Proteome profiling of nasopharynx reveals pathophysiological signature of COVID-19 disease severity (preprint)

An aberrant innate immune system caused by the beta coronavirus SARS-CoV-2 is a characteristic manifestation of severe coronavirus disease 2019 (COVID-19). Here, we performed proteome profiling of nasopharyngeal (NP) swabs from 273 hospitalized patients with mild and severe COVID-19 symptoms, including non-survivors. We identified depletion in STAT1-mediated type I interferon response, retinol metabolism and NRF2 antioxidant system that are associated with disease severity in our patient demography. We found that the dysregulation of glucocorticoid signaling and renin-angiotensin-aldosterone system (RAAS) contribute to the pathophysiology of COVID-19 fatality. Hyperactivation of host innate immune system was observed in severe patients, marked by elevated proteins involved in neutrophil degranulation and platelet aggregation. Our study using high-throughput proteomics on the nasopharynx of COVID-19 patients provides additional evidence on the SARS-CoV-2-induced pathophysiological signatures of disease severity and fatality.

Design and Analysis of Ozone Monitoring System Produced by Plasma Corona Discharge for Disinfectant

Disinfection of a room is very important to note, especially because of the presence of the coronavirus which has been confirmed to be able to spread through the air, stick to objects around it and has a high potential to transmit the virus. This is exacerbated by the presence of a new variant of the coronavirus which causes an increasing number of people to be exposed every day. One of the most effective disinfectants is ozone. Ozone is a gas formed from three oxygen atoms which is highly reactive and more unstable than oxygen. Ozone with the right concentration of about 1 ppm can kill pathogens, such as bacteria and viruses. This research focuses on designing an independent control and monitoring system based on Human Machine Interface (HMI). This control and monitoring system design can be applied to measure ozone concentration and is equipped with a timer and automatic mode. The test results obtained total accuracy value of this device with variables of voltage, current, generator temperature, ambient temperature in the box, humidity in the box, and ozone concentration is 97.3%, while total precision value is 98.5%. This research was conducted by testing the appliance in a 1.2 x 1.5 x 2.5 m room for 10 minutes and the results showed that the voltage used by the appliance is in the range of 216V to 219V with a current dropping from 0.56A to a stability point of 0.46A. The maximum temperature at the generator is around 96oC with an ambient temperature of 38oC, the humidity decreases from 81% to 68% and the ozone concentration produced can be stable around 1 ppm in 1 minute which can be used to kill bacteria and viruses. © 2023 American Institute of Physics Inc.. All rights reserved.

Rapid and Low-Cost Detection of Human Corona Virus Using MEMS ATR-FTIR Spectroscopy

The conventional methods used for the diagnostics of viral infection are either expensive and time-consuming or not accurate enough and dependent on consumable reagents. In the presence of pandemics, a fast and reagent-free solution is needed for mass screening. Recently, the diagnosis of viral infections using infrared spectroscopy has been reported as a fast and low-cost method. In this work a fast and low-cost solution for corona viral detection using infrared spectroscopy based on a compact micro-electro-mechanical systems (MEMS) device and artificial intelligence (AI) suitable for mass deployment is presented. Among the different variants of the corona virus that can infect people, 229E is used in this study due to its low pathogeny. The MEMS ATR-FTIR device employs a 6 reflections ZnSe crystal interface working in the spectral range of 2200-7000 cm-1. The virus was propagated and maintained in a medium for long enough time then cell supernatant was collected and centrifuged. The supernatant was then transferred and titrated using plaque titration assay. Positive virus samples were prepared with a concentration of 105 PFU/mL. Positive and negative control samples were applied on the crystal surface, dried using a heating lamp and the spectrum was captured. Principal component analysis and logistic regression were used as simple AI techniques. A sensitivity of about 90 % and a specificity of about 80 % were obtained demonstrating the potential detection of the virus based on the MEMS FTIR device. © 2023 SPIE.

