COVID-19: Virology, biology and novel laboratory diagnosis

Simultaneous Protein Colorful Imaging via Raman Signal Classification

Protein imaging aids diagnosis and drug development by revealing protein-drug interactions or protein levels. However, the challenges of imaging multiple proteins, reduced sensitivity, and high reliance on specific protein properties such as Raman peaks or refractive index hinder the understanding. Here, we introduce multiprotein colorful imaging through Raman signal classification. Our method utilized machine learning-assisted classification of Raman signals, which are the distinctive features of label-free proteins. As a result, three types of proteins could be imaged simultaneously. In addition, we could quantify individual proteins from a mixture of multiple proteins over a wide detection range (10 fg/mL-1 μg/mL). These results showed a 1000-fold improvement in sensitivity and a 30-fold increase in the upper limit of detection compared to existing methods. These advances will enhance our understanding of biology and facilitate the development of disease diagnoses and treatments.

Factors influencing Jordanian parents' COVID-19 vaccination decision for children: A cross-sectional study

BACKGROUND

Vaccine hesitancy is a major public health problem that emerged post-COVID-19 pandemic, especially for children. Different factors influence parents' perspectives about vaccinating their children and can vary across different populations and contexts.

PURPOSE

This study aimed to explore the vaccine hesitancy among parents in Jordan to vaccinate their children between the ages of 5 and 18.

DESIGN AND METHODS

A descriptive cross-sectional design was used. A convenient sample was used to recruit Jordanian parents. Data was collected via an online questionnaire including demographic data, the Vaccine Hesitancy Questionnaire, the Questionnaire of Vaccine Hesitancy Reasons, and the Vaccine Conspiracy Beliefs Scale.

RESULTS

Over 177 parents, the mean age was 37.74 years (SD = 8.39); the majority of them were females (74%). 51.4% of the participants refused to give the COVID-19 vaccine to their children. Concerns about the safety and efficacy of the vaccine and lack of information about disease and vaccine were the common reasons for the parents' hesitancy. In addition, 54.2% of participants agreement was with the conspiracy theory that pharmaceutical companies cover up the dangers of vaccines. Parents' younger age and fewer children were associated with hesitancy to vaccinate their children with COVID-19.

CONCLUSIONS

Many parents are hesitant to vaccinate their children against COVID-19. Concerns about the vaccine's efficacy and safety as well as potential long-term negative effects were the main reasons for vaccine hesitancy.

PRACTICE IMPLICATIONS

Nurses play a critical role in determining parental hesitancy. Providing detailed, accurate, evidence-based vaccine information is essential to reduce this hesitancy.

Recent Progress in Synthetic and Biological Application of Diorganyl Diselenides

Diorganyl diselenides have emerged as privileged structures because they are easy to prepare, have distinct reactivity, and have broad biological activity. They have also been used in the synthesis of natural products as an electrophile in the organoselenylation of aromatic systems and peptides, reductions of alkenes, and nucleophilic substitution. This review summarizes the advancements in methods for the transformations promoted by diorganyl diselenides in the main functions of organic chemistry. Parallel, it will also describe the main findings on pharmacology and toxicology of diorganyl diselenides, emphasizing anti-inflammatory, hypoglycemic, chemotherapeutic, and antimicrobial activities. Therefore, an examination detailing the reactivity and biological characteristics of diorganyl diselenides provides valuable insights for academic researchers and industrial professionals.

Cell free DNA as a new prognostic biomarker for COVID-19, A prospective cohort study

Predicting the need of hospitalization and intensive care in COVID-19 patients has been challenging with current diagnostic tests since the beginning of the pandemic. We aimed to test cell free DNA (cfDNA) as a novel biomarker for COVID-19 disease severity and mortality. cfDNA concentration was quantified by RT-PCR based test. One hundred and sixty-eight patients(85 outpatients, 61 inpatients,22 ICU) included the study. Mean initial plasma cfDNA levels were significantly different (p < 0.01) in outpatients (1.190,66 ng/ml), inpatients (8.258,10 ng/ml) and ICU patients (84.806,87 ng/ml). ROC analysis showed with 95 % specificity that patients with initial cfDNA concentrations ≥6.389 ng/ml need to be hospitalized and those ≥26.104 ng/ml require ICU referral. cfDNA concentration was correlated with neutrophil/lymphocyte ratio, lymphocyte level, CRP, AST, LDH, CK, fibrinogen, ferritin and D-dimer. Plasma cfDNA levels on admission, well correlating with disease severity and mortality in COVID-19 that found as a useful biomarker.

Morphological Transformations of SARS-CoV-2 Nucleocapsid Protein Biocondensates Mediated by Antimicrobial Peptides

Recently, the discovery of antimicrobial peptides (AMPs) as excellent candidates for overcoming antibiotic resistance has attracted significant attention. AMPs are short peptides active against bacteria, cancer cells, and viruses. It has been shown that the SARS-CoV-2 nucleocapsid protein (N-P) undergoes liquid-liquid phase separation in the presence of RNA, resulting in biocondensate formation. These biocondensates are crucial for viral replication as they concentrate the viral RNA with the host cell's protein machinery required for viral protein expression. Thus, N-P biocondensates are promising targets to block or slow down viral RNA transcription and consequently virion assembly. We investigated the ability of three AMPs to interfere with N-P/RNA condensates. Using microscopy techniques, supported by biophysical characterization, we found that the AMP LL-III partitions into the condensate, leading to clustering. Instead, the AMP CrACP1 partitions into the droplets without affecting their morphology but reducing their dynamics. Conversely, GKY20 leads to the formation of fibrillar structures after partitioning. It can be expected that such morphological transformation severely impairs the normal functionality of the N-P droplets and thus virion assembly. These results could pave the way for the development of a new class of AMP-based antiviral agents targeting biocondensates.

Unwinding circular RNA's role in inflammatory pulmonary diseases

Circular RNAs (circRNAs) have emerged as pivotal regulators of gene expression and cellular processes in various physiological and pathological conditions. In recent years, there has been a growing interest in investigating the role of circRNAs in inflammatory lung diseases, owing to their potential to modulate inflammation-associated pathways and contribute to disease pathogenesis. Inflammatory lung diseases, like asthma, chronic obstructive pulmonary disease (COPD), and COVID-19, pose significant global health challenges. The dysregulation of inflammatory responses demonstrates a pivotal function in advancing these diseases. CircRNAs have been identified as important players in regulating inflammation by functioning as miRNA sponges, engaging with RNA-binding proteins, and participating in intricate ceRNA networks. These interactions enable circRNAs to regulate the manifestation of key inflammatory genes and signaling pathways. Furthermore, emerging evidence suggests that specific circRNAs are differentially expressed in response to inflammatory stimuli and exhibit distinct patterns in various lung diseases. Their involvement in immune cell activation, cytokine production, and tissue remodeling processes underscores their possible capabilities as therapeutic targets and diagnostic biomarkers. Harnessing the knowledge of circRNA-mediated regulation in inflammatory lung diseases could lead to the development of innovative strategies for disease management and intervention. This review summarizes the current understanding of the role of circRNAs in inflammatory lung diseases, focusing on their regulatory mechanisms and functional implications.

COVID-19 Vaccine Acceptance in Pregnancy

OBJECTIVE

 The purpose of the study is to evaluate the acceptance rate of the coronavirus disease 2019 (COVID-19) vaccine among pregnant women at our institution prior to recommendations by national organizations (American College of Obstetricians and Gynecologists/The Society for Maternal-Fetal Medicine) in July 2021 and to determine whether factors including health disparities are associated with acceptance.

STUDY DESIGN

 This is an Institutional Review Board exempt descriptive study. Anonymous surveys were administered from February 2021 to May 2021 to pregnant patients at Mount Sinai South Nassau's affiliated Maternal Fetal Medicine office. The survey was completed by 701 pregnant women. Descriptive statistics were calculated for the overall sample, as well as separately by group (acceptance versus declining/undecided about getting the COVID-19 vaccine). The two groups were compared using the chi-square test or Fisher's exact test and the two-sample t-test. Analysis was compared between two groups (patients who accepted the COVID-19 vaccine and people who declined/undecided about the vaccine). A result was considered statistically significant at the p < 0.05 level of significance.

RESULTS

 Of the 701 pregnant women who completed the survey, 96 patients accepted the vaccine. More pregnant women who were older accepted the COVID-19 vaccine compared with those who were younger (p = 0.0343). Pregnant women willing to get the flu vaccine and/or the Tdap vaccine in pregnancy were more likely to obtain the COVID-19 vaccine (p < 0.05). Pregnant patients who had household members willing to receive the COVID-19 vaccine sought to obtain the vaccine for themselves (p < 0.0001). Interestingly, pregnant women who had an underlying respiratory illness in the pregnancy were less likely to accept the COVID-19 vaccine than those who had either other or no medical problems (p < 0.05).

CONCLUSION

 There is a low rate of COVID-19 vaccine acceptance among pregnant women (13.69%). Efforts should be made to encourage the vaccine in this vulnerable population to protect them from the health risks of the COVID-19 virus.

