Potential Rapid Diagnostics, Vaccine and Therapeutics for 2019 Novel Coronavirus (2019-nCoV): A Systematic Review

A complementary critical appraisal on systematic reviews regarding the most efficient therapeutic strategies for the current COVID-19 (SARS-CoV-2) pandemic

BACKGROUND

This critical appraisal aims to clarify which systematic reviews on COVID-19 treatment are based on high-value evidence. Hereby, the most profitable medicines can be suggested.

METHODS

The mesh terms of "COVID-19 drug treatment" (Supplementary Concept) and "COVID-19 drug treatment" were sequentially utilized as search strategies in Medline and Science direct on October 18, 2020. Searches were confined to systematic reviews/meta-analyses. The Cochrane database was searched on November 1, 2020 with "COVID." With adding up four articles from other resources, 84 systematic reviews were considered for initial screening. Finally, 22 articles fulfilled the criteria and were assessed using PRISMA guidelines.

RESULTS

Increasing number of clinical trials from the onset of the COVID-19 pandemic has revealed that hydroxychloroquine and chloroquine are not only profitable but also deleterious. Lopinavir/ritonavir failed to maintain their initial efficacy in improving clinical symptoms and mortality rate. Steroids and tocilizumab were suggested in patients with intensely severe symptoms. Steroids reduced mechanical ventilation and death in severely ill patients. Plasma or immunoglobulins effects are absolutely controversial. Favorable impressions of remdesivir have been relied on for the early onset of this drug. Hypotension and abnormal liver function tests were realized as its side effects. Favipiravir has resulted in a higher viral clearance than remdesivir. However, this claim needs to be proved with subsequent clinical trials.

CONCLUSIONS

Currently, remdesivir and favipiravir are advantageous drugs that should be administered in the early phases. Their side effects are not well known and need to be found in the following research projects. Steroids and tocilizumab have been considered beneficial in the cytokine storm phase.

rRT-PCR for SARS-CoV-2: Analytical considerations

The COVID-19 pandemic remains a significant problem involving health systems worldwide. Accurate and early detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection is critical for minimizing spread and initiating treatment. Among test methods, real-time reverse-transcriptase polymerase-chain-reaction (rRT-PCR) is considered the gold standard. Although this test has high specificity and relatively high sensitivity, the occurrence of falsely negative results in symptomatic patients and/or having a positive CT scan remains a challenge. Sources of error can be pre-analytical (sampling, storage and processing), analytical (RNA extraction, cDNA synthesis and amplification) and post-analytical (interpretation and analysis and test reporting). These potential sources of error and efforts to mitigate are reviewed in this article with an emphasis on the analytical phase.

Performance Evaluation of the Siemens SARS-CoV-2 Total Antibody and IgG Antibody Test

Objective

In this study, the performance of 2 commercially available SARS-CoV-2 antibody assays is evaluated.

Methods

The Siemens SARS-CoV-2 Total (COV2T) and IgG (COV2G) antibody tests were evaluated on a Siemens Atellica IM1300 analyzer. Imprecision was assessed with the CLSI EP15 protocol using positive controls. Ninety control group specimens were analyzed for specificity, and 175 specimens from 58 patients with polymerase chain reaction–confirmed SARS-CoV-2 were measured for the sensitivity and kinetics of the antibody response.

Results

Within-run and total imprecision were acceptable for both assays. Both tests showed a specificity of 100%. Sensitivity earlier in the disease state was greater for the COV2T assay than for the COV2G assay, but sensitivity >14 days after onset of symptoms approached 100% for both. For all patients, antibody titers remained above the seroconversion cutoff for all follow-up specimens.

Conclusion

This study shows acceptable performance for both the Siemens COV2T and COV2G test, although seroconversion occurs earlier with the COV2T test.

Seroprevalence of SARS-CoV-2 Assessed by Four Chemiluminescence Immunoassays and One Immunocromatography Test for SARS-Cov-2

The onset of the new SARS-CoV-2 coronavirus encouraged the development of new serologic tests that could be additional and complementary to real-time RT-PCR-based assays. In such a context, the study of performances of available tests is urgently needed, as their use has just been initiated for seroprevalence assessment. The aim of this study was to compare four chemiluminescence immunoassays and one immunochromatography test for SARS-Cov-2 antibodies for the evaluation of the degree of diffusion of SARS-CoV-2 infection in Salerno Province (Campania Region, Italy). A total of 3,185 specimens from citizens were tested for anti-SARS-CoV-2 antibodies as part of a screening program. Four automated immunoassays (Abbott and Liaison SARS-CoV-2 CLIA IgG and Roche and Siemens SARS-CoV-2 CLIA IgM/IgG/IgA assays) and one lateral flow immunoassay (LFIA Technogenetics IgG–IgM COVID-19) were used. Seroprevalence in the entire cohort was 2.41, 2.10, 1.82, and 1.85% according to the Liaison IgG, Abbott IgG, Siemens, and Roche total Ig tests, respectively. When we explored the agreement among the rapid tests and the serologic assays, we reported good agreement for Abbott, Siemens, and Roche (Cohen's Kappa coefficient 0.69, 0.67, and 0.67, respectively), whereas we found moderate agreement for Liaison (Cohen's kappa coefficient 0.58). Our study showed that Abbott and Liaison SARS-CoV-2 CLIA IgG, Roche and Siemens SARS-CoV-2 CLIA IgM/IgG/IgA assays, and LFIA Technogenetics IgG-IgM COVID-19 have good agreement in seroprevalence assessment. In addition, our findings indicate that the prevalence of IgG and total Ig antibodies against SARS-CoV-2 at the time of the study was as low as around 3%, likely explaining the amplitude of the current second wave.

CRISPR Systems for COVID-19 Diagnosis

The emergence of the new coronavirus 2019 (COVID-19) was first seen in December 2019, which has spread rapidly and become a global pandemic. The number of cases of COVID-19 and its associated mortality have raised serious concerns worldwide. Early diagnosis of viral infection undoubtedly allows rapid intervention, disease management, and substantial control of the rapid spread of the disease. Currently, the standard approach for COVID-19 diagnosis globally is the RT-qPCR test; however, the limited access to kits and associated reagents, the need for specialized lab equipment, and the need for highly skilled personnel has led to a detection slowdown. Recently, the development of clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostic systems has reshaped molecular diagnosis. The benefits of the CRISPR system such as speed, precision, specificity, strength, efficiency, and versatility have inspired researchers to develop CRISPR-based diagnostic and therapeutic methods. With the global COVID-19 outbreak, different groups have begun to design and develop diagnostic and therapeutic programs based on the efficient CRISPR system. CRISPR-based COVID-19 diagnostic systems have advantages such as a high detection speed (i.e., 30 min from raw sample to reach a result), high sensitivity and precision, portability, and no need for specialized laboratory equipment. Here, we review contemporary studies on the detection of COVID-19 based on the CRISPR system.

