Search results for: SARs

Authors: Hiba Dakroub, Danilo Russo, Luca Cistrone, Francesco Serra, Giovanna Fusco, Esterina De Carlo, Maria Grazia Amoroso

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The question of the origin of SARS-CoV-2 and the cycle of transmission between humans and animals is still unanswered. One serious concern associated with the SARS-CoV-2 pandemic is that the virus might spill back from humans to wildlife, which would render some animal species reservoirs of the human virus. The aim of the present study is to monitor the potential risk of SARS-CoV-2 reverse infection from humans to bats, by performing bat surveillance from different sites in Central-Southern Italy. We collected 240 droppings or saliva from 129 bats and tested them using specific and general primers of SARS-COV-2 and coronaviruses respectively. All samples, including 127 nasal swabs and 113 fecal droppings resulted negative for SARS-COV-2, and these results were confirmed by testing the samples with the Droplet Digital PCR. Also, an end-point RT-PCR was performed and no sample showed specific bands. The absence of SARS-CoV-2 in the bats we surveyed is a first step towards a better understanding of reverse transmission to bats of this virus. We hope our first contribution will encourage the establishment of systematic surveillance of wildlife, and specifically bats, to help prevent reverse zoonotic episodes that would jeopardize human health as well as biodiversity conservation and management.

Keywords: coronaviruses, bats, zoonotic viruses, spillback, SARS-CoV-2

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Authors: Ojo Oo, Akinde S. B., Kiilani A. O., Jayeola Jo, Jogbodo T. M., Ajani Ka, Olaniyan So, Adeagbo Oy, Bolarinwa Ra, Durosomo Ha, Sule W. F.

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Lockdown imposed to control SARS-CoV-2 transmission hampered malaria control services in Nigeria. Considering COVID-19 vaccination, we assessed Plasmodium falciparum (Pf) antigen and SARS-CoV-2 immunoglobulin-G (IgG) positivity among adults in Osogbo, Osun State, Nigeria. Consenting attendees of four Healthcare Centres were consecutively enrolled for blood sampling; relevant socio-demographic/behavioral/clinical/environmental data were collected with a questionnaire. Samples were tested, using commercial rapid test kits, for Pf antigen and SARS-CoV-2 IgG and results were analyzed using logistic regression. Participants' mean age was 40.99 years (n=200), and they were predominantly females (84.5%), traders/businessmen/women (86.0%), with self-reported receipt of COVID-19 vaccine from 123 (61.5%). Pf antigen positivity was 17.5% (95% CI: 12.23–22.77%) with age (p=0.004), marital status (p=0.004), report of stagnant water around the workplace (p=0.041) and bush around homes (p=0.008) being associated. SARS-CoV-2 IgG positivity was 56.5% (95% CI: 49.63–63.37%) with age (p=0.012) and receipt of COVID-19 vaccination (p=0.001) being associated. Although the vaccinated had a 22.8 times higher likelihood of IgG positivity, no factor was predictive of COVID-19 vaccine receipt. We report 17.5% Pf antigen positivity with four predictors, and 56.5% SARS-CoV-2 IgG positivity with two predictors.

Keywords: COVID-19, vaccine, IgG, Plasmodium falciparum, SARS-CoV-2

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Authors: Weldegerima Gebremedhin Hagos

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Background: The Coronavirus disease of 2019 (COVID-19) is a catastrophic emerging global health threat caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). COVID-19 has a wide range of complications and sequels. It is devastating in developing countries, causing serious health and socioeconomic crises as a result of the increasingly overburdened healthcare system. Ethiopia reported the first case of SARS-CoV-2 on 13th March 2020, with community transmission ensuing by mid-May. The aim of this study was conducted to determine the prevalence of SARS-CoV-2 infection in Tigray, Ethiopia. Methods: Facility-based correctional study designs were used on a total of 380 study participants from March 2023 up to May 2023 in two general hospitals and one comprehensive specialized hospital in Tigray, Ethiopia. A pre-structured questionnaire was used to assess information regarding the socio-demographic, clinical data and other risk factors. A nasal swap was taken by trained health professionals, and the laboratory analysis was done by RT-PCR (quant studio 7-flex, applied biosystems) in Tigrai Health Research Institute and Mekelle University Medical Microbiology Research Laboratory. Result: The mean age of the study participants was 31 (SD+/-3.5) years, with 65% being male and 35% female. The overall seropositivity of sars-cov-2 among the study participants was 5.5%. The prevalence was higher in males (6.2%) than females which were (4.7%). Sars-cov-2 infection was significantly associated with a history of lack of vaccination (p-value 0.002). There was no significant association between seropositivity and demographic factors (P > 0.05). Conclusion: The seroprevalence of SARS-CoV-2 among the study participants is high. Those study participants with a previous history of vaccination have a low probability of developing COVID-19 infection. A low SARS-CoV-2 infection rate was recorded in those who frequently use masks.

Keywords: prevalence, SARS-CoV-2, infection, risk factors

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Authors: Gleda Kutrolli, Maksi Kutrolli, Etjon Meco

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SARS-CoV-2 virus is currently one of the most infectious pathogens for humans. It started in China at the end of 2019 and now it is spread in all over the world. The origin and diffusion of the SARS-CoV-2 epidemic, is analysed based on the discussion of viral phylogeny theory. With the aim of understanding the spread of infection in the affected countries, it is crucial to modelize the spread of the virus and simulate its activity. In this paper, the prediction of coronavirus outbreak is done by using SIR model without vital dynamics, applying different numerical technique solving ordinary differential equations (ODEs). We find out that ABM and MRT methods perform better than other techniques and that the activity of the virus will decrease in April but it never cease (for some time the activity will remain low) and the next cycle will start in the middle July 2020 for Norway and Denmark, and October 2020 for Sweden, and September for Finland.

