  
Ho-Jae Lim ◽  
Jung-Eun Park ◽  
Min-Young Park ◽  
Joo-Hwan Baek ◽  
Sunkyung Jung ◽  
...  
Keyword(s):  
Respiratory Infections ◽  
Simultaneous Detection ◽  
Respiratory Viruses ◽  
Analytical Performance ◽  
Nasopharyngeal Swab ◽  
Acid Extraction ◽  
Nucleic Acid Extraction ◽  
Significant Difference ◽  
Z Scores ◽  
Syncytial Virus

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) triggers disease with nonspecific symptoms that overlap those of infections caused by other seasonal respiratory viruses (RVs), such as the influenza virus (Flu) or respiratory syncytial virus (RSV). A molecular assay for accurate and rapid detection of RV and SARS-CoV-2 is crucial to manage these infections. Here, we compared the analytical performance and clinical reliability of Allplex™ SARS-CoV-2/FluA/FluB/RSV (SC2FabR; Seegene Inc., Seoul, South Korea) kit with those of four commercially available RV detection kits. Upon testing five target viral strains (SARS-CoV-2, FluA, FluB, RSV A, and RSV B), the analytical performance of SC2FabR was similar to that of the other kits, with no significant difference (p ≥ 0.78) in z-scores. The efficiency of SC2FabR (E-value, 81–104%) enabled reliable SARS-CoV-2 and seasonal RV detection in 888 nasopharyngeal swab specimens processed using a fully automated nucleic acid extraction platform. Bland–Altman analyses revealed an agreement value of 95.4% (SD ± 1.96) for the kits, indicating statistically similar results for all five. In conclusion, SC2FabR is a rapid and accurate diagnostic tool for both SARS-CoV-2 and seasonal RV detection, allowing for high-throughput RV analysis with efficiency comparable to that of commercially available kits. This can be used to help manage respiratory infections in patients during and after the coronavirus disease 2019 pandemic.

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