RNA Coronaviruses' Outbreaks: Recent Progress on the SARS-CoV-2 Pandemic Diagnostic Tests, Vaccination and Therapeutics

Coronaviruses are RNA-infective viruses that could be considered principal players in universal high-profile outbreaks, namely the Severe Acute Respiratory Syndrome (SARS, 2002-2003), the Middle East Respiratory Syndrome (MERS, 2012) and the continuing novel coronavirus disease (COVID-19, 2019) pandemic. RNA coronaviruses infections raise public health concerns with infections' severity ranging from serious pandemics and highly contagious infections to common influenza episodes. With a wide consensus concerning the seminal role of early detection of the infectious agent on the clinical prognosis, recent technological endeavors have facilitated the rapid, sensitive and specific diagnosis of viral infections. Given that the burst of confirmed cases of the novel coronavirus disease 2019 (COVID-19) are climbing steeply, and we are amid this pandemic, this work will center at the respiratory RNA-viruses outbreaks, including the three coronaviruses-related pandemics, emphasizing on the approved diagnostic approaches, outlining therapeutic clinical trials as well as vaccine candidates. Based on the accumulated data and knowledge on the previous RNA-virus outbreaks, this review aspires to link the current intervention measures against SARS-CoV-2 infection with the previous interventions and to provide a roadmap for any possible future measures.

Phytochemicals from Plant Foods as Potential Source of Antiviral Agents: An Overview

To date, the leading causes of mortality and morbidity worldwide include viral infections, such as Ebola, influenza virus, acquired immunodeficiency syndrome (AIDS), severe acute respiratory syndrome (SARS) and recently COVID-19 disease, caused by the SARS-CoV-2 virus. Currently, we can count on a narrow range of antiviral drugs, especially older generation ones like ribavirin and interferon which are effective against viruses in vitro but can often be ineffective in patients. In addition to these, we have antiviral agents for the treatment of herpes virus, influenza virus, HIV and hepatitis virus. Recently, drugs used in the past especially against ebolavirus, such as remdesivir and favipiravir, have been considered for the treatment of COVID-19 disease. However, even if these drugs represent important tools against viral diseases, they are certainly not sufficient to defend us from the multitude of viruses present in the environment. This represents a huge problem, especially considering the unprecedented global threat due to the advancement of COVID-19, which represents a potential risk to the health and life of millions of people. The demand, therefore, for new and effective antiviral drugs is very high. This review focuses on three fundamental points: (1) presents the main threats to human health, reviewing the most widespread viral diseases in the world, thus describing the scenario caused by the disease in question each time and evaluating the specific therapeutic remedies currently available. (2) It comprehensively describes main phytochemical classes, in particular from plant foods, with proven antiviral activities, the viruses potentially treated with the described phytochemicals. (3) Consideration of the various applications of drug delivery systems in order to improve the bioavailability of these compounds or extracts. A PRISMA flow diagram was used for the inclusion of the works. Taking into consideration the recent dramatic events caused by COVID-19 pandemic, the cry of alarm that denounces critical need for new antiviral drugs is extremely strong. For these reasons, a continuous systematic exploration of plant foods and their phytochemicals is necessary for the development of new antiviral agents capable of saving lives and improving their well-being.

The effect of propolis plus Hyoscyamus niger L. methanolic extract on clinical symptoms in patients with acute respiratory syndrome suspected to COVID-19: A clinical trial

The outbreak of Coronavirus disease 2019 (COVID‐19) has caused a global health crisis. Nevertheless, no antiviral treatment has yet been proven effective for treating COVID‐19 and symptomatic supportive cares have been the most common treatment. Therefore, the present study was designed to evaluate the effects of propolis and Hyoscyamus niger L. extract in patients with COVID‐19. This randomized clinical trial was conducted on 50 cases referred to Akhavan and Sepehri Clinics, Kashan university of medical sciences, Iran. Subjects were divided into two groups (intervention and placebo). This syrup (containing 1.6 mg of methanolic extract along with 450 mg of propolis per 10 mL) was administered three times a day to each patient for 6 days. The clinical symptoms of COVID‐19 such as: dry cough, shortness of breath, sore throat, chest pain, fever, dizziness, headache, abdominal pain, and diarrhea were reduced with propolis plus Hyoscyamus niger L. extract than the placebo group. However, the administration of syrup was not effective in the control of nausea and vomiting. In conclusion, syrup containing propolis and Hyoscyamus niger L. extract had beneficial effects in ameliorating the signs and symptoms of COVID‐19 disease, in comparison with placebo groups.

TRIzol-based RNA extraction for detection protocol for SARS-CoV-2 of coronavirus disease 2019

Diagnostic testing is important for managing the 2019 novel coronavirus (SARS-CoV-2). We developed an optimized protocol for SARS-CoV-2 RNA extraction from the surface of the respiratory mucosa with nasopharyngeal swabs and compared the sensitivity of RNA extraction methods. RNA extraction was performed using three different procedures (TRIzol, QIAamp, VMT-TRIzol) from nine positive SARS-CoV-2 samples. SARS-CoV-2 was detected by real-time reverse transcriptase PCR (RT-PCR) using a detection kit for SARS-CoV-2 (Sun Yat-sen University). Compared to RT-PCR results, there were no discernible differences in detection rates when comparing the three different extraction procedures. On the basis of these results, the use of TRIzol as a transport medium and RNA extraction method for SARS-CoV-2 detection may be a helpful alternative for laboratories facing shortages of commercial testing kits.

False-positive colloidal gold-based immunochromatographic strip assay reactions for antibodies to SARS-CoV-2 in patients with autoimmune diseases

BACKGROUND

The outbreak of the novel 2019 coronavirus disease (COVID-19) was declared a global pandemic by the World Health Organization (WHO) on March 11, 2020. The diagnosis of COVID-19 is frequently based on a positive serological test. We noted the occurrence of false-positive results for COVID-19 in the colloidal gold-based immunochromatographic strip (ICS) assay in sera from patients with autoimmune diseases (ADs). This study aimed to evaluate the possible reasons for the false-positive results in two ICS assays (Wondfo ICS and Innovita ICS) and to investigate the effect of urea dissociation in reducing false-positive results.

METHODS

The sera of 135 patients with ADs, 13 confirmed COVID-19 patients, 95 disease controls, and 120 healthy controls were tested for immunoglobin M (IgM) and IgG against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using Wondfo and Innovita ICS kits. The distributions of auto-antibodies in antibody-positive and antibody-negative groups were also compared, and bivariable logistic regression was used to assess auto-antibodies associated with false-positive results. A urea dissociation test of ICS was performed for the SARS-CoV-2 antibody-positive samples.

RESULTS

Specificity of Wondfo ICS for the 95 disease controls was 94.74% compared to 98.95% and 96.84% for Innovita SARS-CoV-2 IgM and IgG, respectively. Specificity of Wondfo ICS for the 120 healthy controls was 97.5% compared to 100% and 99.17% for Innovita SARS-CoV-2 IgM and IgG, respectively. Specificity of Wondfo ICS for AD patients was 73.33% compared to 97.78% and 96.30% for Innovita SARS-CoV-2 IgM and IgG, respectively. Sensitivity was 74.07% for Wondfo compared to 70.37% for Innovita IgM and 66.67% for Innovita IgG. Using the Wondfo ICS, the percentage of elevated rheumatoid factor (RF) level (>20 IU/mL) was higher in the SARS-CoV-2 antibody-positive group compared with the antibody-negative group [27/36 (75.0%) vs. 34/99 (34.34%), P=0.001]. The elevated RF was associated with antibody positivity, with an odds ratio of 4.671 [95% confidence interval (CI), 1.88-11.69]. The specificity of the Wondfo ICS assay for the AD patients was increased from 73.33% to 94.07% after the urea dissociation assay.

CONCLUSIONS

An elevated serum RF level could lead to false-positive results when detecting SARS-CoV-2 antibodies using the Wondfo ICS kit, and the urea dissociation assay would be helpful in reducing the incidence of false-positive results.

The Inclusive Review on SARS-CoV-2 Biology, Epidemiology, Diagnosis, and Potential Management Options

A novel coronavirus member was reported in Wuhan City, Hubei Province, China, at the end of the year 2019. Initially, the infection spread locally, affecting the Wuhan people, and then expanded rapidly throughout the world. On 11 March 2020, the World Health Organization (WHO) proclaimed it a global pandemic. The virus is a new strain most closely related to a bat coronavirus (RaTG13) which was not previously discovered in humans and is now formally known as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Coronavirus disease 2019 (COVID-19) is the disease syndrome that the SARS-CoV-2 virus triggers. It is suggested that SARS-CoV-2 can be transmitted through aerosols, direct/indirect contact, and also during medical procedures and specimen handling. The infection is characterized by isolated flu-like symptoms, but there may be specific signs of fever, fatigue, cough, and shortness of breath, as well as the loss of smell and breathing difficulty. Within this report, we tried to review the most current scientific literature published by January 2021 on various aspects of the outbreak, including virus structure, pathogenesis, clinical presentation, epidemiology, diagnostic approaches, potential therapeutics and vaccines, and prospects. We hope this article makes a beneficial impact on public education to better deal with the SARS-CoV-2 crisis and push a step forward in the near term towards its prevention and control.

Effect of the COVID-19 Pandemic on Interest in Home-Based Exercise: An Application of Digital Epidemiology

Background and aims: According to the World Health Organization (WHO), immediate self-quarantine is assumed as the best course of action for highly contagious diseases. Since the coronavirus disease 2019 (COVID-19) pandemic, many individuals have become overweight and are also suffering from physical problems. The present study aimed to evaluate the effect of the COVID-19 pandemic on interest in home-based exercise. Methods: This digital epidemiological study used data sources outside the health system. This descriptive study with a comprehensive electronic systematic search in the Google Trends database using the keyword of "home-based exercise" retrieved the relevant data about the Internet search activity of Iranian community members. The data were accordingly obtained within two time intervals, i.e., from February 18, 2020 to October 18, 2020 and eight months prior to the outbreak of COVID-19 (June 18, 2019 to February 18, 2020). To analyze the data, the Wilcoxon test and the Spearman’s correlation coefficient were used. Results: The results showed significant increase in "home-based exercise" Google search in the eight-month time interval during COVID-19 compared with the same period before the pandemic (P<0.001). Moreover, there was a significant correlation between "home-based exercise" Google search and positive COVID-19 cases in the time intervals of February 18, 2020 to April 18, 2020 (r=0.756, P=0.0001), April 18, 2020 to June 18, 2020 (r=-461, P=0.0001), but not June 18, 2020 to August 18, 2020 (r=0.044, P=0.737), August 18, 2020 to October 18, 2020 (r=0.246, P=0.056), and over time (r=-0.083, P=0.0195). Conclusion: The prevalence rate of the COVID-19 pandemic and social constraints including self-quarantine seem to have raised people’s interest in doing exercises, especially home-based exercises.

Sane and safe: Forced social distancing to prevent human-to-human transmission of COVID-19

The current outbreak of COVID-19, originating from the city of Wuhan in China and ultimately involving over 200 countries, is now a global concern. Evidence indicates that COVID-19 spread to humans from wild animals, causing severe respiratory tract infections in humans; the typical symptoms of COVID include cough, high-grade fever, sore throat, and difficulty in breathing. The infection spreads from human to human via droplets. Therefore, social or physical distancing can reduce spread within communities. Asymptomatic spread can also occur during family gatherings or in the workplace; thus, we must enforce physical distancing as much as possible to reduce the spread of cases.

SARS-CoV-2 Proteome-Wide Analysis Revealed Significant Epitope Signatures in COVID-19 Patients

The WHO declared the COVID-19 outbreak a public health emergency of international concern. The causative agent of this acute respiratory disease is a newly emerged coronavirus, named SARS-CoV-2, which originated in China in late 2019. Exposure to SARS−CoV−2 leads to multifaceted disease outcomes from asymptomatic infection to severe pneumonia, acute respiratory distress and potentially death. Understanding the host immune response is crucial for the development of interventional strategies. Humoral responses play an important role in defending viral infections and are therefore of particular interest. With the aim to resolve SARS-CoV-2-specific humoral immune responses at the epitope level, we screened clinically well-characterized sera from COVID-19 patients with mild and severe disease outcome using high-density peptide microarrays covering the entire proteome of SARS-CoV-2. Moreover, we determined the longevity of epitope-specific antibody responses in a longitudinal approach. Here we present IgG and IgA-specific epitope signatures from COVID-19 patients, which may serve as discriminating prognostic or predictive markers for disease outcome and/or could be relevant for intervention strategies.

Ultrasensitive and Highly Specific Lateral Flow Assays for Point-of-Care Diagnosis

Lateral flow assays (LFAs) are paper-based point-of-care (POC) diagnostic tools that are widely used because of their low cost, ease of use, and rapid format. Unfortunately, traditional commercial LFAs have significantly poorer sensitivities (μM) and specificities than standard laboratory tests (enzyme-linked immunosorbent assay, ELISA: pM-fM; polymerase chain reaction, PCR: aM), thus limiting their impact in disease control. In this Perspective, we review the evolving efforts to increase the sensitivity and specificity of LFAs. Recent work to improve the sensitivity through assay improvement includes optimization of the assay kinetics and signal amplification by either reader systems or additional reagents. Together, these efforts have produced LFAs with ELISA-level sensitivities (pM-fM). In addition, sample preamplification can be applied to both nucleic acids (direct amplification) and other analytes (indirect amplification) prior to LFA testing, which can lead to PCR-level (aM) sensitivity. However, these amplification strategies also increase the detection time and assay complexity, which inhibits the large-scale POC use of LFAs. Perspectives to achieve future rapid (<30 min), ultrasensitive (PCR-level), and "sample-to-answer" POC diagnostics are also provided. In the case of LFA specificity, recent research efforts have focused on high-affinity molecules and assay optimization to reduce nonspecific binding. Furthermore, novel highly specific molecules, such as CRISPR/Cas systems, can be integrated into diagnosis with LFAs to produce not only ultrasensitive but also highly specific POC diagnostics. In summary, with continuing improvements, LFAs may soon offer performance at the POC that is competitive with laboratory techniques while retaining a rapid format.

COVID-19 may enhance risk of thrombosis and hemolysis in the G6PD deficient patients

COVID-19 has become a major public health problem since December, 2019 and no highly effective drug has been found until now. Numbers of infected people and deaths by COVID-19 are increasing every day worldwide, therefore self-isolation and protection are highly recommended to prevent the spread of the virus and especially to protect major risk groups such as the elderly population and people with comorbidities including diabetes, hypertension, cancer, cardiovascular diseases and metabolic syndrome. On the other hand, young people without any secondary disease have died by COVID-19 as well. In this study we compared two male patients infected by COVID-19 at the same age and one of them was diagnosed with G6PD deficiency. Both COVID-19 and G6PD deficiency enhance the risk of hemolysis and thrombosis. Serum biochemistry, hemogram and immunological parameters showed that risk of hemolysis and thrombosis may increase in the G6PD deficient patient infected by COVID-19.

Lessons from the COVID-19 Pandemic on the Use of Artificial Intelligence in Digital Radiology: The Submission of a Survey to Investigate the Opinion of Insiders

The development of artificial intelligence (AI) during the COVID-19 pandemic is there for all to see, and has undoubtedly mainly concerned the activities of digital radiology. Nevertheless, the strong perception in the research and clinical application environment is that AI in radiology is like a hammer in search of a nail. Notable developments and opportunities do not seem to be combined, now, in the time of the COVID-19 pandemic, with a stable, effective, and concrete use in clinical routine; the use of AI often seems limited to use in research applications. This study considers the future perceived integration of AI with digital radiology after the COVID-19 pandemic and proposes a methodology that, by means of a wide interaction of the involved actors, allows a positioning exercise for acceptance evaluation using a general purpose electronic survey. The methodology was tested on a first category of professionals, the medical radiology technicians (MRT), and allowed to (i) collect their impressions on the issue in a structured way, and (ii) collect their suggestions and their comments in order to create a specific tool for this professional figure to be used in scientific societies. This study is useful for the stakeholders in the field, and yielded several noteworthy observations, among them (iii) the perception of great development in thoracic radiography and CT, but a loss of opportunity in integration with non-radiological technologies; (iv) the belief that it is appropriate to invest in training and infrastructure dedicated to AI; and (v) the widespread idea that AI can become a strong complementary tool to human activity. From a general point of view, the study is a clear invitation to face the last yard of AI in digital radiology, a last yard that depends a lot on the opinion and the ability to accept these technologies by the operators of digital radiology.

Exploring dynamics and network analysis of spike glycoprotein of SARS-COV-2

The ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 continues to rage with devastating consequences on human health and global economy. The spike glycoprotein on the surface of coronavirus mediates its entry into host cells and is the target of all current antibody design efforts to neutralize the virus. The glycan shield of the spike helps the virus to evade the human immune response by providing a thick sugar-coated barrier against any antibody. To study the dynamic motion of glycans in the spike protein, we performed microsecond-long molecular dynamics simulation in two different states that correspond to the receptor binding domain in open or closed conformations. Analysis of this microsecond-long simulation revealed a scissoring motion on the N-terminal domain of neighboring monomers in the spike trimer. The roles of multiple glycans in shielding of spike protein in different regions were uncovered by a network analysis, in which the high betweenness centrality of glycans at the apex revealed their importance and function in the glycan shield. Microdomains of glycans were identified featuring a high degree of intracommunication in these microdomains. An antibody overlap analysis revealed the glycan microdomains as well as individual glycans that inhibit access to the antibody epitopes on the spike protein. Overall, the results of this study provide detailed understanding of the spike glycan shield, which may be utilized for therapeutic efforts against this crisis.

Leveraging on the genomics and immunopathology of SARS-CoV-2 for vaccines development: prospects and challenges

The incidence and case-fatality rates (CFRs) of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection, the etiological agent for Coronavirus Disease 2019 (COVID-19), have been rising unabated. Even though the entire world has been implementing infection prevention and control measures, the pandemic continues to spread. It has been widely accepted that preventive vaccination strategies are the public health measures for countering this pandemic. This study critically reviews the latest scientific advancement in genomics, replication pattern, pathogenesis, and immunopathology of SARS-CoV-2 infection and how these concepts could be used in the development of vaccines. We also offer a detailed discussion on the anticipated potency, efficacy, safety, and pharmaco-economic issues that are and will be associated with candidate COVID-19 vaccines.

Molecular (real-time reverse transcription polymerase chain reaction) diagnosis of SARS-CoV-2 infections: complexity and challenges

The outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first recorded in Wuhan, China. The World Health Organization initially classified COVID-19 as a public health emergency and subsequently declared the disease a global pandemic. COVID-19 can take at least three distinct forms: severe acute distress syndrome with a potentially fatal outcome, mild respiratory illness (pneumonia with eventual recovery) and asymptomatic infection. All three disease forms have the potential to transmit the infection to healthy contacts. At present, real-time reverse transcription polymerase chain reaction (RT-PCR) is the only available laboratory tool to confirm the presence of viral RNA in patient specimens. These assays are designed to detect one or more (at least 2) SARS-CoV-2 RNA gene targets allowing the detection of the virus. Commercially available RT-PCR assays employ various gene targets of the viral genome in their assay systems. Additionally, there are differences in primer selection for the same gene region of SARS-CoV-2. At present, it is unclear whether the results from different RT-PCR assays are comparable in detecting the spectrum of COVID-19 manifestations. The purpose of the present article is twofold: first, to briefly focus on the findings of these reports; and second, to emphasize the various challenges and flaws that can potentially impact the diagnostic accuracy of RT-PCR testing for SARS-CoV-2.

Development of a multiplex Loop-Mediated Isothermal Amplification (LAMP) assay for on-site diagnosis of SARS CoV-2

A newly identified coronavirus, designated as severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), has spread rapidly from its epicenter in China to more than 150 countries across six continents. In this study, we have designed three reverse-transcription loop-mediated isothermal amplification (RT-LAMP) primer sets to detect the RNA-dependent RNA polymerase (RdRP), Envelope (E) and Nucleocapsid protein (N) genes of SARS CoV-2. For one tube reaction, the detection limits for five combination SARS CoV-2 LAMP primer sets (RdRP/E, RdRP/N, E/N, RdRP/E/N and RdRP/N/Internal control (actin beta)) were evaluated with a clinical nasopharyngeal swab sample. Among the five combination, the RdRP/E and RdRP/N/IC multiplex LAMP assays showed low detection limits. The sensitivity and specificity of the RT-LAMP assay were evaluated and compared to that of the widely used Allplex™ 2019-nCoV Assay (Seegene, Inc., Seoul, South Korea) and PowerChek™ 2019-nCoV Real-time PCR kit (Kogenebiotech, Seoul, South Korea) for 130 clinical samples from 91 SARS CoV-2 patients and 162 NP specimens from individuals with (72) and without (90) viral respiratory infections. The multiplex RdRP (FAM)/N (CY5)/IC (Hex) RT-LAMP assay showed comparable sensitivities (RdRP: 93.85%, N: 94.62% and RdRP/N: 96.92%) to that of the Allplex™ 2019-nCoV Assay (100%) and superior to those of PowerChek™ 2019-nCoV Real-time PCR kit (RdRP: 92.31%, E: 93.85% and RdRP/E: 95.38%).

SARS-CoV-2-mediated immune system activation and potential application in immunotherapy

Although novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-mediated pulmonary inflammation has recently attracted great attention, its pathology and pathogenesis are not clear. Notably, due to both its high infective and pathogenicity, SARS-CoV-2 infection may cause a severe sometimes fatal respiratory disease. A specific vaccine, which relies on the analysis of SARS-CoV-2 structural protein-derived antigenic peptides, is indispensable for restraining the spread and reducing the mortality of SARS-CoV-2. SARS-CoV-2 infections activate cytototxic, myeloid-derived suppressor cells, dendritic cells, macrophages, as well as natural killer, B, helper T, and regulatory T cells, thus further stimulating innate and antigen-specific immune responses. Nevertheless, many immune effector cells cause hyperinflammation and pulmonary immunopathology by releasing proinflammatory cytokines and chemokines, including interferon (IFN)-α, IFN-β, IFN-γ, monocyte chemoattractant protein-1, macrophage inflammatory protein (MIP)-1A, MIP1B, interleukin (IL)-1, IL-2, IL-4, IL-6, IL-7, IL-8, IL-9, IL-12, IL-17, and IL-18, platelet-derived growth factor, fibroblast growth factor, tumor necrosis factor-α, and induced protein 10. Interestingly, related products derived from SARS-CoV-2 are likely to trigger immune evasion. Therefore, investigating SARS-CoV-2-specific vaccines, blocking immunopathology, and prohibiting immune evasion are urgently required for treating SARS-CoV-2 infection. In this review, we emphatically illuminated the development of a SARS-CoV-2-specific vaccine based on the analysis of epitopes, also expounding the molecular mechanisms of SARS-CoV-2-mediated cytokine release syndrome. Furthermore, we comprehensively discussed SARS-CoV-2-associated immune evasion and lung immunopathology. Lastly, potential therapeutic strategies against SARS-CoV-2 were explored.

Cardiovascular implications and complications of the coronavirus disease-2019 pandemic: a world upside down

PURPOSE OF REVIEW

The new pandemic of coronavirus disease-2019 (COVID-19) has produced a global tumult and has overburdened national health systems. We herein discuss the cardiovascular implications and complications of this pandemic analyzing the most recent data clustered over the last several months.

RECENT FINDINGS

COVID-19 afflicts the cardiovascular system producing acute cardiac injury in 10-20% of cases with mild disease but in greater than 50-60% in severe cases, contributing to patients' demise. Other cardiovascular complications include arrhythmias, heart failure, pulmonary embolism and shock. Off-label therapies are being trialed with their own inherent cardiovascular risks, while supportive therapies currently dominate, until more specific and effective antiviral therapies and vaccinations become available. A controversial issue relates to the safety of drugs blocking the renin--angiotensin system as an angiotensin-converting enzyme (ACE) homologue, ACE2, serves as the receptor for viral entry into host cells. However, to-date, no harm has been proven for these drugs.

SUMMARY

In the cardiovascular system, COVID-19 can induce acute cardiac injury, arrhythmias, heart failure, pulmonary embolism, shock and death, whereas anti-COVID therapies also confer serious cardiovascular side-effects. Ongoing extensive efforts focus on specific vaccines and antivirals. Meanwhile, cardiovascular risk factors and diseases should be jointly controlled according to current evidence-based guidelines.

A Retrospective Study of the Epidemiologic and Clinical Characteristics of COVID-19 Among Hospitalized Patients in Quanzhou, China

Coronavirus disease 2019 (COVID-19) has spread throughout China. However, information about COVID-19 in cities and regions outside Wuhan is limited and the indicators that predict the length of hospital stay for patients with COVID-19 are unclear. Therefore, we collected clinical data from 47 patients with COVID-19 in Quanzhou City. The median age was 38 years [interquartile range (IQR): 31-50 years], and 24 (51%) were male. There were 8 mild, 36 moderate, and 3 severe/critical cases. The median interval from exposure to disease onset was 13 days (IQR: 8-18 days). The incidence of severe/critical cases was 33% (3/10) in patients with hypertension. Common symptoms included fever (83%), cough (77%), fatigue (40%), a sore, dry throat (28%), and diarrhea (21%). One patient (2%) developed respiratory distress syndrome on day 13 of inpatient treatment. Six patients had leukopenia, 17 had elevated C-reactive protein (CRP), and 8 had lymphocytopenia and elevated lactate dehydrogenase (LDH). The median length of hospitalization was 22 days (IQR: 16-30 days). Dynamic monitoring of LDH, CRP, and neutrophil-lymphocyte ratio predicted whether length of hospitalization would exceed 21 days. Most patients presented with mild and moderate disease. Patients with hypertension were more likely to become severe or critical. Dynamic monitoring of LDH, CRP, and neutrophil-lymphocyte ratio levels can help predict delayed discharge from the hospital.

Coronavirus Disease 2019-Challenges Today and Tomorrow in Orthodontic Practice: A Review

From the start of 2020, the world has witnessed the biggest health and humanitarian crisis in the modern century named coronavirus disease 2019. The rapid spread of infection created chaos and confusion across the globe. Like all other health professions, a timely and major reorganization of orthodontic services is challenging. Unlike other medical emergencies, an orthodontic emergency does not require immediate attention in most cases. With advances in the modern web-based communication systems, minor problems can be managed online in orthodontic practice. During an emergency, however, orthodontists have a moral obligation to treat and manage patients under the World Health Organization guidelines and protocol.

Importance of Preoperative Screening Strategies for Coronavirus Disease 2019 in Patients Undergoing Cesarean Sections: A Retrospective, Large Single-Center, Observational Cohort Study

During the coronavirus disease 2019 (COVID-19) pandemic, many guidelines have recommended postponing non-emergency operations. However, cesarean sections cannot be indefinitely delayed. Our institution has established a COVID-19 screening strategy for patients undergoing cesarean section. We evaluated the usefulness of this screening strategy. Parturients undergoing cesarean section at our center during the first peak of the COVID-19 outbreak were retrospectively analyzed. Each parturient underwent a questionnaire survey evaluating epidemiological correlation and symptoms at admission. Reverse transcriptase-polymerase chain reaction (RT-PCR) testing and/or chest radiography were performed. In total, 296 parturients underwent cesarean section. All elective and 37 emergency cesarean sections were performed in general operating rooms because they were considered to have a low risk of COVID-19 infection through the screening process. However, 42 emergency cases were performed in negative-pressure operating rooms with full personal protective equipment (PPE) because the RT-PCR results could not be confirmed in a timely manner. None of them were positive for RT-PCR, and there were no cases of nosocomial infection. A comprehensive preoperative screening strategy, including symptomatic and epidemiological correlation, PCR, and/or imaging test, should be performed in patients undergoing cesarian section. Further, cesarean sections in parturients with unconfirmed COVID-19 status should be performed in a negative-pressure operating room with appropriate PPE.

Comparison of clinical and serological features of RT-PCR positive and negative COVID-19 patients

BACKGROUND

In December 2019, an outbreak of coronavirus disease 2019 (COVID-19) began in Wuhan, China, and led to a global epidemic. We aimed to compare the clinical and serological features of COVID-19 patients with positive and negative reverse transcriptase polymerase chain reaction (RT-PCR) tests.

METHODS

This was a retrospective cohort study conducted from 9 February to 4 April 2020. COVID-19 patients at Leishenshan Hospital in Wuhan, China (125 total cases; 87 RT-PCR positive and 38 RT-PCR negative) were included. COVID-19 serology was assessed by colloidal gold assay. All cases were analyzed for demographic, clinical, and serological features.

RESULTS

There were no significant differences in most demographic features, clinical symptoms, complications or treatments of RT-PCR positive and negative COVID-19 patients. Serum IgM/IgG was positive in 82 (94%) and 33 (87%) RT-PCR positive and negative cases, respectively. IgM was detectable as early as 3 days after symptom onset and was undetectable 60 days after symptom onset. By contrast, IgG could be detected only 10 days after symptom onset and reached its peak 60 days after symptom onset.

CONCLUSIONS

Serological tests performed during the appropriate time window of disease progression could be valuable auxiliary methods to RT-PCR in COVID-19 patients.

Immune system response during viral Infections: Immunomodulators, cytokine storm (CS) and Immunotherapeutics in COVID-19

Coronaviruses are non-segmented and single stranded positive-sense RNA (+ssRNA) viruses. To date, 06 human coronaviruses (HCoVs) are reported; α-CoVs (HCoVs-NL63 and HCoVs-229E) and β-CoVs (HCoVs-OC43, HCoVs-HKU1, SARS-CoV, MERS-CoV). While, novel coronavirus (SARS-CoV-2) is the most recent member. The genome sequence of SARS-CoV-2 is 82% similar to SARS-COV-1. The compelling evidences link the progression of viral infection of SARS-CoV-2 with excessive inflammation as a result of the exaggerated immune response and elevated production of "immunocytokines" resulting in cytokine storm (CS); followed by a series of events, like acute organ damage, acute respiratory distress syndrome (ARDS) as well as death. Hence attempts to reduce cytokine storm are now being considered as a new paradigm shift in the clinical management of SARS-CoV-2. Tocilizumab (IL-6 blocker), Baricitinib (JAKs and AAK1 inhibitor), TNFα inhibitors (Infliximab, Adalimumab, Certolizumab) are currently being evaluated for possible block of the CS. Hence, rationalizing anti-inflammatory therapeutics would be the most judicious approach for significant reduction in COVID-19 mortality. In order to elucidate optimized and rationaled use of different therapeutics in COVID-19, we collated latest available information from emerging scientific evidences, integrated previous attempts as well as clinical successes, and various adopted approaches to mitigate past outbreaks with of SARS-CoV and MERS CoV.

The effectiveness of vitamin C for patients with severe viral pneumonia in respiratory failure

Background

Vitamin C is a well-known antioxidant and essential cofactor for numerous biological reactions. Several studies reported that vitamin C can improve the symptoms and prognosis of patients with sepsis and respiratory infection. We aimed to examine the effect of vitamin C when used in viral pneumonia patients with severe respiratory failure.

Methods

Total 201 patients with viral pneumonia were included, of them 35 patients used vitamin C. We performed a statistical analysis through a propensity score matching of the age and baseline characteristics of these patients.

Results

There were differences between the vitamin C group and non-vitamin C group in terms of age (60±15 vs. 66±14, P=0.03), extracorporeal membrane oxygenation (28.6% vs. 5.4%, P<0.001), and procalcitonin (3±8 vs. 9±23, P=0.02). The 28-day mortality was not different between the two groups (20.0% vs. 24.7%, P=0.33). In the propensity-matched group, the 28-day mortality was not significantly different between the two groups (20.0% vs. 37.1%, P=0.07). Moreover, no difference was observed in shock reversal within 14 days (45.7% vs. 25.7%, P=0.08) and recovery after acute kidney injury (52.9% vs. 66.7%, P=0.41) between the two groups. Vitamin C was not a prognostic factor for 28-day mortality (P=0.33).

Conclusions

In this study adjunctive intravenous vitamin C therapy alone was not associated with improvement of the 28-day mortality and prognosis in patients with severe viral pneumonia with respiratory failure.

Surgical management of oncologic patient during and after the COVID-19 outbreak: practical recommendations from the Italian society of Surgical Oncology

The recent outbreak of COVID-19 in Italy caused a limitation of the resources of the health system, which necessarily led to their rationalization in the critical phase (phase 1) and a reorganization of the system in the following phase (phase 2). The Italian Society of Oncological Surgery-SICO has drafted these practical recommendations, calibrated on the most recent scientific literature and taking into account current health regulations and common sense. Surgical activity during phase 1 and 2 should follow a dynamic model, considering architectural structures, hospital mission, organizational models. Surgical delay should not affect oncological prognosis. However, COVID-19-positive cancer patients should be postponed until the infection is cured. The patients to consider more carefully before delaying surgery are those who have completed neoadjuvant therapy, patients with high biological aggressiveness tumors or without therapeutic alternatives. The multidisciplinary discussions are fundamental for sharing clinical decisions; videoconference meetings are preferable and use of telemedicine for follow-up is recommended. Especially in phase 1, maximum effort must be made to reduce the spread of the pandemic. Prefer intra-corporeal rather than open anastomosis during laparoscopy and mechanical rather than hand-sewn anastomosis in open surgery. Consider PPE for caregivers during stoma management. Minimal invasive surgery is not discouraged, because there is little evidence for augmented risk. Specific procedures have to be followed and use of energy devices has to be limited. Training programs with COVID-19 + patients are not recommended. All staff in OR should be trained with specific courses on specific PPE use. Differentiate recommendations are presented for every district cancer. Surgical oncology during phase 2 should be guaranteed by individual and distinct protocols and pathways between cancer patients and COVID-19 + patients with resources specifically addressed to the two distinct kind of patients to limit diagnostic/therapeutic interferences or slowdowns. These recommendations are based on currently available evidence about management of oncologic patients during COVID-19 pandemic, were endorsed by the SICO Executive Board, and are considered suitable for nationwide diffusion. They will be subject to updates and revisions in case of new and relevant scientific acquisitions.

Nature's therapy for COVID-19: Targeting the vital non-structural proteins (NSP) from SARS-CoV-2 with phytochemicals from Indian medicinal plants

BACKGROUND

Containing COVID-19 is still a global challenge. It has affected the "normal" world by targeting its economy and health sector. The effect is shifting of focus of research from life threatening diseases like cancer. Thus, we need to develop a medical solution at the earliest. The purpose of this present work was to understand the efficacy of 22 rationally screened phytochemicals from Indian medicinal plants obtained from our previous work, following drug-likeness properties, against 6 non-structural-proteins (NSP) from SARS-CoV-2.

METHODS

100 ns molecular dynamics simulations were performed, and relative binding free energies were computed by MM/PBSA. Further, principal component analysis, dynamic cross correlation and hydrogen bond occupancy were analyzed to characterize protein-ligand interactions. Biological pathway enrichment analysis was also carried out to elucidate the therapeutic targets of the phytochemicals in comparison to SARS-CoV-2.

RESULTS

The potential binding modes and favourable molecular interaction profile of 9 phytochemicals, majorly from Withania somnifera with lowest free binding energies, against the SARS-CoV-2 NSP targets were identified. It was understood that phytochemicals and 2 repurposed drugs with steroidal moieties in their chemical structures formed stable interactions with the NSPs. Additionally, human target pathway analysis for SARS-CoV-2 and phytochemicals showed that cytokine mediated pathway and phosphorylation pathways were with the most significant p-value.

CONCLUSIONS

To summarize this work, we suggest a global approach of targeting multiple proteins of SARS-CoV-2 with phytochemicals as a natural alternative therapy for COVID-19. We also suggest that these phytochemicals need to be tested experimentally to confirm their efficacy.

Deep COVID DeteCT: an international experience on COVID-19 lung detection and prognosis using chest CT

The Coronavirus disease 2019 (COVID-19) presents open questions in how we clinically diagnose and assess disease course. Recently, chest computed tomography (CT) has shown utility for COVID-19 diagnosis. In this study, we developed Deep COVID DeteCT (DCD), a deep learning convolutional neural network (CNN) that uses the entire chest CT volume to automatically predict COVID-19 (COVID+) from non-COVID-19 (COVID-) pneumonia and normal controls. We discuss training strategies and differences in performance across 13 international institutions and 8 countries. The inclusion of non-China sites in training significantly improved classification performance with area under the curve (AUCs) and accuracies above 0.8 on most test sites. Furthermore, using available follow-up scans, we investigate methods to track patient disease course and predict prognosis.

Exploring salivary diagnostics in COVID-19: a scoping review and research suggestions

INTRODUCTION

Molecular diagnostics for SARS-CoV-2 infection characteristically involves the sampling of the throat or nasopharyngeal swab (NPS). However, these procedures are invasive, require necessary skills for sample collection, cause patient discomfort, and are non-conducive for extensive scale testing. Saliva is increasingly being suggested as an alternate diagnostic sample in SARS-CoV-2 infection.

OBJECTIVES

This scoping review was done with the objective of exploring the evidence on the role of saliva as an alternate diagnostic sample in SARS-CoV-2 condition.

METHODS

Thorough search of the literature in major databases was undertaken in June 2020 using free text and MESH terms, followed by PRISMA to identify 17 studies for data extraction.

RESULTS AND CONCLUSIONS

Evidence was summarised for study characteristics, salivary sampling characteristics, viral load, and longevity of virus in saliva. The literature supports that saliva offers a simple sample collection method compared to technique-sensitive NPS and has the advantage of point-of-care testing for initial screening in community or hospital-based set-up. The additional highlights of this review are heterogeneity in the current literature and the gaps in methodology. Therefore, a robust study design to generate higher levels of evidence has been proposed.

Therapeutic approaches targeting renin-angiotensin system in sepsis and its complications

Sepsis, caused by the inappropriate host response to infection, is characterized by excessive inflammatory response and organ dysfunction, thus becomes a critical clinical problem. Commonly, sepsis may progress to septic shock and severe complications, including acute kidney injury (AKI), acute respiratory distress syndrome (ARDS), sepsis-induced myocardial dysfunction (SIMD), liver dysfunction, cerebral dysfunction, and skeletal muscle atrophy, which predominantly contribute to high mortality. Additionally, the global pandemic of coronavirus disease 2019 (COVID-19) raised the concern of development of effectve therapeutic strategies for viral sepsis. Renin-angiotensin system (RAS) may represent as a potent therapeutic target for sepsis therapy. The emerging role of RAS in the pathogenesis of sepsis has been investigated and several preclinical and clinical trials targeting RAS for sepsis treatment revealed promising outcomes. Herein, we attempt to review the effects and mechanisms of RAS manipulation on sepsis and its complications and provide new insights into optimizing RAS interventions for sepsis treatment.

Rapid SARS-CoV-2 Detection Using Electrochemical Immunosensor

The outbreak of the coronavirus disease (COVID-19) pandemic caused by the novel coronavirus (SARS-CoV-2) has been declared an international public health crisis. It is essential to develop diagnostic tests that can quickly identify infected individuals to limit the spread of the virus and assign treatment options. Herein, we report a proof-of-concept label-free electrochemical immunoassay for the rapid detection of SARS-CoV-2 virus via the spike surface protein. The assay consists of a graphene working electrode functionalized with anti-spike antibodies. The concept of the immunosensor is to detect the signal perturbation obtained from ferri/ferrocyanide measurements after binding of the antigen during 45 min of incubation with a sample. The absolute change in the [Fe(CN)6]3-/4- current upon increasing antigen concentrations on the immunosensor surface was used to determine the detection range of the spike protein. The sensor was able to detect a specific signal above 260 nM (20 µg/mL) of subunit 1 of recombinant spike protein. Additionally, it was able to detect SARS-CoV-2 at a concentration of 5.5 × 105 PFU/mL, which is within the physiologically relevant concentration range. The novel immunosensor has a significantly faster analysis time than the standard qPCR and is operated by a portable device which can enable on-site diagnosis of infection.

Hydroxychloroquine for the treatment and prophylaxis of COVID-19: The journey so far and the road ahead

As mortality and morbidity from novel coronavirus disease (COVID-19) continue to mount worldwide, the scientific community as well as public health systems are under immense pressure to contain the pandemic as well as to develop effective medical countermeasures. Meanwhile, desperation has driven prescribers, researchers as well as administrators to recommend and try therapies supported by little or no reliable evidence. Recently, hydroxychloroquine-sulfate (HCQS) has got significant media and political attention for the treatment as well as prophylaxis of COVID-19 despite the lack of convincing and unequivocal data supporting its efficacy and safety in these patients. This has unfortunately, yet foreseeably led to several controversies and confusion among the medical fraternity, the patient community as well as the general public. Based on the available studies, many with high risk of bias, relatively small sample sizes, and abbreviated follow-ups, HCQS is unlikely to be of dramatic benefit in COVID-19 patients and yet has the potential to cause harm, particularly when used in combination with azithromycin or other medications in high risk individuals with comorbidities. Although definitive data from larger well-controlled randomized trials will be forthcoming in the future, and we may be able to identify specific patient subpopulations likely to benefit from hydroxychloroquine, till that time it will be prudent to prescribe it within investigational trial settings with close safety monitoring. Here we review the current evidence and developments related to the use of HCQS in COVID-19 patients and highlight the importance of risk-benefit assessment and rational use of HCQS during this devastating pandemic.

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.

SARS-COV-2 (COVID-19): Cellular and biochemical properties and pharmacological insights into new therapeutic developments

COVID-19 caused by SARS-COV-2 first appeared in the Wuhan City of China and began to spread rapidly among people. Rapid progression of the outbreak has led to a major global public health problem of a potentially fatal disease. On January 30, 2020, WHO declared the pandemic as the sixth public health emergency of the world. Upon this, the whole country has started to take the necessary precautions. The new coronavirus uses membrane-bound angiotensin-converting enzyme 2 (ACE2) to enter into the cells, such as SARS-CoV, and mostly affects the respiratory tract. Symptoms of COVID-19 patients include fever (93%), fatigue (70%), cough (70%), anorexia (40%) and dyspnoea (34.5%). The elderly and people with underlying chronic diseases are more susceptible to infection and higher mortality. Currently, a large number of drugs and vaccines studies are ongoing. In this review, we discussed the virology, epidemiological data, the replication of the virus, and its relationship with cardiovascular diseases on COVID-19 pandemics, treatment and vaccines. Thereby, this study aims to neatly present scientific data in light of many regarding literature that can be a clue for readers who research this disease prevention and treatment. SIGNIFICANCE OF THE STUDY: This review summarized current information on COVID-19 (epidemiology, pathophysiology, clinical, laboratory, cardiovascular diseases, ACE2 and pharmacological agents) for researchers and reveals guiding data for researchers, especially in the field of cardiovascular system, pharmacology, dysregulation of cellular function in disease, molecular and cell biology and physiology in the regulation of tissue function in health and disease.

Genetics and genomics of SARS-CoV-2: A review of the literature with the special focus on genetic diversity and SARS-CoV-2 genome detection

The outbreak of 2019-novel coronavirus disease (COVID-19), caused by SARS-CoV-2, started in late 2019; in a short time, it has spread rapidly all over the world. Although some possible antiviral and anti-inflammatory medications are available, thousands of people are dying daily. Well-understanding of the SARS-CoV-2 genome is not only essential for the development of new treatments/vaccines, but it also can be used for improving the sensitivity and specificity of current approaches for virus detection. Accordingly, we reviewed the most critical findings related to the genetics of the SARS-CoV-2, with a specific focus on genetic diversity and reported mutations, molecular-based diagnosis assays, using interfering RNA technology for the treatment of patients, and genetic-related vaccination strategies. Additionally, considering the unanswered questions or uncertainties in these regards, different topics were discussed.

Microstructure, pathophysiology, and potential therapeutics of COVID-19: A comprehensive review

There have been over seven million cases and almost 413 372 deaths globally due to the novel coronavirus (2019-nCoV) associated disease COVID-19, as of 11 June 2020. Phylogenetic analysis suggests that there is a common source for these infections. The overall sequence similarities between the spike protein of 2019-nCoV and that of SARS-CoV are known to be around 76% to 78% and 73% to 76% for the whole protein and receptor-binding domain (RBD), respectively. Thus, they have the potential to serve as the drug and/or vaccine candidate. However, the individual response against 2019-nCoV differs due to genetic variations in the human population. Understanding the variations in angiotensin-converting enzyme 2 (ACE2) and human leukocyte antigen (HLA) that may affect the severity of 2019-nCoV infection could help in identifying individuals at a higher risk from the COVID-19. A number of potential drugs/vaccines as well as antibody/cytokine-based therapeutics are in various developmental stages of preclinical/clinical trials against SARS-CoV, MERS-CoV, and 2019-nCoV with substantial cross-reactivity, and may be used against COVID-19. For diagnosis, the reverse-transcription polymerase chain reaction is the gold standard test for initial diagnosis of COVID-19. A kit based on serological tests are also recommended for investigating the spread of COVID-19 but this is challenging due to the antibodies cross-reactivity. This review comprehensively summarizes the recent reports available regarding the host-pathogen interaction, morphological and genomic structure of the virus, and the diagnostic techniques as well as the available potential therapeutics against COVID-19.

COVID-19 lockdown: animal life, ecosystem and atmospheric environment

The outbreak of COVID-19 leads to emergence of the global pandemic, but there is no specific vaccine recommended for COVID-19. More than 216 countries are struggling against the transmission of the disease, recovery and motility. Till date more than 0.948 million deaths out of 30.369 million confirmed cases are reported by WHO. Most of the nations adopted partial or complete 'lockdown' and imposed 'social distancing' to control the rapid transmission of COVID-19 and its consequence. Though global economic growth declined due to nationwide lockdown, there are certain positive impacts on environment. This review article has discussed the effects of nationwide lockdown aiming to community transmission COVID-19 on animal life behaviour and atmospheric environment in different aspects. In the lockdown period, the levels of NO₂ and carbon emission remarkably decrease in atmosphere due to restricted consumption of fossil fuel by industries, thermal power stations and air transportations. The concentration of NO₂ dropped by 45-54% in the atmosphere of most populated cities in Europe. The intensities of particulate matters PM_2.5 and PM₁₀ decreased by 43% and 31% respectively, at lower atmosphere indicating improvement in air qualities in different parts of world caused by less traffic and construction activities. SPM reduced up to 15.9%, showing improvement in surface water quality. New deserted bank has developed due to less river activities in this period. Noise pollution remarkably dropped below 60 db even in crowded cities. Thus, the atmospheric environment has resumed some extent in all respect by means of such global-wide lockdown aiming to control COVID-19 pandemic. The behavioural changes of wild animals, birds, butterfly, pets and street animals that reflected on ecosystem of their relative region indicate the non-interference of human activities on lives of natural creatures during lockdown period. There is certain correlation between atmospheric change with the behavioural changes of natural creature during lockdown period. The objective of this study is to focus the critical analysis of the effect of human activities on atmospheric environment for sustainable ecosystem in long term. Significantly, there is ample scope of research on sustainable development of atmospheric environment and ecosystem of creature in absence of human being.

The Main Molecular and Serological Methods for Diagnosing COVID-19: An Overview Based on the Literature

Diagnostic tests have been considered as the main alternative for the control of coronavirus disease (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as a correct diagnosis allows for decision making when facing the disease, particularly as there is a lack of effective therapeutic protocols and vaccines. Thus, in this review, we summarized the main diagnostic approaches currently available for the diagnosis of SARS-CoV-2 infection in humans based on studies available in article databases. The tests can be organized into two main categories: nucleic acid-based tests, recommended for the initial detection of the virus, and serological tests, recommended for assessing the disease progression. The studies have shown that the performance of diagnostic methods depends on different factors, such as the type of samples and the characteristics of each assay. It was identified that the positivity of the tests is mainly related to the onset of symptoms. We also observed that point-of-care diagnoses are considered as one of the main trends in this area, due to the low-cost and simplicity of the assay; however, the analytical performance must be critically analyzed. Thus, the COVID-19 pandemic has highlighted the critical role of diagnostic technologies in the control of infectious diseases.

COVID-19: A Global Challenge with Old History, Epidemiology and Progress So Far

Humans have witnessed three deadly pandemics so far in the twenty-first century which are associated with novel coronaviruses: SARS, Middle East respiratory syndrome (MERS), and COVID-19. All of these viruses, which are responsible for causing acute respiratory tract infections (ARTIs), are highly contagious in nature and/or have caused high mortalities. The recently emerged COVID-19 disease is a highly transmittable viral infection caused by another zoonotic novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Similar to the other two coronaviruses such as SARS-CoV-1 and MERS-CoV, SARS-CoV-2 is also likely to have originated from bats, which have been serving as established reservoirs for various pathogenic coronaviruses. Although, it is still unknown how SARS-CoV-2 is transmitted from bats to humans, the rapid human-to-human transmission has been confirmed widely. The disease first appeared in Wuhan, China, in December 2019 and quickly spread across the globe, infected 48,539,872 people, and caused 1,232,791 deaths in 215 countries, and the infection is still spreading at the time of manuscript preparation. So far, there is no definite line of treatment which has been approved or vaccine which is available. However, different types of potential vaccines and therapeutics have been evaluated and/or are under clinical trials against COVID-19. In this review, we summarize different types of acute respiratory diseases and briefly discuss earlier outbreaks of coronaviruses and compare their occurrence and pathogenicity with the current COVID-19 pandemic. Various epidemiological aspects of COVID-19 such as mode of spread, death rate, doubling time, etc., have been discussed in detail. