An investigation of a hundred COVID-19 cases and close contacts in Ethiopia, May to June, 2020: A prospective case-ascertained study.

BACKGROUND: Corona Virus Disease 2019 is a novel respiratory disease commonly transmitted through respiratory droplets. The disease has currently expanded all over the world with differing epidemiologic trajectories. This investigation was conducted to determine the basic clinical and epidemiological characteristics of the disease in Ethiopia. METHODS: A prospective case-ascertained study of laboratory-confirmed COVID-19 cases and their close contacts were conducted. The study included 100 COVID-19 laboratory-confirmed cases reported from May 15, 2020 to June 15, 2020 and 300 close contacts. Epidemiological and clinical information were collected using the WHO standard data collection tool developed first-few cases and contacts investigation. Nasopharyngeal and Oropharyngeal samples were collected by using polystyrene tipped swab and transported to the laboratory by viral transport media maintaining an optimal temperature. Clinical and epidemiological parameters were calculated in terms of ratios, proportions, and rates with 95% CI. RESULT: A total of 400 participants were investigated, 100 confirmed COVID-19 cases and 300 close contacts of the cases. The symptomatic proportion of cases was 23% (23) (95% CI: 15.2%-32.5%), the proportion of cases required hospitalization were 8% (8) (95%CI: 3.5%-15.2%) and 2% (95%CI: 0.24% - 7.04%) required mechanical ventilation. The secondary infection rate, secondary clinical attack rate, median incubation period and median serial interval were 42% (126) (95% CI: 36.4%-47.8%), 11.7% (35) (95% CI: 8.3%-15.9%), 7 days (IQR: 4-13.8) and 11 days (IQR: 8-11.8) respectively. The basic reproduction number (RO) was 1.26 (95% CI: 1.0-1.5). CONCLUSION: The proportion of asymptomatic infection, as well as secondary infection rate among close contacts, are higher compared to other studies. The long serial interval and low basic reproduction number might contribute to the observed slow progression of the pandemic, which gives a wide window of opportunities and time to control the spread. Testing, prevention, and control measures should be intensified.

Direct detection of virus-like particles using color images of plasmonic nanostructures.

We propose a measurement method for sensitive and label-free detections of virus-like particles (VLPs) using color images of nanoplasmonic sensing chips. The nanoplasmonic chip consists of 5×5 gold nanoslit arrays and the gold surface is modified with specific antibodies for spike protein. The resonant wavelength of the 430-nm-period gold nanoslit arrays underwater environment is about 570 nm which falls between the green and red bands of the color CCD. The captured VLPs by the specific antibodies shift the plasmonic resonance of the gold nanoslits. It results in an increased brightness of green pixels and decreased brightness of red pixels. The image contrast signals of (green - red) / (red + green) show good linearity with the surface particle density. The experimental tests show the image contrast method can detect 100-nm polystyrene particles with a surface density smaller than 2 particles/µm2. We demonstrate the application for direct detection of SARS-CoV-2 VLPs using a simple scanner platform. A detection limit smaller than 1 pg/mL with a detection time less than 30 minutes can be achieved.

Insight into the microplastics release from disposable face mask: Simulated environment and removal strategy.

The fight against the COVID-19 epidemic significantly raises the global demand for personal protective equipment, especially disposable face masks (DFMs). The discarded DFMs may become a potential source of microplastics (MPs), which has attracted much attention. In this work, we identified the detailed source of MPs released from DFMs with laser direct infrared spectroscopy. Polypropylene (PP) and polyurethane (PU) accounted for 24.5% and 57.1% of released MPs, respectively. The melt-blown fabric was a dominant MPs source, however, previous studies underestimated the contribution of mask rope. The captured polyethylene terephthalate (PET), polyamide (PA), polyethylene (PE), and polystyrene (PS) in airborne only shared 18.4% of released MPs. To deepen the understanding of MPs release from medical mask into the aquatic environment, we investigated the effects of environmental factors on MPs release. Based on regression analysis, the effects of temperature, incubation time, and wearing time significantly affect the release of MPs. Besides, acidity, alkalinity, sodium chloride, and humic acid also contributed to the MPs release through corroding, swelling, or repulsion of fibers. Based on the exposure of medical mask to simulated environments, the number of released MPs followed the order: seawater > simulated gut-fluid > freshwater > pure water. Considering the risk of MPs released from DFMs to the environment, we innovatively established a novel flotation removal system combined with cocoamidopropyl betaine, achieving 86% removal efficiency of MPs in water. This work shed the light on the MPs release from DFMs and proposed a removal strategy for the control of MPs pollution.