Smell disorders associated with COVID-19 infection

Background: We performed a search in the PubMed databases, Web of Science, LILACS, MEDLINE, SciELO, and Cochrane Library using the keywords COVID-19, Novel coronavirus, corona, 2019-nCoV, SARS-CoV-2, ENT, nose, anosmia, hyposmia, smell, olfactory, ORL, different ENT related symptoms. We reviewed published and peer-reviewed studies that reported the ENT manifestations in COVID-19 laboratory-confirmed positive patients. Main text: Within the included 2549 COVID-19 laboratory-confirmed positive patients, smell affection was reported in 1453 patients (57%). The other reported ENT manifestations were taste disorder (49.2%), headache (42.8%), nasal blockage (26.3%), sore throat (25.7%), runny nose or rhinorrhea (21.3%), upper respiratory tract infection (URTI) (7.9%), and frequent sneezing (3.6%). Conclusion(s): Smell affection in COVID-19 is common and could be one of the red flag signs in COVID-19 infection. With a sensitivity of utilized questionnaire in smell identification, a homogenous universal well-defined COVID-19 questionnaire is needed to make the COVID-19 data collection more sensible.Copyright © 2021, The Author(s).

Identifying the Next Mutation of Concern - Exploiting Genomics for Tracking Sars-Cov-2 Mutations and Their Biological Impact in Canada

Intro: Viruses, including SARS-CoV-2, which causes COVID-19, are constantly changing. These genetic changes (aka mutations) occur over time and can lead to the emergence of new variants that may have different characteristics. After the first SARS-CoV-2 genome was published in early 2020, scientists all over the world soon realized the immediate need to obtain as much genetic information from as many strains as possible. However, understanding the functional significance of the mutations harbored by a variant is important to assess its impact on transmissibility, disease severity, immune escape, and the effectiveness of vaccines and therapeutics. Method(s): Here in Canada, we have developed an interactive framework for visualizing and reporting mutations in SARS-CoV-2 variants. This framework is composed of three stand-alone yet connected components;an interactive visualization (COVID-MVP), a manually curated functional annotation database (pokay), and a genomic analysis workflow (nf-ncov-voc). Finding(s): COVID-MVP provides (i) an interactive heatmap to visualize and compare mutations in SARS-CoV-2 lineages classified across different VOCs, VOIs, and VUMs;(ii) mutation profiles including the type, impact, and contextual information;(iii) annotation of biological impacts for mutations where functional data is available in the literature;(iv) summarized information for each variant and/or lineage in the form of a surveillance report;and (v) the ability to upload raw genomic sequence(s) for rapid processing and annotating for real-time classification. Discussion(s): This comprehensive comparison allows microbiologists and public health practitioners to better predict how the mutations in emerging variants will impact factors such as infection severity, vaccine resistance, hospitalization rates, etc. Conclusion(s): This framework is cloud-compatible & standalone, which makes it easier to integrate into other genomic surveillance tools as well. COVID-MVP is integrated into the Canadian VirusSeq data portal (https://virusseqdataportal.ca) - a national data hub for SARS-COV-2 genomic data. COVID-MVP is also used by the CanCOGeN and CoVaRR networks in national COVID-19 genomic surveillance.Copyright © 2023

Acceptance of autonomous delivery robots in urban cities

Autonomous Delivery Robots (ADR), an innovative last-mile delivery method, can be seen as a sustainable solution for the distribution of goods in urban cities. This study combines the modified-TAM (encompassing the Technology Acceptance Model (TAM) and threat elements of the health belief model) and the Theory of Planned Behaviour (TPB) into the stimulus-organism-response framework to explain consumer intention to use ADRs. The responses of 500 respondents living in Singapore were collected via an online questionnaire, and the collected results were obtained using structural equation modelling. Using the modified-TAM and TPB constructs as the main conceptual framework for analysis, the results show significant results for consumers' ADR usage. Based on total effects analysis, attitude shows the largest effect on consumers' intention to use ADRs, followed by perceived usefulness, perceived susceptibility, perceived severity, perceived ease of use, subjective norm, and perceived behavioural control. Overall, the findings give an extensive insight into the key determinants influencing consumers' intention to use ADRs and offer strategic policy recommendations to encourage the use of ADRs.

The importance of combining serological testing with RT-PCR assays for efficient detection of COVID-19 and higher diagnostic accuracy.