Keywords: forecasting, ordinary differential equations, SARS-COV-2 epidemic, SIR model

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Authors: Afia Naheed, Manmohan Singh, David Lucy

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This work is based on a mathematical as well as statistical study of an SEIJTR deterministic model for the interpretation of transmission of severe acute respiratory syndrome (SARS). Based on the SARS epidemic in 2003, the parameters are estimated using Runge-Kutta (Dormand-Prince pairs) and least squares methods. Possible graphical and numerical techniques are used to validate the estimates. Then effect of the model parameters on the dynamics of the disease is examined using sensitivity and uncertainty analysis. Sensitivity and uncertainty analytical techniques are used in order to analyze the affect of the uncertainty in the obtained parameter estimates and to determine which parameters have the largest impact on controlling the disease dynamics.

Keywords: infectious disease, severe acute respiratory syndrome (SARS), parameter estimation, sensitivity analysis, uncertainty analysis, Runge-Kutta methods, Levenberg-Marquardt method

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Authors: Gyaltsen Dakpa, K. J. Senthil Kumar, Nai-Wen Tsao, Sheng-Yang Wang

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Context: Coronavirus disease 2019 (COVID-19) is a severe respiratory illness caused by the SARS-CoV-2 virus. One of the hallmarks of COVID-19 is a change in metabolism, which can lead to increased severity and mortality. The mechanism of SARS-CoV-2-mediated perturbations of metabolic pathways has yet to be fully understood. Research Aim: This study aimed to investigate the metabolic alteration caused by SARS-CoV-2 spike protein in Phorbol 12-myristate 13-acetate (PMA)-induced human monocytes (THP-1) and to examine the regulatory effect of natural compounds like Antcins A on SARS-CoV-2 spike protein-induced metabolic alteration. Methodology: The study used a combination of proton nuclear magnetic resonance (1H-NMR) and MetaboAnalyst 5.0 software. THP-1 cells were treated with SARS-CoV-2 spike protein or control, and the metabolomic profiles of the cells were compared. Antcin A was also added to the cells to assess its regulatory effect on SARS-CoV-2 spike protein-induced metabolic alteration. Findings: The study results showed that treatment with SARS-CoV-2 spike protein significantly altered the metabolomic profiles of THP-1 cells. Eight metabolites, including glycerol-phosphocholine, glycine, canadine, sarcosine, phosphoenolpyruvic acid, glutamine, glutamate, and N, N-dimethylglycine, were significantly different between control and spike-protein treatment groups. Antcin A significantly reversed the changes in these metabolites. In addition, treatment with antacid A significantly inhibited SARS-CoV-2 spike protein-mediated up-regulation of TLR-4 and ACE2 receptors. Theoretical Importance The findings of this study suggest that SARS-CoV-2 spike protein can cause significant metabolic alterations in THP-1 cells. Antcin A, a natural compound, has the potential to reverse these metabolic alterations and may be a potential candidate for developing preventive or therapeutic agents for COVID-19. Data Collection: The data for this study was collected from THP-1 cells that were treated with SARS-CoV-2 spike protein or a control. The metabolomic profiles of the cells were then compared using 1H-NMR and MetaboAnalyst 5.0 software. Analysis Procedures: The metabolomic profiles of the THP-1 cells were analyzed using 1H-NMR and MetaboAnalyst 5.0 software. The software was used to identify and quantify the cells' metabolites and compare the control and spike-protein treatment groups. Questions Addressed: The question addressed by this study was whether SARS-CoV-2 spike protein could cause metabolic alterations in THP-1 cells and whether Antcin A can reverse these alterations. Conclusion: The findings of this study suggest that SARS-CoV-2 spike protein can cause significant metabolic alterations in THP-1 cells. Antcin A, a natural compound, has the potential to reverse these metabolic alterations and may be a potential candidate for developing preventive or therapeutic agents for COVID-19.

Keywords: SARS-CoV-2-spike, ¹H-NMR, metabolomics, antcin-A, taiwanofungus camphoratus

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Authors: Ansah Iris Baffour, Dong-Ho Kim, Sung-Gyu Park

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The ongoing COVID-19 pandemic, caused by the SARS-CoV-2 virus and is gradually shifting to an endemic phase which implies the outbreak is far from over and will be difficult to eradicate. Global cooperation has led to unified precautions that aim to suppress epidemiological spread (e.g., through travel restrictions) and reach herd immunity (through vaccinations); however, the primary strategy to restrain the spread of the virus in mass populations relies on screening protocols that enable rapid on-site diagnosis of infections. Herein, we employed surface enhanced Raman spectroscopy (SERS) for the rapid detection of SARS-CoV-2 lysate on an Au-modified Au nanodimple(AuND)electrode. Through in situone-pot Au electrodeposition on the AuND electrode, Au-lysate nanocomposites were synthesized, generating3D internal hotspots for large SERS signal enhancements within 30 s of the deposition. The capture of lysate into newly generated plasmonic nanogaps within the nanocomposite structures enhanced metal-spike protein contact in 3D spaces and served as hotspots for sensitive detection. The limit of detection of SARS-CoV-2 lysate was 5 x 10-2 PFU/mL. Interestingly, ultrasensitive detection of the lysates of influenza A/H1N1 and respiratory syncytial virus (RSV) was possible, but the method showed ultimate selectivity for SARS-CoV-2 in lysate solution mixtures. We investigated the practical application of the approach for rapid on-site diagnosis by detecting SARS-CoV-2 lysate spiked in normal human saliva at ultralow concentrations. The results presented demonstrate the reliability and sensitivity of the assay for rapid diagnosis of COVID-19.

Keywords: label-free detection, nanocomposites, SARS-CoV-2, surface-enhanced raman spectroscopy

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Authors: Jesmin Akter, Chang Hyuk Ahn, Ilho Kim, Jaiyeop Lee

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Global pandemic coronavirus disease (COVID-19) caused by Severe acute respiratory syndrome SARS-CoV-2, to control the spread of the COVID-19 pandemic, wastewater surveillance has been used to monitor SARS-CoV2 prevalence in the community. The challenging part is establishing wastewater surveillance; there is a need for a well-equipped laboratory for wastewater sample analysis. According to many previous studies, reverse transcription-polymerase chain reaction (RT-PCR) based molecular tests are the most widely used and popular detection method worldwide. However, the RT-qPCR based approaches for the detection or quantification of SARS-CoV-2 genetic fragments ribonucleic acid (RNA) from wastewater require a specialized laboratory, skilled personnel, expensive instruments, and a workflow that typically requires 6 to 8 hours to provide results for just minimum samples. Rapid and reliable alternative detection methods are needed to enable less-well-qualified practitioners to set up and provide sensitive detection of SARS-CoV-2 within wastewater at less-specialized regional laboratories. Therefore, scientists and researchers are conducting experiments for rapid detection methods of COVID-19; in some cases, the structural and molecular characteristics of SARS-CoV-2 are unknown, and various strategies for the correct diagnosis of COVID-19 have been proposed by research laboratories, which are presented in the present study. The ongoing research and development of these highly sensitive and rapid technologies, namely RT-LAMP, ELISA, Biosensors, GeneXpert, allows a wide range of potential options not only for SARS-CoV-2 detection but also for other viruses as well. The effort of this study is to discuss the above effective and regional rapid detection and quantification methods in community wastewater as an essential step in advancing scientific goals.

