New methodology to qualify office microbial air quality with air-handling-unit-filters

The Covid-19 pandemic reminded us the importance of maintaining adequate indoor air quality to reduce the risk of propagation of viral particles. The aim of this study is to use air handling unit (AHU) filters to develop a methodology to identify microbial contaminants present in office indoor air. The methodology involves discs of filter media collected periodically from the extraction filters and analysed by cultural and molecular methods. Results obtained from the 10 months study indicate in particular that the concentration of cultivable microorganisms on the filters display small variations of 37% from average value for the 5-culture media tested (e.g., 3.9×102 CFU/cm2 for LB medium). The genera Aspergillus, Cladosporium and Penicillium are the most represented among the cultivable microorganisms collected on the extraction filter. © 2022 17th International Conference on Indoor Air Quality and Climate, INDOOR AIR 2022. All rights reserved.

Computational Methodology for Discovery of Potential Inhibitory Peptides

In 2020, a new pandemic caused by a coronavirus has impacted the economic and public health landscape on a global level. Named SARS-CoV-2, it causes COVID-19 and, in two years, has caused thousands of deaths. Among its viral particles, SARS-CoV-2 has an important structural protein called Spike (S), and its entry into human cells is mediated by an interaction between the Spike and the human receptor Angiotensin Converting Enzyme 2 (ACE2). This S/ACE2 binding depends on the cleavage of the Spike into three parts (S1, S2 and S2') by host cell proteases. For this, the S protein undergoes a conformational change that exposes a cleavage site between the S1 and S2 domains, being initially cleaved by the Furin enzyme. The S2 part is cleaved by TMPRSS2 (Transmembrane Serine Protease II) to expose the fusion peptide, promoting endocytic entry of the virus. TMPRSS2 can be inhibited by clinically approved serine protease inhibitors, making it a promising target for the treatment of viral infections. Consequently, our objective was to look for peptides that weren't described as inhibitors for SARS-CoV-2 but can be repositioned. In this paper, we propose a computational method to collect, filter, simulate protein-peptide interaction and identify the best hits based on the pattern of interactions. In addition to the main contribution of the paper that is the method, another contribution of this work is the proposal of candidate peptides. © 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.

A Four-Channel Surface Plasmon Resonance Sensor Functionalized Online for Simultaneous Detections of Anti-SARS-CoV-2 Antibody, Free Viral Particles, and Neutralized Viral Particles.

Current tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detect either the constituent nucleic acids/proteins of the viral particles or antibodies specific to the virus, but cannot provide information about viral neutralization by an antibody and the efficacy of an antibody. Such information is important about individuals' vulnerability to severe symptoms or their likelihood of showing no symptoms. We immobilized online SARS-CoV-2 spike (S1) protein and angiotensin-converting enzyme 2 (ACE2) into separate surface plasmon resonance (SPR) channels of a tris-nitrilotriacetic acid (tris-NTA) chip to simultaneously detect the anti-S1 antibody and viral particles in serum samples. In addition, with a high-molecular-weight-cutoff filter, we separated the neutralized viral particles from the free antibody molecules and used a sensing channel immobilized with Protein G to determine antibody-neutralized viral particles. The optimal density of probe molecules in each fluidic channel can be precisely controlled through the closure and opening of the specific ports. By utilizing the high surface density of ACE2, multiple assays can be carried out without regenerations. These three species can be determined with a short analysis time (<12 min per assay) and excellent sensor-to-sensor/cycle-to-cycle reproducibility (RSD < 5%). When coupled with an autosampler, continuous assays can be performed in an unattended manner at a single chip for up to 6 days. Such a sensor capable of assaying serum samples containing the three species at different levels provides additional insights into the disease status and immunity of persons being tested, which should be helpful for containing the SARS-CoV-2 spread during the era of incessant viral mutations.

SARS-CoV-2 Is Persistent in Placenta and Causes Macroscopic, Histopathological, and Ultrastructural Changes.

SARS-CoV-2 is a virus that belongs to the Betacoronavirus genus of the Coronaviridae family. Other coronaviruses, such as SARS-CoV and MERS-CoV, were associated with complications in pregnant women. Therefore, this study aimed to report the clinical history of five pregnant women infected with SARS-CoV-2 (four symptomatic and one asymptomatic who gave birth to a stillborn child) during the COVID-19 pandemic. They gave birth between August 2020 to January 2021, a period in which there was still no vaccination for COVID-19 in Brazil. In addition, their placental alterations were later investigated, focusing on macroscopic, histopathological, and ultrastructural aspects compared to a prepandemic sample. Three of five placentas presented SARS-CoV-2 RNA detected by RT-PCRq at least two to twenty weeks after primary pregnancy infection symptoms, and SARS-CoV-2 spike protein was detected in all placentas by immunoperoxidase assay. The macroscopic evaluation of the placentas presented congested vascular trunks, massive deposition of fibrin, areas of infarctions, and calcifications. Histopathological analysis showed fibrin deposition, inflammatory infiltrate, necrosis, and blood vessel thrombosis. Ultrastructural aspects of the infected placentas showed a similar pattern of alterations between the samples, with predominant characteristics of apoptosis and detection of virus-like particles. These findings contribute to a better understanding of the consequences of SARS-CoV-2 infection in placental tissue, vertical transmission.

An instrumental and computational pipeline for visualizing free viral particles

We are presenting the application of an optical and computational pipeline FAMOUS for revealing the presence of free viral particles named “virions”. The idea of such a protocol is to give rise to images of virions in their environment with a soft solution for recording the native image, contrary to the standard solution of imaging virions with electron microscopy (EM) for visualizing viral particles. The final aim of the current work is to observe free viral particles of SARS-CoV-2, the virions responsible for the worldwide pandemic of Covid-19. But such particles have diameters between 80 and 120 nm, a dimension smaller than the resolution limit of optical-only microscopy solutions. We have chosen to start with the biggest free virions, cytomegalovirus (CMV), a virus from the herpesvirus family also named “Human Herpes Virus 5”. Two kinds of cultures were involved: a fluorescent culture (BAD) and a label-free one (VHLE), both being collected from infected cell culture. VHLE virions were first observed after secondary immunostaining and concentrated with magnetic nanoparticles and then without labelling. The optical protocol rests on a standard solution of multiphoton microscopy combined with a computational strategy based on the point-spread-function (PSF) recordings, its mathematical modeling and the restauration of the image resting on the PSF model. A test with free viral particles of SARS-CoV-2 is led, delivering an optical visualization of the free-viral particles. The visualization of objects aggregates obtained in both situations confirm the relevance of the pipeline FAMOUS for imaging free virions. © 2022 SPIE.

Effect of human movement on a patient's exhaled viral particle transmission: A numerical study

Droplet transmission and aerosol transmission are both possible transmission pathways for many respiratory infections (e.g., COVID-19) and human movements may affect these viral particle transmission pathways. Realistic 3-D human models were used here in a computational fluid dynamics (CFD) study to analyze the effect of human movements on the transmission of virus particles exhaled by a patient. The changes in the airflow, pressure and particle diffusion were compared with experimental data to verify the accuracy of the computations. The results show that when a person passes by a sitting patient in a poorly ventilated room, the wake velocities can reach 1.6~2.0 m/s. The airflow velocity can reach 0.53 m/s at 0.10 m from the moving person, 0.22 m/s at 0.25 m away, and 0.13 m/s at 0.55 m away. The airflow fluctuations can last more than 10 s. Double peak airflow velocities are found near the moving person. The pressure difference of 0.49 Pa caused by the moving person moves the air and the viral particles into the wake of the moving person and slows the nearby droplet deposition. More than 50% of the viral particles are deposited on the moving person's body or spread further. Thus, this study recommends less cross-area movement in epidemic areas and that all people should wear masks and use personalized ventilation equipment. © 2022, Tsinghua University Press. All right reserved.

Demonstrating UVC LEDs inside Automobile HVAC Chambers for Clean Cabin Air and Airborne Transmission Risk Reduction

A global survey in December 2020 revealed a preference for surface and air disinfection in automobiles which may have been accelerated by the COVID-19 pandemic. The observed trend towards healthy cars may remain well after the current pandemic. Additionally, new safety features like CO2 gas sensors, antimicrobial fabrics, and enhanced air purifiers have emerged. While automobile air purifiers trap contaminants using cartridge filters, they are not particularly efficient at removing viral particles and create large pressure drops, which must be compensated with larger fans, increasing power requirements and noise in the vehicle cabin. A HVAC system with integrated UVC-LEDs can inactivating viruses, bacteria, and mold. UVC LEDs are desirable because unlike mercury lamps, they do not pose electrical, glass, and chemical hazards. With the recent improvements in UVC LED lifetime and power, UVC LEDs are becoming a better alternative, as highlighted by recent upsurge of successful in air disinfection studies against SARS-CoV-2 and H1N1. In this paper, the KM model is applied to a vehicle, initial testing on 25 L/s shows half log reduction of E. coli, then a model of a disinfection chamber that could fit a vehicle HVAC is created, and finally a full size mock vehicle is disinfected using Phi6 as a surrogate. It's estimated from this that 90#x00025;of SARS-CoV-2 could be eliminated in 5 minutes. This demonstrates the feasibility of UVC LEDs for aerosol disinfection in vehicles. © 2022 SAE International. All Rights Reserved.