Misdiagnosing suspected COVID-19 individuals could largely contribute to the viruses transmission, therefore, making an accurate diagnosis of infected subjects vital in minimizing and containing the disease. Although RT-PCR is the standard method in detecting COVID-19, it is associated with some limitations, including possible false negative results. Therefore, serological testing has been suggested as a complement assay to RT-PCR to support the diagnosis of acute infections. In this study, 15 out of 639 unvaccinated healthcare workers (HCWs) were tested negative for COVID-19 by RT-PCR and were found seropositive for SARS-CoV-2 nucleocapsid protein-specific IgM and IgG antibodies. These participants underwent additional confirmatory RT-PCR and SARS-CoV-2 spike-specific ELISA tests. Of the 15 individuals, nine participants were found negative by second RT-PCR but seropositive for anti-spike IgM and IgG antibodies and neutralizing antibodies confirming their acute infection. At the time of collection, these nine individuals were in close contact with COVID-19-confirmed patients, with 77.7% reporting COVID-19-related symptoms. These results indicate that including serological tests in the current testing profile can provide better outcomes and help contain the spread of the virus by increasing diagnostic accuracy to prevent future outbreaks rapidly.

A Lecture Centric Automated Distractor Generation for Post-Graduate Software Engineering Courses

Critical circumstances, natural disasters or pandemics like COVID 19 gave rise to the wide applicability of E-learning into education system. Efficient and fair online assessment is very important to utilize the inevitable benefits of E-learning.. In order to make it efficient, the trend of assessment has shifted from the subjective type to the objective type assessments which is mainly based on Multiple Choice Questions (MCQs), generation of MCQs is a tedious, tiresome and time consuming task. To cater this dire need, this study proposes an automated Multiple Choice Question (MCQ) generation by utilizing state of the art transformer based model T5 for the task of question generation and a lexicon based approach Sense2vec for the task of distractor generation. It also presented a domain specific lecture text based test data for performing evaluation on the task of domain specific lecture text based MCQ generation. © 2022 IEEE.

Seroprevalence of SARS-CoV2 Antibodies among Patients and Healthy Individuals of Lahore

Objective: To determine the seroprevalence of SARS-CoV2 antibodies in patients and healthy individuals presenting to a tertiary care hospital in Lahore. Study Design: Cross-sectional study Place and Duration of Study: Pathology Department of Surayya Azeem Hospital, Lahore Pakistan, from May to Jul 2020. Methodology: The study included clinically suspected patients of COVID-19 referred by clinicians and healthy individuals presenting to the hospital for the SARS-CoV-2 antibody test, irrespective of age and gender. Results: The SARS-CoV-2 antibody positivity was 704(59.4%) in our study. Out of 1184 individuals tested, 690 patients had a positive clinical history of COVID-19 infection, and 517(74.9%) were positive for COVID-19 antibodies. Out of 494 asymptomatic healthy individuals, positivity for COVID-19 antibodies was 187(37.8%). It was observed that positivity was significantly higher 169(44.0%) in contacts of COVID-19 infection patients compared to asymptomatic healthy individuals 18(16.3%). Conclusion: Our study shows that the seroprevalence of SARS-CoV-2 antibodies in the general public in Pakistan has greatly increased. © 2023, Army Medical College. All rights reserved.

Pyridone and SARS-CoV-2

COVID-19 is a human coronavirus infectious disease that is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), spreading rapidly across the globe with no treatment currently. Thus, finding the potential therapeutic treatment for this disease is necessary. SARS-CoV-2 main protease (Mpro) is an essential enzyme for viral replication. Different compounds that inhibit SARS-CoV-2 Mpro can be considered effective against the disease. Pyridones were recognized as potential key pharmacophores that inhibit SARS-CoV-2 Mpro. The pyridone system is present in many natural products, vital drugs, and synthetic bioactive compounds. Pyridones have several biological properties, i.e., antimicrobial, anti-inflammatory, antioxidant, antiviral, antitumor, antituberculosis, and antihuman immunodeficiency virus (anti-HIV) activity. The genome of coronavirus encodes Spike and Membrane protein that contribute to the attachment of the virus to the host for viral replication. Pyridones inhibit S protein and M protease of SARS-COV-2. Further investigation is required to evaluate the relationship between pyridones and SARS-CoV-2. © 2023 Elsevier Inc. All rights reserved.