Keywords: rapid detection, SARS-CoV-2, sensitive detection, wastewater surveillance

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Authors: R. Mehta, M. Ghogomu, B. Schoel

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Reports appeared in 2020 about China detecting SARS-Cov-2 (Covid-19) on frozen meat, shrimp, and food packaging material. In this study, we examined the use of swabs for the detection of Covid-19 on meat samples, and chicken breast (CB) was used as a model. Methods: Heat inactivated SARS-Cov-2 virus (IV) from Microbiologics was loaded onto the CB, swabbing was done, and the recovered inactivated virus was subjected to the Machery & Nagel NucleoSpin RNAVirus kit for RNA isolation according to manufacturer's instructions. For RT-PCR, the IDT 2019-nCoV RUO Covid-19 test kit was used with the Taqman Fast Virus 1-step master mix. The limit of detection (LOD) of viral load recovered from the CB was determined under various conditions: first on frozen CB where the IV was introduced on a defined area, then on frozen CB, with IV spread-out, and finally, on thawed CB. Results: The lowest amount of IV which can be reliably detected on frozen CB was a load of 1,000 - 2,000 IV copies where the IV was loaded on one spot of about 1 square inch. Next, the IV was spread out over a whole frozen CB about 16 square inches. The IV could be recovered at a lowest load of 4,000 to 8,000 copies. Furthermore, the effects of temperature change on viral load recovery was investigated i.e., if raw unfrozen meat became contaminated and remains for 1 hour at 4°C or gets refrozen. The amount of IV recovered successfully from CB kept at 4°C and the refrozen CB was similar to the recovery gotten from loading the IV directly on the frozen CB. In conclusion, an assay using swabs was successfully established for the detection of SARS-Cov-2 on frozen or raw (unfrozen) CB with a minimal load of up to 8,000 copies spread over 16 square inches.

Keywords: assay, COVID-19, meat, SARS-Cov-2

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Authors: Jesmin Akter, Chang Hyuk Ahn, Ilho Kim, Fumitake Nishimura, Jaiyeop Lee

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This study aimed to compare two pre-treatment and two RNA extraction methods, namely PEG, and Nano bubble, Viral RNA Soil, and Mini Kit, in terms of their efficiency in detecting SARS-CoV-2 and PMMoV in influent and 1st sedimentation samples from a wastewater treatment plant. The extracted RNA samples were quantified and evaluated for purity, yield, and integrity. The results indicated that the nanobubble PEG method provided the highest yield of RNA, while the QIAamp Viral RNA Mini Kit produced the purest RNA samples. In terms of sensitivity and specificity, all these methods were able to detect SARS-CoV-2 and PMMoV in both influent and 1st sedimentation samples. However, the nanobubble PEG method showed slightly higher sensitivity compared to the other methods. These findings suggest that the choice of RNA extraction method should depend on the downstream application and the quality of the RNA required. The study also highlights the potential of wastewater-based epidemiology as an effective and non-invasive method for monitoring the spread of infectious diseases in a community.

Keywords: influent, PMMoV, SARS-CoV-2, wastewater based epidemiology

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Authors: Jennifer Fane, Mike Gray, Melissa Sager

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Children with diagnosed or suspected learning disabilities frequently experience significant skill gaps in foundational learning areas such as reading, writing, and math. Remedial one-to-one instruction is a highly effective means of supporting children with learning differences in building these foundational skills and closing the learning gap between them and their same-age peers. However, due to the learning challenges children with learning disabilities face, and ensuing challenges with self-confidence, many children with learning differences struggle with motivation and self-regulation within remedial one-to-one learning environments - despite the benefits of these sessions. Socially Assistive Robots (SARs) are an innovative educational technology tool that has been trialled in a range of educational settings to support diverse learning needs. Yet, little is known about the impact of SARs on the learning of children with learning differences in a one-to-one remedial instructional setting. This study sought to explore the impact of SARs on the engagement of children (n=9) with learning differences attending one-to-one remedial instruction sessions at a non-profit remedial education provider. The study used a mixed-methods design to explore learner engagement during learning tasks both with and without the use of a SAR to investigate how the use of SARs impacts student learning. The study took place over five weeks, with each session within the study followed the same procedure with the SAR acting as a teaching assistant when in use. Data from the study included analysis of time-sample video segments of the instructional sessions, instructor recorded information about the student’s progress towards their session learning goal and student self-reported mood and energy levels before and after the session. Analysis of the findings indicates that the use of SARs resulted in fewer instances of off-task behaviour and less need for instructor re-direction during learning tasks, allowing students to work in more sustained ways towards their learning goals. This initial research indicates that the use of SARs does have a material and measurable impact on learner engagement for children with learning differences and that further exploration of the impact of SARs during one-to-one remedial instruction is warranted.

Keywords: engagement, learning differences, learning disabilities, instruction, social robotics.

