MERS coronavirus outbreak: Implications for emerging viral infections

RT-qPCR investigation of post-mortem tissues during COVID-19

In 2020, there were numerous cases in Kazakhstan with clinical symptoms of COVID-19 but negative PCR results in nasopharyngeal and oropharyngeal swabs. The diagnosis was confirmed clinically and by CT scans (computed tomography). The problem with such negative PCR results for SARS-CoV-2 infection confirmation still exists and indicates the need to confirm the diagnosis in the bronchoalveolar lavage in such cases. There is also a lack of information about confirmation of SARS-CoV-2 infection in deceased patients. In this study, various tissue materials, including lungs, bronchi, and trachea, were examined from eight patients who died, presumably from SARS-CoV-2 infection, between 2020 and 2022. Naso/oropharyngeal swabs taken from these patients in hospitals tested PCR negative for SARS-CoV-2. This study presents a modified RNA isolation method based on a comparison of the most used methods for RNA isolation in laboratories: QIAamp Viral RNA Mini Kit and TRIzol-based method. This modified nucleic acid extraction protocol can be used to confirm SARS-CoV-2 infection by RT-qPCR in the tissues of deceased patients in disputed cases. RT-qPCR with RNA of SARS-CoV-2 re-extracted with such method from post-mortem tissues that were stored at -80 °C for more than 32 months still demonstrated high-yielding positive results.

Use of social media for the improvement of safety knowledge and awareness among Saudi Arabian phlebotomists

Purpose

The purpose of this study is to investigate the use of social media for the improvement of safety knowledge and awareness among phlebotomists.

Methods

As this study was intended to arrive at specific conclusions using empirical evidence, a deductive quantitative cross-sectional online survey design was adopted. A total of 521 phlebotomists participated in the survey, and 86 incomplete responders were removed, resulting in a final sample of 435 considered in this study. T-tests and ANOVA were used to analyze the data.

Results

A total of 41.6% stated that social media was very effective, and 31.5% stated that it was somewhat effective in improving safety knowledge and awareness. in addition, this study revealed no major differences between male and female participants (p > 0.05) with respect to the effectiveness of social media. However, statistically significant differences (p < 0.05) among the age groups were identified in relation to the effectiveness of social media and the intention to use it in the future.

Conclusion

Social media applications are effective for knowledge dissemination among healthcare professionals.

The Importance of the One Health Concept in Combating Zoonoses

One Health fundamentally acknowledges that human health is linked to animal health and the environment. One of the pillars One Health is built on is zoonoses. Through the years, zoonotic infections have caused numerous outbreaks and pandemics, as well as millions of fatalities, with the COVID-19 pandemic being the latest one. Apart from the consequences to public health, zoonoses also affect society and the economy. Since its establishment, One Health has contributed significantly to the protection of humans, animals, and the environment, through preparedness, surveillance, and mitigation of such public dangers.

Subunit vaccines with a saponin-based adjuvant boost humoral and cellular immunity to MERS coronavirus

Middle East respiratory syndrome coronavirus (MERS-CoV) outbreaks have constituted a public health issue with drastic mortality higher than 34%, necessitating the development of an effective vaccine. During MERS-CoV infection, the trimeric spike protein on the viral envelope is primarily responsible for attachment to host cellular receptor, dipeptidyl peptidase 4 (DPP4). With the goal of generating a protein-based prophylactic, we designed a subunit vaccine comprising the recombinant S1 protein with a trimerization motif (S1-Fd) and examined its immunogenicity and protective immune responses in combination with various adjuvants. We found that sera from immunized wild-type and human DPP4 transgenic mice contained S1-specific antibodies that can neutralize MERS-CoV infection in susceptible cells. Vaccination with S1-Fd protein in combination with a saponin-based QS-21 adjuvant provided long-term humoral as well as cellular immunity in mice. Our findings highlight the significance of the trimeric S1 protein in the development of MERS-CoV vaccines and offer a suitable adjuvant, QS-21, to induce robust and prolonged memory T cell response.

Ethical uncertainty and COVID-19: exploring the lived experiences of senior physicians at a major medical centre

Given the wide-reaching and detrimental impact of COVID-19, its strain on healthcare resources, and the urgent need for-sometimes forced-public health interventions, thorough examination of the ethical issues brought to light by the pandemic is especially warranted. This paper aims to identify some of the complex moral dilemmas faced by senior physicians at a major medical centre in Saudi Arabia, in an effort to gain a better understanding of how they navigated ethical uncertainty during a time of crisis. This qualitative study uses a semistructured interview approach and reports the findings of 16 interviews. The study finds that participants were motivated by a profession-based moral obligation to provide care during the toughest and most uncertain times of the pandemic. Although participants described significant moral dilemmas during their practice, very few identified challenges as ethical in nature, and in turn, none sought formal ethics support. Rather, participants took on the burden of resolving ethical challenges themselves-whenever possible-rationalising oft fraught decisions by likening their experiences to wartime action or by minimising attention to the moral. In capturing these accounts, this paper ultimately contemplates what moral lessons can, and must be, learnt from this experience.

Delivery of siRNAs against MERS-CoV in Vero and HEK-293 cells: A comparative evaluation of transfection reagents

Background

A new coronavirus was identified in Jeddah, Saudi Arabia in 2012 and designated as Middle East Respiratory Syndrome Coronavirus (MERS-CoV). To date, this virus has been reported in 27 countries. The virus transmission to humans has already been reported from camels. Currently, there is no vaccine or antiviral therapy available against this virus.

Methods

The siRNAs were in silico predicted, designed, and chemically synthesized by using the MERS-CoV-orf1ab region as a target. The antiviral activity was experimentally evaluated by delivering the siRNAs with Lipofectamine™ 2000 and JetPRIME^R as transfection reagents in both Vero cell and HEK-293-T cell lines at two different concentrations (10.0 nM and 5.0 nM). The Ct value of quantitative Real-Time PCR (qRT-PCR) was used to calculate and determine the reduction of viral RNA level in both cell supernatant and cell lysate isolated from both cell lines.

Results

The sequence alignment resulted in the selection of highly conserved regions. The orf1ab region was used to predict and design the siRNAs and a total of twenty-one siRNAs were finally selected from four hundred and twenty-six siRNAs generated by online software. Inhibition of viral replication and significant reduction of viral RNA was observed against selected siRNAs in both cell lines at both concentrations. Based on the Ct value, the siRNAs # 11, 12, 18, and 20 were observed to be the best performing in both cell lines at both concentrations.

Conclusion

Based on the results and data analysis, it is concluded that the use of two different transfection reagents was significantly effective. But the Lipofectamine™ 2000 was found to be a better transfection reagent than the JetPRIME^R for the delivery of siRNAs in both cell lines.

Computational Design and Experimental Evaluation of MERS-CoV siRNAs in Selected Cell Lines

Middle East respiratory syndrome coronavirus (MERS-CoV) is caused by a well-known coronavirus first identified in a hospitalized patient in the Kingdom of Saudi Arabia. MERS-CoV is a serious pathogen affecting both human and camel health globally, with camels being known carriers of viruses that spread to humans. In this work, MERS-CoV genomic sequences were retrieved and analyzed by multiple sequence alignment to design and predict siRNAs with online software. The siRNAs were designed from the orf1ab region of the virus genome because of its high sequence conservation and vital role in virus replication. The designed siRNAs were used for experimental evaluation in selected cell lines: Vero cells, HEK-293-T, and Huh-7. Virus inhibition was assessed according to the cycle threshold value during a quantitative real-time polymerase chain reaction. Out of 462 potential siRNAs, we filtered out 21 based on specific selection criteria without off-target effect. The selected siRNAs did not show any cellular toxicity in the tested cell lines at various concentrations. Based on our results, it was obvious that the combined use of siRNAs exhibited a reduction in MERS-CoV replication in the Vero, HEK-293-T, and Huh-7 cell lines, with the highest efficacy displayed in the Vero cells.