Antiviral Effects of Asian Natural Products Targeting SARS, MERS, and COVID-19

Viral diseases initiated by Coronavirus (CoV) have become the major public health problems worldwide in the last two decades. The recent emergence of the deadly COVID-19 due to SARS-CoV-2 has created unprecedented pandemic situations around the globe making the need for antiviral molecules to treat it. Encountering the health conditions of the patients with synthetic molecules has shown some unpredictable results, including side effects. To face this complex situa-tion, natural products can be good sources of enormous treatment options with fewer side effects. Wide diversity, easy availability, and a good number of scientific researches on Asian origin natural products can be a great tool to meet this critical situation. This paper reviews the currently available Asian natural products with potential antiviral effects on CoV. It includes the potential natural products of whole plant extract, partial plant extract, isolated pure compounds, and isolated pure set of compounds. Besides, the available information of in vitro and in silico from very recent pa-pers are also summarized for the ease of future research. As a rapid search for a potential anti-CoV therapy is undergoing, Asian natural products will provide promising results but still, there are many challenges in front of us, including the robust in vitro assay to confirm the antiviral property, toxicity analysis, and fulfillment of regulatory needs. The use of appropriate natural products with the potential for a safe and more effective anti-CoV property requires multidisciplinary research with preclinical and clinical researchers, which will improve their clinical applications.Copyright © 2021 Bentham Science Publishers.

The impact of age and gender on mortality from COVID19 at A UK Hospital

Rationale: Age poses greater mortality risk to COVID-19 patients. This may be due to co-morbidities and age-related impairment of immunity. It has been shown that females are more likely to be infected however, severe disease is more often seen in males, which could be explained by greater levels of interferon-gamma promoter activity driven by oestrogen in females in addition to higher levels of IgG antibody providing more protection. We aim to investigate the effects of age and gender on the mortality rate in patients with COVID-19. Method(s): A retrospective study of all in-patients aged >= 18 years with a confirmed diagnosis of COVID-19 during the first and second waves of the pandemic. Admission CXRs were analysed. Statistical analysis was performed using the Chi-Squared Test for independence. Result(s): 1759 COVID-19 patients were included in the study, of which 481 were aged <65 years and 982 were aged > 65 years. The study had 967 males and 792 females. We found a higher mortality rate in those aged > 65 (41%) compared to those aged <65 years (18%) (P<0.001). There were no significant differences in the mortality rates between both genders. However, interestingly males had a greater severity of pneumonitis (22%) on CXRs compared to females (13%) (P=0.01). Conclusion(s): Our study demonstrated a positive correlation between increasing age and mortality with males showing a greater disease severity. This data should be considered when stratifying at risk groups and prioritising them for early intervention.

To assess the diagnostic and prognostic ability of CXRs in COVID-19 pneumonitis

Rationale: The COVID-19 pandemic has led to the deaths of millions with its ability to cause severe pneumonia. Diagnosis is based on PCR testing which has many limitations: lengthy turnaround times, lack of universal availability and variance in sensitivity. Imaging such as CXR could be a valuable and faster aid in diagnosing COVID-19 compared to PCR. It is widely available, cheap and can be performed at the bedside- enabling a rapid turnover of patients whilst minimising cross-link infection. However only a few studies have assessed its prognostic value. We aim to analyse the diagnostic accuracy of CXR in COVID-19 and to assess if severity of COVID pneumonitis on CXR correlated with mortality. Method(s): A retrospective study of all in-patients aged >= 18 years with a confirmed diagnosis of COVID-19 during the first and second waves of the pandemic. Admission CXRs and in-patient CT Thorax scans were analysed. Statistical analysis was performed using the Chi-Squared Test for independence. Result(s): 999 COVID-19 patients were included in the study. Severity of COVID pneumonitis on CXR correlated with mortality when patients were grouped into the following categories: normal (n=161, mortality=42%), mild (n=220,mortality=33%) moderate, (n=328, mortality=42%) and severe (n=290, mortality=58%) (P<0.001). 251 patients had both CT and CXRs. CT scans were superior in diagnosing COVID pneumonitis (63%) compared to CXR (47%) (P<0.001). Conclusion(s): Our study showed a positive correlation between the severity of COVID pneumonitis on CXR and mortality, supporting the use of CXR in the ED to help rapidly identify and treat patients at high risk of death.

Comparing the mortality of COPD and non-COPD patients with COVID-19 in a UK hospital

Rationale: Initial reports during the pandemic have shown that COPD patients with COVID-19 have a poorer prognosis due to an increased risk of respiratory failure. It is well known that in COPD, there is an increased expression of angiotensin converting enzyme-2 (ACE2), the receptor which plays a role in SARS-CoV-2 entry into cells. In the absence of infection, ACE2 converts angiotensin-2 (AngII) to angiotensin-1-7- helping regulate inflammation. During COVID-19 infection, ACE2 activity is reduced due to receptor occupancy, resulting in greater levels of AngII- leading to a pro-inflammatory state. We aim to investigate the impact of COPD and COVID-19 on mortality, length of in-patient stay and gender. Method(s): A retrospective study of all in-patients aged >= 18 years with a confirmed diagnosis of COVID-19 during the first wave of the pandemic. Statistical analysis was performed using the Chi-Squared Test for independence. Result(s): 445 COVID-19 patients were included in the study, out of whom 52 (12%) had COPD. Mortality in COPD patients (65%) was found to be significantly higher than non-COPD patients (49%) (P=0.03) There were no significant differences in mortality between COPD and non-COPD patients when grouped for male and female (P=0.68). Furthermore, there were no significant differences in length of in-patient stays of >7 days between COPD and non-COPD patients (P=0.79). Conclusion(s): Our study demonstrated how COPD increases mortality in COVID-19. This data should be considered when highlighting at risk groups- prioritising them for treatment, isolation, and preventative public health measures such as the COVID-19 vaccination programme.

Stability and Bifurcation Analysis of the Caputo Fractional-Order Asymptomatic COVID-19 Model with Multiple Time-Delays

Throughout the last few decades, fractional-order models have been used in many fields of science and engineering, applied mathematics, and biotechnology. Fractional-order differential equations are beneficial for incorporating memory and hereditary properties into systems. Our paper proposes an asymptomatic COVID-19 model with three delay terms τ1,τ2,τ3 and fractional-order α. Multiple constant time delays are included in the model to account for the latency of infection in a vector. We study the necessary and sufficient criteria for stability of steady states and Hopf bifurcations based on the three constant time-delays, τ1, τ2, and τ3. Hopf bifurcation occurs in the addressed model at the estimated bifurcation points τ10, τ20, τ30, and τ10*. The numerical simulations fit to real observations proving the effectiveness of the theoretical results. Fractional-order and time-delays successfully enhance the dynamics and strengthen the stability condition of the asymptomatic COVID-19 model. © 2023 World Scientific Publishing Company.

Unconventional green transport innovations in the post-COVID-19 era. A trade-off between green actions and personal health protection

Irrefutable evidence attributes environmental challenges, such as air and noise pollution, to unsustainable transportation, especially in urban settings. In this context, urban public transport is a sustainable mobility system with ecological benefits. However, limited research focuses on understanding the factors that promote urban public transport adoption in the face of disruptive events, such as the COVID-19 pandemic. This study integrates the push-pull-mooring (PPM) model and institutional theory to examine urban commuters' intentions to switch to urban public transport in the post-COVID-19 era. This study is the first to investigate the trade-offs consumers perceive between green actions and personal health protection in the COVID-19 context. Our results indicate that regulative and normative environments, public transport's economic viability and commuters' pro-environmental concerns and identities significantly influence their intentions to switch to public transportation. Furthermore, hygiene concerns and choice uncertainty partially moderate the tested associations. The study thus provides unique insights into the nuances of individual decision-making regarding public transport use. Leveraging our findings, we present implications for theory and practice. We also offer a possible framework for classifying consumers of green urban public transport, which can be used to create targeted communication to encourage commuters to switch to routine public transport use for sustainability and environmental protection. © 2022 The Authors

Assessment of Medical Students Burnout during COVID-19 Pandemic.

