Eight influenza virus cellular manipulations which can boost concurrent SARS-CoV-2 infections to severe outcomes.

Viral pathogens in the lungs can cause severe outcomes, including acute lung injury and acute respiratory distress syndrome. Dangerous respiratory pathogens include some influenza A and B viruses, and the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Unfortunately, concurrent infections of influenza virus and SARS-CoV-2 increase severe outcome probabilities. Influenza viruses have eight cellular manipulations which can assist concurrent SARS-CoV-2 viral infections. The eight cellular manipulations include: (1) viral protein binding with cellular sensors to block antiviral transcription factors and cytokine expressions, (2) viral protein binding with cell proteins to impair cellular pre-messenger ribonucleic acid splicing, (3) increased ribonucleic acid virus replication through the phosphatidylinositol 3-kinase/Akt (protein kinase B) pathway, (4) regulatory ribonucleic acids to manipulate cellular sensors and pathways to suppress antiviral defenses, (5) exosomes to transmit influenza virus to uninfected cells to weaken cellular defenses before SARS-CoV-2 infection, (6) increased cellular cholesterol and lipids to improve virion synthesis stability, quality and virion infectivity, (7) increased cellular autophagy, benefiting influenza virus and SARS-CoV-2 replications and (8) adrenal gland stimulation to produce glucocorticoids, which suppress immune cells, including reduced synthesis of cytokines, chemokines and adhesion molecules. Concurrent infections by one of the influenza viruses and SARS-CoV-2 will increase the probability of severe outcomes, and with sufficient synergy potentially enable the recurrence of tragic pandemics.

Four thermostatic steps: A novel CRISPR-Cas12-based system for the rapid at-home detection of respiratory pathogens.

The outbreak of coronavirus disease 2019 (COVID-19) in 2019 has severely damaged the world's economy and public health and made people pay more attention to respiratory infectious diseases. However, traditional quantitative real-time polymerase chain reaction (qRT-PCR) nucleic acid detection kits require RNA extraction, reverse transcription, and amplification, as well as the support of large-scale equipment to enrich and purify nucleic acids and precise temperature control. Therefore, novel, fast, convenient, sensitive and specific detection methods are urgently being developed and moving to proof of concept test. In this study, we developed a new nucleic acid detection system, referred to as 4 Thermostatic steps (4TS), which innovatively allows all the detection processes to be completed in a constant temperature device, which performs extraction, amplification, cutting of targets, and detection within 40 min. The assay can specifically and sensitively detect five respiratory pathogens, namely SARS-CoV-2, Mycoplasma felis (MF), Chlamydia felis (CF), Feline calicivirus (FCV), and Feline herpes virus (FHV). In addition, a cost-effective and practical small-scale reaction device was designed and developed to maintain stable reaction conditions. The results of the detection of the five viruses show that the sensitivity of the system is greater than 94%, and specificity is 100%. The 4TS system does not require complex equipment, which makes it convenient and fast to operate, and allows immediate testing for suspected infectious agents at home or in small clinics. Therefore, the assay system has diagnostic value and significant potential for further reducing the cost of early screening of infectious diseases and expanding its application. KEY POINTS: • The 4TS system enables the accurate and specific detection of nucleic acid of pathogens at 37 °C in four simple steps, and the whole process only takes 40 min. •A simple alkali solution can be used to extract nucleic acid. • A small portable device simple to operate is developed for home diagnosis and detection of respiratory pathogens.

Evaluation of BioFire Respiratory Panel 2 plus for Detection of Bordetella pertussis in Nasopharyngeal Swab Specimens from Children with Clinically Suspected Pertussis.