Murine Hepatitis Virus, a Biosafety Level 2 Model for SARS-CoV-2, Can Remain Viable on Meat and Meat Packaging Materials for at Least 48 Hours.

In 2020 and 2021, many meat processing plants faced temporary closures due to outbreaks of COVID-19 cases among the workers. There are several factors that could potentially contribute to the increased numbers of COVID-19 cases in meat processing plants: the survival of viable SARS-CoV-2 on meat and meat packaging materials, difficulties in maintaining workplace physical distancing, personal hygiene, and crowded living and transportation conditions. In this study, we used murine hepatitis virus (MHV) as a biosafety level 2 (BSL2) surrogate for SARS-CoV-2 to determine viral survival on the surface of meat, namely, stew-cut beef and ground beef, and commonly used meat packaging materials, such as plastic wrap, meat-absorbent material, and Styrofoam. From our studies, we observed the infectivity of MHV inoculated on ground beef and stew-cut beef for 48 h and saw no significant loss in infectivity for MHV from 0 to 6 h postinoculation (hpi) (unpaired t test). However, beginning at 9 hpi, viral infectivity steadily decreased, resulting in a 1.12-log reduction for ground beef and a 0.46-log reduction for stew-cut beef by 48 hpi. We also observed a significant persistence of MHV on meat packaging materials, with Styrofoam supporting the highest viability (3.25 × 103 ± 9.57 × 102 PFU/mL, a 0.91-log reduction after 48 hpi), followed by meat-absorbent material (75 ± 50 PFU/mL, a 1.10-log reduction after 48 hpi), and lastly, plastic wrap (no detectable PFU after 3 hpi, a 3.12-log reduction). Despite a notable reduction in infectivity, the virus was able to survive and remain infectious for up to 48 h at 7°C on four of the five test surfaces. Our results provide evidence that coronaviruses, such as SARS-CoV-2, could potentially survive on meat, meat-absorbent materials. and Styrofoam for up to 2 days, and potentially longer. IMPORTANCE The meat industry has been faced with astronomical challenges with the rampant spread of COVID-19 among meat processing plant workers. This has resulted in meat processing and packaging plant closures, creating bottlenecks everywhere in the chain, from farms to consumers, subsequently leading to much smaller production outputs and higher prices for all parties involved. This study tested the viability of meat and meat packaging materials as potential reservoirs for SARS-CoV-2, allowing the virus to survive and potentially spread among the workers. We used murine hepatitis virus (MHV) as a biosafety level 2 (BSL2) surrogate for SARS-CoV-2. Our results suggest that ground beef, stew-cut beef, meat-absorbent material, and Styrofoam can harbor coronavirus particles, which can remain viable for at least 48 h. Furthermore, our study provides evidence that the environmental and physical conditions within meat processing facilities can facilitate the survival of viable virus.

Molecular Dynamics Simulations of Adsorption of SARS-CoV-2 Spike Protein on Polystyrene Surface.