KEY POINTS

· COVID-19 vaccine acceptance rates in our population were 13.6%.. · Accepting Tdap and influenza vaccines increased the likelihood of accepting the COVID vaccine.. · Pregnant patients with respiratory illnesses were more likely to decline the COVID vaccine..

Matrix metalloproteinases are associated with severity of disease among COVID-19 patients: A possible pharmacological target

COVID-19 is a devastating disease and imbalanced matrix metalloproteinase (MMP) activity may contribute to its pathophysiology. This exploratory study examined whether increased circulating concentrations of MMP-2 and MMP-9, and their endogenous inhibitors, the tissue inhibitors of MMP (TIMP)-1, TIMP-2, TIMP-3 and TIMP-4 are persistently found in patients 2 weeks after their recovery from severe or critical COVID-19 as compared with those in healthy controls. Subjects who had severe (n = 26) or critical (n = 25) PCR-confirmed COVID-19 and healthy controls (n = 21) had blood samples drawn 2 weeks after recovery and serum MMP-2, MMP-9, TIMP-1, TIMP-2, TIMP-3 and TIMP-4 were determined using two Human Luminex® Discovery Assays. Circulating MMP activity was also determined by gel zymography. Patients who had severe or critical COVID-19 had increased circulating MMP-9 and MMP-2 concentrations, with increased MMP-9/TIMP-1 and MMP-2/TIMP-2 ratios indicating increased MMP activity, confirmed by gel zymography (all p < 0.05). Higher circulating MMP-9 (but not MMP-2) concentrations were found in critical versus severe COVID-19 (p < 0.05). We found increased circulating MMP-9 and MMP-2 concentrations and activity many days after recovery from the acute disease, with MMP-9 levels associated with disease severity. These biochemical alterations suggest that MMP-2 and MMP-9 may be important pharmacological targets in COVID-19.

Clinical characteristics of COVID-19 patients treated in emergency COVID-19 hospitals in Vietnam: Experience from Phutho province, Vietnam

Background: This study aimed to evaluate the clinical characteristics, patient's management approaches, and outcomes of the COVID-19 patients in Phu Tho Province, Vietnam. Methods: A retrospective, multicenter study of 2166 COVID-19 patients in 13 hospitals in Phutho Province, Vietnam. The subjects were divided into 3 groups based on vaccination status: unvaccinated group, 1st dose of vaccine group, 2nd dose of vaccine group. The clinical characteristics, management approaches, and outcomes were collected and compared between the 3 groups. Results: The hospitalization rate of the 3 groups decreased from the unvaccinated group, the 1st dose of vaccinated group, to the 2nd dose of vaccinated group, 42.61%; 30,24% and 27,15% respectively. The 19-40 years old group had the highest hospitalization rate (38,1%) together with the group that had not accepted the full COVID 19 vaccination dose (57,64%). The 2nd dose of vaccinated group had the lowest percentages of high temperature, cough, dyspnea, chest pain and sore throat. The unvaccinated group had the highest heart rate, respiratory rate and SpO2 compared to the two other groups. The percentage needing Immunomodulation and Anticoagulant Therapy was highest (6.8% and 1.4 % respectively) in the unvaccinated group. The percentage receiving Antiviral Therapy was highest (42,5%) in those who had received the 2nd dose of vaccine. Conclusions: COVID-19 vaccination improved the symptoms of the patients and should be accepted in all ages.

EG.5 (Eris) and BA.2.86 (Pirola) two new subvariants of SARS-CoV-2: a new face of old COVID-19

BACKGROUND

The World Health Organization announced the end of the Coronavirus Disease of 2019 (COVID-19) global health emergency on May 5, 2023. However, the reports from different countries indicate an elevation in the number of COVID-19-related hospitalizations and deaths through the last months. The subvariant XBB.1.5 (Kraken) was the cause of 49.1% of COVID-19 cases by the end of January 2023. Although, the subvariant EG.5 (Eris) has surpassed the XBB.1.5 recently. EG.5 is a close subvariant descending from XBB.1.9.2 subvariant of Omicron. EG.5.1 is a sublineage carrying two crucial spike mutations F456L and Q52H. Up to now, it is not well-established whether its infectivity, severity, and immune evasion have shown any change or not. Also, BA.2.86 another subvariant of Omicron descending from BA.2 bears over 30 mutations which could affect its infectivity and transmissibility.

METHODS

Scopus, PubMed, Google Scholar, and Google were searched with six keywords up to 20 November 2023 and highly reliable research and reports were selected to refer to in this article.

PURPOSE

This brief review aims to overview the most reliable data about EG.5 and BA.2.86 based on scientific evidence.

CONCLUSION

Based on the currently available data these two new subvariants have similar features with currently circulating variants of Omicron and are less immune evasive than ancestral SARS-CoV-2.

COVID-19 and Its Ophthalmic Manifestations: A Literature Review

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus discovered in late 2019 in Wuhan, Hubei Province, China. The virus has now developed into a full-scale global pandemic affecting hundreds of millions of people to date. A majority of cases present with nonspecific acute upper respiratory symptoms. A wide range of systemic symptoms has been reported, with some patients presenting with nonspecific extrapulmonary symptoms. Recently, there has been an increased association of COVID-19-positive patients presenting with ocular symptoms. As an increasing number of patients present with ophthalmic manifestations, recognizing these visual symptoms is of utmost importance. Some patients may present with ocular symptoms as the first indication of COVID-19 infection; quickly isolating and starting treatment can aid in stopping the spread of this novel coronavirus. This review will describe the current epidemiology and pathophysiology of SARS-CoV-2, emphasizing the ophthalmic manifestations and their clinical course progression. Further, we will be reporting on the growing number of rare ocular manifestations that have occurred in some COVID-19-positive patients, along with the route of transmission, specific manifestations, and the treatment methods for both these pulmonary and extrapulmonary symptoms, specifically the ocular manifestations.

COVID-19 Virus Structural Details: Optical and Electrochemical Detection

The increasing viral species have ruined people's health and the world's economy. Therefore, it is urgent to design bio-responsive materials to provide a vast platform for detecting a different family's passive or active virus. One can design a reactive functional unit for that moiety based on the particular bio-active moieties in viruses. Nanomaterials as optical and electrochemical biosensors have enabled better tools and devices to develop rapid virus detection. Various material science platforms are available for real-time monitoring and detecting COVID-19 and other viral loads. In this review, we discuss the recent advances of nanomaterials in developing the tools for optical and electrochemical sensing COVID-19. In addition, nanomaterials used to detect other human viruses have been studied, providing insights for developing COVID-19 sensing materials. The basic strategies for nanomaterials develop as virus sensors, fabrications, and detection performances are studied. Moreover, the new methods to enhance the virus sensing properties are discussed to provide a gateway for virus detection in variant forms. The study will provide systematic information and working of virus sensors. In addition, the deep discussion of structural properties and signal changes will offer a new gate for researchers to develop new virus sensors for clinical applications.

Adverse Events of SARS-CoV-2 Therapy: A Pharmacovigilance Study of the FAERS Database

BACKGROUND

Over the past 2 years of the several strategies recommended to help fight COVID-19, nirmatrelvir/ritonavir is a novel drug shown in the EPIC-HR phase 2 to 3 clinical trial to lower COVID-19-related death or hospitalization at day 28 when compared with placebo.

OBJECTIVE

Our study's aim was to explore the reported adverse events (AEs) associated with nirmatrelvir/ritonavir use for COVID-19.

METHOD

We conducted a retrospective analysis using the FDA Adverse Event Reporting System (FAERS) database for AEs, listing nirmatrelvir/ritonavir as the primary drug between January and June 2022. The primary outcome was the incidence of reported AEs associated with nirmatrelvir/ritonavir. The OpenFDA database was queried using Python 3.10 to collect the AEs and Stata 17 was used to analyze the database. Adverse events were analyzed by associated medication, with "Covid-19" excluded.

RESULTS

A total of 8098 reports were identified between January and June 2022. Most reported complaints in the AE system were COVID-19 and disease recurrence. The most common symptomatic AEs were dysgeusia, diarrhea, cough, fatigue, and headache. Event rates significantly rose between April and May. Disease recurrence and dysgeusia were the most commonly reported complaints for the top 8 concomitant drugs identified. Cardiac arrest, tremor, akathisia, and death were reported in 1, 3, 67, and 5 cases, respectively.

CONCLUSIONS AND RELEVANCE

This is the first retrospective study done on reported AEs associated with nirmatrelvir/ritonavir use for COVID-19. COVID-19 and disease recurrence were the most reported AEs. Further monitoring of the FAERS database is warranted to periodically reassess the safety profile of this medication.