The objective of this study was to compare the performances of BioFire Respiratory Panel 2 (RP2) plus, quantitative real-time PCR (qPCR), and culture for the detection of Bordetella pertussis in nasopharyngeal swab (NPS) specimens. Consecutive NPS specimens were collected from patients with clinically suspected pertussis from 1 March 1 to 31 July 2018 in Shenzhen Children's Hospital. All the specimens were tested in parallel by RP2 plus, qPCR, and culture methods. A total of 464 children were enrolled in this study. The positive pertussis rates of culture, RP2 plus, and qPCR were 23.1%, 39.0%, and 38.4%, respectively. Compared to the combined reference standard, the sensitivity, specificity, positive predictive value, and negative predictive values were, respectively, 56.6% (95% confidence interval [CI], 49.2 to 63.7%), 100% (98.3 to 100%), 100% (95.7 to 100%), and 77.0% (72.2 to 81.2%) for culture, 89.9% (84.5 to 93.7%), 96.0% (92.8 to 97.9%), 93.9% (89.1 to 96.8%), and 93.3% (89.5 to 95.8%) for RP2 plus, and 86.8% (80.9 to 91.1%), 94.9% (91.4 to 97.1%), 92.1% (86.9 to 95.5%), and 91.3% (87.2 to 94.2%) for qPCR. The most prevalent codetected pathogen was human rhinovirus/enterovirus (n = 99, 52.4%), followed by parainfluenza virus (n =32, 16.9%) and respiratory syncytial virus (n = 29, 15.3%), in children with B. pertussis present, which was consistent with the top three pathogens previously found in children with B. pertussis absent. Turnaround times for RP2 plus, qPCR, and culture were 2 h, 8 h, and 120 h, respectively. RP2 plus quickly and accurately detected B. pertussis, providing valuable information for an early clinical diagnosis and optimal choice of therapy. IMPORTANCE In recent years, there have been some epidemic or local outbreaks of pertussis in countries with high vaccination rates. One of the crucial factors in controlling pertussis is early diagnosis, which is based on specific laboratory measurements, including culture, serological tests, and PCR assays. Compared to culture and serological tests, PCR is more suitable for clinical application, with a fast detection speed of several hours independent of the disease stage and individual vaccination status. BioFire Respiratory Panel 2 plus, a multiplex PCR assay for simultaneously detecting 22 respiratory pathogens, facilitates the quick detection of Bordetella pertussis and coinfecting respiratory pathogens. It also provides valuable information for an early clinical diagnosis and optimal choice of therapy for children with clinically suspected pertussis.

Lipid Nanoparticles as Promising Carriers for mRNA Vaccines for Viral Lung Infections.

In recent years, there has been an increase in deaths due to infectious diseases, most notably in the context of viral respiratory pathogens. Consequently, the focus has shifted in the search for new therapies, with attention being drawn to the use of nanoparticles in mRNA vaccines for targeted delivery to improve the efficacy of these vaccines. Notably, mRNA vaccine technologies denote as a new era in vaccination due to their rapid, potentially inexpensive, and scalable development. Although they do not pose a risk of integration into the genome and are not produced from infectious elements, they do pose challenges, including exposing naked mRNAs to extracellular endonucleases. Therefore, with the development of nanotechnology, we can further improve their efficacy. Nanoparticles, with their nanometer dimensions, move more freely in the body and, due to their small size, have unique physical and chemical properties. The best candidates for vaccine mRNA transfer are lipid nanoparticles (LNPs), which are stable and biocompatible and contain four components: cationic lipids, ionizable lipids, polyethylene glycols (PEGs), and cholesterol, which are used to facilitate cytoplasmic mRNA delivery. In this article, the components and delivery system of mRNA-LNP vaccines against viral lung infections such as influenza, coronavirus, and respiratory syncytial virus are reviewed. Moreover, we provide a succinct overview of current challenges and potential future directions in the field.

Exploring the Possible Phenomenon of Viral Interference Between the Novel Coronavirus and Common Respiratory Viruses.

At the peak of the 2021 wave of the SARS-CoV-2 alpha variant in North America, there was concern for a superimposed wave of viral respiratory infections. There was, however, an apparent shift in the usual epidemiology of these pathogens, especially during the traditional influenza season from approximately October 2020 to March 2021. This article seeks to briefly describe the epidemiology of notable respiratory pathogens during the first wave of the COVID-19 pandemic and to focus on one possible factor for the trends observed. There are many contributory elements to the observed viral trends, but in particular, we present a synopsis of the data supporting the phenomenon of viral interference in relation to the clinically relevant early variants of SARS-CoV-2 (ancestral lineage, alpha, delta, omicron). Viral interference has been implicated in previous pandemics and is currently not well characterized in the setting of the COVID-19 pandemic. It is important to understand this dynamic and its effect on the predominant variants of COVID-19 thus far so that we may appropriately consider its possible influence in patient pathology going forward.