Spatial Models and Masks in Indoor Analysis for the Spread of COVID-19

Face masks have been shown to slow or stop the spread of airborne COVID-19 droplets and aerosols. There is an apparent lack of research examining the effect of different types of masks used at the same time, and their impact on the spread of viral particles in a spatial sense. We introduce a rapid prototype model to overcome the issues in the available research using the Cell-DEVS formalism. We also build scenarios for the model to examine the effectiveness of all types of masks and respirators recommended by the World Health Organization on the spread of viral particles in an indoor environment. © 2021 IEEE.

Can spike fragments of SARS-CoV-2 induce genomic instability and DNA damage in the guppy, Poecilia reticulate? An unexpected effect of the COVID-19 pandemic.

The identification of SARS-CoV-2 particles in wastewater and freshwater ecosystems has raised concerns about its possible impacts on non-target aquatic organisms. In this particular, our knowledge of such impacts is still limited, and little attention has been given to this issue. Hence, in our study, we aimed to evaluate the possible induction of mutagenic (via micronucleus test) and genotoxic (via single cell gel electrophoresis assay, comet assay) effects in Poecilia reticulata adults exposed to fragments of the Spike protein of the new coronavirus at the level of 40 µg/L, denominated PSPD-2002. As a result, after 10 days of exposure, we have found that animals exposed to the peptides demonstrated an increase in the frequency of erythrocytic nuclear alteration (ENA) and all parameters assessed in the comet assay (length tail, %DNA in tail and Olive tail moment), suggesting that PSPD-2002 peptides were able to cause genomic instability and erythrocyte DNA damage. Besides, these effects were significantly correlated with the increase in lipid peroxidation processes [inferred by the high levels of malondialdehyde (MDA)] reported in the brain and liver of P. reticulata and with the reduction of the superoxide dismutase (SOD) and catalase (CAT) activity. Thus, our study constitutes a new insight and promising investigation into the toxicity associated with the dispersal of SARS-CoV-2 peptide fragments in freshwater environments.

Cloning of a Passage-Free SARS-CoV-2 Genome and Mutagenesis Using Red Recombination.

The ongoing pandemic coronavirus (CoV) disease 2019 (COVID-19) by severe acute respiratory syndrome CoV-2 (SARS-CoV-2) has already caused substantial morbidity, mortality, and economic devastation. Reverse genetic approaches to generate recombinant viruses are a powerful tool to characterize and understand newly emerging viruses. To contribute to the global efforts for countermeasures to control the spread of SARS-CoV-2, we developed a passage-free SARS-CoV-2 clone based on a bacterial artificial chromosome (BAC). Moreover, using a Lambda-based Red recombination, we successfully generated different reporter and marker viruses, which replicated similar to a clinical isolate in a cell culture. Moreover, we designed a full-length reporter virus encoding an additional artificial open reading frame with wild-type-like replication features. The virus-encoded reporters were successfully applied to ease antiviral testing in cell culture models. Furthermore, we designed a new marker virus encoding 3xFLAG-tagged nucleocapsid that allows the detection of incoming viral particles and, in combination with bio-orthogonal labeling for the visualization of viral RNA synthesis via click chemistry, the spatiotemporal tracking of viral replication on the single-cell level. In summary, by applying BAC-based Red recombination, we developed a powerful, reliable, and convenient platform that will facilitate studies answering numerous questions concerning the biology of SARS-CoV-2.

Passive Tracer Visualization to Simulate Aerodynamic Virus Transport in Noninvasive Respiratory Support Methods.