An Open One-Step RT-qPCR for SARS-CoV-2 detection

The COVID-19 pandemic has resulted in millions of deaths globally, and while several diagnostic systems were proposed, real-time reverse transcription polymerase chain reaction (RT-PCR) remains the gold standard. However, diagnostic reagents, including enzymes used in RT-PCR, are subject to centralized production models and intellectual property restrictions, which present a challenge for less developed countries. With the aim of generating a standardized One-Step open RT-qPCR protocol to detect SARS-CoV-2 RNA in clinical samples, we purified and tested recombinant enzymes and a non-proprietary buffer. The protocol utilized M-MLV RT and Taq DNA pol enzymes to perform a Taqman probe-based assay. Synthetic RNA samples were used to validate the One-Step RT-qPCR components, demonstrating sensitivity comparable to a commercial kit routinely employed in clinical settings for patient diagnosis. Further evaluation on 40 clinical samples (20 positive and 20 negative) confirmed its comparable diagnostic accuracy. This study represents a proof of concept for an open approach to developing diagnostic kits for viral infections and diseases, which could provide a cost-effective and accessible solution for less developed countries.

Improving the detection capability and efficiency of SARS-CoV-2 RNA specimens by the specimen turn-around process with multi-department cooperation

Objective

Improving the detection capability and efficiency of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA specimens is very important for the prevention and control of the outbreak of Coronavirus disease 2019 (COVID-19). In this study, we evaluated the detection capability and efficiency of two outbreaks of COVID-19 before and after the process re-engineering in April and July 2022.

Methods

This retrospective cross-sectional study involved 359,845 SARS-CoV-2 RNA specimens 2 weeks before and 2 weeks after the two outbreaks of COVID-19 in April and July. The number, transportation time and detection time of specimens, and the number of reports of more than 24 h were analyzed by SPSS software.

Results

While 16.84% of people chose nasopharyngeal swabs (NPS) specimens, 83.16% chose oropharyngeal swabs (OPS) specimens to detect SARS-CoV-2 RNA. There were significant upward trends in the percentage of 10 sample pooling (P-10) from April before process re-engineering to July after process re-engineering (p < 0.001). Compared with April, the number of specimens in July increased significantly not only 2 weeks before but also 2 weeks after the outbreak of COVID-19, with an increase of 35.46 and 93.94%, respectively. After the process re-engineering, the number of reports more than 24 h in the 2 weeks before and after the outbreak of COVID-19 in July was significantly lower than that in April before process re-engineering (0% vs. 0.06% and 0 vs. 0.89%, both p < 0.001).

Conclusion

The present study shows that strengthening the cooperation of multi-departments in process re-engineering, especially using the P-10 strategy and whole process informatization can improve the detection capability and efficiency of SARS-CoV-2 RNA specimens.

Applications of Mass Spectrometry in the Characterization, Screening, Diagnosis, and Prognosis of COVID-19

Mass spectrometry (MS) is a powerful analytical technique that plays a central role in modern protein analysis and the study of proteostasis. In the field of advanced molecular technologies, MS-based proteomics has become a cornerstone that is making a significant impact in the post-genomic era and as precision medicine moves from the research laboratory to clinical practice. The global dissemination of COVID-19 has spurred collective efforts to develop effective diagnostics, vaccines, and therapeutic interventions. This chapter highlights how MS seamlessly integrates with established methods such as RT-PCR and ELISA to improve viral identification and disease progression assessment. In particular, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) takes the center stage, unraveling intricate details of SARS-CoV-2 proteins, revealing modifications such as glycosylation, and providing insights critical to formulating therapies and assessing prognosis. However, high-throughput analysis of MALDI data presents challenges in manual interpretation, which has driven the development of programmatic pipelines and specialized packages such as MALDIquant. As we move forward, it becomes clear that integrating proteomic data with various omic findings is an effective strategy to gain a comprehensive understanding of the intricate biology of COVID-19 and ultimately develop targeted therapeutic paradigms.

Network Pharmacology and Experimental Validation of Qingwen Baidu Decoction Therapeutic Potential in COVID-19-related Lung Injury

BACKGROUND AND PURPOSE

Coronavirus disease 2019 (COVID-19) is a lifethreatening disease worldwide due to its high infection and serious outcomes resulting from acute lung injury. Qingwen Baidu decoction (QBD), a well-known herbal prescription, has shown significant efficacy in patients with Coronavirus disease 2019. Hence, this study aims to uncover the molecular mechanism of QBD in treating COVID-19-related lung injury.

METHODS

Traditional Chinese Medicine Systems Pharmacology database (TCMSP), DrugBanks database, and Chinese Knowledge Infrastructure Project (CNKI) were used to retrieve the active ingredients of QBD. Drug and disease targets were collected using UniProt and Online Mendelian Inheritance in Man databases (OMIM). The core targets of QBD for pneumonia were analyzed by the Protein-Protein Interaction Network (PPI), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) to reveal the underlying molecular mechanisms. The analysis of key targets using molecular docking and animal experiments was also validated.

RESULTS

A compound-direct-acting target network mainly containing 171 compounds and 110 corresponding direct targets was constructed. The key targets included STAT3, c-JUN, TNF-α, MAPK3, MAPK1, FOS, PPARG, MAPK8, IFNG, NFκB1, etc. Moreover, 117 signaling pathways mainly involved in cytokine storm, inflammatory response, immune stress, oxidative stress and glucose metabolism were found by KEGG. The molecular docking results showed that the quercetin, alanine, and kaempferol in QBD demonstrated the strongest affinity to STAT3, c- JUN, and TNF-α. Experimental results displayed that QBD could effectively reduce the pathological damage to lung tissue by LPS and significantly alleviate the expression levels of the three key targets, thus playing a potential therapeutic role in COVID-19.

CONCLUSION

QBD might be a promising therapeutic agent for COVID-19 via ameliorating STAT3-related signals.

Development and Clinical Performance of InteliSwab® COVID-19 Rapid Test: Evaluation of Antigen Test for the Diagnosis of SARS-CoV-2 and Analytical Sensitivity to Detect Variants of Concern Including Omicron and Subvariants

BACKGROUND AND OBJECTIVES

Timely detection of SARS-CoV-2 infection with subsequent contact tracing and rapid isolation are considered critical to containing the pandemic, which continues with the emergence of new variants. Hence, there is an ongoing need for reliable point-of-care antigen rapid diagnostic tests (Ag-RDT). This report describes the development, evaluation, and analytical sensitivity of the diagnostic performance of the InteliSwab® COVID-19 Rapid Test. Methods: Samples from 165 symptomatic subjects were tested with InteliSwab® and the results were compared to RT-PCR to determine the antigen test performance. The analytical sensitivity of InteliSwab® for the detection of different variants was assessed by limit of detection (LOD) determination using recombinant nucleocapsid proteins (NPs) and testing with virus isolates. Western immunoblot independently confirmed that each monoclonal Ab is capable of binding to all variants tested thus far.

RESULTS

The overall positivity rate by RT-PCR was 37% for the 165 symptomatic subjects. Based on RT-PCR results as the reference standard, InteliSwab® showed clinical sensitivity and specificity of 85.2% (95% CI, 74.3-92.0%) and 98.1% (95% CI, 93.3-99.7%), respectively. The overall agreement was 93.3% (Kappa index value 0.85; 95% CI, 0.77-0.74) between RT-PCR and InteliSwab® test results. Furthermore, the evaluation of analytical sensitivity for different SARS-CoV-2 variants by InteliSwab® was comparable in the detection of all the variants tested, including Omicron subvariants, BA.4, BA.5, and BQ.1.

CONCLUSIONS

Due to the surge of infections caused by different variants from time to time, there is a critical need to evaluate the sensitivity of rapid antigen-detecting tests for new variants. The study findings showed the robust diagnostic performance of InteliSwab® and analytical sensitivity in detecting different SARS-CoV-2 variants, including the Omicron subvariants. With the integrated swab and excellent sensitivity and variant detection, this test has high potential as a point-of-care Ag-RDT in various settings when molecular assays are in limited supply and rapid diagnosis of SARS-CoV-2 is necessary.

Lived experience of Iranian pre-hospital medical staff during the COVID-19 pandemic: a descriptive phenomenological study

Background

Pre-hospital medical staff faced numerous challenges during the COVID-19 pandemic. However, these challenges specific to pre-hospital services have not been thoroughly explored in Iran. This qualitative study aimed to examine the essence of pre-hospital care during the COVID-19 pandemic.

Methods

This phenomenological study was conducted from June to August 2021 in Tehran, Iran. Semi-structured interviews were conducted with pre-hospital medical staff. Data analysis was performed using Colaizzi's approach, and rigor was ensured by adhering to the consolidated criteria for qualitative reporting research.

Results

A total of 17 pre-hospital medical staff were interviewed, and five themes were extracted from the data: workload and resilience, damage, lack of control, under preparedness, and post-traumatic growth. These themes highlight the resilience demonstrated by pre-hospital medical staff, who faced an unprecedented crisis with limited preparedness and significant damage.

Conclusion

The findings of this study indicate that pre-hospital medical staff in Iran encountered challenges during the COVID-19 pandemic due to a lack of preparedness and substantial damage. Despite these adversities, the participants exhibited resilience and experienced post-traumatic growth. The study emphasizes the importance of proper planning and preparedness to enhance the resilience of emergency medical services during pandemics. Furthermore, the results underscore the need to address the challenges faced by pre-hospital medical staff and improve the quality of care provided to patients during crises such as the COVID-19 pandemic.