The Clinical Performance of the BioCode Respiratory Pathogen Panel for the Detection of Viruses and Bacteria from Nasopharyngeal Swabs.

Early detection of microbial pathogens causing respiratory tract infection plays a crucial role in clinical management. The BioCode Respiratory Pathogen Panel (BioCode RPP) utilizes reverse transcriptase PCR (RT-PCR) in combination with barcoded magnetic beads to amplify, detect, and identify respiratory pathogens. This panel qualitatively detects and identifies 14 viruses, including influenza virus A with H1 pdm09, H1, and H3 subtyping; influenza B; respiratory syncytial virus (RSV); human metapneumovirus; parainfluenza virus 1; parainfluenza virus 2; parainfluenza virus 3; parainfluenza virus 4; coronavirus (229E, NL63, OC43, and HKU1); adenovirus; and human rhinovirus/enterovirus, and 3 bacteria, including Chlamydia pneumoniae, Mycoplasma pneumoniae, and Bordetella pertussis. Reproducibility, which was assessed with contrived specimens containing 12 targets at 3 clinical sites, with 2 operators at each site for 5 days, was 99.4% for Flu A H3 and Flu B, 98.9% for RSV, and 100% for the remaining 9 targets assayed. A multicenter clinical trial evaluated the performance of the BioCode RPP with 2,647 nasopharyngeal swab specimens from 5 geographically distinct sites and revealed comparable performance between the BioCode RPP and FilmArray Respiratory Panel (FA-RP). Specifically, the positive percent agreements (PPAs) for various pathogens ranged between 80.8% and 100% compared with the FA-RP (1.7 and 2.0). Negative percent agreement ranged from 98.4% to 100% for BioCode RPP. The BioCode RPP also offers scalable automated testing capability of up to 96 specimens in a single run with total sample-to-result time under 5 h. The invalid rate of the BioCode RPP on initial testing was 1.0% (26/2,649). IMPORTANCE Early detection of microbial pathogens causing respiratory tract infection plays a crucial role in clinical management. The BioCode Respiratory Pathogen Panel (BioCode RPP) is a high-throughput test that utilizes RT-PCR in combination with barcoded magnetic beads to amplify, detect, and identify 17 respiratory pathogens, including 14 viruses and 3 bacteria. This study summarizes data generated from a multicenter clinical trial evaluating the performance of the BioCode RPP on 2,647 nasopharyngeal swab specimens from five geographically distinct sites.

Evaluation of the ePlex Respiratory pathogen panel 2 to detect viral and bacterial pathogens, including SARS-CoV-2 Omicron in nasopharyngeal swabs

The simultaneous detection and specific identification of multiple pathogens from patients exhibiting respiratory symptoms is important for directing pathogen-specific treatments. The ePlex Respiratory Pathogen Panel 2 (ePlex RP2 panel) is a multiplex molecular test for the qualitative detection of many viral and bacterial pathogens including SARS-CoV-2 in respiratory tract infections. The ePlex RP2 panel received FDA emergency use authorization for nasopharyngeal swab specimens collected in viral transport media. In the evaluation using the ePlex RP2, a total of 67 nasopharyngeal swab specimens were compared to the ePlex RP panel and the CDC 2019-nCoV Real-Time RT-PCR assay as the reference methods. The overall agreement of the ePlex RP2 panel was 100%. The ePlex RP2 panel could detect Omicron BA1 and BA2. The ePlex RP2 panel is a rapid, sensitive and specific "specimen-to-answer" platform to detect simultaneously multiple viruses and bacteria in the upper respiratory tract.Copyright © 2022 The Authors

Comparison of common human respiratory pathogens among hospitalized children aged ≤ 6 years in Hainan Island, China, during spring and early summer in 2019-2021.

