2019-nCoV (Wuhan virus), a novel Coronavirus: human-to-human transmission, travel-related cases, and vaccine readiness

A comprehensive review on nutritional interventions and nutritive elements: Strengthening immunity for effective defense mechanism during pandemic

The pandemic has brought attention to the importance of a healthy immune system in preventing infectious diseases. In this in-depth review, the process by which nutritional interventions and fundamental nutrients affect immune function has been discussed with the goal of enhancing the body's natural defenses against viral infections. We explored the complex interplay between diet and immunology, highlighting the essential nutrients, vitamins, minerals, and bioactive substances that are crucial for enhancing immune response. We also investigated the effect of dietary patterns and supplementation methods on immune function. We assessed the effectiveness and potential mechanisms of action of various nutritional therapies in modifying immune responses through a thorough examination of scientific literature. Additionally, we go through the significance of individualized nutrition and highlight possible factors to consider for vulnerable groups, such as the elderly and people with chronic conditions. This review attempts to provide a thorough understanding of the role of diet in boosting immunity by synthesizing available research. It also offers insights into practical methods for enhancing the immune function during the current epidemic and in the future.

Nigella sativa and its chemical constituents: pre-clinical and clinical evidence for their potential anti-SARS-CoV-2 effects

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused over 500 million reported cases of COVID-19 worldwide with relatively high morbidity and mortality. Although global vaccination drive has helped control the pandemic, the newer variant of the virus still holds the world in ransom. Several medicinal herbs with antiviral properties have been reported, and one such promising herb is Nigella sativa (NS). Recent molecular docking, pre-clinical, and clinical studies have shown that NS extracts may have the potential to prevent the entry of coronaviruses into the host cell as well as to treat and manage COVID-19 symptoms. Several active compounds from NS, such as nigelledine, α-hederin, dithymoquinone (DTQ), and thymoquinone (TQ), have been proposed as excellent ligands to target angiotensin-converting enzyme 2 (ACE2 receptors) and other targets on host cells as well as the spike protein (S protein) on SARS-CoV-2. By binding to these target proteins, these ligands could potentially prevent the binding between ACE2 and S protein. Though several articles have been published on the promising therapeutic role of NS and its constituents against SARS-CoV-2 infection, in this review, we consolidate the published information on NS and SARS-CoV-2, focusing on pre-clinical in silico studies as well as clinical trials reported between 2012 and 2023.

Applying the digital data and the bioinformatics tools in SARS-CoV-2 research

Bioinformatics has been playing a crucial role in the scientific progress to fight against the pandemic of the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The advances in novel algorithms, mega data technology, artificial intelligence and deep learning assisted the development of novel bioinformatics tools to analyze daily increasing SARS-CoV-2 data in the past years. These tools were applied in genomic analyses, evolutionary tracking, epidemiological analyses, protein structure interpretation, studies in virus-host interaction and clinical performance. To promote the in-silico analysis in the future, we conducted a review which summarized the databases, web services and software applied in SARS-CoV-2 research. Those digital resources applied in SARS-CoV-2 research may also potentially contribute to the research in other coronavirus and non-coronavirus viruses.

The NSP4 T492I mutation increases SARS-CoV-2 infectivity by altering non-structural protein cleavage

The historically dominant SARS-CoV-2 Delta variant and the currently dominant Omicron variants carry a T492I substitution within the non-structural protein 4 (NSP4). Based on in silico analyses, we hypothesized that the T492I mutation increases viral transmissibility and adaptability, which we confirmed with competition experiments in hamster and human airway tissue culture models. Furthermore, we showed that the T492I mutation increases the replication capacity and infectiveness of the virus and improves its ability to evade host immune responses. Mechanistically, the T492I mutation increases the cleavage efficiency of the viral main protease NSP5 by enhancing enzyme-substrate binding, which increases production of nearly all non-structural proteins processed by NSP5. Importantly, the T492I mutation suppresses viral-RNA-associated chemokine production in monocytic macrophages, which may contribute to the attenuated pathogenicity of Omicron variants. Our results highlight the importance of NSP4 adaptation in the evolutionary dynamics of SARS-CoV-2.

Efficacy and safety of integrated traditional Chinese and Western medicine against COVID-19: A systematic review and meta-analysis

Although plenty of clinical trials have confirmed the efficacy and safety of integrated traditional Chinese and Western medicine (ITCWM) against COVID-19, the role of ITCWM remains controversial. So we conducted a systematic review and meta-analysis of published studies in eight major databases that report the outcomes of interest in COVID-19 patients receiving ITCWM. RevMan5.4 software was used for meta-analysis, while the quality of RCTs was assessed by the Cochrane risk of bias tool and the retrospective studies were assessed by Newcastle-Ottawa Scale. Eventually, a total of 53 studies with 5425 COVID-19 patients was identified. The meta-analysis results showed that ITCWM was significantly better than western medicine treatment (WMT) alone in the percentage of cases changing to severe/critical [RR = 0.40, 95%CI (0.33, 0.49), p < .00001, I2  = 10%], overall clinical effectiveness [RR = 1.26, 95% CI (1.18, 1.35), p < .00001, I2  = 50%], time to defervescencer [MD = -1.45, 95% CI (-1.82, -1.07), p < .00001, I2  = 83%], disappearing time of cough [MD = -2.11, 95% CI (-2.98, -1.25), p < .00001, I2  = 93%], time of RT-PCR negativity [MD = -3.35, 95% CI (-4.74, -1.95), p < .00001, I2  = 92%], length of hospital stay [MD = -4.05, 95% CI (-5.24, -2.85), p < .00001, I2  = 91%], improvement in CT scan [RR = 1.22, 95% CI (1.17, 1.28), p < .00001, I2  = 46%], TCM syndrome score [MD = -3.95, 95% CI (-5.07, -2.82), p < .00001, I2  = 92%], disappearance rate of fever [RR = 1.23, 95% CI (1.10, 1.38), p < .00001, I2  = 85%], disappearance rate of cough [RR = 1.43, 95% CI (1.25, 1.63), p < .00001, I2  = 60%], level of CRP [MD = -9.23, 95% CI (-10.94, -7.52), p < .00001, I2  = 97%], and WBC [MD = -9.23, 95% CI (-10.94, -7.52), p < .00001, I2  = 97%]. There is no significant difference between ITCWM and WMT in the adverse reaction rate [RR = 0.85, 95% CI(0.71, 1.03), p = .10, I2  = 25%]. Our results showed evidence of clinical efficacy and safety benefit in COVID-19 patients treated with ITCWM. In spite of some limitations, the rapidly developing global pandemic warrants further high-quality and multicenter clinical studies to confirm the contribution of ITCWM.

Efficacy of Dexamethasone and Methylprednisolone in Hospitalization Outcomes of COVID-19 Patients: A Comparative Retrospective Study

Background: Control of the COVID-19 pandemic, its treatment, and prevention of mortality and morbidity have been the main focus of researchers over the past two years. Due to disagreement on the usefulness of different corticosteroids in the treatment of COVID-19, this work compared the efficacy of dexamethasone and methylprednisolone in the treatment outcomes of intensive critical care (ICU) patients. Methods: The present retrospective cohort study examined clinical records of 105 COVID-19 patients hospitalized in the ICUs of Firoozabadi Hospital in 2021. Clinical outcomes, including the length of hospital stay, the need for a ventilator, and mortality, were compared between patients who received either dexamethasone (DXM) or methylprednisolone (MP). Data were analyzed by SPSS V.20 software at P < 0.05 as statistical significance. Results: The mean ± SD ages of the patients in the DXM and MP groups were 58.82 ± 19.29 and 60.66 ± 14.17 years, respectively, without a statistically significant difference (P > 0.05). The mean duration of hospitalization was 8.14 ± 4.36 days in the DXM group and 6.80 ± 3.34 days in the MP group (P = 0.295). Also, 19 (33.3%) cases in the DXM group an, 19 (39.6%) in the MP group needed mechanical ventilation during hospitalization (P = 0.546). Finally, 30 (52.6%) patients in the DXM group and 27 (56.2%) in the MP group died. Conclusions: The findings indicated no significant difference in the mean duration of hospitalization, the need for a ventilator, and mortality in COVID-19 ICU patients treated with methylprednisolone or dexamethasone. There is a need to perform meta-analyses owing to conflicting results regarding the effects of different corticosteroids on the COVID-19 course.