Epidemiological clustered characteristics of coronavirus disease 2019 (COVID-19) in three phases of transmission in Jilin Province, China

The current epidemiological status of the new coronary pneumonia epidemic in China is being explored to prevent and control the localized dissemination of aggregated outbreaks. This study analyzed the characteristics of new outbreaks of coronavirus disease 2019 (COVID-19) at three stages of aggregated outbreaks in Jilin Province, China, to provide a reference for the prevention and control of aggregated outbreaks. Case information were collected from all patients in Jilin Province from January 12, 2020 to the present. The epidemic was divided into three stages according to the time of onset. The first stage comprised 97 cases reported from January 12, 2020 to February 19, 2020, during which 17 aggregated outbreaks occurred. The second comprised 43 cases reported from April 25, 2020 and May 23, 2020, involving one aggregated outbreak. The third comprised 435 cases reported on January 10, 2021 and February 9, 2021, involving one aggregated outbreak. The relationship between aggregated and non-aggregated cases in the first phase of the outbreak and the difference between imported and local cases during the aggregated outbreak were assess using statistical analysis, and the differences in the baseline information between the three phases were analyzed. The incubation periods of the three phases were 10 days, 8 days, and 5 days. The number of aggregated epidemic events in Jilin Province tended to increase and then decrease over time. The clustered events in Jilin Province were divided into four categories: household contact (14 times, 51 cases); household contact and public places (one time, three cases); household contact, public places, and gatherings (one time, six cases); and household contact, public places, gatherings, and work (three times, 495 cases). Clustered events occurred mainly between January 22, 2020, and February 4, 2020. Among all cases in the first phase of the outbreak, the method of detection and the time from diagnosis to discharge were longer in aggregated cases than in non-aggregated cases, and that the source of infection and renewal cases were more frequent and more likely to be detected in the outpatient clinics during aggregated outbreaks than the imported cases. The second phase of the epidemic showed significant spatial variability (Moran's I<0, P<0.05). The third stage of the epidemic occurred in a higher proportion of individuals aged 50-90 years and within a shorter incubation period compared with the first two stages. The current focus of prevention and control of the COVID-19 epidemic in Jilin Province is to strictly implement the restrictions on gatherings and to perform timely screening and isolation of close contacts of infectious sources while strengthening the supervision of the inflow of people from outside the region. Simultaneously, more targeted prevention and control measures can be implemented for different age groups and occupations.

Evaluation and removal efficiencies of a rural WWTP for metals and anions in Lufkin, East Texas (USA)

The present study quantified element concentrations and evaluated the removal efficiencies of the Lufkin Wastewater Treatment Plant (LWWTP): a public municipal wastewater treatment plant in East Texas. Macroelements (Na, K, Mg, Ca, Al, Fe, Se, Zn, P, and S) and microelements (Ni, Pb, Mn, Cr, Mo, Cu, Co, V, As, B, Ba) were detected using ICP-OES and ICP-MS. In addition, the anion concentrations (Br^-, NO₃^-, NO₂^-, PO₄^3-, F^-, Cl^-, and SO₄^2-) and their percent removal from the LWWTP were assessed by using ion chromatography. Whereas macroelements in the influent were above the maximum ceiling limits, the total metal concentrations in the effluent were found below the USEPA (below μg/L) guidelines. In general, the removal efficiencies for metals in LWWTP were ≥ 94%. The removal efficiencies of the anions were > 100% (Br^-), 16.42% (Cl^-), 78.89% (F^-), 182.59% (NO₃^-), > 100% (NO₂^-), 51.81% (PO₄^3-), and 67.01% (SO₄^2-). In addition, Pierson correlation coefficients between the anions and cations, and implications for usage and suggested improvements of the treatment plants are proposed.

Immunogenicity of two doses of BNT162b2 and mRNA-1273 vaccines for solid cancer patients on treatment with or without a previous SARS-CoV-2 infection

Previous studies on the immunogenicity of SARS-CoV-2 mRNA vaccines showed a reduced seroconversion in cancer patients. The aim of our study is to evaluate the immunogenicity of two doses of mRNA vaccines in solid cancer patients with or without a previous exposure to the virus. This is a single-institution, prospective, nonrandomized study. Patients in active treatment and a control cohort of healthy people received two doses of BNT162b2 (Comirnaty, BioNTech/Pfizer, The United States) or mRNA-1273 (Spikevax, Moderna). Vaccine was administered before starting anticancer therapy or on the first day of the treatment cycle. SARS-CoV-2 antibody levels against S1, RBD (to evaluate vaccine response) and N proteins (to evaluate previous infection) were measured in plasma before the first dose and 30 days after the second one. From January to June 2021, 195 consecutive cancer patients and 20 healthy controls were enrolled. Thirty-one cancer patients had a previous exposure to SARS-CoV-2. Cancer patients previously exposed to the virus had significantly higher median levels of anti-S1 and anti-RBD IgG, compared to healthy controls (P = .0349) and to cancer patients without a previous infection (P < .001). Vaccine type (anti-S1: P < .0001; anti-RBD: P = .0045), comorbidities (anti-S1: P = .0274; anti-RBD: P = .0048) and the use of G-CSF (anti-S1: P = .0151) negatively affected the antibody response. Conversely, previous exposure to SARS-CoV-2 significantly enhanced the response to vaccination (anti-S1: P < .0001; anti-RBD: P = .0026). Vaccine immunogenicity in cancer patients with a previous exposure to SARS-CoV-2 seems comparable to that of healthy subjects. On the other hand, clinical variables of immune frailty negatively affect humoral immune response to vaccination.

Covariance predicts conserved protein residue interactions important for the emergence and continued evolution of SARS-CoV-2 as a human pathogen

SARS-CoV-2 is one of three recognized coronaviruses (CoVs) that have caused epidemics or pandemics in the 21st century and that likely emerged from animal reservoirs. Differences in nucleotide and protein sequence composition within related β-coronaviruses are often used to better understand CoV evolution, host adaptation, and their emergence as human pathogens. Here we report the comprehensive analysis of amino acid residue changes that have occurred in lineage B β-coronaviruses that show covariance with each other. This analysis revealed patterns of covariance within conserved viral proteins that potentially define conserved interactions within and between core proteins encoded by SARS-CoV-2 related β-coronaviruses. We identified not only individual pairs but also networks of amino acid residues that exhibited statistically high frequencies of covariance with each other using an independent pair model followed by a tandem model approach. Using 149 different CoV genomes that vary in their relatedness, we identified networks of unique combinations of alleles that can be incrementally traced genome by genome within different phylogenic lineages. Remarkably, covariant residues and their respective regions most abundantly represented are implicated in the emergence of SARS-CoV-2 and are also enriched in dominant SARS-CoV-2 variants.

Comparative evaluation of chlorous acid and sodium hypochlorite activity against SARS-CoV-2

A novel coronavirus, named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), suddenly emerged in China in 2019, spread globally and caused the present COVID-19 pandemic. Therefore, to mitigate SARS-CoV-2 infection effective measures are essential. Chlorous acid (HClO₂) has been shown to be an effective antimicrobial agent. However, at present there is no experimental evidence showing that HClO₂ can inactivate SARS-CoV-2. Therefore, in this study, we examined the potential of HClO₂ to inactivate SARS-CoV-2 in presence or absence of organic matter and the results were compared with that of sodium hypochlorite (NaClO), another potent antimicrobial agent. When concentrated SARS-CoV-2 was incubated with 10 ppm HClO₂ for 10 s, viral titre was decreased by 5 log of 50% tissue culture infective dose per mL (TCID₅₀ ml⁻¹). However, the same concentration of NaClO could not inactivate SARS-CoV-2 as effectively as HClO₂ did even after incubation for 3 min. Furthermore, 10 ppm HClO₂ also inactivated more than 4.0 log of TCID₅₀ within 10 s in the presence of 5 % fetal bovine serum used as mixed organic matters. Our results obtained with HClO₂ are more effective against SARS-CoV-2 as compared to NaClO that can be used for disinfectant against SARS-CoV-2 .