The coronavirus disease 2019 (COVID-19) pandemic and related public health intervention measures have been reported to have resulted in the reduction of infections caused by influenza viruses and other common respiratory viruses. However, the influence may be varied in areas that have different ecological, economic, and social conditions. This study investigated the changing epidemiology of 8 common respiratory pathogens, including Influenza A (IFVA), Influenza B (IFVB), Respiratory syncytial virus (HRSV), rhinovirus (RV), Human metapneumovirus Adenovirus, Human bocavirus, and Mycoplasma pneumoniae, among hospitalized children during spring and early summer in 2019-2021 in two hospitals in Hainan Island, China, in the COVID-19 pandemic era. The results revealed a significant reduction in the prevalence of IFVA and IFVB in 2020 and 2021 than in 2019, whereas the prevalence of HRSV increased, and it became the dominant viral pathogen in 2021. RV was one of the leading pathogens in the 3 year period, where no significant difference was observed. Phylogenetic analysis revealed close relationships among the circulating respiratory viruses. Large scale studies are needed to study the changing epidemiology of seasonal respiratory viruses to inform responses to future respiratory virus pandemics.

Clinical Evaluation of a Multiplex PCR Assay for Simultaneous Detection of 18 Respiratory Pathogens in Patients with Acute Respiratory Infections.

Reliable diagnostics are necessary to identify influenza infections, and coronavirus disease 2019 (COVID-19) highlights the need to develop highly specific and sensitive viral detection methods to distinguish severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory pathogens to prevent their further spread. In this prospective study, 1070 clinical respiratory samples were collected from patients with acute respiratory infections from January 2019 to February 2021 to evaluate the diagnostic performance of a multiplex probe amplification (MPA) assay, designed to screen 18 pathogens, mainly those causing acute respiratory infections. Ninety-six positive samples and twenty negative samples for the 18 respiratory pathogens defined by the MPA assay and reverse transcription polymerase chain reaction (RT-PCR) were further confirmed by reference next-generation sequencing (NGS). The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the MPA assay were 95.00%, 93.75%, 98.96% and 75.00%, respectively. Additionally, the co-infection rate for these positive samples were 25% (24/95). The MPA assay demonstrated a highly concordant diagnostic performance with NGS in the diagnosis of 18 respiratory pathogens and might play an important role in clinical respiratory pathogen diagnosis.

Sharp decline in rates of community respiratory viral detection among NIH Clinical Center patients during the COVID-19 pandemic.

OBJECTIVE: The objective of this study was to analyze the frequency and rates of community respiratory virus infections detected in NIH Clinical Center (NIHCC) patients from January 2015 through March 2021, comparing the trends before and during the COVID-19 pandemic. METHODS: We conducted a retrospective study comparing frequency and rates of community respiratory viruses detected in NIHCC patients from January 2015 through March 2021. Test results from nasopharyngeal swabs/washes, bronchoalveolar lavages, and bronchial washes were included in this study. Results from viral challenge studies and repeat positives were excluded. A quantitative data analysis was completed using cross tabulations; comparisons were done using mixed models, applying Dunnett's correction for multiplicity. RESULTS: Frequency of all respiratory pathogens declined from an annual range of 0.88-1.97% from January 2015 through March 2020 to 0.29% between April 2020 and March 2021. Individual viral pathogens declined sharply in frequency during the same timeframe, with zero cases of influenza A/B or parainfluenza and one case of RSV. Rhino/enterovirus detection continued, but with a substantially lower frequency of 4.27% between April 2020 and March 2021, compared with an annual range of 8.65-18.28% from January 215 through March 2020. DISCUSSION: The decrease in viral respiratory infections detected in NIHCC patients during the pandemic was likely due to the layered COVID-19 prevention and mitigation measures implemented in the community and the hospital. Hospitals should consider continued use of nonpharmaceutical interventions in the future to prevent nosocomial transmission of respiratory viruses during times of high community viral load.