BACKGROUND: Various forms of noninvasive respiratory support methods are used in the treatment of hypoxemic CO-VID-19 patients, but limited data are available about the corresponding respiratory droplet dispersion. OBJECTIVES: The aim of this study was to estimate the potential spread of infectious diseases for a broad selection of oxygen and respiratory support methods by revealing the therapy-induced aerodynamics and respiratory droplet dispersion. METHODS: The exhaled air-smoke plume from a 3D-printed upper airway geometry was visualized by recording light reflection during simulated spontaneous breathing, standard oxygen mask application, nasal high-flow therapy (NHFT), continuous positive airway pressure (CPAP), and bilevel positive airway pressure (BiPAP). The dispersion of 100 µm particles was estimated from the initial velocity of exhaled air and the theoretical terminal velocity. RESULTS: Estimated droplet dispersion was 16 cm for unassisted breathing, 10 cm for Venturi masks, 13 cm for the nebulizer, and 14 cm for the nonrebreathing mask. Estimated droplet spread increased up to 34 cm in NHFT, 57 cm in BiPAP, and 69 cm in CPAP. A nonsurgical face mask over the NHFT interface reduced estimated droplet dispersion. CONCLUSIONS: During NHFT and CPAP/BiPAP with vented masks, extensive jets with relatively high jet velocities were observed, indicating increased droplet spread and an increased risk of droplet-driven virus transmission. For the Venturi masks, a nonrebreathing mask, and a nebulizer, estimated jet velocities are comparable to unassisted breathing. Aerosols are transported unboundedly in all these unfiltered therapies. The adequate use of protective measures is of vital importance when using noninvasive unfiltered therapies in infectious respiratory diseases.

Heterogeneity of SARS-CoV-2 virus produced in cell culture revealed by shotgun proteomics and supported by genome sequencing.

COVID-19 is the most disturbing pandemic of the past hundred years. Its causative agent, the SARS-CoV-2 virus, has been the subject of an unprecedented investigation to characterize its molecular structure and intimate functioning. While markers for its detection have been proposed and several diagnostic methodologies developed, its propensity to evolve and evade diagnostic tools and the immune response is of great concern. The recent spread of new variants with increased infectivity requires even more attention. Here, we document how shotgun proteomics can be useful for rapidly monitoring the evolution of the SARS-CoV-2 virus. We evaluated the heterogeneity of purified SARS-CoV-2 virus obtained after culturing in the Vero E6 cell line. We found that cell culture induces significant changes that are translated at the protein level, such changes being detectable by tandem mass spectrometry. Production of viral particles requires careful quality control which can be easily performed by shotgun proteomics. Although considered relatively stable so far, the SARS-CoV-2 genome turns out to be prone to frequent variations. Therefore, the sequencing of SARS-CoV-2 variants from patients reporting only the consensus genome after its amplification would deserve more attention and could benefit from more in-depth analysis of low level but crystal-clear signals, as well as complementary and rapid analysis by shotgun proteomics.

Are the Portable Air Cleaners (PAC) really effective to terminate airborne SARS-CoV-2?

The transmission of SARS-CoV-2 virus through aerosols has become an outstanding issue, where plenty of spread aspects are being analyzed. Portable Air Cleaners (PAC) with high-efficiency particulate air (HEPA) filters have been discussed as an adjunctive means for indoor environments coronavirus decontamination. This study evaluates, first, the air and surfaces SARS-COV-2 RNA contamination due to positive patients in households, and second, the efficiency of a PAC with HEPA filter to eliminate virus. A total of 29 air and surface samples were collected inside 9 households, by using an air portable collector with gelatin filters and swabs. SARS-CoV-2 RNA detection was performed using real-time reverse transcription polymerase chain reaction (RT-PCR). Overall, all the air samples collected before using PAC and 75% of swab samples were positive for SARS-CoV-2. After the PAC usage, all samples except one were negative, displaying a 80% device effectiveness. Portable HEPA cleaners usage allowed the removal of SARS CoV-2 and, therefore, they could be recommended for places with inadequate ventilation, considering the limitations and functionality of the device.

A technical review of face mask wearing in preventing respiratory COVID-19 transmission.

Since the outbreak of the COVID-19 pandemic, most countries have recommended their citizens to adopt social distance, hand hygiene, and face mask wearing. However, wearing face masks has not been well adopted by many citizens. While the reasons are complex, there is a general perception that the evidence to support face mask wearing is lacking, especially for the general public in a community setting. Face mask wearing can block or filter airborne virus-carrying particles through the working of colloid and interface science. This paper assesses current knowledge behind the design and functioning of face masks by reviewing the selection of materials, mask specifications, relevant laboratory tests, and respiratory virus transmission trials, with an overview of future development of reusable masks for the general public. This review highlights the effectiveness of face mask wearing in the prevention of COVID-19 infection.