A prominent feature of coronaviruses is the presence of a large glycoprotein spike (S) protruding from the viral particle. The specific interactions of a material with S determine key aspects such as its possible role for indirect transmission or its suitability as a virucidal material. Here, we consider all-atom molecular dynamics simulations of the interaction between a polymer surface (polystyrene) and S in its up and down conformations. Polystyrene is a commonly used plastic found in electronics, toys, and many other common objects. Also, previous atomic force microscopy (AFM) experiments showed substantial adhesion of S over polystyrene, stronger than in other common materials. Our results show that the main driving forces for the adsorption of the S protein over polystyrene were hydrophobic and π-π interactions with S amino acids and glycans. The interaction was stronger for the case of S in the up conformation, which exposes one highly flexible receptor binding domain (RBD) that adjusts its conformation to interact with the polymer surface. In this case, the interaction has similar contributions from the RBD and glycans. In the case of S in the down conformation, the interaction with the polystyrene surface was weaker and it was dominated by glycans located near the RBD. We do not find significant structural changes in the conformation of S, a result which is in deep contrast to our previous results with another hydrophobic surface (graphite). Our results suggest that SARS-CoV-2 virions may adsorb strongly over plastic surfaces without significantly affecting their infectivity.

Tracking SARS-CoV-2 in rivers as a tool for epidemiological surveillance.

The aim of this work was to evaluate if rivers could be used for SARS-CoV-2 surveillance. Five sampling points from three rivers (AR-1 and AR-2 in Arenales River, MR-1 and MR-2 in Mojotoro River, and CR in La Caldera River) from Salta (Argentina), two of them receiving discharges from wastewater plants (WWTP), were monitored from July to December 2020. Fifteen water samples from each point (75 in total) were collected and characterized physico-chemically and microbiologically and SARS-CoV-2 was quantified by RT-qPCR. Also, two targets linked to human contributions, human polyomavirus (HPyV) and RNase P, were quantified and used to normalize SARS-CoV-2 concentration, which was compared to reported COVID-19 cases. Statistical analyses allowed us to verify the correlation between SARS-CoV-2 and the concentration of fecal indicator bacteria (FIB), as well as to find similarities and differences between sampling points. La Caldera River showed the best water quality; FIBs were within acceptable limits for recreational activities. Mojotoro River's water quality was not affected by the northern WWTP of the city. Instead, Arenales River presented the poorest water quality; at AR-2 was negatively affected by the discharges of the southern WWTP, which contributed to significant increase of fecal contamination. SARS-CoV-2 was found in about half of samples in low concentrations in La Caldera and Mojotoro Rivers, while it was high and persistent in Arenales River. No human tracers were detected in CR, only HPyV was found in MR-1, MR-2 and AR-1, and both were quantified in AR-2. The experimental and normalized viral concentrations strongly correlated with reported COVID-19 cases; thus, Arenales River at AR-2 reflected the epidemiological situation of the city. This is the first study showing the dynamic of SARS-CoV-2 concentration in an urban river highly impacted by wastewater and proved that can be used for SARS-CoV-2 surveillance to support health authorities.

Toxic impact of polystyrene microplastic particles in freshwater organisms.

The ongoing COVID-19 pandemic is leading to an increase of the global production of plastics since the use of personal protective equipment (PPEs, i.e. gloves, gowns, masks, packaging items), has become mandatory to prevent the spread of the virus. Plastic breaks down into micro/nano particles due to physical or chemical or biological actions into environment. Due to small dimensions, ubiquitous and persistent nature, the plastic particles represent a significant threat to ecosystems and can entry into food chains. Among the plastic polymers used for PPEs, polystyrene is less studied regarding its eco-geno-toxicity. This study aims to investigate acute, chronic and subchronic effects of the microplastic polystyrene beads (PS-MP, size 1.0 µm) on three freshwater species, the alga Raphidocelis subcapitata, the rotifer Brachionus calyciflorus, the crustacean Ceriodaphnia dubia and the benthic ostracod Heterocypris incongruens. Furthermore, the potential genotoxicity and the ROS production due to the PS-MP were also determined in C. dubia. Results revealed that the acute effects occurred at concentrations of PS-MP in the order of dozens of mg/L in B. calyciflorus and C. dubia and hundreds of mg/L in H. incongruens. Regarding long-term toxicity, increasing chronic effects with EC50s in the order of units (C. dubia), hundreds (B. calyciflorus) and thousands (R. subcapitata) of µg/L were observed. Both for acute and chronic/sub chronic toxicity, daphnids were more sensitive to polystyrene than ostracods. Moreover, when C. dubia neonates were exposed to the PS-MP, alterations in genetic material as well as the production of ROS occurred, starting from concentrations in the order of units of µg/L, probably due to inflammatory responses. At last, the risk quotient (RQ) as a measure of risk posed by PS-MPs in freshwater environment, was calculated obtaining a value of 7.2, higher than the threshold value of 1.

High-throughput fabrication of high aspect ratio Ag/Al nanopillars for optical detection of biomarkers.

Nanomaterial-based optical techniques for biomarker detection have garnered tremendous attention from the nanofabrication community due to their high precision and enhanced limit of detection (LoD) features. These nanomaterials are highly responsive to local refractive index (RI) fluctuations, and their RI unit sensitivity can be tuned by varying the chemical composition, geometry, and dimensions of the utilized nanostructures. To improve the sensitivity and LoD values of these nanomaterials, it is common to increase both dimensions and aspect ratios of the fabricated nanostructures. However, limited by the complexity, prolonged duration, and elevated costs of the available nanofabrication techniques, mass production of these nanostructures remains challenging. To address not only high accuracy, but also speed and production effectiveness in these nanostructures' fabrication, our work reports, for the first time, a fast, high-throughput, and cost-effective nanofabrication protocol for routine manufacturing of polymer-based nanostructures with high sensitivity and calculated LoD in the pM range by utilizing anodized aluminum oxide (AAO) membranes as templates. Specifically, our developed platform consists of arrays of nearly uniform polystyrene nanopillars with an average diameter of ∼185 nm and aspect ratio of ∼11. We demonstrate that these nanostructures can be produced at a high speed and a notably low price, and that they can be efficiently applied for biosensing purposes after being coated with aluminum-doped silver (Ag/Al) thin films. Our platform successfully detected very low concentrations of human C-reactive protein (hCRP) and SARS-CoV-2 spike protein biomarkers in human plasma samples with LoDs of 11 and 5 pM, respectively. These results open new opportunities for day-to-day fabrication of high aspect ratio arrays of nanopillars that can be used as a base for nanoplasmonic sensors with competitive LoD values. This, in turn, contributes to the development of point-of-care devices and further improvement of the existing nanofabrication techniques, thereby enriching the fields of pharmacology, clinical analysis, and diagnostics.

Toward Rapid and Sensitive Detection of SARS-CoV-2 with Functionalized Magnetic Nanoparticles.

The outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) threatens global medical systems and economies and rules our daily living life. Controlling the outbreak of SARS-CoV-2 has become one of the most important and urgent strategies throughout the whole world. As of October 2020, there have not yet been any medicines or therapies to be effective against SARS-CoV-2. Thus, rapid and sensitive diagnostics is the most important measures to control the outbreak of SARS-CoV-2. Homogeneous biosensing based on magnetic nanoparticles (MNPs) is one of the most promising approaches for rapid and highly sensitive detection of biomolecules. This paper proposes an approach for rapid and sensitive detection of SARS-CoV-2 with functionalized MNPs via the measurement of their magnetic response in an ac magnetic field. For proof of concept, mimic SARS-CoV-2 consisting of spike proteins and polystyrene beads are used for experiments. Experimental results demonstrate that the proposed approach allows the rapid detection of mimic SARS-CoV-2 with a limit of detection of 0.084 nM (5.9 fmole). The proposed approach has great potential for designing a low-cost and point-of-care device for rapid and sensitive diagnostics of SARS-CoV-2.

Rapid molecular diagnostics of COVID-19 by RT-LAMP in a centrifugal polystyrene-toner based microdevice with end-point visual detection.

Infection caused by the new coronavirus (SARS-CoV-2) has become a serious worldwide public health problem, and one of the most important strategies for its control is mass testing. Loop-mediated isothermal amplification (LAMP) has emerged as an important alternative to simplify the diagnostics of infectious diseases. In addition, an advantage of LAMP is that it allows for easy reading of the final result through visual detection. However, this step must be performed with caution to avoid contamination and false-positive results. LAMP performed on microfluidic platforms can minimize false-positive results, in addition to having potential for point-of-care applications. Here, we describe a polystyrene-toner (PS-T) centrifugal microfluidic device manually controlled by a fidget spinner for molecular diagnosis of COVID-19 by RT-LAMP, with integrated and automated colorimetric detection. The amplification was carried out in a microchamber with 5 µL capacity, and the reaction was thermally controlled with a thermoblock at 72 °C for 10 min. At the end of the incubation time, the detection of amplified RT-LAMP fragments was performed directly on the chip by automated visual detection. Our results demonstrate that it is possible to detect COVID-19 in reactions initiated with approximately 10-3 copies of SARS-CoV-2 RNA. Clinical samples were tested using our RT-LAMP protocol as well as by conventional RT-qPCR, demonstrating comparable performance to the CDC SARS-CoV-2 RT-qPCR assay. The methodology described in this study represents a simple, rapid, and accurate method for rapid molecular diagnostics of COVID-19 in a disposable microdevice, ideal for point-of-care testing (POCT) systems.

Synthesis of polystyrene-based fluorescent quantum dots nanolabel and its performance in H5N1 virus and SARS-CoV-2 antibody sensing.

Quantum dots (QDs) based fluorescent nanobeads are considered as promising materials for next generation point-of-care diagnosis systems. In this study, we carried out, for the first time, the synthesis of QDs nanobeads using polystyrene (PS) nanobead as the template. QDs loading on PS nanobead surface in this method can be readily achieved by the use of polyelectrolyte, avoiding the time-consuming and uncontrollable silane reagents-involved functionalization procedure that conventional synthesis of silica-based QDs nanobeads often suffer from. Notably, the application of QDs nanobeads in suspension microarray for H5N1 virus detection leads to a sensitivity lower than 25 PFU/mL. In addition, QDs nanobead was also incorporated into lateral flow assay for SARS-CoV-2 antibody detection, leading to more than one order of magnitude detection sensitivity as compared to that of commercial one based on colloid gold.

A Nanomechanical Study on Deciphering the Stickiness of SARS-CoV-2 on Inanimate Surfaces.

The SARS-CoV-2 virus that causes the COVID-19 epidemic can be transmitted via respiratory droplet-contaminated surfaces or fomites, which urgently requires a fundamental understanding of intermolecular interactions of the coronavirus with various surfaces. The corona-like component of the outer surface of the SARS-CoV-2 virion, named spike protein, is a key target for the adsorption and persistence of SARS-CoV-2 on various surfaces. However, a lack of knowledge in intermolecular interactions between spike protein and different substrate surfaces has resulted in ineffective preventive measures and inaccurate information. Herein, we quantified the surface interaction and adhesion energy of SARS-CoV-2 spike protein with a series of inanimate surfaces via atomic force microscopy under a simulated respiratory droplet environment. Among four target surfaces, polystyrene was found to exhibit the strongest adhesion, followed by stainless steel (SS), gold, and glass. The environmental factors (e.g., pH and temperature) played a role in mediating the spike protein binding. According to systematic quantification on a series of inanimate surfaces, the adhesion energy of spike protein was found to be (i) 0-1 mJ/m2 for hydrophilic inorganics (e.g., silica and glass) due to the lack of hydrogen bonding, (ii) 2-9 mJ/m2 for metals (e.g., alumina, SS, and copper) due to the variation of their binding capacity, and (iii) 6-11 mJ/m2 for hydrophobic polymers (e.g., medical masks, safety glass, and nitrile gloves) due to stronger hydrophobic interactions. The quantitative analysis of the nanomechanics of spike proteins will enable a protein-surface model database for SARS-CoV-2 to help generate effective preventive strategies to tackle the epidemic.