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Authors: Hueiwang Anna Jeng, Norou Diawara, Nancy Welch, Cynthia Jackson, Rekha Singh, Kyle Curtis, Raul Gonzalez, David Jurgens, Sasanka Adikari

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Modeling effort is needed to predict the COVID-19 trends for developing management strategies and adaptation measures. The objective of this study was to assess whether SARS-CoV-2 viral load in wastewater could serve as a predictor for forecasting COVID-19 cases, hospitalization cases, and death cases using copula-based time series modeling. SARS-CoV-2 RNA load in raw wastewater in Chesapeake VA was measured using the RT-qPCR method. Gaussian copula time series marginal regression model, incorporating an autoregressive moving average model and the copula function, served as a forecasting model. COVID-19 cases were correlated with wastewater viral load, hospitalization cases, and death cases. The forecasted trend of COVID-19 cases closely paralleled one of the reported cases, with over 90% of the forecasted COVID-19 cases falling within the 99% confidence interval of the reported cases. Wastewater SARS-CoV-2 viral load could serve as a predictor for COVID-19 cases and hospitalization cases.

Keywords: COVID-19, modeling, time series, copula function

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Authors: Atlal El-Assaad

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Viruses change with time through mutations and result in new variants that may persist or disappear. A Mutation refers to an actual change in the virus genetic sequence, and a variant is a viral genome that may contain one or more mutations. Critical mutations may cause the virus to be more transmissible, with high disease severity, and more vulnerable to diagnostics, therapeutics, and vaccines. Thus, variants carrying such mutations may increase the risk to human health and are considered variants of concern (VOC). Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) - the contagious in humans, positive-sense single-stranded RNA virus that caused coronavirus disease 2019 (COVID-19) - has been studied thoroughly, and several variants were revealed across the world with their corresponding mutations. SARS-CoV-2 has four structural proteins, known as the S (spike), E (envelope), M (membrane), and N (nucleocapsid) proteins, but prior study and vaccines development focused on genetic mutations in the S protein due to its vital role in allowing the virus to attach and fuse with the membrane of a host cell. Specifically, subunit S1 catalyzes attachment, whereas subunit S2 mediates fusion. In this perspective, we studied all charged amino acid mutations of the SARS-CoV-2 viral spike protein S1 when bound to Antibody CC12.1 in a crystal structure and assessed the effect of different mutations. We generated all missense mutants of SARS-CoV-2 protein amino acids (AAs) within the SARS-CoV-2:CC12.1 complex model. To generate the family of mutants in each complex, we mutated every charged amino acid with all other charged amino acids (Lysine (K), Arginine (R), Glutamic Acid (E), and Aspartic Acid (D)) and studied the new binding of the complex after each mutation. We applied Poisson-Boltzmann electrostatic calculations feeding into free energy calculations to determine the effect of each mutation on binding. After analyzing our data, we identified charged amino acids keys for binding. Furthermore, we validated those findings against published experimental genetic data. Our results are the first to propose in silico potential life-threatening mutations of SARS-CoV-2 beyond the present mutations found in the five common variants found worldwide.

Keywords: SARS-CoV-2, variant, ionic amino acid, protein-protein interactions, missense mutation, AESOP

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Authors: Manal Kamel, Sara Maher, Hanan El Baz, Faten Salah, Omar Sayyouh, Zeinab Demerdash

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In the recent COVID 19 pandemic, experts of public health have emphasized testing, tracking infected people, and tracing their contacts as an effective strategy to reduce the spread of the virus. Development of rapid and sensitive diagnostic assays to replace reverse transcription polymerase chain reaction (RT-PCR) is mandatory..Our innovative test strip relying on the application of nanoparticles conjugated to recombinant nanobodies for SARS-COV-2 spike protein (S1) & angiotensin-converting enzyme 2 (that is responsible for the virus entry into host cells) for rapid detection of SARS-COV-2 spike protein (S1) in saliva or sputum specimens. Comparative tests with RT-PCR will be held to estimate the significant effect of using COVID 19 nanobodies for the first time in the development of lateral flow test strip. The SARS-CoV-2 S1 (3 ng of recombinant proteins) was detected by our developed LFIA in saliva specimen of COVID-19 Patients No cross-reaction was detected with Middle East respiratory syndrome coronavirus (MERS-CoV) or SARS- CoV antigens..Our developed system revealed 96 % sensitivity and 100% specificity for saliva samples compared to 89 % and 100% sensitivity and specificity for nasopharyngeal swabs. providing a reliable alternative for the painful and uncomfortable nasopharyngeal swab process and the complexes, time consuming PCR test. An increase in testing compliances to be expected.

Keywords: COVID 19, diagnosis, LFIA, nanobodies, ACE2

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Authors: Adam M. Pitz, Gillian L. Phillipson, Jayant E. Khanolkar, Andrew M. Middleton

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New emerging evidence suggests that the nose is the predominant route for entry of the SARS-CoV-2 virus into the host. A virucidal suspension test (conforming in principle to the European Standard EN14476) was conducted to determine whether a commercial liquid gel intranasal spray containing 1% of the mucoadhesive hydroxypropyl methylcellulose (HPMC) could inhibit the cellular infectivity of the SARS-CoV-2 coronavirus. Virus was added to the test product samples and to controls in a 1:8 ratio and mixed with one part bovine serum albumin as an interfering substance. The test samples were pre-equilibrated to 34 ± 2°C (representing the temperature of the nasopharynx) with the temperature maintained at 34 ± 2°C for virus contact times of 1, 5 and 10 minutes. Neutralized aliquots were inoculated onto host cells (Vero E6 cells, ATCC CRL-1586). The host cells were then incubated at 36 ± 2°C for a period of 7 days. The residual infectious virus in both test and controls was detected by viral-induced cytopathic effect. The 50% tissue culture infective dose per mL (TCID50/mL) was determined using the Spearman-Karber method with results reported as the reduction of the virus titer due to treatment with test product, expressed as log10. The controls confirmed the validity of the results with no cytotoxicity or viral interference observed in the neutralized test product samples. The HPMC formulation reduced SARS-CoV-2 titer, expressed as log10TCID50, by 2.30 ( ± 0.17), 2.60 ( ± 0.19), and 3.88 ( ± 0.19) with the respective contact times of 1, 5 and 10 minutes. The results demonstrate that this 1% HPMC gel formulation can reduce the cellular infectivity of the SARS-CoV-2 virus with an increasing viral inhibition observed with increasing exposure time. This 1% HMPC gel is well tolerated and can reside, when delivered via nasal spray, for up to one hour in the nasal cavity. We conclude that this intranasal gel spray with 1% HPMC repeat-dosed every few hours may offer an effective preventive or early intervention solution to limit the transmission and impact of the SARS-CoV-2 coronavirus.

Keywords: hydroxypropyl methylcellulose, mucoadhesive nasal spray, respiratory viruses, SARS-CoV-2

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Authors: Mark Osborn

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Clustered, regularly interspaced short palindromic repeat (CRISPR/Cas) proteins can be designed to bind specified DNA and RNA sequences and hold great promise for the accurate detection of nucleic acids for diagnostics. Commercially available reagents were integrated into a CRISPR/Cas9-based lateral flow assay that can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequences with single-base specificity. This approach requires minimal equipment and represents a simplified platform for field-based deployment. A rapid, multiplex fluorescence CRISPR/Cas9 nuclease cleavage assay capable of detecting and differentiating SARS-CoV-2, influenza A and B, and respiratory syncytial virus in a single reaction was also developed. These findings provide proof of principle for CRISPR/Cas9 point-of-care diagnosis that can detect specific SARS-CoV-2 strain(s). Further, Cas9 cleavage allows for a scalable fluorescent platform for identifying respiratory viral pathogens with overlapping symptomology. Collectively, this approach is a facile platform for diagnostics with broad application to user-defined sequence interrogation and detection.

Keywords: CRISPR/Cas9, lateral flow assay, SARS-Co-V2, single-nucleotide resolution

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Authors: Mohammad Hossein Modarressi, Mozhgan Mondeali, Khabat Barkhordari, Ali Etemadi

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The COVID-19 pandemic, caused by SARS-CoV-2, has led to significant concerns worldwide due to its catastrophic effects on public health. The SARS-CoV-2 infection is initiated with the binding of the receptor-binding domain (RBD) in its spike protein to the ACE2 receptor in the host cell membrane. Due to the error-prone entity of the viral RNA-dependent polymerase complex, the virus genome, including the coding region for the RBD, acquires new mutations, leading to the appearance of multiple variants. These variants can potentially impact transmission, virulence, antigenicity and evasive immune properties. S477N mutation located in the RBD has been observed in the SARS-CoV-2 omicron (B.1.1. 529) variant. In this study, we investigated the consequences of S477N mutation at the molecular level using computational approaches such as molecular dynamics simulation, protein-protein interaction analysis, immunoinformatics and free energy computation. We showed that displacement of Ser with Asn increases the stability of the spike protein and its affinity to ACE2 and thus increases the transmission potential of the virus. This mutation changes the folding and secondary structure of the spike protein. Also, it reduces antibody neutralization, raising concern about re-infection, vaccine breakthrough and therapeutic values.

Keywords: S477N, COVID-19, molecular dynamic, SARS-COV2 mutations

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Authors: Werner Roux Uys

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The Commissioner for the South African Revenue Service (SARS) holds a high position of trust in South African society and a lack of trust by taxpayers in the Commissioner’s actions or conduct could compromise SARS’ management of public finances. Tax morality – which is implicit in the social contract between taxpayers and the state – includes distinct phenomena that can cause a breakdown if there is a perceived lack of action on the part of the Commissioner to ensure public finances are kept safe. To promote tax morality, the Commissioner must support the judiciary in the exercise of its discretion to punish fraudulent tax activities and corrupt tax practices. For several years the political meddling in the Commissioner’s actions and conduct have caused perceived abuse of power at SARS, and taxpayers believed their hard-earned income paid over to SARS would be fruitless and wasteful expenditure. The purpose of this article is to identify and analyse previous decisions held by the South African judiciary regarding the Commissioner’s actions and conduct in tax matters, as well as consider important political statements and newspaper bulletins for the purpose of this research. The study applies a qualitative research approach and exploratory case study technique. Keywords were selected and inserted in the LexisNexis electronic database to systematically identify applicable case law where the ratio decidendi of the court referred to the actions and/or conduct of the Commissioner. Specific real-life statements, including political statements and newspaper bulletins, were selected to support the topic at hand. The purpose of the study is to educate the public about the perceptions that have transformed taxpayers’ behaviour towards the Commissioner for SARS since South Africa’s fledgling constitutional democracy was inaugurated in 1994. The study adds to the literature by identifying key characteristics or distinct phenomena regarding the actions and conduct of the Commissioner affecting taxpayers’ behaviour, including discretionary decision-making. From the findings, it emerged that SARS must abide by its (own) laws and that there is a need to educate not only South African taxpayers about tax morality, but also the public in general.

Keywords: commissioner, SARS, action and conduct, judiciary, discretionry, decsion-making

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Authors: Teklay Gebrecherkos

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Background: Serological testing for SARS-CoV-2 plays an important role in epidemiological studies, in aiding the diagnosis of COVID-19 and assess vaccine responses. Little is known about the dynamics of SARS-CoV-2 serology in African settings. Here, we aimed to characterize the longitudinal antibody response profile to SARS-CoV-2 in Ethiopia. Methods: In this prospective study, a total of 102 PCR-confirmed COVID-19 patients were enrolled. We obtained 802 plasma samples collected serially. SARS-CoV-2 antibodies were determined using four lateral flow immune assays (LFIAs) and an electrochemiluminescent immunoassay. We determined longitudinal antibody response to SARS-CoV-2 as well as seroconversion dynamics. Results: Serological positivity rate ranged between 12%-91%, depending on timing after symptom onset. There was no difference in the positivity rate between severe and non-severe COVID-19 cases. The specificity ranged between 90%-97%. Agreement between different assays ranged between 84%-92%. The estimated positive predictive value (PPV) for IgM or IgG in a scenario with seroprevalence at 5% varies from 33% to 58%. Nonetheless, when the population seroprevalence increases to 25% and 50%, there is a corresponding increase in the estimated PPVs. The estimated negative-predictive value (NPV) in a low seroprevalence scenario (5%) is high (>99%). However, the estimated NPV in a high seroprevalence scenario (50%) for IgM or IgG is reduced significantly from 80% to 85%. Overall, 28/102 (27.5%) seroconverted by one or more assays tested within a median time of 11 (IQR: 9–15) days post symptom onset. The median seroconversion time among symptomatic cases tended to be shorter when compared to asymptomatic patients [9 (IQR: 6–11) vs. 15 (IQR: 13–21) days; p = 0.002]. Overall, seroconversion reached 100% 5.5 weeks after the onset of symptoms. Notably, of the remaining 74 COVID-19 patients included in the cohort, 64 (62.8%) were positive for antibodies at the time of enrollment, and 10 (9.8%) patients failed to mount a detectable antibody response by any of the assays tested during follow-up. Conclusions: Longitudinal assessment of antibody response in African COVID-19 patients revealed heterogeneous responses. This underscores the need for a comprehensive evaluation of serum assays before implementation. Factors associated with failure to seroconvert need further research.

Keywords: COVID-19, antibody, rapid diagnostic tests, ethiopia

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Authors: Mohamad Ammar Ayass, Natalya Griko, Victor Pashkov, Wanying Cao, Kevin Zhu, Jin Zhang, Lina Abi Mosleh

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Respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent for coronavirus disease 2019 (COVID-19). Early evidence pointed at the angiotensin-converting enzyme 2 (ACE-2) expressed on the epithelial cells of the lung as the main entry point of SARS-CoV-2 into the cells. The viral entry is mediated by the binding of the Receptor Binding Domain (RBD) of the spike protein that is expressed on the surface of the virus to the ACE-2 receptor. As the number of SARS-CoV-2 variants continues to increase, mutations arising in the RBD of SARS-CoV-2 may lead to the ineffectiveness of RBD targeted neutralizing antibodies. To address this limitation, the objective of this study is to develop a combination of aptamers that target different regions of the RBD, preventing the binding of the spike protein to ACE-2 receptor and subsequent viral entry and replication. A safe and innovative biomedical tool was developed to inhibit viral infection and reduce the harms of COVID-19. In the present study, DNA aptamers were developed against a recombinant trimer S protein using the Systematic Evolution of Ligands by Exponential enrichment (SELEX). Negative selection was introduced at round number 7 to select for aptamers that bind specifically to the RBD domain. A series of 9 aptamers (ADI2010, ADI2011, ADI201L, ADI203L, ADI205L, ADIR68, ADIR74, ADIR80, ADIR83) were selected and characterized with high binding affinity and specificity to the RBD of the spike protein. Aptamers (ADI25, ADI2009, ADI203L) were able to bind and pull down endogenous spike protein expressed on the surface of SARS-CoV-2 virus in COVID-19 positive patient samples and determined by liquid chromatography- tandem mass spectrometry analysis (LC-MS/MS). LC-MS/MS data confirmed that aptamers can bind to the RBD of the spike protein. Furthermore, results indicated that the combination of the 9 best aptamers inhibited the binding of the purified trimer spike protein to the ACE-2 receptor found on the surface of Vero E6 cells. In the same experiment, the combined aptamers displayed a better neutralizing effect than antibodies. The data suggests that the selected aptamers could be used in therapy to neutralize the effect of the SARS-CoV-2 virus by inhibiting the interaction between the RBD and ACE-2 receptor, preventing viral entry into target cells and therefore blocking viral replication.

Keywords: aptamer, ACE-2 receptor, binding inhibitor, COVID-19, spike protein, SARS-CoV-2, treatment

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Authors: Dmitriy Babenko, Sergey Yegorov, Ilya Korshukov, Aidana Sultanbekova, Valentina Barkhanskaya, Tatiana Bashirova, Yerzhan Zhunusov, Yevgeniya Li, Viktoriya Parakhina, Svetlana Kolesnichenko, Yeldar Baiken, Aruzhan Pralieva, Zhibek Zhumadilova, Matthew S. Miller, Gonzalo H. Hortelano, Anar Turmuhambetova, Antonella E. Chesca, Irina Kadyrova

Abstract:

Introduction: The rapidly evolving COVID-19 pandemic, along with the re-emergence of pathogens causing acute respiratory infections (ARI), has necessitated the development of novel diagnostic tools to differentiate various causes of ARI. MALDI-MS, due to its wide usage and affordability, has been proposed as a potential instrument for diagnosing SARS-CoV-2 versus non-SARS-CoV-2 ARI. The aim of this study was to investigate the potential of MALDI-MS in conjunction with a machine learning model to accurately distinguish between symptomatic infections caused by SARS-CoV-2 and non-SARS-CoV-2 during both the early and later phases of the pandemic. Furthermore, this study aimed to analyze mass spectrometry (MS) data obtained from nasal swabs of healthy individuals. Methods: We gathered mass spectra from 252 samples, comprising 108 SARS-CoV-2-positive samples obtained in 2020 (Covid 2020), 7 SARS-CoV- 2-positive samples obtained in 2023 (Covid 2023), 71 samples from symptomatic individuals without SARS-CoV-2 (Control non-Covid ARVI), and 66 samples from healthy individuals (Control healthy). All the samples were subjected to RT-PCR testing. For data analysis, we employed the caret R package to train and test seven machine-learning algorithms: C5.0, KNN, NB, RF, SVM-L, SVM-R, and XGBoost. We conducted a training process using a five-fold (outer) nested repeated (five times) ten-fold (inner) cross-validation with a randomized stratified splitting approach. Results: In this study, we utilized the Covid 2020 dataset as a case group and the non-Covid ARVI dataset as a control group to train and test various machine learning (ML) models. Among these models, XGBoost and SVM-R demonstrated the highest performance, with accuracy values of 0.97 [0.93, 0.97] and 0.95 [0.95; 0.97], specificity values of 0.86 [0.71; 0.93] and 0.86 [0.79; 0.87], and sensitivity values of 0.984 [0.984; 1.000] and 1.000 [0.968; 1.000], respectively. When examining the Covid 2023 dataset, the Naive Bayes model achieved the highest classification accuracy of 43%, while XGBoost and SVM-R achieved accuracies of 14%. For the healthy control dataset, the accuracy of the models ranged from 0.27 [0.24; 0.32] for k-nearest neighbors to 0.44 [0.41; 0.45] for the Support Vector Machine with a radial basis function kernel. Conclusion: Therefore, ML models trained on MALDI MS of nasopharyngeal swabs obtained from patients with Covid during the initial phase of the pandemic, as well as symptomatic non-Covid individuals, showed excellent classification performance, which aligns with the results of previous studies. However, when applied to swabs from healthy individuals and a limited sample of patients with Covid in the late phase of the pandemic, ML models exhibited lower classification accuracy.

Keywords: SARS-CoV-2, MALDI-TOF MS, ML models, nasopharyngeal swabs, classification

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Authors: Getu Hailu, Catelynn Hettick, Niklas Pieper, Paul Kim, Augustine Hamner

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Airborne transmission is a problem that all viral respiratory diseases have in common. In late 2019, a disease outbreak, now known as SARS-CoV-2, suddenly expanded across China and the rest of the world in a matter of months. Research on the spread and transmission of SARS-CoV-2 airborne particles is ongoing, as well as the development of strategies for the prevention of the spread of these pathogens using indoor air quality (IAQ) methods. By evaluating the surface area of pollutants on the surface of a mannequin in a mock-based clinic room, this study aims to better understand how altering temperature and relative humidity affect aerosol spread and contamination. Four experiments were carried out at a constant temperature of 70 degrees Fahrenheit but with four different humidity levels of 0%, 30%, 45 percent, and 60%. The mannequin was placed in direct aerosol flow since it was discovered that this was the position with the largest exposed surface area. The findings demonstrate that as relative humidity increased while the temperature remained constant, the amount of surface area infected by virus particles decreased. These findings point to approaches to reduce the spread of viral particles, such as SARS-CoV-2 and emphasize the significance of IAQ controls in enclosed environments.

Keywords: IAQ, ventilation, COVID-19, humidity, temperature

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Authors: Manal Kamel, Sara Maher

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Development of sensitive non-invasive tests for detection of SARS-CoV-2 antigens is imperative to manage the extent of infection throughout the population, yet, it is still challenging. Here, we designed and optimized a sandwich enzyme-linked immunosorbent assay (ELISA) for SARS-CoV-2 S1 antigen detection in saliva. Both saliva samples and nasopharyngeal swapswere collected from 170 PCR-confirmed positive and negative cases. Gold nanoparticles (AuNPs) were conjugated with S1protein receptor binding domain (RBD) nanobodies. Recombinant S1 monoclonal antibodies (S1mAb) as primery antibody and gold conjugated nanobodies as secondary antibody were employed in sandwich ELISA. Our developed system were optimized to achieve 87.5 % sensitivity and 100% specificity for saliva samples compared to 89 % and 100% for nasopharyngeal swaps, respectively. This means that saliva could be a suitable replacement for nasopharyngeal swaps No cross reaction was detected with other corona virus antigens. These results revealed that our developed ELISAcould be establishedas a new, reliable, sensitive, and non-invasive test for diagnosis of SARS-CoV-2 infection, using the easily collected saliva samples.

Keywords: COVID 19, diagnosis, ELISA, nanobodies

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Authors: Le-Quyen Nguyen, Hoang Van Bui, Ngoc Thi Tran, Binh Thanh Le, Linus Olson, Thanh Quang Le

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Objective: We compared of outcomes between infected and non-infected COVID-19 pregnant at the largest obstetrics and gynecology hospital in southern Vietnam. Materials and Methods: A retrospective study was conducted at gestational age (GA) 28-42 weeks, who terminated pregnancy and had a real-time PCR test for SARS-CoV-2 at Tu Du Hospital. Demographic, clinical, laboratory, and epidemiological data were collected from hospital electronic-medical-records. Diagnosis and screening of SARS-CoV-2 used Real-time-PCR. Results: From July to October 2021, 9,246 pregnant with GA of 28-42 weeks were delivered, including 664 infected with COVID-19 and 8,582 non-infected. The cesarean section (CS) rates of pregnant with and without COVID-19 were 47.3% and 46.0%. At GA 32-34 weeks, the rate of CS with COVID-19 was 5.07 times higher than without. The rate of postpartum hemorrhage (PPH) and the Apgar score between these two groups were similar. The mortality rate of infected pregnants was 2.26%. Conclusions: COVID-19 infection increased the CS rate in the group of preterm pregnancies from 32 to less than 34 weeks. COVID-19 did not increase the risk of complications related to adverse pregnancy outcomes such as PPH, Apgar scores, the ratio of stillbirths, deaths due to malformation, and fetal deaths in labor.

Keywords: COVID-19, SARS-CoV-2, pregnancy, outcome, vietnam

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Authors: Busra Mutlu Ipek, Merve Mutlu, Ahmet Mutlu

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Novel coronavirus COVID-19, which has recently influenced the world, poses a great threat to humanity. In order to overcome this challenging situation, scientists are working on developing effective vaccine against coronavirus. Many experts and researchers have also produced articles and done studies on this highly important subject. In this direction, this special topic was chosen for article to make a contribution to this area. The purpose of this article is to perform RNA sequence analysis of selected virus forms in the Coronaviridae family and predict/classify SARS-CoV-2 (COVID-19) from other selected complete genomes in coronaviridae family using proposed Artificial Neural Network(ANN) algorithm.

Keywords: Coronaviridae family, COVID-19, RNA sequencing, ANN, neural network

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Authors: Alireza Jalalvand, Maryam Saleh, Somayeh Behjat Khatouni, Zahra Bahri Najafi, Foroozan Fatahinia, Narges Ismailzadeh, Behrokh Farahmand

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Object: In the last two decades, the recent outbreak of Coronavirus (SARS-CoV-2) imposed a global pandemic in the world. Despite the increasing prevalence of the disease, there are no effective drugs to treat it. A suitable and rapid way to afford an effective drug and treat the global pandemic is a computational drug study. This study used molecular docking methods to examine the potential inhibition of over 50 antiviral drugs against three fundamental proteins of SARS-CoV-2. METHODS: Through a literature review, three important proteins (a key protease, RNA-dependent RNA polymerase (RdRp), and spike) were selected as drug targets. Three-dimensional (3D) structures of protease, spike, and RdRP proteins were obtained from the Protein Data Bank. Protein had minimal energy. Over 50 antiviral drugs were considered candidates for protein inhibition and their 3D structures were obtained from drug banks. The Autodock 4.2 software was used to define the molecular docking settings and run the algorithm. RESULTS: Five drugs, including indinavir, lopinavir, saquinavir, nelfinavir, and remdesivir, exhibited the highest inhibitory potency against all three proteins based on the binding energies and drug binding positions deduced from docking and hydrogen-bonding analysis. Conclusions: According to the results, among the drugs mentioned, saquinavir and lopinavir showed the highest inhibitory potency against all three proteins compared to other drugs. It may enter laboratory phase studies as a dual-drug treatment to inhibit SARS-CoV-2.

Keywords: covid-19, drug repositioning, molecular docking, lopinavir, saquinavir

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Authors: Saleh Alkarri, Melinda Frame, Dimple Sharma, John Cairney, Lee Maddan, Jin H. Kim, Jonathan O. Rayner, Teresa M. Bergholz, Muhammad Rabnawaz

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Reported herein is an investigation of anti-bacterial and anti-virus properties, mode of action of Mg(OH)₂ and copper-infused Mg(OH)₂ nanoplatelets (NPs) on melt-compounded and thermally embossed polypropylene (PP) surfaces. The anti-viral activity for the NPs was studied in aqueous liquid suspensions against SARS-CoV-2, and the mode of action was investigated on neat NPs and PP samples that were thermally embossed with NPs. Anti-bacterial studies for melt-compounded NPs in PP confirmed approximately 1 log reduction of E. coli populations in 24 h, while for thermally embossed NPs, an 8 log reduction of E. coli populations was observed. In addition, the NPs exhibit anti-viral activity against SARS-CoV-2. Fluorescence microscopy revealed that reactive oxygen species (ROS) is the main mode of action through which Mg(OH)₂ and Cu-Infused Mg(OH)₂act against microbes. Plastics with anti-microbial surfaces from where biocides are non-leachable are highly desirable. This work provides a general fabrication strategy for developing anti-microbial plastic surfaces.

Keywords: anti-microbial activity, E. coli K-12 MG1655, anti-viral activity, SARS-CoV-2, copper-infused magnesium hydroxide, non-leachable, ROS, compounding, surface embossing, dyes

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Authors: C. Recchia, M. Bourel, B. Recchia

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Microorganisms (viruses, bacteria, fungi) are responsible for most communicable diseases, threatening human health. For domestic use, chemical agents are often criticized because of their potential dangerousness, and natural solutions are needed. Application of the “dry microfine steam” (DMS) technology was tested on a selection of common pathogens (SARS-CoV-2, enterovirus EV-71, human coronavirus 229E, E. coli, S. aureus, C. albicans), on different innate surfaces, for 5 to 10 seconds. Quantification of the remaining pathogens was performed, and the reduction rates ranged from 99.8% (S. aureus on plastic) to over 99.999%. DMS showed high efficacy in the elimination of common microorganisms and could be seen as a natural alternative to chemical agents to improve domestic hygiene.

Keywords: steam, SARS-CoV-2, bactericidal, virucidal, fungicidal, sterilization

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Authors: Aghasadeghi MR., Bahramali G., Sadat SM., Sadeghi SA., Yousefi M., Khodaei K., Ghorbani M., Sadat Larijani M.

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Background:The emerging COVID-19 pandemic is a serious concernfor the public health worldwide. Despite the many mutations in the virus genome, it is important to find an effective vaccine against viral mutations. Therefore, in current study, we aimed at immunoinformatic evaluation of the virus proteins immunogenicity to design a preventive vaccine candidate, which could elicit humoral and cellular immune responses as well. Methods:Three antigenic regions are included;Spike, Membrane, and Nucleocapsid amino acid sequences were obtained, and possible fusion proteins were assessed andcompared by immunogenicity, structural features, and population coverage. The best fusion protein was also evaluated for MHC-I and MHC-II T-cell epitopes and the linear and conformational B-cell epitopes. Results: Among the four predicted models, the truncated Spike protein in fusion with M and N proteins is composed of 24 highly immunogenic human MHC class I and 29 MHC class II, along with 14 B-cell linear and 61 discontinues epitopes. Also, the selected protein has high antigenicity and acceptable population coverage of 82.95% in Iran and 92.51% in Europe. Conclusion: The data indicate that the truncated Spike-M-N SARS-CoV-2form which could be potential targets of neutralizing antibodies. The protein also has the ability to stimulate humoral and cellular immunity. The in silico study provided the fusion protein as a potential preventive vaccine candidate for further in vivo evaluation.

Keywords: SARS-CoV-2, immunoinformatic, protein, vaccine

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Authors: Lucia Salvioni, Pietro Giorgio Lovaglio, Valerio Leoni, Miriam Colombo, Luisa Fiandra

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The involvement of plasmatic surfactant protein-D (SP-D) in pulmonary diseases has been long investigated, and over the last two years, more interest has been directed to determine its role as a marker of COVID-19. In this direction, several studies aimed to correlate pulmonary surfactant proteins with the clinical manifestations of the virus indicated SP-D as a prognostic biomarker of COVID-19 pneumonia severity. The present work has performed a retrospective study on a relatively large cohort of patients of Hospital Pio XI of Desio (Lombardia, Italy) with the aim to assess differences in the hematic SP-D concentrations among COVID-19 patients and healthy donors and the role of SP-D as a prognostic marker of severity and/or of mortality risk. The obtained results showed a significant difference in the mean of log SP-D levels between COVID-19 patients and healthy donors, so as between dead and survived patients. SP-D values were significantly higher for both hospitalized COVID-19 and dead patients, with threshold values of 150 and 250 ng/mL, respectively. SP-D levels at admission and increasing differences among follow-up and admission values resulted in the strongest significant risk factors of mortality. Therefore, this study demonstrated the role of SP-D as a predictive marker of SARS-CoV-2 infection and its outcome. A significant correlation of SP-D with patient mortality indicated that it is also a prognostic factor in terms of mortality, and its early detection should be considered to design adequate preventive treatments for COVID-19 patients.

Keywords: SARS-CoV-2 infection, COVID-19, surfactant protein-D (SP-D), mortality, biomarker

Procedia PDF Downloads 46