Overview SARS-CoV-2 Pandemic as January-February 2022: Likely Cometary Origin, Global Spread, Prospects for Future Vaccine Efficacy

As the SARS-CoV-2 pandemic is nearing its eventual end we focus on what we believe are two key omissions from the mainstream scientific literature and which have significant implications for how mankind manages the next global pandemic. We therefore review data, observations, analyses and conclusions from our series of papers published through 2020 and 2021 on its likely cometary origin and global spread. We also revisit our long held understanding of the superior effectiveness of intra-nasal vaccines against respiratory tract pathogens that involve induction of dimeric secretory IgA antibodies. While these two oversights seem disparate, together they provide us with new insights into our collective awareness of how we might view and address the next global pandemic. We begin with our hypothesis of the likely cometary origin of the SARS-CoV-2 virus via a bolide strike in the stratosphere on the night of October 11 2019 on the 40o N line over Jilin in NE China. Further global spread most likely occurred via prevailing wind systems transporting both the pristine cometary virus followed by continuing strikes from the same primary source as well as prior human-passaged virus transmitted by person to person spread and through contaminated dust in global wind systems. We also include a discussion of our prior work on data relating to vaccine protective efficacy. Finally we review the totality of evidence concerning the likely origin and global spread of the predominant variants of the virus ‘Omicron' (+Delta mix?) from early to mid-December 2021 and extending into the first week January 2022. We describe the striking data showing the large numbers of infectious cases per day and outline the scale of what appears to be a global pandemic phenomenon, the causes of which are unclear and not completely understood. Firstly, these essentially simultaneous and sudden global-wide epidemic COVID-19 out breaks, appear to be largely correlated with events external to the Earth, probably causing globally correlated precipitation events. They appear related broadly to "Space Weather” events that render the Earth vulnerable to cosmic pandemic pathogen attack particularly during times of the minima of the Sunspot Solar Cycle which we are now currently passing through. Secondly, we argue that these sudden global-wide epidemic outbreaks of COVID-19 are specifically largely influenced by global wind transport and deposition mechanisms, the physics of which we need to further explore and comprehend. We conclude on an optimistic note for mankind. Given our prior knowledge of the effectiveness against respiratory tract pathogens of mucosal immunity involving induction of dimeric secretory IgA antibodies, we consider that the recently published intra-nasal vaccine data from laboratories based at the University of California, San Francisco and, independently at Yale University. These latter studies hold out great promise for the future development of both panspecific and specific immunity against future pandemics caused by suddenly emergent respiratory pathogens, whether viral, bacterial or fungal. © 2022 by World Scientific Publishing Co. Pte. Ltd.

High detection rate of viral pathogens in nasal discharge in children aged 0 till 5 years.

Respiratory tract infections (RTI) in children remain a cause of disease burden worldwide. Nasopharyngeal (NP) & oropharyngeal (OP) swabs are used for respiratory pathogen detection, but hold disadvantages particularly for children, highlighting the importance and preference for a child friendly detection method. We aimed to evaluate the performance and tolerability of a rhinorrhea swab (RS) in detecting viral pathogens when compared to a combined OP(/NP) or mid-turbinate (MT) nasal swab. This study was conducted between September 2021 and July 2022 in the Netherlands. Children aged 0-5 years, with an upper RTI and nasal discharge, were included and received a combined swab and a RS. Multiplex polymerase chain reaction (PCR) and severe acute respiratory syndrome coronavirus-2 PCR were used for viral pathogen detection. Tolerability was evaluated with a questionnaire and visual analog scale (VAS) scores. During 11 months 88 children were included, with a median age of 1.00 year [interquartile range 0.00-3.00]. In total 122 viral pathogens were detected in 81 children (92%). Sensitivity and specificity of the RS compared to a combined swab were respectively 97% (95% confidence interval [CI] 91%-100%) and 78% (95% CI 45%-94%). Rhinorrhea samples detected more pathogens than the (combined) nasal samples, 112 versus 108 respectively. Median VAS scores were significantly lower for the RS in both children (2 vs. 6) and their parents (0 vs. 5). A RS can therefore just as effectively/reliably detect viral pathogens as the combined swab in young children and is better tolerated by both children and their parents/caregivers.

Impact of multiplex polymerase chain reaction syndromic panel on antibiotic use among hospitalized children with respiratory tract illness during COVID-19 pandemic.

BACKGROUND/PURPOSE: Precise detection of respiratory pathogens by molecular method potentially may shorten the time to diagnose and reduce unnecessary antibiotic use. METHODS: Medical records of hospitalized children from January 2020 to June 2021 with acute respiratory illness who received a FilmArray RP for respiratory pathogens were reviewed and compared with data from diagnosis-matched patients without receiving the test. RESULTS: In total, 283 patients and 150 diagnosis-matched controls were included. Single pathogen was detected in 84.3% (193/229) of the patients. The most common pathogen was human rhinovirus/enterovirus (31.6%, 84/266), followed by respiratory syncytial virus (18.8%, 50/266) and adenovirus (15%, 40/266). Although antimicrobial days of therapy (DOT) was significantly longer in FilmArray group than the control [7.1 ± 4.9 days vs 5.7 ± 2.7 days, P = 0.002], the former showed a higher intensive care unit (ICU) admission rate (3.9% vs 0%; P = 0.010). All ICU admissions were in FilmArray RP-positive group. There was no difference in antimicrobial DOT between FilmArray RP-positive and the negative groups, in all admissions, even after excluding ICU admissions. Antimicrobial DOT was shorter in the positive than negative group in patients with lower respiratory tract infections without admission to ICU [median (IQR): 6 (4-9) days vs 9 (4-12) days, P = 0.047]. CONCLUSIONS: Shorter antimicrobial DOTs were identified in children with lower respiratory tract infection admitted to general pediatric ward and with an identifiable respiratory pathogen, indicating a role of the multiplex PCR in reducing antimicrobial use for children with respiratory tract infection.

Viral and Bacterial Respiratory Pathogens during the COVID-19 Pandemic in Israel.

BACKGROUND: previous worldwide reports indicated a substantial short-term reduction in various respiratory infections during the early phase of the SARS-CoV-2 pandemic. AIMS: exploring the long-term impact of the COVID-19 pandemic on respiratory pathogens. METHODS: retrospective analysis of bacterial and viral positivity rate in respiratory samples, between 1 January 2017-30 June 2022 in a tertiary hospital in Jerusalem, Israel. RESULTS: A decline in overall respiratory tests and positivity rate was observed in the first months of the pandemic. Respiratory isolations of Hemophilus influenza and Streptococcus pneumoniae were insignificantly affected and returned to their monthly average by November 2020, despite a parallel surge in COVID-19 activity, while Mycoplasma pneumoniae was almost eliminated from the respiratory pathogens scene. Each viral pathogen acted differently, with adenovirus affected only for few months. Human-metapneumovirus and respiratory-syncytial-virus had reduced activity for approximately a year, and influenza A virus resurged in November 2021 with the elimination of Influenza-B. CONCLUSIONS: After an immediate decline in non-SARS-CoV-2 respiratory infections, each pathogen has a different pattern during a 2-year follow-up. These patterns might be influenced by intrinsic factors of each pathogen and different risk reduction behaviors of the population. Since some of these measures will remain in the following years, we cannot predict the timing of return to pre-COVID-19 normalcy.

Changes in the Epidemiology of Respiratory Pathogens in Children during the COVID-19 Pandemic.

Since the outbreak of the COVID-19 pandemic, a significant decrease in non-COVID-19 respiratory illnesses were observed, suggesting that the implementation of measures against COVID-19 affected the transmission of other respiratory pathogens. The aim of this study was to highlight the changes in the epidemiology of respiratory pathogens in children during the COVID-19 pandemic. All children with Severe Acute respiratory illness admitted to the pediatric departments between January 2018 and December 2021 with negative COVID-19 PCR, were enrolled. The detection of respiratory pathogens was made by the Film Array Respiratory Panel. A total of 902 respiratory specimens were tested. A significantly lower positivity rate during the COVID-19 period was found (p = 0.006), especially in infants under 6 months (p = 0.008). There was a substantial absence of detection of Respiratory Syncytial Virus and Influenza A during the winter season following the outbreak of the pandemic (p < 0.05; p = 0.002 respectively). An inter-seasonal resurgence of Respiratory Syncytial Virus was noted. Human Rhinovirus was detected throughout the year, and more prevalent in winter during COVID-19 (p = 0.0002). These changes could be explained by the impact of the implementation of preventive measures related to the COVID-19 pandemic on the transmission of respiratory pathogens in children.