Direct hemoperfusion using a polymyxin B-immobilized polystyrene column for COVID-19.

OBJECTIVE: To evaluate the efficacy and safety of direct hemoperfusion using a polymyxin B-immobilized polystyrene column (PMX-DHP) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-positive pneumonia patients. METHODS: This study was a case series conducted at a designated infectious diseases hospital. Twelve SARS-CoV-2-positive patients with partial pressure of arterial oxygen/percentage of inspired oxygen (P/F) ratio < 300 were treated with PMX-DHP on two consecutive days each during hospitalization. We defined day 1 as the first day when PMX-DHP was performed. PMX-DHP efficacy was assessed on days 7 and 14 after the first treatment based on eight categories. Subsequently, improvement in P/F ratio and urinary biomarkers on days 4 and 8, malfunctions, and ventilator and extracorporeal membrane oxygenation avoidance rates were also evaluated. RESULTS: On day 14 after the first treatment, disease severity decreased in 58.3% of the patients. P/F ratio increased while urine ß2-microglobulin decreased on days 4 and 8. Cytokine measurement pre- and post-PMX-DHP revealed decreased levels of interleukin-6 and the factors involved in vascular endothelial injury, including vascular endothelial growth factor. Twenty-two PMX-DHPs were performed, of which seven and five PMX-DHPs led to increased inlet pressure and membrane coagulation, respectively. When the membranes coagulated, the circuitry needed to be reconfigured. Circuit problems were usually observed when D-dimer and fibrin degradation product levels were high before PMX-DHP. CONCLUSIONS: Future studies are expected to determine the therapeutic effect of PMX-DHP on COVID-19. Because of the relatively high risk of circuit coagulation, coagulation capacity should be assessed beforehand.

Hemoperfusion with CytoSorb as Adjuvant Therapy in Critically Ill Patients with SARS-CoV2 Pneumonia.

We report a preliminary experience of adjuvant therapy with Hemoperfusion (HP) in patients with Severe Acute Respiratory Syndrome-CoronaVirus 2 (SARS-CoV2) pneumonia. Currently, there are no approved treatments for CoronaVirus Disease 19 (COVID-19); however, therapeutic strategies based on the preclinical evidence include supportive measures, such as oxygen supplementation, antiviral, and anticoagulant agents. Despite these treatments, 10% of patients worsen and develop severe acute respiratory distress syndrome (ARDS). Since the pathogenic mechanism of ARDS is an uncontrolled inflammatory state, we speculate that removing inflammation effectors from blood may contrast tissue injury and improve clinical outcome. In a scenario of dramatic medical emergency, we conducted an observational study on 9 consecutive patients hospitalized in COVID Intensive Care Unit, where 5 of 9 consecutive patients were treated with HP, due to the emergency overload made it impossible to deliver blood purification in the other 4 patients. COVID-19 was diagnosed through the identification of virus sequences by reverse transcription-PCR on respiratory specimens. All patients had severe pneumonia requiring continuous positive airway pressure. HP was started in all patients 6-7 days after hospital admission. The treated patients (T) received 2 consecutive sessions of HP using CytoSorb cartridge. Our results show a better clinical course of T compared to control patients (C), in fact all T except 1 survived, and only 2 of them were intubated, while all C required intubation and died. Lymphocytopenia worsened in C but not in T. C-reactive protein decreased in both patients, but to a greater extent in T. IL-6, IL-8, and TNF-α decreased after HP, IL-10 did not change. Respiratory function remained stable and did not worsen in T compared to C. The limited sample size and observational study design preclude a sound statement about the potential effectiveness of HP in COVID-19 patients, but our experience suggests a potential therapeutic role of adjuvant CytoSorb HP in the early course of CO-VID-19 pneumonia. A randomized clinical trial is ongoing.