This study estimated the prevalence of burnout and its determinants among medical students at Jazan University during the COVID-19 pandemic. A total of 444 medical students completed an online survey containing the Maslach burnout inventory. The prevalence of burnout was 54.5%. Burnout reached its peak during the fourth year whereas it was the lowest in the internship year. Being a resident in mountain areas, being delayed in college-level, being divorced, and having divorced parents were all associated with an increased risk of burnout. During their time at medical school, students generally showed a trend of consistently high scores in the personal accomplishment subscale, a decreasing trend in the emotional exhaustion subscale, and an increasing trend in the depersonalization subscale. The most important predictive factor was having separated parents. Perceived study satisfaction appeared to be a significant protective factor in a dose-response manner. These findings suggest that burnout among medical students during the COVID-19 pandemic is a concern that should be monitored and prevented.

Effect of Lockdown on the Air Quality of Four Major Cities in Pakistan During the COVID-19 Pandemic

This study attempted to evaluate the effect of lockdown on the air quality of four major cities in Pakistan: Karachi, Lahore, Islamabad, and Peshawar. Particulate matter (PM2.5) concentration and U.S. Environmental Protection Agency Air Quality Index (AQI) were used to determine air quality before and after lockdown. We found that air quality in all the cities improved after lockdown was imposed: PM2.5 concentrations in Karachi and Lahore decreased by 62% and in Peshawar and Islamabad by 57% and 55%, respectively. AQI in Karachi and Islamabad improved from Unhealthy to Moderate and in Peshawar and Lahore from Unhealthy to Unhealthy for Sensitive Groups. Formal complete lockdown in Pakistan was imposed on March 24, 2020, and lasted until May 10, 2020, after which partial or smart lockdown was still in place. Maximum improvement in air quality was observed in April 2020, with concentrations starting to increase in May 2020 following the ease of restrictions. © 2023, National Environmental Health Association. All rights reserved.

MERS-CoV infection elicits long-lasting specific antibody, T and B cell immune responses in recovered individuals.

BACKGROUND: The Middle East respiratory syndrome coronavirus (MERS-CoV) is a highly pathogenic zoonotic betacoronaviruses and a global public health concern. Better undersetting of the immune responses to MERS-CoV is needed to characterize the correlates of protection and durability of the immunity and to aid in developing preventative and therapeutic interventions. While MERS-CoV-specific circulating antibodies could persist for several years post-recovery, their waning raises concerns about their durability and role in protection. Nonetheless, memory B and T cells could provide long-lasting protective immunity despite the serum antibodies levels. METHODS: Serological and flow cytometric analysis of MERS-CoV-specific immune responses were performed on samples collected from a cohort of recovered individuals who required intensive care unit (ICU) admission as well as hospital or home isolation several years after infection to characterize the longevity and quality of humoral and cellular immune responses. RESULTS: Our data showed that MERS-CoV infection could elicit robust long-lasting virus-specific binding and neutralizing antibodies as well as T and B cell responses up to 6.9 years post-infection regardless of disease severity or need for ICU admission. Apart from the persistent high antibody titers, this response was characterized by B cell subsets with antibody-independent functions as demonstrated by their ability to produce TNF-α, IL-6, and IFN-γ cytokines in response to antigen stimulation. Furthermore, virus-specific activation of memory CD8+ and CD4+ T cell subsets from MERS-recovered patients resulted in secretion of high levels of TNF-α, IL-17 and IFN-γ. CONCLUSIONS: MERS-CoV infection could elicit robust long-lasting virus-specific humoral and cellular responses.

Therapeutic Properties of Vanadium Complexes

Vanadium is a hard, silver-grey transition metal found in at least 60 minerals and fossil fuel deposits. Its oxide and other vanadium salts are toxic to humans, but the toxic effects depend on the vanadium form, dose, exposure duration, and route of intoxication. Vanadium is used by some life forms as an active center in enzymes, such as the vanadium bromoperoxidase of ocean algae and nitrogenases of bacteria. The structure and biochemistry of vanadate resemble those of phosphate, hence vanadate can be regarded as a phosphate competitor in a variety of biochemical enzymes such as kinases and phosphatases. In this review, we describe the biochemical pathways regulated by vanadium compounds and their potential therapeutic benefits for a range of disorders including type 2 diabetes, cancer, cardiovascular disease, and microbial pathology.