Trained Immunity as a Prospective Tool against Emerging Respiratory Pathogens.

Although parental vaccines offer long-term protection against homologous strains, they rely exclusively on adaptive immune memory to produce neutralizing antibodies that are ineffective against emerging viral variants. Growing evidence highlights the multifaceted functions of trained immunity to elicit a rapid and enhanced innate response against unrelated stimuli or pathogens to subsequent triggers. This review discusses the protective role of trained immunity against respiratory pathogens and the experimental models essential for evaluating novel inducers of trained immunity. The review further elaborates on the potential of trained immunity to leverage protection against pathogens via the molecular patterns of antigens by pathogen recognition receptors (PPRs) on innate immune cells. The review also focuses on integrating trained innate memory with adaptive memory to shape next-generation vaccines by coupling each one's unique characteristics.

A Digital Microfluidic RT-qPCR Platform for Multiple Detections of Respiratory Pathogens.

The coronavirus disease 2019 pandemic has spread worldwide and caused more than six million deaths globally. Therefore, a timely and accurate diagnosis method is of pivotal importance for controlling the dissemination and expansions. Nucleic acid detection by the reverse transcription-polymerase chain reaction (RT-PCR) method generally requires centralized diagnosis laboratories and skilled operators, significantly restricting its use in rural areas and field settings. The digital microfluidic (DMF) technique provides a better option for simultaneous detections of multiple pathogens with fewer specimens and easy operation. In this study, we developed a novel digital microfluidic RT-qPCR platform for multiple detections of respiratory pathogens. This method can simultaneously detect eleven respiratory pathogens, namely, mycoplasma pneumoniae (MP), chlamydophila pneumoniae (CP), streptococcus pneumoniae (SP), human respiratory syncytial virus A (RSVA), human adenovirus (ADV), human coronavirus (HKU1), human coronavirus 229E (HCoV-229E), human metapneumovirus (HMPV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza A virus (FLUA) and influenza B virus (FLUB). The diagnostic performance was evaluated using positive plasmids samples and clinical specimens compared with off-chip individual RT-PCR testing. The results showed that the limit of detections was around 12 to 150 copies per test. The true positive rate, true negative rate, positive predictive value, negative predictive value, and accuracy of DMF on-chip method were 93.33%, 100%, 100%, 99.56%, and 99.85%, respectively, as validated by the off-chip RT-qPCR counterpart. Collectively, this study reported a cost-effective, high sensitivity and specificity on-chip DMF RT-qPCR system for detecting multiple respiratory pathogens, which will greatly contribute to timely and effective clinical management of respiratory infections in medical resource-limited settings.

Counter-propagating Gaussian beam enhanced Raman spectroscopy for rapid reagentless detection of respiratory pathogens in nasal swab samples

Co-circulation of respiratory viruses compounded by similarities in clinical presentation and mode of transmission underscores the need for broad range pathogen detection. Accurate identification and diagnosis at the point-of-need is critical to limiting disease spread. A novel point-of-need Raman spectroscopy-based platform is described for rapid detection of multiple respiratory pathogens in nasal swab samples with high sensitivity and specificity. The system takes advantage of a counter-propagating Gaussian beam focused within the sample chamber that augments the Raman signal of pathogens. Combined with multiclass machine learning spectral analysis via Gradient Boosting Machine, accurate identification of SARS-CoV-2, human coronaviruses OC43, NL63, 229E, Influenza A (H1N1), respiratory syncytial virus, and Streptococcus pyogenes in spiked clinical nasal swab samples was demonstrated at 99% sensitivity and 93% specificity. The limit of detection was assessed using binary class Support Vector Machine with SARS-CoV-2 in nasal swab samples against negative control at 2.2 × 104 virions/swab. The spectrometer can be operated by minimally trained personnel with software-generated diagnostic yes/no results in 2 min or less, making it well suited for point-of-need applications. Furthermore, adaptive algorithms can detect and differentiate new and emerging variants using a Raman spectral database.