A review on the impacts of COVID-19 on the auditory system: Implications for public health promotion research

Background

Currently, there are few studies on the relationship between COVID-19 and the auditory system. In the current study, a review of the studies conducted in the fields of etiopathology, clinical manifestations, research, and treatment of hearing loss caused byCOVID-19 was conducted, which can be used as a baseline for future studies.

Methods

We utilized the research approach suggested by Arksey and O'Malley to carry out this scoping review. Search was conducted in Farsi and English with a focus on the onset of hearing loss in patients with COVID-19 through Medline and PubMed, and Google Scholar search engine. Studies included were those involving adult patients diagnosed with COVID-19 who experienced hearing loss, ear pain, ear discharge, and otitis media. Studies were eligible for inclusion if there was a description of the otologic dysfunction, specifically onset, duration, or clinical outcomes.

Results

Among 90 studies identified, 35 studies were included in the review process. Our findings suggest several possible mechanisms for sudden sensorineural hearing loss (SSNHL) in COVID-19 patients, and COVID-19 infection could have deleterious effects on the inner ear, specifically on the hair cells of the cochlea despite patients being asymptomatic and early identification of SSNHL in COVID-19patients can save the hearing and also patient.

Conclusion

Hearing loss in COVID-19 infection has not received much attention by health care professionals. Sensorineural hearing loss (SNHL), tinnitus, and/or vertigo have been shown to occur during and following COVID-19 infection. Due to lack of research studies, and the inconsistency and even contradictory of the findings, it remains questionable whether COVID-19 contributes to the high incidence of hearing loss. The proper understanding of the mechanisms behind hearing loss in COVID-19 infections needs further research. However, it seems likely that SNHL could be included among the manifestations of those-called "long COVID" syndrome.

Targeting the cGAS-STING pathway as an inflammatory crossroad in coronavirus disease 2019 (COVID-19)

CONTEXT AND OBJECTIVE

The emerging pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has imposed significant mortality and morbidity on the world. An appropriate immune response is necessary to inhibit SARS-CoV-2 spread throughout the body.

RESULTS

During the early stages of infection, the pathway of stimulators of interferon genes (STING), known as the cGAS-STING pathway, has a significant role in the induction of the antiviral immune response by regulating nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) and Interferon regulatory factor 3 (IRF3), two key pathways responsible for proinflammatory cytokines and type I IFN secretion, respectively.

DISCUSSION

During the late stages of COVID-19, the uncontrolled inflammatory responses, also known as cytokine storm, lead to the progression of the disease and poor prognosis. Hyperactivity of STING, leading to elevated titers of proinflammatory cytokines, including Interleukin-I (IL-1), IL-4, IL-6, IL-18, and tissue necrosis factor-α (TNF-α), is considered one of the primary mechanisms contributing to the cytokine storm in COVID-19.

CONCLUSION

Exploring the underlying molecular processes involved in dysregulated inflammation can bring up novel anti-COVID-19 therapeutic options. In this article, we aim to discuss the role and current studies targeting the cGAS/STING signaling pathway in both early and late stages of COVID-19 and COVID-19-related complications and the therapeutic potential of STING agonists/antagonists. Furthermore, STING agonists have been discussed as a vaccine adjuvant to induce a potent and persistent immune response.

The impact of early therapies for COVID-19 on death, hospitalization and persisting symptoms: a retrospective study

PURPOSE

Oral antivirals (nirmatrelvir/ritonavir and molnupiravir), intravenous short treatment of remdesivir and anti-SARS-CoV-2 monoclonal antibodies (mAbs) have been used for early COVID-19 treatments in high risk of disease progression patients. The term long COVID has been used to refer to a range of new, returning, or ongoing symptoms after SARS-CoV-2 infection. Little is known about the impact of such therapies on long COVID.

METHODS

This is a retrospective observational study, including all outpatients evaluated from April 2021 to March 2022 in Brescia, Lombardy, northern Italy. Patients were stratified in three groups: (a) treated with mAbs, (b) treated with antivirals drugs and (c) controls (patients eligible for a or b who refused treatment). Data were collected at baseline and at month 1 and 3 (data on self-reported symptoms were collected using a telephone-administered questionnaire). We assessed early COVID-19 therapies effectiveness in preventing hospitalization, death at 1 or 3 months and persisting symptoms at 3 months after the onset of SARS-CoV-2 infection.

RESULTS

A total of 649 patients were included in the study, of which 242 (37.3%) were treated with mAbs, 197 (30.3%) with antiviral drugs and 210 (32.4%) were not treated. Patients most frequently reported cerebro-cardiovascular diseases (36.7%) followed by obesity (22%). Overall, 29 patients (4.5%) died or were hospitalized at 1 or 3-month follow-up. Death or hospitalization was positively associated with older ages, with a significant linear trend (OR 3.05; 95% CI 1.16-8.06, for patients aged 80 or more years compared to those aged less than 65). Data on long COVID at 3 months were available for 323 (49.8%) patients. A positive association emerged for females compared to men, with an OR of 2.14 (95% CI 1.30-3.53) for any symptoms. Conversely, inverse associations were found for treatment groups as compared to the control one, with significant estimates among patients treated with antiviral drugs for any symptoms (OR 0.43, 95% CI 0.21-0.87) and patients treated with mAbs for any neuro-behavioral symptoms (OR 0.48, 95% CI 0.25-0.92).

CONCLUSIONS

We report beneficial effect of early use of anti-SARS-CoV-2 antivirals and mAbs on long COVID.

Obtaining a high titer of polyclonal antibodies from rats to the SARS-CoV-2 nucleocapsid protein and its N- and C-terminal domains for diagnostic test development

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is an enveloped, plus-stranded RNA virus responsible for the Coronavirus Disease 2019 (COVID-19). Patients infected with COVID-19 may be asymptomatic or have symptoms ranging from mild manifestations to severe cases of the disease that could lead to death. The SARS-CoV-2 genome encodes 4 structural proteins, including the Spike protein (S), the Nucleocapsid protein (N), Membrane protein (M) and, the Envelope protein (E). The N protein forms a major component of the ribonucleoprotein complex within the virus particle and play a vital role in its transcription and replication. Nevertheless, the S protein was the most important protein in the development of vaccines against COVID-19. However, the decrease in number of registered immunizations against the disease and the rapid drop in neutralizing antibody titers together with looser preventive measures for virus transmission, favored the rapid appearance of new variants of concerns (VOCs) that primarily show mutations in the S protein. This fact makes the N protein a good candidate for the development of diagnostic tests, due to its stability, amino acid conservation, high immunogenicity, and the smaller likelihood of mutation. With the aim of developing a new diagnostic kit based on the N protein, we evaluated the humoral response in female Wistar rats against this target. Three constructions of the N protein were used to inoculate the animals: the full-length protein (Cfull), the N- (NTD), and the C-terminal (CTD) portion of the protein. The immunizations induced the animal's immune response, with specific polyclonal IgG antibodies against the Cfull protein and its fragments. There were not non-specific bind to the protein used as negative control. Anti-Cfull antibodies demonstrated high efficiency in binding to the NTD protein and the antibodies present in the anti-CTD and anti-NTD sera have recognized the Cfull protein, but they were not able to recognize the NTD and CTD proteins, respectively. Our results indicate an efficient protocol for obtaining high antibody titers against the N recombinant protein of SARS-CoV-2 and its fragments highlighting the Cfull protein, which can be used in the development of new diagnostic kits.

Emerging infectious diseases, focus on infection prevention, environmental survival and germicide susceptibility: SARS-CoV-2, Mpox, and Candida auris

BACKGROUND

New and emerging infectious diseases continue to represent a public health threat. Emerging infectious disease threats include pathogens increasing in range (eg, Mpox), zoonotic microbes jumping species lines to cause sustained infections in humans via person-to-person transmission (SARS-CoV-2) and multidrug-resistant pathogens (eg, Candida auris).

MATERIALS AND METHODS

We searched the published English literature and reviewed the selected articles on SARS-CoV-2, Mpox, and Candida auris with a focus on environmental survival, contamination of the patient's hospital environment, susceptibility of the pathogen to antiseptics and disinfectants and infection prevention recommendations.

RESULTS

All three pathogens (ie, SARS-CoV-2, Mpox, and Candida auris) can survive on surfaces for minutes to hours and for Mpox and C auris for days. Currently available antiseptics (eg, 70%-90% alcohol hand hygiene products) are active against SARS-CoV-2, Mpox and C auris. The U.S Environmental Protection Agency provides separate lists of surface disinfectants active against SARS-CoV-2, Mpox, and C auris.

DISCUSSION

The risk of environment-to-patient transmission of SARS-CoV-2, Mpox and Candida auris, is very low, low-moderate and high, respectively. In the absence of appropriate patient isolation and use of personal protection equipment, the risk of patient-to-health care provider transmission of SARS-CoV-2, Mpox, and C auris is high, moderate and low, respectively.

CONCLUSIONS

Appropriate patient isolation, use of personal protective equipment by health care personnel, hand hygiene, and surface disinfection can protect patients and health care personnel from acquiring SARS-CoV-2, Mpox, and C auris from infected patients.

Differences in door-to-balloon time and outcomes in SARS-CoV-2-positive ST-segment elevation myocardial infarction patients undergoing primary percutaneous coronary intervention: A systematic review and meta-analysis

BACKGROUND

The coronavirus disease 2019 infection has significantly impacted the world and placed a heavy strain on the medical system and the public, especially those with cardiovascular diseases. Hoverer, the differences in door-to-balloon time and outcomes in ST-segment elevation myocardial infarction (STEMI) patients undergoing primary percutaneous coronary intervention after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are not known too much.

METHODS

Web of Science, EMBASE, PubMed, Cochrane Library, Wanfang, VIP, and China's National Knowledge Infrastructure were utilized to perform a systematic literature search until April 30, 2023. We computed the odds ratios (ORs) and their corresponding 95% confidence intervals (CIs) to determine the correlation. A random-effects model was used for the meta-analysis if the study had significant heterogeneity. Meanwhile, sensitivity analysis and Trial sequential analysis were also accomplished using Rveman5.4 and trial sequential analysis 0.9.5.10 Beta software, respectively.

RESULTS

A total of 5 eligible studies were explored in our meta-analysis, including 307 cases and 1804 controls. By meta-analysis, the pooled data showed that SARS-CoV-2-positive STEMI patients undergoing percutaneous coronary intervention had a longer door-to-balloon time (OR 6.31, 95% CI 0.99, 11.63, P = .02) than the negative subjects. The glycoprotein IIb/IIIa inhibitor use after SARS-CoV-2 infection (OR 2.71, 95% CI 1.53, 4.81, P = .0006) was relatively frequent compared with controls, and the postoperative Thrombolysis in Myocardial Infarction blood flow (OR 0.48, 95% CI 0.34, 0.67, P < .0001) was worse compared that. The in-hospital mortality (OR 5.16, 95% CI 3.53, 7.53, P < .00001) was higher than non-SARS-CoV-2 infection ones. In addition, we also discovered that age, gender (male), hypertension, diabetes mellitus, hyperlipidemia, smoking, previous myocardial infarction, total ischemia time, and thrombus aspiration use did not have a significant association with the development of STEMI patients with SARS-CoV-2.

CONCLUSION

SARS-CoV-2 positivity is significantly associated with longer door-to-balloon time and higher in-hospital mortality in STEMI patients undergoing primary percutaneous coronary intervention.

Impact of SARS-CoV-2 Infection on Maternal and Neonatal Outcome in Correlation with Sociodemographic Aspects: A Retrospective Case-Control Study

BACKGROUND

As the COVID-19 pandemic evolved, concerns grew about its impact on pregnant women. This study aimed to determine how SARS-CoV-2 affects pregnancy, birth, and newborns, in order to identify vulnerable individuals and provide proper care.

METHODS

This is a retrospective case-control study of 398 pregnant women who delivered at the Emergency Clinical County Hospital in Sibiu, Romania from 1 February 2020 to 31 March 2022. Patients were initially grouped and compared based on their RT-PCR SARS-CoV-2 test results into the COVID group (cases) (N = 199) and non-COVID group (control) (N = 199). The COVID cases were further divided and compared according to the pre-Delta (N = 105) and Delta/Omicron (N = 94) SARS-CoV-2 variants. COVID cases and control groups were compared to identify correlations between sociodemographic factors, pregnancy outcomes, and SARS-CoV-2 infection. The same comparisons were performed between pre-Delta and Delta/Omicron groups.

RESULTS

There were no significant differences concerning maternal residence, while educational level and employment proportion were higher among the positively tested patients. No significant differences were found for neonatal and pregnancy complications between COVID cases and control groups. Except for a lower mean gestational age, no significant differences were found between pre-Delta and Delta/Omicron periods. The maternal mortality in the infected group was 0.5% (1 case).

CONCLUSIONS

Our study showed that SARS-CoV-2 infection at birth did not significantly affect maternal and neonatal outcomes, not even considering the SARS-CoV-2 strain.

Increased Expression of lncRNA AC000120.7 and SENP3-EIF4A1 in Patients with Acute Respiratory Distress Syndrome Induced by SARS-CoV-2 Infection: A Pilot Study

COVID-19, a disease caused by the SARS-CoV-2 virus, poses significant threats to the respiratory system and other vital organs. Long non-coding RNAs have emerged as influential epigenetic regulators and promising biomarkers in respiratory ailments. The objective of this study was to identify candidate lncRNAs in SARS-CoV-2-positive individuals compared to SARS-CoV-2-negative individuals and investigate their potential association with ARDS-CoV-2 (acute respiratory distress syndrome). Employing qRT-PCR, we meticulously examined the expression profiles of a panel comprising 84 inflammation-related lncRNAs in individuals presenting upper respiratory infection symptoms, categorizing them into those testing negative or positive for SARS-CoV-2. Notably, first-phase PSD individuals exhibited significantly elevated levels of AC000120.7 and SENP3-EIF4A1. In addition, we measured the expression of two lncRNAs, AC000120.7 and SENP3-EIF4A1, in patients with ARDS unrelated to SARS-CoV-2 (n = 5) and patients with ARDS induced by SARS-CoV-2 (ARDS-CoV-2, n = 10), and interestingly, expression was also higher among patients with ARDS. Intriguingly, our interaction pathway analysis unveiled potential interactions between lncRNA AC000120.7, various microRNAs, and genes associated with inflammation. This study found higher expression levels of lncRNAs AC000120.7 and SENP3-EIF4A1 in the context of infection-positive COVID-19, particularly within the complex landscape of ARDS.

Asthma and COVID-19: a controversial relationship

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection induces a spectrum of clinical manifestations that depend on the immune response of the patient, i.e., from an asymptomatic form to an inflammatory response with multiorgan deterioration. In some cases, severe cases of SARS-CoV-2 are characterized by an excessive, persistent release of inflammatory mediators known as a cytokine storm. This phenomenon arises from an ineffective T helper (Th)-1 response, which is unable to control the infection and leads to a reinforcement of innate immunity, causing tissue damage. The evolution of the disease produced by SARS-CoV2, known as COVID-19, has been of interest in several research fields. Asthma patients have been reported to present highly variable outcomes due to the heterogeneity of the disease. For example, the Th2 response in patients with allergic asthma is capable of decreasing Th1 activation in COVID-19, preventing the onset of a cytokine storm; additionally, IL-33 released by damaged epithelium in the context of COVID-19 potentiates either Th1 or T2-high responses, a process that contributes to poor outcomes. IL-13, a T2-high inflammatory cytokine, decreases the expression of angiotensin converting enzyme-2 (ACE2) receptor, hindering SARS-CoV-2 entry; finally, poor outcomes have been observed in COVID-19 patients with severe neutrophilic asthma. In other contexts, the COVID-19 lockdown has had interesting effects on asthma epidemiology. The incidence of asthma in the most populated states in Mexico, including Tamaulipas, which has the highest asthma incidence in the country, showed similar tendencies independent of how strict the lockdown measures were in each state. As described worldwide for various diseases, a decrease in asthma cases was observed during the COVID-19 lockdown. This decrease was associated with a drop in acute respiratory infection cases. The drop in cases of various diseases, such as diabetes, hypertension or depression, observed in 2020 was restored in 2022, but not for asthma and acute respiratory infections. There were slight increases in asthma cases when in-person classes resumed. In conclusion, although many factors were involved in asthma outcomes during the pandemic, it seems that acute respiratory infection is intimately linked to asthma cases. Social distancing during remote learning, particularly school lockdown, appears to be an important cause of the decrease in cases.

Monkeypox: Virology, laboratory diagnosis and therapeutic approach

Monkeypox infection outbreaks have been observed sporadically in Africa, usually as a result of interaction with wildlife reservoirs. The genomes of the new strain range in size from 184.7 to 198.0 kb and are identified with 143-214 open reading frames. Viral cores are rapidly carried on microtubules away from the cell's perimeter and deeper into the cytoplasm once the virus and cell membranes fuse. Depending on the kind of exposure, patients with monkeypox may experience a febrile prodrome 5-13 days after exposure, which frequently includes lymphadenopathy, malaise, headaches, and muscle aches. A different diagnostic approach is available for monkeypox, including histopathological analysis, electron microscopy, immunoassays, polymerase chain reaction, genome sequencing, microarrays, loop-mediated isothermal amplification technology and CRISPR (i.e., "clustered regularly interspaced short palindromic repeats"). There are currently no particular, clinically effective treatments available for the monkeypox virus. An initial treatment is cidofovir. As a monophosphate nucleotide analog, cidofovir is transformed into an inhibitor of viral DNA polymerase by cellular kinases, which is analogous to cidofovir's function in inhibiting viral DNA synthesis. The European Medicine Agency and the Food and Drug Administration have both granted permission for IMVAMUNE, a replication-deficient, attenuated third-generation modified vaccinia Ankara vaccine, to be used for the prevention of smallpox and monkeypox in adults.

The defense of Shangri-La: Protecting isolated communities by periodic infection screening in the worst future pandemic

In the worst future pandemic, effective vaccines and medicines could be unavailable for a long time. In such circumstances, it is necessary to evaluate whether a periodic screening can protect isolated communities and critical facilities and avoid a complete shutdown. In this study, we introduced an epidemiological model that included the essential parameters of infection transmission and screening. With varying parameters, we studied the dynamics of viral infection in the isolated communities. In the scenario with a periodic infection screening once per 3 days and a viral basic reproduction number 3.0, >85% of the infection waves have a duration <7 days and the infection size in each of the waves is generally <4 individuals when the efficiency of infection discovery is 0.9 in the screening. When the period of screening was elongated to once per 7 days, the cases of infection dramatically increased to 5 folds of that mentioned previously. Further, with a weak discovery efficiency of 0.7 and the aforementioned low screening frequency, the spread of infection would be out of control. Our study suggests that frequent periodic screening is capable of controlling a future epidemic in isolated communities without other measures.

SARS-CoV-2-assoziierte Todesfälle innerhalb des ersten Jahres der COVID-19-Pandemie: eine Autopsiestudie

Background

COVID-19 now exists for more than 3 years and has caused almost 7 million deaths worldwide. At the beginning of this study only little was known on the patients’ characteristics and comparative autopsy studies are still rare.

Material and methods

Between 11 March 2020 and 10 March 2021, 55 consecutive and complete autopsies of individuals who died in association with SARS-CoV‑2 infections were performed shortly after death (median PMI 6.8 h) by the same team. Clinical data were available in 45 of 55 cases. 1st vs. 2nd infection wave cases and male vs. female cases were compared.

Results

Thirty-five patients were male (63.6%) 20 were female (36.4%), average age 72.4 years. Seventeen cases (30.9%) could be assigned to the 1st and 38 cases (69.1%) to the 2nd infection wave. Forty-two of the decedents (76.4%) died due to COVID-19. Arterial hypertension, obesity, and cardiac hypertrophy were the most frequent detected comorbidities.

Discussion

The present study corroborates previous research data but also reveals new approaches for further comparative studies. Patient-specific personal and general ICU-related risk factors for the development of thromboembolisms oppose the effects of changes in anticoagulant medication.

Nanopore sequencing technology and its applications

Since the development of Sanger sequencing in 1977, sequencing technology has played a pivotal role in molecular biology research by enabling the interpretation of biological genetic codes. Today, nanopore sequencing is one of the leading third-generation sequencing technologies. With its long reads, portability, and low cost, nanopore sequencing is widely used in various scientific fields including epidemic prevention and control, disease diagnosis, and animal and plant breeding. Despite initial concerns about high error rates, continuous innovation in sequencing platforms and algorithm analysis technology has effectively addressed its accuracy. During the coronavirus disease (COVID-19) pandemic, nanopore sequencing played a critical role in detecting the severe acute respiratory syndrome coronavirus-2 virus genome and containing the pandemic. However, a lack of understanding of this technology may limit its popularization and application. Nanopore sequencing is poised to become the mainstream choice for preventing and controlling COVID-19 and future epidemics while creating value in other fields such as oncology and botany. This work introduces the contributions of nanopore sequencing during the COVID-19 pandemic to promote public understanding and its use in emerging outbreaks worldwide. We discuss its application in microbial detection, cancer genomes, and plant genomes and summarize strategies to improve its accuracy.

Autoimmune Heart Disease: A Comprehensive Summary for Forensic Practice

Autoimmune heart disease is a non-random condition characterised by immune system-mediated aggression against cardiac tissue. Cardiac changes often exhibit nonspecific features and, if unrecognised, can result in fatal outcomes even among seemingly healthy young individuals. In the absence of reliable medical history, the primary challenge lies in differentiating between the various cardiopathies. Numerous immunohistochemical and genetic studies have endeavoured to characterise distinct types of cardiopathies, facilitating their differentiation during autopsy examinations. However, the presence of a standardised protocol that forensic pathologists can employ to guide their investigations would be beneficial. Hence, this summary aims to present the spectrum of autoimmune cardiopathies, including emerging insights such as SARS-CoV-2-induced cardiopathies, and proposes the utilisation of practical tools, such as blood markers, to aid forensic pathologists in their routine practice.

Coinfections and Superinfections Associated with COVID-19 in Colombia: A Narrative Review

The COVID-19 pandemic has had significant impacts on healthcare systems around the world, including in Latin America. In Colombia, there have been over 23,000 confirmed cases and 100 deaths since 2022, with the highest number of cases occurring in females and the highest number of deaths in males. The elderly and those with comorbidities, such as arterial hypertension, diabetes mellitus, and respiratory diseases, have been particularly affected. Coinfections with other microorganisms, including dengue virus, Klebsiella pneumoniae, and Mycobacterium tuberculosis, have also been a significant factor in increasing morbidity and mortality rates in COVID-19 patients. It is important for surveillance systems to be improved and protocols to be established for the early detection and management of coinfections in COVID-19. In addition to traditional treatments, alternatives such as zinc supplementation and nanomedicine may have potential in the fight against COVID-19. It is also crucial to consider the social, labor, educational, psychological, and emotional costs of the pandemic and to address issues such as poverty and limited access to potable water in order to better prepare for future pandemics.

Molecular Biomarker Identification Using a Network-Based Bioinformatics Approach That Links COVID-19 With Smoking

The COVID-19 coronavirus, which primarily affects the lungs, is the source of the disease known as SARS-CoV-2. According to "Smoking and COVID-19: a scoping review," about 32% of smokers had a severe case of COVID-19 pneumonia at their admission time and 15% of non-smokers had this case of COVID-19 pneumonia. We were able to determine which genes were expressed differently in each group by comparing the expression of gene transcriptomic datasets of COVID-19 patients, smokers, and healthy controls. In all, 37 dysregulated genes are common in COVID-19 patients and smokers, according to our analysis. We have applied all important methods namely protein-protein interaction, hub-protein interaction, drug-protein interaction, tf-gene interaction, and gene-MiRNA interaction of bioinformatics to analyze to understand deeply the connection between both smoking and COVID-19 severity. We have also analyzed Pathways and Gene Ontology where 5 significant signaling pathways were validated with previous literature. Also, we verified 7 hub-proteins, and finally, we validated a total of 7 drugs with the previous study.

Identification of a Putative SARS-CoV-2 Main Protease Inhibitor through In Silico Screening of Self-Designed Molecular Library

There have been outbreaks of SARS-CoV-2 around the world for over three years, and its variants continue to evolve. This has become a major global health threat. The main protease (M^pro, also called 3CL^pro) plays a key role in viral replication and proliferation, making it an attractive drug target. Here, we have identified a novel potential inhibitor of M^pro, by applying the virtual screening of hundreds of nilotinib-structure-like compounds that we designed and synthesized. The screened compounds were assessed using SP docking, XP docking, MM-GBSA analysis, IFD docking, MD simulation, ADME/T prediction, and then an enzymatic assay in vitro. We finally identified the compound V291 as a potential SARS-CoV-2 M^pro inhibitor, with a high docking affinity and enzyme inhibitory activity. Moreover, the docking results indicate that His41 is a favorable amino acid for pi-pi interactions, while Glu166 can participate in salt-bridge formation with the protonated primary or secondary amines in the screened molecules. Thus, the compounds reported here are capable of engaging the key amino acids His41 and Glu166 in ligand-receptor interactions. A pharmacophore analysis further validates this assertion.

Hematocytological, biochemical, and hemostasis parameters' role in predicting the possibility of the various forms of the COVID-19 course in hospitalized Ukrainian patients: A cross-sectional study

Background and Aims

The main objective of this study is to establish the characteristics of blood laboratory parameters in hospitalized coronavirus disease 2019 (COVID-19) Ukrainian patients and the significance of the above-mentioned parameters for predicting the course of the disease.

Methods

Hematocytological, biochemical, and hemostasis methods of research have been used. Groups of patients with different forms of the coronavirus disease course have been analyzed (lethality - recovery, recovery with a severe and mild course).

Results and Conclusion

Age is one of the risk factors for COVID-19 mortality. Absolute values of neutrophils, neutrophil-lymphocyte ratio (NLR), systemic inflammation index, d-dimer, C-reactive protein, and soluble fibrin complex can be used by clinicians to effectively differentiate between two possible outcomes (lethality vs. recovery). A higher number of stab leukocytes, d-NLR, and platelets concentration have been recorded in patients with severe COVID-19 cases, compared to mild ones. The risk of adverse COVID-19 outcome (lethality) is significantly linked with d-dimer and NLR (odds ratio 1.42). The risk of a severe course of the disease was significantly associated with the count of leukocytes (odds ratio 4.96).

Quantitative Evaluation of COVID-19 Pneumonia CT Using AI Analysis-Feasibility and Differentiation from Other Common Pneumonia Forms

PURPOSE: To implement the technical feasibility of an AI-based software prototype optimized for the detection of COVID-19 pneumonia in CT datasets of the lung and the differentiation between other etiologies of pneumonia. METHODS: This single-center retrospective case-control-study consecutively yielded 144 patients (58 female, mean age 57.72 ± 18.25 y) with CT datasets of the lung. Subgroups including confirmed bacterial (n = 24, 16.6%), viral (n = 52, 36.1%), or fungal (n = 25, 16.6%) pneumonia and (n = 43, 30.7%) patients without detected pneumonia (comparison group) were evaluated using the AI-based Pneumonia Analysis prototype. Scoring (extent, etiology) was compared to reader assessment. RESULTS: The software achieved an optimal sensitivity of 80.8% with a specificity of 50% for the detection of COVID-19; however, the human radiologist achieved optimal sensitivity of 80.8% and a specificity of 97.2%. The mean postprocessing time was 7.61 ± 4.22 min. The use of a contrast agent did not influence the results of the software (p = 0.81). The mean evaluated COVID-19 probability is 0.80 ± 0.36 significantly higher in COVID-19 patients than in patients with fungal pneumonia (p < 0.05) and bacterial pneumonia (p < 0.001). The mean percentage of opacity (PO) and percentage of high opacity (PHO ≥ -200 HU) were significantly higher in COVID-19 patients than in healthy patients. However, the total mean HU in COVID-19 patients was -679.57 ± 112.72, which is significantly higher than in the healthy control group (p < 0.001). CONCLUSION: The detection and quantification of pneumonia beyond the primarily trained COVID-19 datasets is possible and shows comparable results for COVID-19 pneumonia to an experienced reader. The advantages are the fast, automated segmentation and quantification of the pneumonia foci.

New era of medical education: asynchronous and synchronous online teaching during and after COVID-19

COVID-19 struck the world suddenly and unexpectedly. Since traditional education requires face-to-face communication, to avoid further spreading of the virus a majority part of that education has moved online. Our study attempts to compare the differences between online medical education with a unique course design and traditional face-to-face education. We conducted a retrospective analysis of a total of 4,098 medical students between 2019 and 2020, including two groups of students who received online education and classroom education for the same subjects, respectively. Freshmen enrolled in September 2018 received traditional classroom physiology and pharmacology education in the spring semester of 2019. Because of the impact of the COVID-19 pandemic, freshmen who were enrolled in September 2019 received online physiology and pharmacology education in the spring semester of 2020. The final marks of the two groups of students were recorded and compared. Data on students participating in online discussions, learning, homework, and watching instructional videos were also recorded. There was no significant difference in the final academic performance between the two groups [average mark: 55.93 (online education) vs. 56.27 (classroom education), P = 0.488]. Further analysis showed that student participation rates in online discussions, online learning, and online viewing of instructional videos were closely correlated with final grades in online courses (P < 0.01). In conclusion, our results suggest that the pedagogical effects of online education during COVID-19 were promising, and we provide a well-designed medical online course to inspire further improvements in online education.NEW & NOTEWORTHY The COVID-19 pandemic has led to a massive temporary conversion of offline education to online education worldwide. Previous studies have noted that more students believed they had better learning experience in face-to-face learning. However, with our method of online teaching, we still showed a relatively similar performance result compared with offline education.

Ketogenic Diet and Ketone Bodies as Clinical Support for the Treatment of SARS-CoV-2-Review of the Evidence

One of the proposed nutritional therapies to support drug therapy in COVID-19 is the use of a ketogenic diet (KD) or ketone bodies. In this review, we summarized the evidence from tissue, animal, and human models and looked at the mechanisms of action of KD/ketone bodies against COVID-19. KD/ketone bodies were shown to be effective at the stage of virus entry into the host cell. The use of β-hydroxybutyrate (BHB), by preventing the metabolic reprogramming associated with COVID-19 infection and improving mitochondrial function, reduced glycolysis in CD4+ lymphocytes and improved respiratory chain function, and could provide an alternative carbon source for oxidative phosphorylation (OXPHOS). Through multiple mechanisms, the use of KD/ketone bodies supported the host immune response. In animal models, KD resulted in protection against weight loss and hypoxemia, faster recovery, reduced lung injury, and resulted in better survival of young mice. In humans, KD increased survival, reduced the need for hospitalization for COVID-19, and showed a protective role against metabolic abnormalities after COVID-19. It appears that the use of KD and ketone bodies may be considered as a clinical nutritional intervention to assist in the treatment of COVID-19, despite the fact that numerous studies indicate that SARS-CoV-2 infection alone may induce ketoacidosis. However, the use of such an intervention requires strong scientific validation.

An Open One-Step RT-qPCR for SARS-CoV-2 detection

The COVID-19 pandemic has resulted in millions of deaths globally, and while several diagnostic systems were proposed, real-time reverse transcription polymerase chain reaction (RT-PCR) remains the gold standard. However, diagnostic reagents, including enzymes used in RT-PCR, are subject to centralized production models and intellectual property restrictions, which present a challenge for less developed countries. With the aim of generating a standardized One-Step open RT-qPCR protocol to detect SARS-CoV-2 RNA in clinical samples, we purified and tested recombinant enzymes and a non-proprietary buffer. The protocol utilized M-MLV RT and Taq DNA pol enzymes to perform a Taqman probe-based assay. Synthetic RNA samples were used to validate the One-Step RT-qPCR components, and the kit showed comparable sensitivity to approved commercial kits. The One-Step RT-qPCR was then tested on clinical samples and demonstrated similar performance to commercial kits in terms of positive and negative calls. This study represents a proof of concept for an open approach to developing diagnostic kits for viral infections and diseases, which could provide a cost-effective and accessible solution for less developed countries.

The Influence of Different SARS-CoV-2 Strains on Changes in Maximal Oxygen Consumption, Ventilatory Efficiency and Oxygen Pulse of Elite Athletes

PURPOSE

The aim of this study was to evaluate the influence of different SARS-CoV-2 strains on the functional capacity of athletes.

METHODS

In total, 220 athletes underwent cardiopulmonary exercise testing (CPET) after coronavirus infection and before returning to sports activities. Eighty-eight athletes were infected by the Wuhan virus, and 66 were infected during the Delta and Omicron strain periods of the pandemic.

RESULTS

The CPET results showed significantly decreased maximal oxygen consumption, ventilatory efficiency, and oxygen pulse in athletes who were infected with Wuhan and Delta strains compared to athletes who suffered from Omicron virus infection. An early transition from aerobic to anaerobic metabolic pathways for energy production was observed in the Wuhan and Delta groups but not in athletes who were infected with the Omicron strain. There were no differences in the obtained results when Wuhan and Delta virus variants were compared.

CONCLUSION

These results suggest that the Wuhan and Delta virus strains had a significantly greater negative impact on the functional abilities of athletes compared to the Omicron virus variant, especially in terms of aerobic capacity and cardiorespiratory function.

COVID-19 in early 2023: Structure, replication mechanism, variants of SARS-CoV-2, diagnostic tests, and vaccine & drug development studies

Coronavirus Disease-19 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome-coronaviruses-2 (SARS-CoV-2), a highly pathogenic and transmissible coronavirus. Most cases of COVID-19 have mild to moderate symptoms, including cough, fever, myalgias, and headache. On the other hand, this coronavirus can lead to severe complications and death in some cases. Therefore, vaccination is the most effective tool to prevent and eradicate COVID-19 disease. Also, rapid and effective diagnostic tests are critical in identifying cases of COVID-19. The COVID-19 pandemic has a dynamic structure on the agenda and contains up-to-date developments. This article has comprehensively discussed the most up-to-date pandemic situation since it first appeared. For the first time, not only the structure, replication mechanism, and variants of SARS-CoV-2 (Alpha, Beta, Gamma, Omicron, Delta, Epsilon, Kappa, Mu, Eta, Zeta, Theta, lota, Lambda) but also all the details of the pandemic, such as how it came out, how it spread, current cases, what precautions should be taken, prevention strategies, the vaccines produced, the tests developed, and the drugs used are reviewed in every aspect. Herein, the comparison of diagnostic tests for SARS-CoV-2 in terms of procedure, accuracy, cost, and time has been presented. The mechanism, safety, efficacy, and effectiveness of COVID-19 vaccines against SARS-CoV-2 variants have been evaluated. Drug studies, therapeutic targets, various immunomodulators, and antiviral molecules applied to patients with COVID-19 have been reviewed.

Immune evasion of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2); molecular approaches

In December 2019, a new betacoronavirus, known as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), caused an outbreak at the Wuhan seafood market in China. The disease was further named coronavirus disease 2019 (COVID-19). In March 2020, the World Health Organization (WHO) announced the disease to be a pandemic, as more cases were reported globally. SARS-CoV-2, like many other viruses, employs diverse strategies to elude the host immune response and/or counter immune responses. The infection outcome mainly depends on interactions between the virus and the host immune system. Inhibiting IFN production, blocking IFN signaling, enhancing IFN resistance, and hijacking the host's translation machinery to expedite the production of viral proteins are among the main immune evasion mechanisms of SARS-CoV-2. SARS-CoV-2 also downregulates the expression of MHC-I on infected cells, which is an additional immune-evasion mechanism of this virus. Moreover, antigenic modifications to the spike (S) protein, such as deletions, insertions, and also substitutions are essential for resistance to SARS-CoV-2 neutralizing antibodies. This review assesses the interaction between SARS-CoV-2 and host immune response and cellular and molecular approaches used by SARS-CoV-2 for immune evasion. Understanding the mechanisms of SARS-CoV-2 immune evasion is essential since it can improve the development of novel antiviral treatment options as well as vaccination methods.

The impact of Covid-19 pandemic on modification of medical teaching in Italy: A narrative review

During the first wave of Covid-19 in Italy, there was a problem with University. Universities couldn't do face-to-face (FTF) lessons and started to do online lessons (OL). This study investigates the impressions of students, teachers, and institutions during the first wave situation. A search was conducted on the main international databases, and only studies conducted in Italy starting during the Covid-19 pandemic are considered. 9 studies tell about the impressions of students about OL lessons, and 10 studies speak about medical resident's situation and teacher's impressions. Studies about students give conflicting results, teachers are generally satisfied with the contents, but agree on the difficulty of not having relationships with students. Medical residents have reduced significantly the clinical and surgical practice, sometimes increasing the research. In the future, it is indispensable to create a system that guarantees the efficacy of FTF lessons for practice, it is still low in sanitary and medical courses in Italy during the pandemic period.

Analysis of Optical Coherence Tomography (OCT) and Optical Coherence Tomography Angiography (OCTA) Parameters in Young Adults after SARS-CoV-2 Infection (COVID-19) Compared with Healthy Young Controls

Purpose: To compare retinal changes in young adults with previous SARS-CoV-2 infection with healthy young controls using optical coherence tomography (OCT) and optical coherence tomography angiography (OCTA). Methods: This prospective single-center study was conducted at the University Hospital of Zurich, Zurich, Switzerland. Participants were imaged from May to November 2021 using the SOLIX device (Visionix International SAS, Pont-de-l’Arche, France). We performed 12 mm × 12 mm, 6.4 mm × 6.4 mm, 6 mm × 6 mm and 3 mm × 3 mm OCT and OCTA scans, as well as fundus photography of each participant’s eyes. Results: In total, 466 participants were imaged. Of these, 233 were healthy controls with negative RT-PCR tests for SARS-CoV-2, 168 were young adults who had a SARS-CoV-2 infection at least 180 days previously, 19 were participants who had a SARS-CoV-2 infection < 180 days previously, and 46 were participants with asymptomatic SARS-CoV-2 infection (i.e., serologically positive but with no symptoms). Compared with healthy controls, statistically significant differences were found for OCTA recordings of the optic disc for the whole image (WI) and WI capillary vessel density, with both being higher in the SARS-CoV-2 group. Conclusion: Statistically significant results were only observed for selected variables, and in parts, only unilaterally, with relatively large p values (p = 0.02–0.03). Thus, we did not interpret these as clinically significant, leading to the conclusion that young and otherwise healthy individuals (mainly men) seem to recover from mild COVID-19 infections with no ophthalmological residues.

A triple-target reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid and accurate detection of SARS-CoV-2 virus

The spreading of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) across the world has impacted people's health and lives worldwide in recent years. Rapid and accurate diagnosis is crucial for curbing the pandemic of coronavirus disease 2019 (COVID-19). Reverse transcription loop-mediated isothermal amplification (RT-LAMP) has great potential for SARS-CoV-2 detection but fails to completely replace conventional PCR due to the high false-positive rate (FPR). We proposed a triple-target RT-LAMP method for dual-signal, sensitive, and simultaneous detection of conserved genes of SARS-CoV-2. Multiple LAMP primer sets were designed for N, E, and M genes and their amplification efficacy were screened. Then, using artificial plasmids and RNA, the optimal primer set for each gene was examined on specificity, sensitivity, and detection range. The RT-LAMP initiated by these primer sets exhibited better specificity and sensitivity than that of RT-qPCR, and the triple-target RT-LAMP could determine different variants of SARS-CoV-2. By testing 78 artificial RNA samples, the total FPR of triple-target RT-LAMP was eliminated compared with that of mono-target RT-LAMP. The triple-target RT-LAMP method precisely identified throat swab specimens through colorimetry and fluorescent signals within 60 min, and the limit of detection (LOD) was as low as 187 copies/reaction. In the future, the triple-target RT-LAMP can be applied to in-field and on-site diagnosis of symptomatic and asymptomatic virus carriers.

Challenges and Recent Advancements in COVID-19 Vaccines

Vaccination is the most effective method for the prevention of COVID-19 caused by SARS-CoV-2, which is still a global epidemic. However, the evolution of SARS-CoV-2 is so rapid that various variants, including the Alpha, Beta, Gamma, Delta, and Omicron variants, have emerged, lowering the protection rate of vaccines and even resulting in breakthrough infections. Additionally, some rare but severe adverse reactions induced by COVID-19 vaccines may raise safety concerns and hinder vaccine promotion; however, clinical studies have shown that the benefits of vaccination outweigh the risks caused by adverse reactions. Current vaccines approved with emergency use authorization (EUA) were originally adaptive for adults only, and infants, children, and adolescents are not included. New-generation vaccines are needed to overcome the challenges of limited adaptive age population, breakthrough infection (mainly due to virus variant emergencies), and critical adverse reactions. Fortunately, some advances in COVID-19 vaccines have been obtained regarding enlarged adaptive populations for clinical applications, such as the Pfizer/BioNTech vaccine and the Moderna vaccine. In this article, we provide a review on the challenges and recent advancements in COVID-19 vaccines. The development of next-generation COVID-19 vaccines should lay emphasis on the expansion of adaptive age populations in all individuals, the induction of immune responses to viral variants, the avoidance or alleviation of rare but potentially critical adverse reactions, and the discovery of subunit vaccines with adjuvants encapsulated in nanoparticles.

Performance Evaluation of a BZ COVID-19 NALF Assay for Rapid Diagnosis of SARS-CoV-2

Coronavirus disease (COVID-19) caused by SARS-CoV-2 infection has been a global pandemic for more than two years, and it is important to quickly and accurately diagnose and isolate patients with SARS-CoV-2 infection. The BZ COVID-19 NALF Assay could sensitively detect SARS-CoV-2 from a nasopharyngeal swab because it adopts both a loop-mediated isothermal amplification and lateral flow immunochromatography technology. In this study, a total of 389 nasopharyngeal swab samples, of which 182 were SARS-CoV-2 PCR positive and 207 were negative samples, were recruited. Compared to the Allplex™ SARS-CoV-2 Assay, the BZ COVID-19 NALF Assay showed 95.05% sensitivity and 99.03% specificity for detecting SARS-CoV-2. The concordance rate between the BZ COVID-19 NALF Assay and Allplex™ SARS-CoV-2 Assay was 97.69%. The turnaround time of the BZ COVID-19 NALF Assay is only about 40~55 min. The BZ COVID-19 NALF Assay is an accurate, easy, and quick molecular diagnostic test compared to the conventional PCR test for detection of SARS-CoV-2. In addition, the BZ COVID-19 NALF Assay is thought to be very useful in small size medical facilities or developing countries where it is difficult to operate a clinical laboratory.

Genetic predisposition between coronavirus disease 2019 and rheumatic diseases: A 2-sample Mendelian randomization study

OBJECTIVE

The causalities between the coronavirus disease 2019 (COVID-19) and the risk of rheumatic diseases remain unclear. The purpose of this study was to investigate the causal effect of COVID-19 on rheumatic disease occurrence.

METHODS

Single nucleotide polymorphisms (SNPs), acquired from published genome-wide association studies, were used to perform 2-sample Mendelian randomization (MR) on cases diagnosed with COVID-19 (n = 13 464), rheumatic diseases (n = 444 199), juvenile idiopathic arthritis (JIA, n = 15 872), gout (n = 69  374), systemic lupus erythematosus (SLE, n = 3094), ankylosing spondylitis (n = 75 130), primary biliary cholangitis (PBC, n = 11 375) and primary Sjögren's syndrome (n = 95 046). Three MR methods were used in the analysis based on different heterogeneity and pleiotropy using the Bonferroni correction.

RESULTS

The results revealed a causality between COVID-19 and rheumatic diseases with an odds ratio (OR) of 1.010 (95% confidence interval [CI], 1.006-1.013; P = .014). In addition, we observed that COVID-19 was causally associated with an increased risk of JIA (OR 1.517; 95%CI, 1.144-2.011; P = .004), PBC (OR 1.370; 95%CI, 1.149-1.635; P = .005), but a decreased risk of SLE (OR 0.732; 95%CI, 0.590-0.908; P = .004). Using MR, 8 SNPs were identified to associate with COVID-19 and recognized as significant variables. None of them were previously reported in any other diseases.

CONCLUSIONS

This is the first study to use MR to explore the impact of COVID-19 on rheumatic diseases. From a genetic perspective, we found that COVID-19 could increase the risk of rheumatic diseases, such as PBC and JIA, but decrease that of SLE, thereby suggesting a potential surge in the disease burden of PBC and JIA following the COVID-19 pandemic.