Strain Variation Based on Spike Glycoprotein Gene of SARS-CoV-2 in Kuwait from 2020 to 2021

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19), which was first identified in Wuhan, China, in December 2019. With the global transmission of the virus, many SARS-CoV-2 variants have emerged due to the alterations of the spike glycoprotein. Therefore, the S glycoprotein encoding gene has widely been used for the molecular analysis of SARS-Co-2 due to its features affecting antigenicity and immunogenicity. We analyzed the S gene sequences of 35 SARS-CoV-2 isolates in Kuwait from March 2020 to February 2021 using the Sanger method and MinION nanopore technology to confirm novel nucleotide alterations. Our results show that the Kuwaiti strains from clade 19A and B were the dominant variants early in the pandemic, while clade 20I (Alpha, V1) was the dominant variant from February 2021 onward. Besides the known mutations, 21 nucleotide deletions in the S glycoprotein in one Kuwaiti strain were detected, which might reveal a recombinant SARS-CoV-2 with the defective viral genome (DVG). This study emphasizes the importance of closely perceiving the emerging clades with these mutations during this continuous pandemic as some may influence the specificity of diagnostic tests, such as RT-PCR and even vaccine design directing these positions.

Longitudinal determination of BNT162b2 vaccine induced strongly binding SARS-CoV-2 IgG antibodies in a cohort of Romanian healthcare workers

Mass vaccination against the disease caused by the novel coronavirus (COVID-19) was a crucial step in slowing the spread of SARS-CoV-2 in 2021. Even in the face of new variants, it still remains extremely important for reducing hospitalizations and COVID-19 deaths. In order to better understand the short- and long-term dynamics of humoral immune response, we present a longitudinal analysis of post-vaccination IgG levels in a cohort of 166 Romanian healthcare workers vaccinated with BNT162b2 with weekly follow-up until 35 days past the first dose and monthly follow-up up to 6 months post-vaccination. A subset of the patients continued with follow-up after 6 months and either received a booster dose or got infected during the Delta wave in Romania. Tests were carried out on 1694 samples using a CE-marked IgG ELISA assay developed in-house, containing S1 and N antigens of the wild type virus.

Participants infected with SARS-CoV-2 before vaccination mount a quick immune response, reaching peak IgG levels two weeks after the first dose, while IgG levels of previously uninfected participants mount gradually, increasing abruptly after the second dose. Overall higher IgG levels are maintained for the previously infected group throughout the six month primary observation period (e.g. 36–65 days after the first dose, the median value in the previously infected group is 5.29 AU/ml, versus 3.58 AU/ml in the infection naïve group, p less than 0.001). The decrease of IgG levels is gradual, with lower median values in the infection naïve cohort even 7–8 months after vaccination, compared to the previously infected cohort (0.7 AU/ml versus 1.29 AU/ml, p = 0.006). Administration of a booster dose yielded higher median IgG antibody levels than post second dose in the infection naïve group and comparable levels in the previously infected group.

Molecular characteristics, immune evasion, and impact of SARS-CoV-2 variants

The persistent COVID-19 pandemic since 2020 has brought an enormous public health burden to the global society and is accompanied by various evolution of the virus genome. The consistently emerging SARS-CoV-2 variants harboring critical mutations impact the molecular characteristics of viral proteins and display heterogeneous behaviors in immune evasion, transmissibility, and the clinical manifestation during infection, which differ each strain and endow them with distinguished features during populational spread. Several SARS-CoV-2 variants, identified as Variants of Concern (VOC) by the World Health Organization, challenged global efforts on COVID-19 control due to the rapid worldwide spread and enhanced immune evasion from current antibodies and vaccines. Moreover, the recent Omicron variant even exacerbated the global anxiety in the continuous pandemic. Its significant evasion from current medical treatment and disease control even highlights the necessity of combinatory investigation of the mutational pattern and influence of the mutations on viral dynamics against populational immunity, which would greatly facilitate drug and vaccine development and benefit the global public health policymaking. Hence in this review, we summarized the molecular characteristics, immune evasion, and impacts of the SARS-CoV-2 variants and focused on the parallel comparison of different variants in mutational profile, transmissibility and tropism alteration, treatment effectiveness, and clinical manifestations, in order to provide a comprehensive landscape for SARS-CoV-2 variant research.

Mental Health Conditions Among E-Learning Students During the COVID-19 Pandemic

Aim

The COVID-19 pandemic has forced the education system to undergo changes, which have also affected universities. E-learning became the main form of education, reducing interpersonal contacts, which could affect the mental wellbeing of students. The aim of this study was to investigate the prevalence of depressive symptoms and the level of perceived stress during e-learning among Polish students and to identify the factors for predicting higher levels of depression symptoms.

Methods

The study included 753 participants with a mean age of 22.47 (±4.02) years. The Perception of Stress Questionnaire (PSQ) and Beck Depression Inventory (BDI-II) were used to measure the severity of stress and level of depression. Furthermore, our own survey was used to assess the impact of e-learning on various aspects of life. To examine how much stress can explain a statistically significant amount of variance in depression, three-step hierarchical multiple regression was used. In addition, our own questionnaire was used to assess the impact of e-learning on education, social contacts and technical abilities.

Results

A total of 58% of the students characterized by an increased level of stress. 56% show symptoms of depression and 18% of the participants had suicidal thoughts. The most significant predictor of depression is high stress levels and factors related to e-learning: isolation from friends and acquaintances, negative impact on level of knowledge, reduced motivation to learn, and worsening grades. This predictors may explain about 66% of the variance of depression.

Conclusion

Universities should implement interventions and educational programmes, providing ad hoc assistance in the form of individual or group meetings with a psychologist (also in a remote form) and organizing workshops and webinars on strategies for managing stress.

The Negative Impact of Social Media during COVID-19 Pandemic

The coronavirus pandemic is a global pandemic of Coronavirus Disease 2019 (COVID-19) resulting from the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2). Despite its numerous benefits for sharing health information, social media has raised several concerns in terms of posing panic among the general population around the world during the COVID-19 pandemic. The main objective of this study was to investigate the negative impact of social media during the COVID-19 outbreak. A web-based poll was used to collect data from social media users. Snowball sampling was used to acquire information from participants for 1 month, from September 1 to September 30, 2020. To examine the effect of social media on fear among participants, the study employed Cohen’s d statistic, analysis of variance, Chi-squared test, and linear regression analysis. The study results showed that more than three-fourth (73.26%) used Facebook followed by Telegram by 14.49%. Health news was the most frequently seen, read, or heard with 88.20% of the total. Moreover, 86.73% of respondents experienced panic, while only 13.27% was not. Compared to males, females were more likely to follow health news (p < 0.001). The majority of participants reported being psychologically affected, while only a few were physically affected. Females were substantially more affected mentally and reported significantly more fear than males (p < 0.001). The effect of social media panic is associated with participants’ age, and gender at a 5% level of significance. A significant positive link between social media and the diffusion of COVID-19 fear has been shown in this study. According to the result of regression analysis, social media usage has a significant effect on the spread of panic among participants at a 5% level of significance. Study revealed that social media use has a significant impact on the development of panic among people regarding the COVID-19 epidemic, with possibly detrimental psychological and mental health repercussions.This study also discovered a strong correlation between COVID-19 fear and social media. According to the findings, the impact of social media on respondents’ terror levels differs depending on their age and gender. The government should take steps to punish those who spread false information or fake news to the public.

Acute Respiratory Distress Syndrome due to COVID-19 in India and efficacy of Indian Siddha drugs - A Trial of Lopinavir-Ritonavir

Novel coronavirus pneumonia (COVID-19) is a respiratory infection caused by infecting lungs and respiratory pathways which has rapidly spread to 216 countries. It is causing serious harm to the world’s entire population and a huge social burden, which can spread mainly by droplets produced during coughing and sneezing from animal to animal or human to human. There were no drugs or vaccines available as of May 2020. Though the severity and infectious behavior and mortality rate of COVID-19 led to the discovery of various vaccines and drugs that are available to control COVID-19 pandemic. India has two vaccines: Covishield and Covaxin approved by the Government of India on 2nd January 2021. Of this sudden and lethal disease, the traditional Indian siddha medicine was proficient as an alternative source, in performing differentiation with fewer side effects and better ability to prevent and control. In this article, we have comprehensively analyzed the case study and the efficacy of Indian Siddha medicine Kabasura Kudineer chooranam. Naturally occurring Indian Siddha medicinal (Kabasura Kudineer chooranam) compounds and its treatment as prevention measures so as to provide strategy and suggestions for the disease COVID-19 are discussed.