Bioactivity and Pharmacological Potential of Date Palm (Phoenix dactylifera L.) Against Pandemic COVID-19: a Comprehensive Review

A novel coronavirus disease (COVID-19) or severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2), transmitted from person to person, has quickly emerged as the pandemic responsible for the current global health crisis. This infection has been declared a global pandemic, resulting in a concerning number of deaths as well as complications post-infection, primarily among vulnerable groups particularly older people and those with multiple comorbidities. In this article, we review the most recent research on the role of date palm (Phoenix dactylifera L.) fruits (DPFs) to prevent or treat COVID-19 infection. The mechanisms underlying this preventive or therapeutic effect are also discussed in terms of bioactivity potentials in date palm, e.g., antimicrobial, antioxidant, anticancer, anti-diabetic, anti-inflammatory, neuroprotective, and hemolytic potential, as well as prospect against COVID-19 disease and the potential product development. Therefore, it can be concluded that regular consumption of DPFs may be associated with a lower risk of some chronic diseases. Indeed, DPFs have been widely used in folk medicine since ancient times to treat a variety of health conditions, demonstrating the importance of DPFs as a nutraceutical and source of functional nourishment. This comprehensive review aims to summarize the majority of the research on DPFs in terms of nutrient content and biologically active components such as phenolic compounds, with an emphasis on their roles in improving overall health as well as the potential product development to ensure consumers’ satisfaction in a current pandemic situation. In conclusion, DPFs can be given to COVID-19 patients as a safe and effective add-on medication or supplement in addition to routine treatments.

COVID 19 in pregnant women and neonates: Clinical characteristics and laboratory and imaging findings. An overview of systematic reviews

Introduction: SARS-CoV-2 infection in the perinatal period may be associated with an increased risk of morbidity and mortality in both the mother and the neonate. Objective: To describe the clinical characteristics and, laboratory and imaging findings in pregnant women with COVID-19 and their newborns. Materials and methods: We searched PubMed, Scopus, Web of Science, and Cochrane databases for systematic reviews published between February 1, 2020, and May 30, 2021, describing clinical characteristics and laboratory and imaging (chest) findings in pregnant women with COVID-19 and their newborns; there were no language restrictions. Data were reanalyzed by means of Bayesian meta-analysis using Markov Chain Monte Carlo methods. The study protocol is registered in PROSPERO under code CRD42020178329. Results: Six systematic reviews were retrieved (for a total of 617 primary studies). A narrative synthesis of the proportions of signs, symptoms, and imaging and laboratory findings of both mothers and neonates was performed. The Odds ratios (OR) between pregnant women with and without COVID-19 were as follows: fetal well-being involvement: 1.9 (95%CI:1.09-3.63); stillbirth: 1.73 (95%CI:1.01-2.94); preterm birth: 1.77 (95%CI:1.25-2.61); maternal admission to the intensive care unit (ICU): 6.75 (95%CI:1-31.19). Regarding symptomatology, the following OR was obtained for myalgia between pregnant women and non-pregnant women with COVID-19: 0.67 (95% CI:0.51-0.93). Conclusions: Cough, fever, dyspnea, and myalgia are the most common symptoms in pregnant women with COVID-19; in addition, there is a higher risk of admission to the ICU. Regarding complementary testing, the most frequent alterations are lymphopenia and the evidence of lesions in chest imaging studies. The presence of COVID-19 in pregnant women is associated with premature birth. It seems that SARS-CoV-2 infection in neonates is not serious and the risk of vertical transmission is low, since no data about congenital malformations attributable to the virus were found.

Post-Immune Antibodies in HIV-1 Infection in the Context of Vaccine Development: A Variety of Biological Functions and Catalytic Activities

Unlike many other viruses, HIV-1 is highly variable. The structure of the viral envelope changes as the infection progresses and is one of the biggest obstacles in developing an HIV-1 vaccine. HIV-1 infection can cause the production of various natural autoantibodies, including catalytic antibodies hydrolyzing DNA, myelin basic protein, histones, HIV-integrase, HIV-reverse transcriptase, β-casein, serum albumin, and some other natural substrates. Currently, there are various directions for the development of HIV-1 vaccines: stimulation of the immune response on the mucous membranes; induction of cytotoxic T cells, which lyse infected cells and hold back HIV-infection; immunization with recombinant Env proteins or vectors encoding Env; mRNA-based vaccines and some others. However, despite many attempts to develop an HIV-1 vaccine, none have been successful. Here we review the entire spectrum of antibodies found in HIV-infected patients, including neutralizing antibodies specific to various viral epitopes, as well as antibodies formed against various autoantigens, catalytic antibodies against autoantigens, and some viral proteins. We consider various promising targets for developing a vaccine that will not produce unwanted antibodies in vaccinated patients. In addition, we review common problems in the development of a vaccine against HIV-1.

Nanoparticle and virus-like particle vaccine approaches against SARS-CoV-2

The global spread of coronavirus disease 2019 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has provoked an urgent need for prophylactic measures. Several innovative vaccine platforms have been introduced and billions of vaccine doses have been administered worldwide. To enable the creation of safer and more effective vaccines, additional platforms are under development. These include the use of nanoparticle (NP) and virus-like particle (VLP) technology. NP vaccines utilize self-assembling scaffold structures designed to load the entire spike protein or receptor-binding domain of SARS-CoV-2 in a trimeric configuration. In contrast, VLP vaccines are genetically modified recombinant viruses that are considered safe, as they are generally replication-defective. Furthermore, VLPs have indigenous immunogenic potential due to their microbial origin. Importantly, NP and VLP vaccines have shown stronger immunogenicity with greater protection by mimicking the physicochemical characteristics of SARS-CoV-2. The study of NP- and VLP-based coronavirus vaccines will help ensure the development of rapid-response technology against SARS-CoV-2 variants and future coronavirus pandemics.

Why All the Fury over Furin?

Analysis of the SARS-CoV-2 sequence revealed a multibasic furin cleavage site at the S1/S2 boundary of the spike protein distinguishing this virus from SARS-CoV. Furin, the best-characterized member of the mammalian proprotein convertases, is an ubiquitously expressed single pass type 1 transmembrane protein. Cleavage of SARS-CoV-2 spike protein by furin promotes viral entry into lung cells. While furin knockout is embryonically lethal, its knockout in differentiated somatic cells is not, thus furin provides an exciting therapeutic target for viral pathogens including SARS-CoV-2 and bacterial infections. Several peptide-based and small-molecule inhibitors of furin have been recently reported, and select cocrystal structures have been solved, paving the way for further optimization and selection of clinical candidates. This perspective highlights furin structure, substrates, recent inhibitors, and crystal structures with emphasis on furin's role in SARS-CoV-2 infection, where the current data strongly suggest its inhibition as a promising therapeutic intervention for SARS-CoV-2.

A review on COVID-19 transmission, epidemiological features, prevention and vaccination

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused hundreds of millions of infections and millions of deaths over past two years. Currently, many countries have still not been able to take the pandemic under control. In this review, we systematically summarized what we have done to mitigate the COVID-19 pandemic, from the perspectives of virus transmission, public health control measures, to the development and vaccination of COVID-19 vaccines. As a virus most likely coming from bats, the SARS-CoV-2 may transmit among people via airborne, faecal-oral, vertical or foodborne routes. Our meta-analysis suggested that the R₀ of COVID-19 was 2.9 (95% CI: 2.7–3.1), and the estimates in Africa and Europe could be higher. The median R_t could decrease by 23–96% following the nonpharmacological interventions, including lockdown, isolation, social distance, and face mask, etc. Comprehensive intervention and lockdown were the most effective measures to control the pandemic. According to the pooled R₀ in our meta-analysis, there should be at least 93.3% (95% CI: 89.9–96.2%) people being vaccinated around the world. Limited amount of vaccines and the inequity issues in vaccine allocation call for more international cooperation to achieve the anti-epidemic goals and vaccination fairness.

Myocardial injuries among patients with COVID-19: a systematic review

This is a systematic review of the literature specifically aimed to explore myocardial injury in coronavirus disease-19 (COVID-19) patients who were hospitalized with severe complicated infections. The medical literature was examined through the large medical databases, including Medline, Ovid, PubMed, and Embase, over the last year between January 2020 and May 2021. The search terms used were a combination of "myocardial injury" AND "COVID-19" AND "Hospitalization". Then we applied a step to filter the results to select original research articles only evaluating the myocardial injuries in severe COVID-19 hospitalized patients. Selected trials mentioned the type of myocardial injury detected with the infection. A total of 245 articles were extracted. Considering the exclusion of ineligible articles, 42 articles appeared. A total of 42 articles were eligible and were included in the review. These studies included a total of 4326 COVID-19 patients. The 30-day mortality was found to be associated with increased cardiac troponin and myocardial infarction could be a systemic reaction rather than the direct action of COVID-19. Patients with myocardial injury were significantly older and with co-morbid conditions. Studies also found a correlation of higher concentrations of cardiac enzymes with disease severity and increased in-hospital mortality. Myocardial injury was a significant predictor for severe COVID-19 infection and in-hospital mortality. Cardiac enzymes should be monitored in hospitalized patients with severe COVID-19 infections.

Covariance predicts conserved protein residue interactions important to the emergence and continued evolution of SARS-CoV-2 as a human pathogen.. [PMID: 35169805 PMCID: PMC8845505 DOI: 10.1101/2022.01.13.476204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

SARS-CoV-2 is one of three recognized coronaviruses (CoVs) that have caused epidemics or pandemics in the 21st century and that likely emerged from animal reservoirs. Differences in nucleotide and protein sequence composition within related β-coronaviruses are often used to better understand CoV evolution, host adaptation, and their emergence as human pathogens. Here we report the comprehensive analysis of amino acid residue changes that have occurred in lineage B β-coronaviruses that show covariance with each other. This analysis revealed patterns of covariance within conserved viral proteins that potentially define conserved interactions within and between core proteins encoded by SARS-CoV-2 related β-coranaviruses. We identified not only individual pairs but also networks of amino acid residues that exhibited statistically high frequencies of covariance with each other using an independent pair model followed by a tandem model approach. Using 149 different CoV genomes that vary in their relatedness, we identified networks of unique combinations of alleles that can be incrementally traced genome by genome within different phylogenic lineages. Remarkably, covariant residues and their respective regions most abundantly represented are implicated in the emergence of SARS-CoV-2 are also enriched in dominant SARS-CoV-2 variants.

Impact of sewer overflow on public health: A comprehensive scientometric analysis and systematic review

Sewer overflow (SO), which has attracted global attention, poses serious threat to public health and ecosystem. SO impacts public health via consumption of contaminated drinking water, aerosolization of pathogens, food-chain transmission, and direct contact with fecally-polluted rivers and beach sediments during recreation. However, no study has attempted to map the linkage between SO and public health including Covid-19 using scientometric analysis and systematic review of literature. Results showed that only few countries were actively involved in SO research in relation to public health. Furthermore, there are renewed calls to scale up environmental surveillance to safeguard public health. To safeguard public health, it is important for public health authorities to optimize water and wastewater treatment plants and improve building ventilation and plumbing systems to minimize pathogen transmission within buildings and transportation systems. In addition, health authorities should formulate appropriate policies that can enhance environmental surveillance and facilitate real-time monitoring of sewer overflow. Increased public awareness on strict personal hygiene and point-of-use-water-treatment such as boiling drinking water will go a long way to safeguard public health. Ecotoxicological studies and health risk assessment of exposure to pathogens via different transmission routes is also required to appropriately inform the use of lockdowns, minimize their socio-economic impact and guide evidence-based welfare/social policy interventions. Soft infrastructures, optimized sewer maintenance and prescreening of sewer overflow are recommended to reduce stormwater burden on wastewater treatment plant, curtail pathogen transmission and marine plastic pollution. Comprehensive, integrated surveillance and global collaborative efforts are important to curtail on-going Covid-19 pandemic and improve resilience against future pandemics.

Impact of metabolic and cardiovascular disease on COVID-19 mortality: A systematic review and meta-analysis

BACKGROUND AND AIMS

This meta-analysis aims to highlight the impact of cardio-metabolic comorbidities on COVID-19 severity and mortality.

METHODS

A thorough search on major online databases was done for studies describing the clinical outcomes of COVID-19 patients. We used random-effects model to compute pooled estimates for critical or fatal disease.

RESULTS

A total of 20,475 patients from 33 eligible studies were included. Maximum risk of development of critical or fatal COVID-19 disease was seen in patients with underlying cardiovascular disease [OR: 3.44, 95% CI: 2.65-4.48] followed by chronic lung disease, hypertension and diabetes mellitus. Of the total cases, 64% had one of the four comorbidities with the most prevalent being hypertension with a pooled prevalence of 27%.

CONCLUSIONS

Presence of comorbidities like cardiovascular disease, chronic lung disease, hypertension and diabetes mellitus led to a higher risk of development of critical or fatal COVID-19 disease, with maximum risk seen with underlying cardiovascular disease.

Effect of ORF7 of SARS-CoV-2 on the Chemotaxis of Monocytes and Neutrophils In Vitro

Coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently the most significant public health threat worldwide. Patients with severe COVID-19 usually have pneumonia concomitant with local inflammation and sometimes a cytokine storm. Specific components of the SARS-CoV-2 virus trigger lung inflammation, and recruitment of immune cells to the lungs exacerbates this process, although much remains unknown about the pathogenesis of COVID-19. Our study of lung type II pneumocyte cells (A549) demonstrated that ORF7, an open reading frame (ORF) in the genome of SARS-CoV-2, induced the production of CCL2, a chemokine that promotes the chemotaxis of monocytes, and decreased the expression of IL-8, a chemokine that recruits neutrophils. A549 cells also had an increased level of IL-6. The results of our chemotaxis Transwell assay suggested that ORF7 augmented monocyte infiltration and reduced the number of neutrophils. We conclude that the ORF7 of SARS-CoV-2 may have specific effects on the immunological changes in tissues after infection. These results suggest that the functions of other ORFs of SARS-CoV-2 should also be comprehensively examined.

Hypochlorous acid solution is a potent antiviral agent against SARS-CoV-2

Aim

A novel coronavirus, termed severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) suddenly appeared in Wuhan, China, and has caused pandemic. In this study, we evaluated antiviral activity of purified hypochlorous acid (HClO) against coronaviruses such as SARS‐CoV‐2 and transmissible gastroenteritis virus (TGEV) responsible for pig diseases.

Materials and Results

In a suspension test, 28.1 ppm HClO solution inactivated SARS‐CoV‐2 in phosphate‐buffered saline with the reduction of 10⁴ of 50% tissue culture infectious dose per ml (TCID₅₀ per ml) within 10 s. When its concentration increased to 59.4 ppm, the virus titre decreased to below the detection limit (reduction of 5 logs TCID₅₀) within 10 s even in the presence of 0.1% foetal bovine serum. In a carrier test, incubation with 125 ppm HClO solution for 10 min or 250 ppm for 5 min inactivated SARS‐CoV‐2 by more than 4 logs TCID₅₀ per ml or below the detection limit. Because the titre of TGEV was 10‐fold higher, TGEV was used for SARS‐CoV‐2 in a suspension test. As expected, 56.3 ppm HClO solution inactivated TGEV by 6 logs TCID₅₀ within 30 s.

Conclusions

In a carrier test, 125 ppm HClO solution for 10 min incubation is adequate to inactivate 4 logs TCID₅₀ per ml of SARS‐CoV‐2 or more while in a suspension test 56.3 ppm HClO is adequate to inactivate 5 logs TCID₅₀ per ml of SARS‐CoV‐2 when incubated for only 10 s regardless of presence or absence of organic matter.

Significance and Impact of the Study

Effectiveness of HClO solution against SARS‐CoV‐2 was demonstrated by both suspension and carrier tests. HClO solution inactivated SARS‐CoV‐2 by 5 logs TCID₅₀ within 10 s. HClO solution has several advantages such as none toxicity, none irritation to skin and none flammable. Thus, HClO solution can be used as a disinfectant for SARS‐CoV‐2.

COVID-19 in Pregnancy-Perinatal Outcomes and Vertical Transmission Preventative Strategies, When Considering More Transmissible SARS-CoV-2 Variants

The COVID-19 pandemic affected the physical and mental health of people around the world and left unprepared health care systems struggling to mount an adequate response. Understanding the impact of COVID-19 on pregnancy in terms of perinatal and fetal outcomes is essential to propose strategies for mminimising viral transmission. Overall, 91 pregnant women in labour, or with indication for induction of labour, with COVID-19 were admitted to hospital. On the day of admission, each pregnant woman underwent a nasopharyngeal swab to validate SARS-CoV-2 infection. Whenever delivery was by caesarean section, an amniotic fluid sample was collected after uterus incision. Neonates were tested twice: first by nasopharyngeal swab at birth and secondly either at 24 h after (when babies were isolated) or at discharge (when rooming-in). All samples underwent rRT-PCR testing for SARS-CoV-2. The SARS-CoV-2 RNA tests by nasopharyngeal swab of the pregnant women produced positive results in 47 patients. This cohort gave birth to 48 infants who were double tested by nasopharyngeal swab and included in the prospective observational study. Moreover, in this same cohort, 39 amniotic fluid samples were taken during caesarean section. All samples underwent rRT-PCR testing for SARS-CoV-2 and came back negative. The study results suggest a low risk of vertical transmission of COVID-19 and favourable perinatal outcomes due to adequate preventative strategies. This approach may prove to be more beneficial in the new SARS-CoV-2 variants era.

The lethal internal face of the coronaviruses: Kidney tropism of the SARS, MERS, and COVID19 viruses

The kidney is one of the main targets attacked by viruses in patients with a coronavirus infection. Until now, SARS-CoV-2 has been identified as the seventh member of the coronavirus family capable of infecting humans. In the past two decades, humankind has experienced outbreaks triggered by two other extremely infective members of the coronavirus family; the MERS-CoV and the SARS-CoV. According to several investigations, SARS-CoV causes proteinuria and renal impairment or failure. The SARS-CoV was identified in the distal convoluted tubules of the kidney of infected patients. Also, renal dysfunction was observed in numerous cases of MERS-CoV infection. And recently, during the 2019-nCoV pandemic, it was found that the novel coronavirus not only induces acute respiratory distress syndrome (ARDS) but also can induce damages in various organs including the liver, heart, and kidney. The kidney tissue and its cells are targeted massively by the coronaviruses due to the abundant presence of ACE2 and Dpp4 receptors on kidney cells. These receptors are characterized as the main route of coronavirus entry to the victim cells. Renal failure due to massive viral invasion can lead to undesirable complications and enhanced mortality rate, thus more attention should be paid to the pathology of coronaviruses in the kidney. Here, we have provided the most recent knowledge on the coronaviruses (SARS, MERS, and COVID19) pathology and the mechanisms of their impact on the kidney tissue and functions.

Anxiety, OCD, delusions, and religiosity among the general public during the COVID-19 pandemic

The COVID-19 outbreak has not only affected the physical health of the public but also resulted in severe psychological outcomes. This study aims to investigate the psychological effects of the COVID-19 outbreak on Pakistan's general public. In order to identify the main psychological factors that have emerged due to the current pandemic, extensive literature and opinion pieces of psychologists were reviewed. After a thorough study of the existing scholarship, four main psychological factors were investigated: stress and anxiety, obsessive compulsive disorder (OCD), delusions of getting infected from the disease, and religiosity. A research survey was circulated among the sample population online. A total 356 valid responses were received in the period of two to three weeks. Findings showed that the respondents reported a moderate level of anxiety, occasional symptoms of OCD, and delusions. However, respondents showed a high inclination toward religion during the current pandemic situation. Furthermore, respondents highlighted a few other psychological factors, such as financial strain and loneliness, in the survey. The primary sources of COVID-19-related information were social media and television among the general public of Pakistan. Finally, guidelines and tips from the reviewed psychologists and psychiatrists on overcoming the highlighted psychological problems that have arisen due to the COVID-19 outbreak were summarised.

Why the COVID-19 Is Not Significantly Reduced in Iran?

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was transported from China to Iran via passengers. The virus is transmitted through droplets from coughing, sneezing, talking and contact with infected surfaces. Due to high transmissibility in places such as clinics, medical offices, buses and offices where there are large crowds, it spread rapidly in Iran and caused the mortality of a significant number of people, especially the elderly with underlying disease. Preventing travel and gatherings, as well as applying house quarantine in Apr 2020, reduced COVID-19 somewhat but then due to lack of attention to social distancing, reducing the use of masks by the people and inappropriate decisions by the national committee on combating coronavirus (NCCC), including reducing the working hours of public offices and shops, reducing the staff of government offices, monopoly on the distribution of essential materials and supplies, the presence of overcrowding in clinics of medical centers, hospitals, and private clinics caused the decline of the disease in the country to decrease. Measures can be taken to prevent the spread of the virus as much as possible, including: rapid detection of infected people, their isolation, contact tracing, quarantine of people over 65 and under 15, protection of the elderly, prevention of gatherings, forcing the use of protective equipment in possible gatherings, and electronicizing public services.

Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-1) and Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infections in pregnancy - An overview

Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-1) and Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infections, like most other viruses that affect the respiratory tract can cause severe maternal illness and adverse pregnancy outcomes. They are not only highly transmissible (acquired through droplets), but Host reservoirs such as dromedary camels for MERS-CoV and masked palm civet for SARS-CoV-1 are critical links in the onset of outbreaks. Clinically they present with flu-like symptoms and therefore a high index of suspicion is required to ensure timely diagnosis and tailored management. Although there are not many reported series on these infections in pregnancy they seem to be associated with an increased risk of preterm delivery and maternal mortality. Diagnosis is made by PCR from nasopharyngeal swabs. There are currently no effective anti-viral agents for these viruses but following infections various agents have been administered to patients. The most important aspect of management should be early identification of deterioration and intensive support and prevention of transmission. Our understanding of the evidence of the impact of both infections on pregnancies suggests the potential for future repeat outbreaks, hence the importance of maintaining vigilance across healthcare systems.

Care needs and preferences from the perspective of COVID-19 patients: A qualitative study

Background: The COVID-19 epidemic is one of the major health problems worldwide due to its inconceivable spreading power and potential damage. Given the increasing prevalence of the disease, the identification of care needs and preferences of patients could play an important role in providing effective training and caring programs. This study was conducted to explain the preferences and needs of care based on the experiences of patients with COVID-19.

Methods: This qualitative study with a content analysis approach was performed in 2 months at a referral general hospital and quarantine centers of COVID-19 in Tehran, the capital of Iran, in 2020. The participants consisted of 15 COVID-19 patients selected through purposive sampling. The data analysis was performed using the conventional content analysis method according to the procedure proposed by Graneheim and Lundman.

Results: The results were classified into 5 main categories: (1) access to desirable care and comfort services; (2) access to education and information from credible sources; (3) access to specialized care; (4) support social needs; and (5) need for deep emotional interactions.

Conclusion: According to our results, identifying priorities and care needs from the perspective of patients with COVID-19 can help improve knowledge, reduce unrealistic patient concerns, and improve emotional interactions between patients and health care providers.

Maternal death related to COVID-19: A systematic review and meta-analysis focused on maternal co-morbidities and clinical characteristics

Background

Besides reducing the quality of obstetric care, the direct impact of COVID‐19 on pregnancy and postpartum is uncertain.

Objective

To evaluate the characteristics of pregnant women who died due to COVID‐19.

Search strategy

Cochrane Library, Embase, MEDLINE, Scopus, and Google Scholar were searched from inception to February 2021.

Selection criteria

Studies that compared deceased and survived pregnant women with COVID‐19.

Data collection and analysis

Relevant data were extracted and tabulated. The primary outcome was maternal co‐morbidity.

Main results

Thirteen studies with 154 deceased patients were included. Obesity doubled the risk of death (relative risk [RR] 2.48, 95% confidence interval [CI] 1.41–4.36, I² = 0%). No differences were found for gestational diabetes (RR 5.71; 95% CI 0.77–42.44, I² = 94%) or asthma (RR 2.05, 95% CI 0.81–5.15, I² = 0%). Overall, at least one severe co‐morbidity showed a twofold increased risk of death (RR 2.26, 95% CI 1.77–2.89, I² = 76%). Admission to intensive care was related to a fivefold increased risk of death (RR 5.09, 95% CI 2.00–12.98, I² = 56%), with no difference in need for respiratory support (RR 0.53, 95% CI 0.23–1.48, I² = 95%) or mechanical ventilation (RR 4.34, 95% CI 0.96–19.60, I² = 58%).

Conclusion

COVID‐19 with at least one co‐morbidity increases risk of intensive care and mortality.

Pregnant women with COVID‐19 infection and at least one severe co‐morbidity experience increased risk of death and admission to the intensive care unit.

Changes in healthcare workers' knowledge, attitudes, practices, and stress during the COVID-19 pandemic

Coronavirus disease 2019 (COVID-19) has caused an unprecedented health crisis around the world, not least because of its heterogeneous clinical presentation and course. The new information on the pandemic emerging daily has made it challenging for healthcare workers (HCWs) to stay current with the latest knowledge, which could influence their attitudes and practices during patient care.This study is a follow-up evaluation of changes in HCWs' knowledge, attitudes, and practices as well as anxiety levels regarding COVID-19 since the beginning of the pandemic. Data were collected through an anonymous, predesigned, self-administered questionnaire that was sent online to HCWs in Saudi Arabia.The questionnaire was sent to 1500 HCWs, with a 63.8% response rate (N = 957). The majority of respondents were female (83%), and the most common age group was 31 to 40 years (52.2%). Nurses constituted 86.3% of the respondents. HCWs reported higher anxiety during the COVID-19 pandemic which increased from 4.91 ± 2.84 to 8.6 ± 2.27 on an 11-point Likert scale compared to other viral outbreaks. HCWs believed that their own preparedness as well as that of their hospital's intensive care unit or emergency room was higher during the COVID-19 pandemic than during the Middle East respiratory syndrome coronavirus pandemic (2012-2015). About 58% of HCWs attended one or more simulations concerning the management of COVID-19 patients in their intensive care unit/emergency room, and nearly all had undergone N95 mask fit testing. The mean score of HCWs' knowledge of COVID-19 was 9.89/12. For most respondents (94.6%), the perception of being at increased risk of infection was the main cause of anxiety related to COVID-19; the mean score of anxiety over COVID-19 increased from 4.91 ± 2.84 before to 8.6 ± 2.27 during the pandemic in Saudi Arabia.HCWs' anxiety levels regarding COVID-19 have increased since a pandemic was declared. It is vital that healthcare facilities provide more emotional and psychological support for all HCWs.

In Vitro Inhibitory Analysis of Rationally Designed siRNAs against MERS-CoV Replication in Huh7 Cells

MERS-CoV was identified for the first time in Jeddah, Saudi Arabia in 2012 in a hospitalized patient. This virus subsequently spread to 27 countries with a total of 939 deaths and 2586 confirmed cases and now has become a serious concern globally. Camels are well known for the transmission of the virus to the human population. In this report, we have discussed the prediction, designing, and evaluation of potential siRNA targeting the ORF1ab gene for the inhibition of MERS-CoV replication. The online software, siDirect 2.0 was used to predict and design the siRNAs, their secondary structure and their target accessibility. ORF1ab gene folding was performed by RNAxs and RNAfold software. A total of twenty-one siRNAs were selected from 462 siRNAs according to their scoring and specificity. siRNAs were evaluated in vitro for their cytotoxicity and antiviral efficacy in Huh7 cell line. No significant cytotoxicity was observed for all siRNAs in Huh7 cells. The in vitro study showed the inhibition of viral replication by three siRNAs. The data generated in this study provide preliminary and encouraging information to evaluate the siRNAs separately as well as in combination against MERS-CoV replication in other cell lines. The prediction of siRNAs using online software resulted in the filtration and selection of potential siRNAs with high accuracy and strength. This computational approach resulted in three effective siRNAs that can be taken further to in vivo animal studies and can be used to develop safe and effective antiviral therapies for other prevalent disease-causing viruses.

Identification of Epidemiological Traits by Analysis of SARS-CoV-2 Sequences

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the ongoing global COVID-19 pandemic that began in late December 2019. The rapid spread of SARS-CoV-2 is primarily due to person-to-person transmission. To understand the epidemiological traits of SARS-CoV-2 transmission, we conducted phylogenetic analysis on genome sequences from >54K SARS-CoV-2 cases obtained from two public databases. Hierarchical clustering analysis on geographic patterns in the resulting phylogenetic trees revealed a co-expansion tendency of the virus among neighboring countries with diverse sources and transmission routes for SARS-CoV-2. Pairwise sequence similarity analysis demonstrated that SARS-CoV-2 is transmitted locally and evolves during transmission. However, no significant differences were seen among SARS-CoV-2 genomes grouped by host age or sex. Here, our identified epidemiological traits provide information to better prevent transmission of SARS-CoV-2 and to facilitate the development of effective vaccines and therapeutics against the virus.

Current Understanding of Novel Coronavirus: Molecular Pathogenesis, Diagnosis, and Treatment Approaches

An outbreak of “Pneumonia of Unknown Etiology” occurred in Wuhan, China, in late December 2019. Later, the agent factor was identified and coined as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the disease was named coronavirus disease 2019 (COVID-19). In a shorter period, this newly emergent infection brought the world to a standstill. On 11 March 2020, the WHO declared COVID-19 as a pandemic. Researchers across the globe have joined their hands to investigate SARS-CoV-2 in terms of pathogenicity, transmissibility, and deduce therapeutics to subjugate this infection. The researchers and scholars practicing different arts of medicine are on an extensive quest to come up with safer ways to curb the pathological implications of this viral infection. A huge number of clinical trials are underway from the branch of allopathy and naturopathy. Besides, a paradigm shift on cellular therapy and nano-medicine protocols has to be optimized for better clinical and functional outcomes of COVID-19-affected individuals. This article unveils a comprehensive review of the pathogenesis mode of spread, and various treatment modalities to combat COVID-19 disease.

The Integration of Human and Veterinary Studies for Better Understanding and Management of Crimean-Congo Haemorrhagic Fever

Outbreaks that occur as a result of zoonotic spillover from an animal reservoir continue to highlight the importance of studying the disease interface between species. One Health approaches recognise the interdependence of human and animal health and the environmental interplay. Improving the understanding and prevention of zoonotic diseases may be achieved through greater consideration of these relationships, potentially leading to better health outcomes across species. In this review, special emphasis is given on the emerging and outbreak pathogen Crimean-Congo Haemorrhagic Fever virus (CCHFV) that can cause severe disease in humans. We discuss the efforts undertaken to better understand CCHF and the importance of integrating veterinary and human research for this pathogen. Furthermore, we consider the use of closely related nairoviruses to model human disease caused by CCHFV. We discuss intervention approaches with potential application for managing CCHFV spread, and how this concept may benefit both animal and human health.

SEAHIR: A Specialized Compartmental Model for COVID-19

The SEIR (Susceptible-Exposed-Infected-Removed) model is widely used in epidemiology to mathematically model the spread of infectious diseases with incubation periods. However, the SEIR model prototype is generic and not able to capture the unique nature of a novel viral pandemic such as SARS-CoV-2. We have developed and tested a specialized version of the SEIR model, called SEAHIR (Susceptible-Exposed-Asymptomatic-Hospitalized-Isolated-Removed) model. This proposed model is able to capture the unique dynamics of the COVID-19 outbreak including further dividing the Infected compartment into: (1) “Asymptomatic”, (2) “Isolated” and (3) “Hospitalized” to delineate the transmission specifics of each compartment and forecast healthcare requirements. The model also takes into consideration the impact of non-pharmaceutical interventions such as physical distancing and different testing strategies on the number of confirmed cases. We used a publicly available dataset from the United Arab Emirates (UAE) as a case study to optimize the main parameters of the model and benchmarked it against the historical number of cases. The SEAHIR model was used by decision-makers in Dubai’s COVID-19 Command and Control Center to make timely decisions on developing testing strategies, increasing healthcare capacity, and implementing interventions to contain the spread of the virus. The novel six-compartment SEAHIR model could be utilized by decision-makers and researchers in other countries for current or future pandemics.

PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses

Viral co-infections occur in COVID-19 patients, potentially impacting disease progression and severity. However, there is currently no dedicated method to identify viral co-infections in patient RNA-seq data. We developed PACIFIC, a deep-learning algorithm that accurately detects SARS-CoV-2 and other common RNA respiratory viruses from RNA-seq data. Using in silico data, PACIFIC recovers the presence and relative concentrations of viruses with > 99% precision and recall. PACIFIC accurately detects SARS-CoV-2 and other viral infections in 63 independent in vitro cell culture and patient datasets. PACIFIC is an end-to-end tool that enables the systematic monitoring of viral infections in the current global pandemic.

A Comprehensive Summary of the Knowledge on COVID-19 Treatment

Currently, the world is challenged by the coronavirus disease 2019 (COVID-19) pandemic. Epidemiologists and researchers worldwide are invariably trying to understand and combat this precarious new disease. Scrutinizing available drug options and developing potential new drugs are urgent needs to subdue this pandemic. Several intervention strategies are being considered and handled worldwide with limited success, and many drug candidates are yet in the trial phase. Despite these limitations, the development of COVID-19 treatment strategies has been accelerated to improve the clinical outcome of patients with COVID-19, and some countries have efficiently kept it under control. Recently, the use of natural and traditional medicine has also set the trend in coronavirus treatment. This review aimed to discuss the prevailing COVID-19 treatment strategies available globally by examining their efficacy, potential mechanisms, limitations, and challenges in predicting a future potential treatment candidate and bridging them with the effective traditional Chinese medicine (TCM). The findings might enrich the knowledge on traditional alternative medication and its complementary role with Western medicine in managing the COVID-19 epidemic.

Structure of Nonstructural Protein 1 from SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. One protein known to play a critical role in the coronavirus life cycle is nonstructural protein 1 (nsp1).

The periodic emergence of novel coronaviruses (CoVs) represents an ongoing public health concern with significant health and financial burdens worldwide. The most recent occurrence originated in the city of Wuhan, China, where a novel coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) emerged causing severe respiratory illness and pneumonia. The continual emergence of novel coronaviruses underscores the importance of developing effective vaccines as well as novel therapeutic options that target either viral functions or host factors recruited to support coronavirus replication. The CoV nonstructural protein 1 (nsp1) has been shown to promote cellular mRNA degradation, block host cell translation, and inhibit the innate immune response to virus infection. Interestingly, deletion of the nsp1-coding region in infectious clones prevented the virus from productively infecting cultured cells. Because of nsp1’s importance in the CoV life cycle, it has been highlighted as a viable target for both antiviral therapy and vaccine development. However, the fundamental molecular and structural mechanisms that underlie nsp1 function remain poorly understood, despite its critical role in the viral life cycle. Here, we report the high-resolution crystal structure of the amino globular portion of SARS-CoV-2 nsp1 (residues 10 to 127) at 1.77-Å resolution. A comparison of our structure with the SARS-CoV-1 nsp1 structure reveals how mutations alter the conformation of flexible loops, inducing the formation of novel secondary structural elements and new surface features. Paired with the recently published structure of the carboxyl end of nsp1 (residues 148 to 180), our results provide the groundwork for future studies focusing on SARS-CoV-2 nsp1 structure and function during the viral life cycle.

IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. One protein known to play a critical role in the coronavirus life cycle is nonstructural protein 1 (nsp1). As such, it has been highlighted in numerous studies as a target for both the development of antivirals and the design of live-attenuated vaccines. Here, we report the high-resolution crystal structure of nsp1 derived from SARS-CoV-2 at 1.77-Å resolution. This structure will facilitate future studies focusing on understanding the relationship between structure and function for nsp1. In turn, understanding these structure-function relationships will allow nsp1 to be fully exploited as a target for both antiviral development and vaccine design.

Coronavirus Pneumonia and Pulmonary Thromboembolism

Abstract In 2019, a novel pneumonia, called coronavirus disease 2019 (COVID-19), spread rapidly throughout the world. This novel global pandemic severely threatened public respiratory health and medical services. To date, except for the common respiratory symptoms, coagulation disorders, especially pulmonary thromboembolism (PTE), has been proven as an important complication in severe COVID-19 patients, and the incidence of PTE causes poor clinical outcome and increased fatality. Therefore, it is important that healthcare providers, including respiratory physicians, emergency medicine specialists, hematologists, cardiologists, infectious disease specialists, and other specialists, recognize that patients with COVID-19 are at increased risk of PTE, and ensure that appropriate prophylaxis is administered to the appropriate patients, and that they effectively manage PTE when it does occur. The mechanism of PTE in patients with coronavirus pneumonia consists of endothelial injury, activated platelet, cytokine storm, and a suppressed fibrinolytic system. Early prophylaxis, antiviral therapy, anticoagulation, and supportive treatment are beneficial to COVID-19 patients. In this review, we summarize the harm that coronavirus pneumonia wreaks and highlight the clinical relationship between PTE and coronavirus infection. The potential mechanism and the prophylaxis and therapeutic measures are also discussed to call for more effort and research to investigate the strategies for PTE in COVID-19.

Product of natural evolution (SARS, MERS, and SARS-CoV-2); deadly diseases, from SARS to SARS-CoV-2

SARS-CoV-2, the virus causing COVID-19, is a single-stranded RNA virus belonging to the order Nidovirales, family Coronaviridae, and subfamily Coronavirinae. SARS-CoV-2 entry to cellsis initiated by the binding of the viral spike protein (S) to its cellular receptor. The roles of S protein in receptor binding and membrane fusion makes it a prominent target for vaccine development. SARS-CoV-2 genome sequence analysis has shown that this virus belongs to the beta-coronavirus genus, which includes Bat SARS-like coronavirus, SARS-CoV and MERS-CoV. A vaccine should induce a balanced immune response to elicit protective immunity. In this review, we compare and contrast these three important CoV diseases and how they inform on vaccine development.

Knowledge of COVID-19 and its implications in dental treatment, and practices of personal protective equipment among dentists: A survey-based assessment

BACKGROUND

Oral health-care providers are always at a risk of transmitting or acquiring airborne, saliva-borne, or blood-borne infections due to their proximity to the patient's mouth, contact with saliva, and handling of sharp instruments. the aim this study was to evaluate the knowledge of the dentists regarding COVID-19, methods to prevent its transmission, and implications of COVID-19 in dental treatment.