ANALYZING INDOOR PATHOGEN DISPERSION AND VENTILATION STRATEGIES TO REDUCE THE RISK OF CORONAVIRUS INFECTION

The COVID-19 pandemic has refocused attention to the significance of indoor air quality and how air moves during the circulation process. Contaminants, especially aerosols (≤ 5 µm), remain airborne for prolonged periods and travel long distances increasing the risk of infection to occupants. This study investigated the movement of air and respiratory particles in a clinical setting and an isolation system using computational fluid dynamics. The ventilation system distributes a combination of outdoor and indoor air to reduce energy consumption. The recirculated air carries contaminants smaller than 1 µm, which are distributed to other spaces in the building, increasing the risk of infection to other occupants. Therefore, the efficacy of an air-sterilization unit that integrates with a building air handling system was examined. It was observed that a larger percentage of aerosols were exhausted compared to droplets, as larger particles deposit on surfaces under the influence of gravity. Using the air sterilization unit reduced the pathogen concentration in the clinical setting by 25%. The air sterilization system had a significant impact when used in an isolation system with a negative pressure and a positive pressure room. Contaminants from the negative pressure room were distributed to the positive pressure room with the conventional ventilation system. However, sterilizing the recirculated air ensured complete safety of the patient (or other occupants) in the positive pressure room. The findings of these studies can be generalized to any scenario where a centralized ventilation system is employed for thermal comfort and air quality control. © 2022 Begell House Inc.. All rights reserved.

Quantification of Respirable Aerosol Particles from Speech and Language Therapy Exercises.

INTRODUCTION: Voice assessment and treatment involve the manipulation of all the subsystems of voice production, and may lead to production of respirable aerosol particles that pose a greater risk of potential viral transmission via inhalation of respirable pathogens (eg, SARS-CoV-2) than quiet breathing or conversational speech. OBJECTIVE: To characterise the production of respirable aerosol particles during a selection of voice assessment therapy tasks. METHODS: We recruited 23 healthy adult participants (12 males, 11 females), 11 of whom were speech-language pathologists specialising in voice disorders. We used an aerodynamic and an optical particle sizer to measure the number concentration and particle size distributions of respirable aerosols generated during a variety of voice assessment and therapy tasks. The measurements were carried out in a laminar flow operating theatre, with a near-zero background aerosol concentration, allowing us to quantify the number concentration and size distributions of respirable aerosol particles produced from assessment/therapy tasks studied. RESULTS: Aerosol number concentrations generated while performing assessment/therapy tasks were log-normally distributed among individuals with no significant differences between professionals (speech-language pathologists) and non-professionals or between males and females. Activities produced up to 32 times the aerosol number concentration of breathing and 24 times that of speech at 70-80 dBA. In terms of aerosol mass, activities produced up to 163 times the mass concentration of breathing and up to 36 times the mass concentration of speech. Voicing was a significant factor in aerosol production; aerosol number/mass concentrations generated during the voiced activities were 1.1-5 times higher than their unvoiced counterpart activities. Additionally, voiced activities produced bigger respirable aerosol particles than their unvoiced variants except the trills. Humming generated higher aerosol concentrations than sustained /a/, fricatives, speaking (70-80 dBA), and breathing. Oscillatory semi-occluded vocal tract exercises (SOVTEs) generated higher aerosol number/mass concentrations than the activities without oscillation. Water resistance therapy (WRT) generated the most aerosol of all activities, ∼10 times higher than speaking at 70-80 dBA and >30 times higher than breathing. CONCLUSIONS: All activities generated more aerosol than breathing, although a sizeable minority were no different to speaking. Larger number concentrations and larger particle sizes appear to be generated by activities with higher suspected airflows, with the greatest involving intraoral pressure oscillation and/or an oscillating oral articulation (WRT or trilling).