Occurrence and decay of SARS-CoV-2 in community sewage drainage systems

The rapid spread of the coronavirus disease (COVID-19) pandemic in over 200 countries poses a substantial threat to human health. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes COVID-19, can be discharged with feces into the drainage system. However, a comprehensive understanding of the occurrence, presence, and potential transmission of SARS-CoV-2 in sewers, especially in community sewers, is still lacking. This study investigated the virus occurrence by viral nucleic acid testing in vent stacks, septic tanks, and the main sewer outlets of community where confirmed patients had lived during the outbreak of the epidemic in Wuhan, China. The results indicated that the risk of long-term emission of SARS-CoV-2 to the environment via vent stacks of buildings was low after confirmed patients were hospitalized. SARS-CoV-2 were mainly detected in the liquid phase, as opposed to being detected in aerosols, and its RNA in the sewage of septic tanks could be detected for only four days after confirmed patients were hospitalized. The surveillance of SARS-CoV-2 in sewage could be a sensitive indicator for the possible presence of asymptomatic patients in the community, though the viral concentration could be diluted more than 10 times, depending on the sampling site, as indicated by the Escherichia coli (E. coli) test. The comprehensive investigation of the community sewage drainage system is helpful to understand the occurrence characteristics of SARS-CoV-2 in sewage after excretion with feces and the feasibility of sewage surveillance for COVID-19 pandemic monitoring.

Adaptive Evolution of the Fox Coronavirus Based on Genome-Wide Sequence Analysis

Purpose. To report the first complete fox coronavirus (CoV) genome sequence obtained through genome-wide amplifications and to understand the adaptive evolution of fox CoV. Methods. Anal swab samples were collected from 35 foxes to detect the presence of CoV and obtain the virus sequence. Phylogenetic analysis was conducted using MrBayes. The possibility of recombination within these sequences was assessed using GARD. Analysis of the levels of selection pressure experienced by these sequences was assessed using methods on both the PAML and Data Monkey platforms. Results. Of the 35 samples, two were positive, and complete genome sequences for the viruses were obtained. Phylogenetic analysis, using Bayesian methods, of these sequences, together with other CoV sequences, revealed that the fox CoV sequences clustered with canine coronavirus (CCoV) sequences, with sequences from other carnivores more distantly related. In contrast to the feline, ferret and mink CoV sequences that clustered into species-specific clades, the fox CoV fell within the CCoV clade. Minimal evidence for recombination was found among the sequences. A total of 7, 3, 14, and 2 positively selected sites were identified in the M, N, S, and 7B genes, respectively, with 99, 111, and 581 negatively selected sites identified in M, N, and S genes, respectively. Conclusion. The complete genome sequence of fox CoV has been obtained for the first time. The results suggest that the genome sequence of fox CoV may have experienced adaptive evolution in the genes replication, entry, and virulence. The number of sites in each gene that experienced negative selection is far greater than the number that underwent positive selection, suggesting that most of the sequence is highly conserved and important for viral survive. However, positive selection at a few sites likely aided these viruses to adapt to new environments.

Recombinant subunits of SARS‐CoV‐2 spike protein as vaccine candidates to elicit neutralizing antibodies

Objectives

The spike protein has been reported as one of the most critical targets for vaccine design strategies against the SARS‐CoV‐2 infection. Hence, we have designed, produced, and evaluated the potential use of three truncated recombinant proteins derived from spike protein as vaccine candidates capable of neutralizing SARS‐CoV‐2 virus.

Methods

In silico tools were used to design spike‐based subunit recombinant proteins (RBD (P₁), fusion peptide (P₂), and S1/S2 cleavage site (P₃)). These proteins were checked for their ability to be identified by the anti‐SARS‐CoV‐2 antibodies by exposing them to COVID‐19 serum samples. The proteins were also injected into mice and rabbit, and the antibody titers were measured for 390 days to assess their neutralization efficiency.

Results

The antibodies that existed in the serum of COVID‐19 patients were identified by designed proteins. The anti‐spike antibody titer was increased in the animals injected with recombinant proteins. The VNT results revealed that the produced antibodies could neutralize the cultured live virus.

Conclusion

Truncated subunit vaccines could also be considered as robust tools for effective vaccination against COVID‐19. Using a combination of in silico, in vitro, and in vivo experiments, it was shown that the injection of spike‐based truncated recombinant proteins could stimulate long‐lasting and neutralizing antibody responses.

Mutations and Phylogenetic Analyses of SARS-CoV-2 Among Imported COVID-19 From Abroad in Nanjing, China

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a pandemic and is threatening human health globally. The rapid genome sequencing and bioinformatic analysis of SARS-CoV-2 have become a helpful tool in the battle against the COVID-19. Here, we report the genetic characteristics, variations and phylogenetic analysis of SARS-CoV-2 sequenced from 42 clinical specimens. The complete genomes sequencing of SARS-CoV-2 were performed using Oxford Nanopore sequencing. All genomes accumulated mutations compared to the Wuhan-Hu-1 (GenBank Accession No: MN908947.3). Our data of the 42 whole genomes revealed 16 different lineages. The B.1.1 lineage was the most frequent, and 5, 2, 2, 3, and 1 sequences were classified as lineages of B.1.1.7, B.1.351, P.1, B.1.617.2, and C.37, respectively. A total of 328 nucleotide mutation sites were found in 42 genomes, among which A23403G mutation (D614G amino acid change in the spike protein) was the most common substitution. The phylogenetic trees of 42 SARS-CoV-2 sequences and GISAID-available SARS-CoV-2 sequences were constructed and its taxonomic status was supported. These results will provide scientific basis for tracing the source and prevention and control of SARS-CoV-2 imported from abroad in Nanjing, China.

Seroprevalence of SARS-CoV-2 Antibodies in Employees of Three Hospitals of a Secondary Care Hospital Network in Germany and an Associated Fire Brigade: Results of a Repeated Cross-Sectional Surveillance Study Over 1 Year

Healthcare workers (HCWs) are playing a vital role in the current SARS-CoV-2 pandemic. This study investigated how infection spreads within three local hospitals and an associated fire brigade in Germany by testing employees for the presence of SARS-CoV-2 IgG antibodies over one year. The three observational periods corresponded to the initial three pandemic waves: first wave: June-September 2020, second wave: October 2020-January 2021, and third wave: February-June 2021. We analysed 3285 serum samples of 1842 employees, which represents 65.7% of all employees. Altogether, 13.2% employees were seropositive: 194/1411 HCWs (13.7%) and 49/431 non-HCWs (11.4%) with a clear increase of seroprevalence from the first (1.1%) to the second (13.2%) and third (29.3%) pandemic wave. HCWs presumably had an additional occupational risk for infection in the second and third wave due to an increase of infection pressure with more COVID-19 patients treated, showing possible weak points in the recommended infection prevention strategy.

Analysing lecturers' perceptions on traditional vs. distance learning: A conceptual study of emergency transferring to distance learning during COVID-19 pandemic

In recent years, and also due to the COVID-19 pandemic, education institutions worldwide have changed their education paradigm from a traditional to an online system. These institutions have rapidly accomplished their educational programs and activities by supporting various web applications, allowing the completion of the education process remotely. This motivated us to investigate the general perceptions of the faculty members who are teaching different courses for undergraduate students using the distance education system. The proposed technique is based on the use of advanced analysis methods to test the hypothesis of instructors' perceptions of online teaching effectiveness, compared with traditional teaching, will not be affected by the following eight factors, including gender, academic major, age, academic degree, country of teaching, teaching experience in traditional classes, teaching experience in virtual classes (VCs), and whether or not the department/faculty provided e-learning courses before the COVID-19 pandemic. A total of 187 lecturers from 71 departments in 24 educational institutions located in 11 countries participated in this research. Results indicate that the perceptions of instructors regarding the online teaching system generally do not change based on the studied factors. Furthermore, the quantitative analyses illustrate that no significant differences exist in all dimension scales in terms of gender, major specification, age, country of teaching, and virtual experience. Significant differences are found in the dimension scale of distance education effectiveness in terms of academic degree and the educator status in terms of supporting VCs and traditional experience dimension scales. Additionally, the study provides various recommendations, including that the departments should encourage instructors to positively adapt with online teaching by developing the required skills and knowledge. Moreover, departments and institutions should support the teaching staff with specialized education tools. In addition, instructors should strive to decrease the communication and interaction gap between distance education and traditional in-class teaching.

Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2

Previous work found that the co-occurring mutations R203K/G204R on the SARS-CoV-2 nucleocapsid (N) protein are increasing in frequency among emerging variants of concern or interest. Through a combination of in silico analyses, this study demonstrates that R203K/G204R are adaptive, while large-scale phylogenetic analyses indicate that R203K/G204R associate with the emergence of the high-transmissibility SARS-CoV-2 lineage B.1.1.7. Competition experiments suggest that the 203K/204R variants possess a replication advantage over the preceding R203/G204 variants, possibly related to ribonucleocapsid (RNP) assembly. Moreover, the 203K/204R virus shows increased infectivity in human lung cells and hamsters. Accordingly, we observe a positive association between increased COVID-19 severity and sample frequency of 203K/204R. Our work suggests that the 203K/204R mutations contribute to the increased transmission and virulence of select SARS-CoV-2 variants. In addition to mutations in the spike protein, mutations in the nucleocapsid protein are important for viral spreading during the pandemic.

Changes implemented in the work environment of nurses in the COVID-19 pandemic

OBJECTIVE

to describe the changes implemented in the work environment of nurses in university hospitals considering the COVID-19 pandemic.

METHODS

this qualitative and descriptive research was developed from an online survey with 75 nurses from three Brazilian university hospitals. Data processing occurred through textual analysis with the aid of software IRAMUTEQ.

RESULTS

five semantic classes were obtained: Organization of units for exclusive care of patients with COVID-19; Adaptations in the use of personal protective equipment; Physical structure adaptation; Care flow institution; Increased number of beds and training courses. Final considerations: the results show the effort of healthcare and nursing professionals/managers in the development of structural adaptations and reorganizations of care processes, in the hospital context, to respond with quality and efficiency to the demands arising from the COVID-19 pandemic.

Fighting the pandemic with collaboration at heart: Report from cardiologists in a COVID-19-dedicated Portuguese intensive care unit

INTRODUCTION AND OBJECTIVES

The coronavirus disease 2019 (COVID-19) spread quickly around the world. Although mainly a respiratory illness, there is growing interest in non-respiratory manifestations, particularly cardiovascular ones. At our center, mobilization of cardiologists with intensive care training was needed. Our aim is to describe patients with severe COVID-19 admitted to a Portuguese intensive care unit (ICU), the cardiovascular impact of the disease and the experience of cardiologists working in a COVID-19 ICU.

METHODS

Data from adult patients with COVID-19 admitted to the ICU of Centro Hospitalar de Vila Nova de Gaia/Espinho between 16 March 2020 and 21 April 2020 were analyzed retrospectively.

RESULTS

Thirty-five patients were admitted. Mean age was 62.6±6.0 years and 23 (65.7%) were male. Dyslipidemia was the most common cardiovascular risk factor (65.7%, n=23), followed by hypertension (57.1%, n=20). Mean ICU stay time was 15.9±10.0 days. Patients had high rates of mechanical ventilation (88.6%, n=31) and vasopressor support (88.6%, n=31). Low rates of new onset left systolic dysfunction were detected (8.5%, n=2). One patient required venoarterial extra-corporeal membrane oxygenation. Mortality was 25% (n=9). Acute myocardial injury and N-terminal pro-B-type natriuretic peptide (NT-proBNP) elevation was detected in 62.9% (n=22). Patients that died had higher NT-proBNP compared to those discharged alive (p<0.05). Care by cardiologists frequently changed decision making.

CONCLUSIONS

The cardiovascular impact of COVID-19 seems relevant but is still widely unknown. Studies are needed to clarify the role of cardiac markers in COVID-19 prognosis. Multidisciplinary care most likely results in improved patient care.

Knowledge and attitude of dental professionals toward COVID-19 in Riyadh, Saudi Arabia: a cross-sectional survey

Background

Coronavirus disease-2019 (COVID-19) is a life-threatening global pandemic. The dental profession is considered a high-risk group in the transmission of the responsible virus.

Objective

To assess the knowledge and attitude among dental professionals in response to the COVID-19 pandemic.

Methods

We conducted a cross-sectional study of dental graduates, interns, postgraduates, and dental faculty from May to July 2020. A standardized questionnaire was developed to assess knowledge and attitude of 650 participants. The questionnaire comprised 14 questions to assess general knowledge about COVID-19, 11 questions regarding knowledge about prevention of COVID-19 in dental practice, and 10 questions regarding the attitude toward preventing COVID-19.

Results

Among the study population, only 376 (57.8%) knew the causative virus for COVID-19. Only 425 (65.3%) knew about rinsing the mouth with an antimicrobial solution or 1% hydrogen peroxide before the dental procedure. Regarding the hand hygiene guidelines, 357 (54.9%) had knowledge of the Centers for Disease Control and Prevention (CDC) and 377 (58.0%) about World Health Organization (WHO) guidelines. At the time of our survey, 72% of the participants showed sufficient knowledge, while 28% had low or insufficient knowledge about COVID-19.

Conclusion

While there was a lack of knowledge among dental professionals in Riyadh, Saudi Arabia about COVID-19, there was an excellent positive attitude toward preventing disease. Greater awareness is needed to control the spread of this disease.

Fighting the pandemic with collaboration at heart: Report from cardiologists in a COVID-19-dedicated Portuguese intensive care unit

INTRODUCTION AND OBJECTIVES

The coronavirus disease 2019 (COVID-19) spread quickly around the world. Although mainly a respiratory illness, there is growing interest in non-respiratory manifestations, particularly cardiovascular ones. At our center, mobilization of cardiologists with intensive care training was needed. Our aim is to describe patients with severe COVID-19 admitted to a Portuguese intensive care unit (ICU), the cardiovascular impact of the disease and the experience of cardiologists working in a COVID-19 ICU.

METHODS

Data from adult patients with COVID-19 admitted to the ICU of Centro Hospitalar de Vila Nova de Gaia/Espinho between 16 March 2020 and 21 April 2020 were analyzed retrospectively.

RESULTS

Thirty-five patients were admitted. Mean age was 62.6±6.0 years and 23 (65.7%) were male. Dyslipidemia was the most common cardiovascular risk factor (65.7%, n=23), followed by hypertension (57.1%, n=20). Mean ICU stay time was 15.9±10.0 days. Patients had high rates of mechanical ventilation (88.6%, n=31) and vasopressor support (88.6%, n=31). Low rates of new onset left systolic dysfunction were detected (8.5%, n=2). One patient required venoarterial extra-corporeal membrane oxygenation. Mortality was 25% (n=9). Acute myocardial injury and N-terminal pro-B-type natriuretic peptide (NT-proBNP) elevation was detected in 62.9% (n=22). Patients that died had higher NT-proBNP compared to those discharged alive (p<0.05). Care by cardiologists frequently changed decision making.

CONCLUSIONS

The cardiovascular impact of COVID-19 seems relevant but is still widely unknown. Studies are needed to clarify the role of cardiac markers in COVID-19 prognosis. Multidisciplinary care most likely results in improved patient care.

Ultra-sensitive and fast optical detection of the spike protein of the SARS-CoV-2 using AgNPs/SiNWs nanohybrid based sensors

Severe acute respiratory syndrome SARS-CoV-2 virus led to notable challenges amongst researchers in view of development of new and fast detecting techniques. In this regard, surface-enhanced Raman spectroscopy (SERS) technique, providing a fingerprint characteristic for each material, would be an interesting approach. The current study encompasses the fabrication of a SERS sensor to study the SARS-CoV-2 S1 (RBD) spike protein of the SARS-CoV-2 virus family. The SERS sensor consists of a silicon nanowires (SiNWs) substrate decorated with plasmonic silver nanoparticles (AgNPs). Both SiNWs fabrication and AgNPs decoration were achieved by a relatively simple wet chemical processing method. The study deliberately projects the factors that influence the growth of silicon nanowires, uniform decoration of AgNPs onto the SiNWs matrix along with detection of Rhodamine-6G (R6G) to optimize the best conditions for enhanced sensing of the spike protein. Increasing the time period of etching process resulted in enhanced SiNWs' length from 0.55 to 7.34 µm. Furthermore, the variation of the immersion time in the decoration process of AgNPs onto SiNWs ensued the optimum time period for the enhancement in the sensitivity of detection. Tremendous increase in sensitivity of R6G detection was perceived on SiNWs etched for 2 min (length=0.90 µm), followed by 30s of immersion time for their optimal decoration by AgNPs. These SiNWs/AgNPs SERS-based sensors were able to detect the spike protein at a concentration down to 9.3 × 10^-12 M. Strong and dominant peaks at 1280, 1404, 1495, 1541 and 1609 cm^-1 were spotted at a fraction of a minute. Moreover, direct, ultra-fast, facile, and affordable optoelectronic SiNWs/AgNPs sensors tuned to function as a biosensor for detecting the spike protein even at a trace level (pico molar concentration). The current findings hold great promise for the utilization of SERS as an innovative approach in the diagnosis domain of infections at very early stages.

Meta-analysis of arbidol versus lopinavir/ritonavir in the treatment of coronavirus disease 2019

Objectives

To systematically evaluate the efficacy and safety of arbidol and lopinavir/ritonavir (LPV/r) in the treatment of coronavirus disease 2019 (COVID‐19) using a meta‐analysis method.

Methods

The China Knowledge Network, VIP database, WanFang database PubMed database, Embase database, and Cochrane Library were searched for a collection of comparative studies on arbidol and lopinavir/ritonavir in the treatment of COVID‐19. Meta‐analysis was used to evaluate the efficacy and safety of Arbidol and lopinavir/ritonavir in the treatment of COVID‐19.

Results

The results of the systematic review indicated that Arbidol had a higher positive‐to‐negative conversion rate of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) nucleic acid on Day 7 (p = 0.03), a higher positive‐to‐negative conversion rate of SARS‐CoV‐2 nucleic acid on Day 14 (p = 0.006), a higher improvement rate of chest computed tomography on Day 14 (p = 0.02), a lower incidence of adverse reactions (p = 0.002) and lower rate of mortality (p = 0.007). There was no difference in the rate of cough disappearance on Day 14 (p = 0.24) or the rate of severe/critical illness (p = 0.07) between the two groups.

Conclusions

Arbidol may be superior to lopinavir/ritonavir in the treatment of COVID‐19. However, due to the small number of included studies and the number of patients, high‐quality multicenter large‐sample randomized double‐blind controlled trials are still needed for verification.

SARS-CoV-2 spillover into hospital outdoor environments

Facing the ongoing coronavirus infectious disease-2019 (COVID-19) pandemic, many studies focus on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in indoor environment, on solid surface or in wastewater. It remains unclear whether SARS-CoV-2 can spill over into outdoor environments and impose transmission risks to surrounding people and communities. In this study, we investigated the presence of SARS-CoV-2 by measuring viral RNA in 118 samples from outdoor environment of three hospitals in Wuhan. We detected SARS-CoV-2 in soils (205-550 copies/g), aerosols (285-1,130 copies/m3) and wastewaters (255-18,744 copies/L) in locations close to hospital departments receiving COVID-19 patients or in wastewater treatment sectors. These findings revealed a significant viral spillover in hospital outdoor environments that was possibly caused by respiratory droplets from patients or aerosolized particles from wastewater containing SARS-CoV-2. In contrast, SARS-CoV-2 was not detected in other areas or on surfaces with regular implemented disinfection. Soils may behave as viral warehouse through deposition and serve as a secondary source spreading SARS-CoV-2 for a prolonged time. For the first time, our findings demonstrate that there are high-risk areas out of expectation in hospital outdoor environments to spread SARS-CoV-2, calling for sealing of wastewater treatment unit and complete sanitation to prevent COVID-19 transmission risks.

COVID-19 Risk Mapping with Considering Socio-Economic Criteria Using Machine Learning Algorithms

The reduction of population concentration in some urban land uses is one way to prevent and reduce the spread of COVID-19 disease. Therefore, the objective of this study is to prepare the risk mapping of COVID-19 in Tehran, Iran, using machine learning algorithms according to socio-economic criteria of land use. Initially, a spatial database was created using 2282 locations of patients with COVID-19 from 2 February 2020 to 21 March 2020 and eight socio-economic land uses affecting the disease-public transport stations, supermarkets, banks, automated teller machines (ATMs), bakeries, pharmacies, fuel stations, and hospitals. The modeling was performed using three machine learning algorithms that included random forest (RF), adaptive neuro-fuzzy inference system (ANFIS), and logistic regression (LR). Feature selection was performed using the OneR method, and the correlation between land uses was obtained using the Pearson coefficient. We deployed 70% and 30% of COVID-19 patient locations for modeling and validation, respectively. The results of the receiver operating characteristic (ROC) curve and the area under the curve (AUC) showed that the RF algorithm, which had a value of 0.803, had the highest modeling accuracy, which was followed by the ANFIS algorithm with a value of 0.758 and the LR algorithm with a value of 0.747. The results showed that the central and the eastern regions of Tehran are more at risk. Public transportation stations and pharmacies were the most correlated with the location of COVID-19 patients in Tehran, according to the results of the OneR technique, RF, and LR algorithms. The results of the Pearson correlation showed that pharmacies and banks are the most incompatible in distribution, and the density of these land uses in Tehran has caused the prevalence of COVID-19.

Evolutionary trajectory of SARS-CoV-2 and emerging variants

The emergence of a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and more recently, the independent evolution of multiple SARS-CoV-2 variants has generated renewed interest in virus evolution and cross-species transmission. While all known human coronaviruses (HCoVs) are speculated to have originated in animals, very little is known about their evolutionary history and factors that enable some CoVs to co-exist with humans as low pathogenic and endemic infections (HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1), while others, such as SARS-CoV, MERS-CoV and SARS-CoV-2 have evolved to cause severe disease. In this review, we highlight the origins of all known HCoVs and map positively selected for mutations within HCoV proteins to discuss the evolutionary trajectory of SARS-CoV-2. Furthermore, we discuss emerging mutations within SARS-CoV-2 and variants of concern (VOC), along with highlighting the demonstrated or speculated impact of these mutations on virus transmission, pathogenicity, and neutralization by natural or vaccine-mediated immunity.

Contribution of SARS-CoV-2 Accessory Proteins to Viral Pathogenicity in K18 Human ACE2 Transgenic Mice

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the viral pathogen responsible for the current coronavirus disease 2019 (COVID-19) pandemic. As of 19 May 2021, John Hopkins University’s COVID-19 tracking platform reported 3.3 million deaths associated with SARS-CoV-2 infection. Currently, the World Health Organization has granted emergency use listing (EUL) to six COVID-19 vaccine candidates. However, much of the pathogenesis observed during SARS-CoV-2 infection remains elusive. To gain insight into the contribution of individual accessory open reading frame (ORF) proteins in SARS-CoV-2 pathogenesis, we used our recently described reverse-genetics system approach to successfully engineer recombinant SARS-CoV-2 (rSARS-CoV-2) constructs; we removed individual viral ORF3a, −6, −7a, −7b, and −8 proteins from them, and we characterized the resulting recombinant viruses in vitro and in vivo. Our results indicate differences in plaque morphology, with ORF-deficient (ΔORF) viruses producing smaller plaques than those of the wild type (rSARS-CoV-2/WT). However, growth kinetics of ΔORF viruses were like those of rSARS-CoV-2/WT. Interestingly, infection of K18 human angiotensin-converting enzyme 2 (hACE2) transgenic mice with the ΔORF rSARS-CoV-2s identified ORF3a and ORF6 as the major contributors of viral pathogenesis, while ΔORF7a, ΔORF7b, and ΔORF8 rSARS-CoV-2s induced pathology comparable to that of rSARS-CoV-2/WT. This study demonstrates the robustness of our reverse-genetics system to generate rSARS-CoV-2 constructs and the major role for ORF3a and ORF6 in viral pathogenesis, providing important information for the generation of attenuated forms of SARS-CoV-2 for their implementation as live attenuated vaccines for the treatment of SARS-CoV-2 infection and associated COVID-19.

IMPORTANCE Despite great efforts put forward worldwide to combat the current coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to be a human health and socioeconomic threat. Insights into the pathogenesis of SARS-CoV-2 and the contribution of viral proteins to disease outcome remain elusive. Our study aims (i) to determine the contribution of SARS-CoV-2 accessory open reading frame (ORF) proteins to viral pathogenesis and disease outcome and (ii) to develop a synergistic platform combining our robust reverse-genetics system to generate recombinant SARS-CoV-2 constructs with a validated rodent model of infection and disease. We demonstrate that SARS-CoV-2 ORF3a and ORF6 contribute to lung pathology and ultimately disease outcome in K18 hACE2 transgenic mice, while ORF7a, ORF7b, and ORF8 have little impact on disease outcome. Moreover, our combinatory platform serves as a foundation for generating attenuated forms of the virus to develop live attenuated vaccines for the treatment of SARS-CoV-2.

A meta-analysis for Lianhua Qingwen on the treatment of Coronavirus disease 2019 (COVID-19)

Background

Traditional Chinese medicine (TCM) has been proven to played a great important role on the treatment of COVID-19. As one of the drugs recommended in Chinese guidelines, Lianhua Qingwen Granules or Capsules (LQ) are widely used.This systematic review and meta-analysis amis to evaluate the clinical efficacy of LQ on the treatment of COVID-19.

Methods

Seven databases (PubMed, EMBASE, CENTRAL, CNKI, VIP, CBM and Wanfang) were searched to include all appropriate clinical trials that explore the efficacy of LQ on the treatment of COVID-19.

Result

A total of 3 trials including 245 COVID-19 patients were eventually enrolled.Compared with the control group,the LQ group showed great significant difference on reducing the rate of clinical change to severe or critical condition[RR = 0.38, 95 %CI (0.17,0.85), P < 0.05]and the fever time (SMD =-0.57,95 %CI (-0.96,-0.17), P<0.05),as well as the significant improvement on the disappearance rate of the clinical symptoms: fever [RR = 1.36,95 %CI (1.14,1.61), P < 0.05],cough[RR = 1.99,95 %CI (1.39,2.86), P < 0.05],fatigue[RR = 1.52,95 %CI (1.15,2.01), P < 0.05] and anhelation [RR = 4.18,95 %CI (1.99,8.81), P < 0.05], but no significance on expectoration[RR = 2.46,95 %CI (0.81,7.51), P < 0.05].

Conclusion

The clinical application of LQ on the treatment of COVID-19 has significant efficacy in improving clinical symptoms and reducing the rate of clinical change to severe or critical condition. Nevertheless, due to the limited quantity and quality of the included studies, more and higher quality trials with more observational indicators are expected to be published.

Integrating Proteomics for Facilitating Drug Identification and Repurposing During an Emerging Virus Pandemic

The coronavirus disease 2019 (COVID-19) pandemic has disrupted global healthcare and economic systems throughout 2020 with no clear end in sight. While the pandemic continues to have deleterious effects across the globe, mechanisms for disrupting disease transmission have relied on behavioral controls (e.g., social distancing, masks, and hygiene) as there are currently no vaccines approved for use and limited therapeutic options. As this pandemic has demonstrated our vulnerability to newly emerging viruses, there has been strong interest in utilizing proteomics approaches to identify targets for repurposed drugs as novel therapeutic candidates that could be fast-tracked for human use. Building on a previous discussion on the combination of proteomics technologies with clinical data for combating emerging viruses, we discuss how these technologies are being employed for COVID-19 and the current state of knowledge regarding repurposed drugs in these efforts.

COVID-19: Hotspot hospital?- seroprevalence of SARS-CoV-2 antibodies in hospital employees in a secondary care hospital network in Germany: Intermediate results of a prospective surveillance study

Purpose

The objective of the ongoing study was to investigate how SARS-CoV-2 infection spread within two hospitals in North Rhine-Westphalia, Germany by testing the employees working in high-risk, intermediate-risk and low-risk-areas for the presence of SARS-CoV-2 IgG antibodies. Presented intermediate results evaluate the first infection period until the end of September 2020.

Methods

The study “COVID-19: Hotspot hospital?- Seroprevalence of SARS-CoV-2 antibodies in hospital employees in a secondary care hospital network in Germany " is a prospective, single centre observational cohort study conducted at the St. Vincenz Hospital Datteln with 316 beds. The presented data include one other hospital: St. Laurentius Stift Waltrop, Germany with 172 beds.

Results

Between June 2020 and September 2020 we analyzed serum samples of 907 employees which represents 62.1% of all employees. Thirteen employees (1.4%), respectively 13/696 healthcare workers (HCWs) (1.9%) had detectable SARS-CoV-2 IgG antibodies. Among them, 4 (30.8%) were aware of COVID-19 exposure, and 5 (38.5%) reported clinical symptoms. HCWs working in high-risk areas had a seroprevalence rate of 1.6% (1/64), HCWs working in intermediate-risk area 1.7% (11/632) and 0.5% employees (1/211) in low-risk areas with no contact to patients were seropositive.

Conclusion

Even if we treated COVID-19 positive patients, we found no clear evidence that infection was transmitted to HCWs in contact to these patients. As knowledge about SARS-CoV-2 transmission evolves, the concept of infection prevention must be continuously reviewed and adapted as needed to keep hospitals a safe place.

The Anti-Viral and Anti-Inflammatory Properties of Edible Bird's Nest in Influenza and Coronavirus Infections: From Pre-Clinical to Potential Clinical Application

Edible bird's nest (BN) is a Chinese traditional medicine with innumerable health benefits, including anti-viral, anti-inflammatory, neuroprotective, and immunomodulatory effects. A small number of studies have reported the anti-viral effects of EBN against influenza infections using in vitro and in vivo models, highlighting the importance of sialic acid and thymol derivatives in their therapeutic effects. At present, studies have reported that EBN suppresses the replicated virus from exiting the host cells, reduces the viral replication, endosomal trafficking of the virus, intracellular viral autophagy process, secretion of pro-inflammatory cytokines, reorient the actin cytoskeleton of the infected cells, and increase the lysosomal degradation of viral materials. In other models of disease, EBN attenuates oxidative stress-induced cellular apoptosis, enhances proliferation and activation of B-cells and their antibody secretion. Given the sum of its therapeutic actions, EBN appears to be a candidate that is worth further exploring for its protective effects against diseases transmitted through air droplets. At present, anti-viral drugs are employed as the first-line defense against respiratory viral infections, unless vaccines are available for the specific pathogens. In patients with severe symptoms due to exacerbated cytokine secretion, anti-inflammatory agents are applied. Treatment efficacy varies across the patients, and in times of a pandemic like COVID-19, many of the drugs are still at the experimental stage. In this review, we present a comprehensive overview of anti-viral and anti-inflammatory effects of EBN, chemical constituents from various EBN preparation techniques, and drugs currently used to treat influenza and novel coronavirus infections. We also aim to review the pathogenesis of influenza A and coronavirus, and the potential of EBN in their clinical application. We also describe the current literature in human consumption of EBN, known allergenic or contaminant presence, and the focus of future direction on how these can be addressed to further improve EBN for potential clinical application.

A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics

Coronavirus disease (COVID-19) rapidly expands to a global pandemic and its impact on public health varies from country to country. It is caused by a new virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It is imperative for relapsing current antiviral therapeutics owing to randomized genetic drift in global SARS-CoV-2 isolates. A molecular mechanism behind the emerging genomic variants is not yet understood for the prioritization of selective antivirals. The present computational study was aimed to repurpose existing antivirals for Indian SARS-CoV-2 isolates by uncovering a hijack mechanism based on structural and functional characteristics of protein variants. Forty-one protein mutations were identified in 12 Indian SARS-CoV-2 isolates by analysis of genome variations across 460 genome sequences obtained from 30 geographic sites in India. Two unique mutations such as W6152R and N5928H found in exonuclease of Surat (GBRC275b) and Gandhinagar (GBRC239) isolates. We report for the first time the impact of folding rate on stabilizing/retaining a sequence-structure-function-virulence link of emerging protein variants leading to accommodate hijack ability from current antivirals. Binding affinity analysis revealed the effect of point mutations on virus infectivity and the drug-escaping efficiency of Indian isolates. Emodin and artinemol suggested herein as repurposable antivirals for the treatment of COVID-19 patients infected with Indian isolates. Our study concludes that a protein folding rate is a key structural and evolutionary determinant to enhance the receptor-binding specificity and ensure hijack ability from the prevalent antiviral therapeutics.

Prevalence and Risk Factors for Anxiety and Depression in Patients With COVID-19 in Wuhan, China

OBJECTIVE

Infectious diseases can cause psychological changes in patients. This study aimed to evaluate the prevalence and related risk factors for anxiety and depression in patients with COVID-19.

METHODS

A cross-sectional study was performed on patients with COVID-19 admitted to the Sino-French New City branch of Wuhan Tongji Hospital from January to February 2020. The Zung Self-Rating Anxiety and Depression Scales were used to evaluate the prevalence of anxiety and depression. Demographic, clinical, and sociological data were also collected. Multivariable logistic regression analysis was used to identify independent risk factors of anxiety and depression in patients with COVID-19.

RESULTS

In the current study, 183 patients were enrolled (mean age = 53 ± 9 years; 41.1% women). The prevalences of anxiety and depression were 56.3% and 39.3%, respectively. Logistic regression analysis revealed that older age, female sex, being divorced or widowed, COVID-19 disease duration, renal disease, and depression were identified as independent risk factors for anxiety in patients with COVID-19. Factors that were associated with depression were female sex, being widowed, COVID-19 disease duration, and anxiety.

CONCLUSIONS

This study demonstrates a high prevalence of anxiety and depression in patients with COVID-19 at the peak of the epidemic in Wuhan, China. The identification of demographic, clinical, and social factors may help identify health care professionals to provide psychological care as part of treatment for patients with COVID-19 and other life-threatening infectious diseases.

Biosensors promising bio-device for pandemic screening "COVID-19"

Undoubtedly, the coronavirus pandemic is one of the most influential events not only in medicine but also in the economic field in the world. Rapid transmission and high mortality rates, as well as prolonged and asymptomatic communal periods, are the most important reasons for the global panic due to coronavirus. Since coronavirus treatment and specific vaccines are not yet available, early detection of the virus is critical. A rapid and accurate diagnosis can play a crucial role in the treatment and control of the COVID 19 disease. Serological, ELISA, and molecular-based tests, including PCR and RT-PCR, are among the most important routine methods for detecting coronaviruses. False-positive/negative results, low sensitivity and specificity, and the need for advanced equipment are among the disadvantages and problems of routine methods. To eliminate the drawbacks of routine methods, new technologies are being developed. Biosensors are one of the most important ones. This paper is a summary of the up-to-date states of innovative bio-sensing tools for the ultrasensitive detection of coronaviruses (COVID 19) with encouraging uses for future challenges in disease diagnosis.

Research on International Cooperative Governance of the COVID-19

Since the first case of the novel coronavirus (SARS-CoV-2) was reported in Wuhan, China, in December 2019, the coronavirus disease (COVID-19) has quickly spread to all the corners of the world. Amid the global public health threats posed by the COVID-19 pandemic, active cooperative governance has gradually emerged as the most powerful weapon against its spread. To facilitate international cooperation for pandemic governance, this paper applied the evolutionary game theory to analyze the factors influencing active cooperative governance and, based on the results, proposed a series of recommendations for promoting international cooperation. (1) leveraging the role of international organizations to reduce the cost of realizing the strategy of active cooperative governance, (2) promoting the international exchange of related experiences to lower the cost of active pandemic governance, (3) sustaining productive and daily activities during the pandemic in a classified and hierarchical manner to reduce the economic loss incurred by active pandemic governance, and (4) optimizing the incentive measures of international organizations to facilitate the selection of active cooperative governance. Finally, from the four aspects of resource management of pandemic treatment, supply management of living materials, population flow cooperation management, and governance fund cooperation management, this paper gives the path of international pandemic cooperative governance.

Nurse Leaders Advocate for Nurses Across a Health Care System: COVID-19

The COVID-19 pandemic emphasizes the importance of nursing care globally. Nurses are the frontline staff in the care of individuals stricken with this highly infectious and deadly illness. Nurse leaders must advocate for nursing staff when staff are immersed in often overwhelming conditions. Through a case study, this article outlines how one healthcare system's Chief Nursing Officer council worked collaboratively, jointly and with the Emergency Incident Command Structure, to operationalize CDC guidelines and support, protect, educate, and empower staff. These initiatives resulted in creative solutions, technological advances for the system, and nursing staff and leaders rising to the challenge.

Bovine Coronavirus and the Associated Diseases

Coronaviruses (CoVs) possess the largest and most complex RNA genome (up to 32 kb) that encodes for 16 non-structural proteins regulating RNA synthesis and modification. Coronaviruses are known to infect a wide range of mammalian and avian species causing remarkably diverse disease syndromes. Variable tissue tropism and the ability to easily cross interspecies barriers are the well-known characteristics of certain CoVs. The 21st century epidemics of severe acute respiratory CoV (SARS-CoV), Middle East respiratory CoV and the ongoing SARS-CoV-2 pandemic further highlight these characteristics and emphasize the relevance of CoVs to the global public health. Bovine CoVs (BCoVs) are betacoronaviruses associated with neonatal calf diarrhea, and with winter dysentery and shipping fever in older cattle. Of interest, no distinct genetic or antigenic markers have been identified in BCoVs associated with these distinct clinical syndromes. In contrast, like other CoVs, BCoVs exist as quasispecies. Besides cattle, BCoVs and bovine-like CoVs were identified in various domestic and wild ruminant species (water buffalo, sheep, goat, dromedary camel, llama, alpaca, deer, wild cattle, antelopes, giraffes, and wild goats), dogs and humans. Surprisingly, bovine-like CoVs also cannot be reliably distinguished from BCoVs using comparative genomics. Additionally, there are historical examples of zoonotic transmission of BCoVs. This article will discuss BCoV pathogenesis, epidemiology, interspecies transmission, immune responses, vaccines, and diagnostics.

MCCS: a novel recognition pattern-based method for fast track discovery of anti-SARS-CoV-2 drugs

Given the scale and rapid spread of the coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, or 2019-nCoV), there is an urgent need to identify therapeutics that are effective against COVID-19 before vaccines are available. Since the current rate of SARS-CoV-2 knowledge acquisition via traditional research methods is not sufficient to match the rapid spread of the virus, novel strategies of drug discovery for SARS-CoV-2 infection are required. Structure-based virtual screening for example relies primarily on docking scores and does not take the importance of key residues into consideration, which may lead to a significantly higher incidence rate of false-positive results. Our novel in silico approach, which overcomes these limitations, can be utilized to quickly evaluate FDA-approved drugs for repurposing and combination, as well as designing new chemical agents with therapeutic potential for COVID-19. As a result, anti-HIV or antiviral drugs (lopinavir, tenofovir disoproxil, fosamprenavir and ganciclovir), antiflu drugs (peramivir and zanamivir) and an anti-HCV drug (sofosbuvir) are predicted to bind to 3CLPro in SARS-CoV-2 with therapeutic potential for COVID-19 infection by our new protocol. In addition, we also propose three antidiabetic drugs (acarbose, glyburide and tolazamide) for the potential treatment of COVID-19. Finally, we apply our new virus chemogenomics knowledgebase platform with the integrated machine-learning computing algorithms to identify the potential drug combinations (e.g. remdesivir+chloroquine), which are congruent with ongoing clinical trials. In addition, another 10 compounds from CAS COVID-19 antiviral candidate compounds dataset are also suggested by Molecular Complex Characterizing System with potential treatment for COVID-19. Our work provides a novel strategy for the repurposing and combinations of drugs in the market and for prediction of chemical candidates with anti-COVID-19 potential.

Management Challenges in Chronic Obstructive Pulmonary Disease in the COVID-19 Pandemic: Telehealth and Virtual Reality

For the treatment of chronic obstructive pulmonary disease (COPD), early diagnosis and unconditionally correct management at the initial stage of the disease are very important when the symptoms are not yet too worrying. In this way, the progress of the disease can be slowed down, as can the occurrence of late, life-threatening symptoms. Pulmonary rehabilitation is an essential component of the management of COPD. The selection of appropriate exercises, which are determined during the classification of patients into a suitable improvement program, is of key importance in the process of rehabilitation. The coronavirus disease 2019 (COVID-19) pandemic has resulted in major limitations to public health care. Health systems were largely unprepared for an outbreak of this magnitude. Searching for new, attractive technologies that help patients with chronic diseases seems to be justified. This may be driven by telehealth platforms, likewise with the use of virtual reality (VR). Analysis of the available literature indicates promising effectiveness, high patient acceptance, and high motivations to undertake physical activity with the use of such a solution. Thus, the management of patients with COPD during the COVID-19 pandemic should include options for remote delivery of pulmonary rehabilitation, including home-based, telerehabilitation, and computer-based virtual programs.

A simple, safe and sensitive method for SARS-CoV-2 inactivation and RNA extraction for RT-qPCR

The SARS‐CoV‐2 pandemic has created an urgent need for diagnostic tests to detect viral RNA. Commercial RNA extraction kits are often expensive, in limited supply, and do not always fully inactivate the virus. Together, this calls for the development of safer methods for SARS‐CoV‐2 extraction that utilize readily available reagents and equipment present in most standard laboratories. We optimized and simplified a RNA extraction method combining a high molar acidic guanidinium isothiocyanate (GITC) solution, phenol and chloroform. First, we determined the GITC/RNA dilution thresholds compatible with an efficient two‐step RT‐qPCR for B2M mRNA in nasopharyngeal (NP) or oropharyngeal (OP) swab samples. Second, we optimized a one‐step RT‐qPCR against SARS‐CoV‐2 using NP and OP samples. We furthermore tested a SARS‐CoV‐2 dilution series to determine the detection threshold. The method enables downstream detection of SARS‐CoV‐2 by RT‐qPCR with high sensitivity (~4 viral RNA copies per RT‐qPCR). The protocol is simple, safe, and expands analysis capacity as the inactivated samples can be used in RT‐qPCR detection tests at laboratories not otherwise classified for viral work. The method takes about 30 min from swab to PCR‐ready viral RNA and circumvents the need for commercial RNA purification kits.

A comparative review of pathogenesis and host innate immunity evasion strategies among the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), severe acute respiratory syndrome coronavirus (SARS-CoV) and the Middle East respiratory syndrome coronavirus (MERS-CoV)

COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has put the global public health at its highest threat around the world. Previous epidemic caused by the acute respiratory syndrome coronavirus (SARS-CoV) in 2002 is also considered since both the coronaviruses resulted in the similar clinical complications. The outbreak caused by the Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 had a low rate of disease transmission and death cases. Modes of entry by MERS and SARS coronaviruses are similar to that of SARS-CoV-2, except MERS-CoV utilize different receptor. They all belong to the lineage C of β-coronavirus. Based on the information from the previous reports, the present review is mainly focused on the mechanisms of disease progression by each of these viruses in association to their strategies to escape the host immunity. The viral entry is the first step of pathogenesis associated with attachment of viral spike protein with host receptor help releasing the viral RNA into the host cell. Models of molecular pathogenesis are outlined with virus strategies escaping the host immunity along with the role of various inflammatory cytokines and chemokines in the process. The molecular aspects of pathogenesis have also been discussed.

An Epidemiological Neural Network Exploiting Dynamic Graph Structured Data Applied to the COVID-19 Outbreak

With the recent COVID-19 outbreak, we have assisted to the development of new epidemic models or the application of existing methodologies to predict the virus spread and to analyze how the different lock-down strategies can effectively influence the epidemic diffusion. In this paper, we propose a novel machine learning based framework able to estimate the parameters of any epidemiological model, such as contact rates and recovery rates, based on static and dynamic features of places. In particular, we model mobility data through a graph series whose spatial and temporal features are investigated by combining Graph Convolutional Neural Networks (GCNs) and Long short-term memories (LSTMs) in order to infer the parameters of SIR and SIRD models. We evaluate the proposed approach using data related to the COVID-19 dynamics in Italy and we compare the forecasts of the trained model with available data about the epidemic spread.

Presentation of a developed sub-epidemic model for estimation of the COVID-19 pandemic and assessment of travel-related risks in Iran

The COVID-19 pandemic is one of the contagious diseases involving all the world in 2019-2020. Also, all people are concerned about the future of this catastrophe and how the continuous outbreak can be prevented. Some countries are not successful in controlling the outbreak; therefore, the incidence is observed in several peaks. In this paper, firstly single-peak SIR models are used for historical data. Regarding the SIR model, the termination time of the outbreak should have been in early June 2020. However, several peaks invalidate the results of single-peak models. Therefore, we should present a model to support pandemics with several extrema. In this paper, we presented the generalized logistic growth model (GLM) to estimate sub-epidemic waves of the COVID-19 outbreak in Iran. Therefore, the presented model simulated scenarios of two, three, and four waves in the observed incidence. In the second part of the paper, we assessed travel-related risk in inter-provincial travels in Iran. Moreover, the results of travel-related risk show that typical travel between Tehran and other sites exposed Isfahan, Gilan, Mazandaran, and West Azerbaijan in the higher risk of infection greater than 100 people per day. Therefore, controlling this movement can prevent great numbers of infection, remarkably.

Elevation in viral entry genes and innate immunity compromise underlying increased infectivity and severity of COVID-19 in cancer patients

Multiple studies have reported a doubling in risk of Coronavirus Disease-2019 (COVID-19) among cancer patients. Here, we examine the potential biological rationale behind this recurrent epidemiological observation. By leveraging large-scale genome-wide transcriptional data of normal and malignant tissues from adults and children, we found evidence of increased expression of SARS-CoV-2 viral entry genes in the cancer state, particularly in respiratory, gastrointestinal, and genitourinary tract tissues, with decreased expression in pediatric vs. adult samples. Additionally, by interrogating the temporal effects of radiotherapy on human peripheral blood mononuclear and mucosal cells, we observed important treatment-related alterations in host innate immunity, specifically type I interferon responses. Overall, cancers enhance expression of critical viral entry genes, and innate viral defenses can be dysregulated transiently during radiation treatments. These factors may contribute to the observed increased susceptibility to SARS-CoV-2 entry and severity of COVID-19 in cancer patients.

SARS-CoV-2 spillover transmission due to recombination event

In late 2019, a novel Coronavirus emerged in China. Perceiving the modulating factors of cross-species virus transmission is critical to elucidate the nature of virus emergence. Using bioinformatics tools, we analyzed the mapping of the SARS-CoV-2 genome, modeling of protein structure, and analyze the evolutionary origin of SARS-CoV-2, as well as potential recombination events. Phylogenetic tree analysis shows that SARS-CoV-2 has the closest evolutionary relationship with Bat-SL-CoV-2 (RaTG13) at the scale of the complete virus genome, and less similarity to Pangolin-CoV. However, the Receptor Binding Domain (RBD) of SARS-CoV-2 is almost identical to Pangolin-CoV at the aa level, suggesting that spillover transmission probably occurred directly from pangolins, but not bats. Further recombination analysis revealed the pathway for spillover transmission from Bat-SL-CoV-2 and Pangolin-CoV. Here, we provide evidence for recombination event between Bat-SL-CoV-2 and Pangolin-CoV that resulted in the emergence of SARS-CoV-2. Nevertheless, the role of mutations should be noted as another influencing factor in the continuing evolution and resurgence of novel SARS-CoV-2 variants.

Early stage risk communication and community engagement (RCCE) strategies and measures against the coronavirus disease 2019 (COVID-19) pandemic crisis

Coronavirus disease 2019 (COVID-19) pandemic has proven to be tenacious and shows that the global community is still poorly prepared to handling such emerging pandemics. Enhancing global solidarity in emergency preparedness and response, and the mobilization of conscience and cooperation, can serve as an excellent source of ideas and measures in a timely manner. The article provides an overview of the key components of risk communication and community engagement (RCCE) strategies at the early stages in vulnerable nations and populations, and highlight contextual recommendations for strengthening coordinated and sustainable RCCE preventive and emergency response strategies against COVID-19 pandemic. Global solidarity calls for firming governance, abundant community participation and enough trust to boost early pandemic preparedness and response. Promoting public RCCE response interventions needs crucially improving government health systems and security proactiveness, community to individual confinement, trust and resilience solutions. To better understand population risk and vulnerability, as well as COVID-19 transmission dynamics, it is important to build intelligent systems for monitoring isolation/quarantine and tracking by use of artificial intelligence and machine learning systems algorithms. Experiences and lessons learned from the international community is crucial for emerging pandemics prevention and control programs, especially in promoting evidence-based decision-making, integrating data and models to inform effective and sustainable RCCE strategies, such as local and global safe and effective COVID-19 vaccines and mass immunization programs.

Deltacoronavirus Evolution and Transmission: Current Scenario and Evolutionary Perspectives

Deltacoronavirus (DCoV)–the only coronavirus that can infect multiple species of mammals and birds–was initially identified in several avian and mammalian species, including pigs, in China in 2009–2011. Porcine DCoV has since spread worldwide and is associated with multiple outbreaks of diarrheal disease of variable severity in farmed pigs. In contrast, avian DCoV is being reported in wild birds in different countries without any evidence of disease. The DCoV transboundary nature and the recent discovery of its remarkably broad reactivity with its cellular receptor–aminopeptidase N (APN)–from different species emphasize its epidemiological relevance and necessitate additional research. Further, the ability of porcine DCoV to infect and cause disease in chicks and turkey poults and gnotobiotic calves is suggestive of its increased potential for interspecies transmission or of its avian origin. Whether, porcine DCoVs were initially acquired by one or several mammalian species from birds and whether avian and porcine DCoVs continue co-evolving with frequent spillover events remain to be major unanswered questions. In this review, we will discuss the current information on the prevalence, genetic diversity, and pathogenic potential of porcine and avian DCoVs. We will also analyze the existing evidence of the ongoing interspecies transmission of DCoVs that may provide novel insights into their complex evolution.