MATERIALS AND METHODS

It was a cross-sectional online survey. There were 35 questions in total, divided into sections of knowledge of COVID-19, practices of personal protective equipment (PPE), and knowledge of implications of COVID-19 in dental treatment. Both convenience sampling and snowball sampling were used, so that maximal participation could be ensured. The results were analyzed using descriptive statistics and making comparisons among various groups. The data were summarized as proportions and percentages (%). All the associations were tested using the Chi-square test, ANOVA, and Pearson's correlation coefficient. Statistical analyses were performed using SPSS version 19.0.

RESULTS

26.8% of respondents had a high knowledge, 61.5% had good knowledge, 10.1% had low knowledge, and 6 (1.5%) had nil knowledge about COVID-19. No significant association was found between qualification and knowledge level among the respondents (P = 0.053). Both graduates and postgraduates had low knowledge regarding effective PPE components (P = 0.053), donning (P = 0.888), and doffing (P = 0.745). Only 52.9% of postgraduates and 43.7% graduates answered correctly about the sequence of donning, and 47.9% of postgraduates and 46.1% of graduates had knowledge regarding correct doffing sequence of PPE. Furthermore, knowledge was low regarding the implications of COVID-19 in dental treatment.

CONCLUSION

Although the dentists were found to have high/good knowledge scores regarding COVID-19, there was a lack of knowledge regarding hand hygiene, proper use of PPE, and implications of COVID-19 in dental treatment. Thus, they need to be trained and sensitized regarding the same.

Vertical transmission of coronavirus disease 2019: a systematic review and meta-analysis

OBJECTIVE

This study aimed to conduct a systematic review of the current literature to determine estimates of vertical transmission of coronavirus disease 2019 based on early RNA detection of severe acute respiratory syndrome coronavirus 2 after birth from various neonatal or fetal sources and neonatal serology.

DATA SOURCES

Eligible studies published until May 28, 2020, were retrieved from PubMed, EMBASE, medRxiv, and bioRxiv collection databases.

STUDY ELIGIBILITY CRITERIA

This systematic review included cohort studies, case series, and case reports of pregnant women who received a coronavirus disease 2019 diagnosis using severe acute respiratory syndrome coronavirus 2 viral RNA test and had reported data regarding the testing of neonates or fetuses for severe acute respiratory syndrome coronavirus 2 immediately after birth and within 48 hours of birth. A total of 30 eligible case reports describing 43 tested neonates and 38 cohort or case series studies describing 936 tested neonates were included.

STUDY APPRAISAL AND SYNTHESIS METHODS

The methodological quality of all included studies was evaluated by a modified version of the Newcastle-Ottawa scale. Quantitative synthesis was performed on cohort or case series studies according to the neonatal biological specimen site to reach pooled proportions of vertical transmission.

RESULTS

Our quantitative synthesis revealed that of 936 neonates from mothers with coronavirus disease 2019, 27 neonates had a positive result for severe acute respiratory syndrome coronavirus 2 viral RNA test using nasopharyngeal swab, indicating a pooled proportion of 3.2% (95% confidence interval, 2.2-4.3) for vertical transmission. Of note, the pooled proportion of severe acute respiratory syndrome coronavirus 2 positivity in neonates by nasopharyngeal swab in studies from China was 2.0% (8/397), which was similar to the pooled proportion of 2.7% (14/517) in studies from outside of China. Severe acute respiratory syndrome coronavirus 2 viral RNA testing in neonatal cord blood was positive in 2.9% of samples (1/34), 7.7% of placenta samples (2/26), 0% of amniotic fluid (0/51), 0% of urine samples (0/17), and 9.7% of fecal or rectal swabs (3/31). Neonatal serology was positive in 3 of 82 samples (3.7%) (based on the presence of immunoglobulin M).

CONCLUSION

Vertical transmission of severe acute respiratory syndrome coronavirus 2 is possible and seems to occur in a minority of cases of maternal coronavirus disease 2019 infection in the third trimester. The rates of infection are similar to those of other pathogens that cause congenital infections. However, given the paucity of early trimester data, no assessment can yet be made regarding the rates of vertical transmission in early pregnancy and potential risk for consequent fetal morbidity and mortality.

Coagulopathy: Another side effect of coronavirus infection

Recently, coronavirus disease 2019 (COVID-19) has been considered as a major health problem around the globe. This severe acute respiratory syndrome has a bunch of features, such as high transmission rate, which are adding to its importance. Overcoming this disease relies on a complete understanding of the viral structure, receptors, at-risk cells or tissues, and pathogenesis. Currently, researches have shown that besides the lack of a proper anti-viral therapeutic method, complications provided by this virus are also standing in the way of decreasing its mortality rate. One of these complications is believed to be a hematologic manifestation. Commonly, three kinds of coagulopathies are detected in COVID-19 patients: disseminated intravascular coagulation (DIC), pulmonary embolism (PE), and deep vein thrombosis (DVT). In this paper, we have reviewed the relation between these conditions and coronavirus-related diseases pathogenesis, severity, and mortality rate.

COVID-19 Epidemic in Bangladesh among Rural and Urban Residents: An Online Cross-Sectional Survey of Knowledge, Attitudes, and Practices

As other nations around the world, Bangladesh is facing enormous challenges with the novel coronavirus (COVID-19) epidemic. To design a prevention and control strategy for this new infectious disease, it is essential to first understand people's knowledge, attitudes, and practices (KAP) regarding COVID-19. This study sought to determine KAP among rural and urban residents as well as predictors of preventive practices associated with COVID-19 in Bangladesh. A social media-based (Facebook) cross-sectional survey was conducted to explore these variables among Bangladeshi adults. Of 1520 respondents who completed the questionnaire, low level of good or sufficient knowledge of COVID-19 (70.8%) and practices associated with COVID-19 (73.8%) were found. Despite the low level of knowledge and practices, respondents' attitude (78.9%) towards COVID-19 was relatively high. Results suggest that compared to urban, rural residents are at a particularly high risk of COVID-19 because they were found to have significantly lower knowledge (p = 0.001) and practice levels (p = 0.002) than were urban residents. Multivariable logistic regression analysis identified gender, education, knowledge of COVID-19 transmission, signs and symptoms, and sources of information as factors significantly associated with preventive practices against COVID-19. Further attention and effort should be directed toward increasing both knowledge and practices targeting the general population in Bangladesh, particularly the rural and less educated residents. Findings from this study provide baseline data that can be used to promote integrated awareness of and effective health education programs about COVID-19 prevention and control strategies in Bangladesh, and similar COVID-19 endemic countries.

COVID-19 Epidemic in Bangladesh among Rural and Urban Residents: An Online Cross-Sectional Survey of Knowledge, Attitudes, and Practices

As other nations around the world, Bangladesh is facing enormous challenges with the novel coronavirus (COVID-19) epidemic. To design a prevention and control strategy for this new infectious disease, it is essential to first understand people's knowledge, attitudes, and practices (KAP) regarding COVID-19. This study sought to determine KAP among rural and urban residents as well as predictors of preventive practices associated with COVID-19 in Bangladesh. A social media-based (Facebook) cross-sectional survey was conducted to explore these variables among Bangladeshi adults. Of 1520 respondents who completed the questionnaire, low level of good or sufficient knowledge of COVID-19 (70.8%) and practices associated with COVID-19 (73.8%) were found. Despite the low level of knowledge and practices, respondents' attitude (78.9%) towards COVID-19 was relatively high. Results suggest that compared to urban, rural residents are at a particularly high risk of COVID-19 because they were found to have significantly lower knowledge (p = 0.001) and practice levels (p = 0.002) than were urban residents. Multivariable logistic regression analysis identified gender, education, knowledge of COVID-19 transmission, signs and symptoms, and sources of information as factors significantly associated with preventive practices against COVID-19. Further attention and effort should be directed toward increasing both knowledge and practices targeting the general population in Bangladesh, particularly the rural and less educated residents. Findings from this study provide baseline data that can be used to promote integrated awareness of and effective health education programs about COVID-19 prevention and control strategies in Bangladesh, and similar COVID-19 endemic countries.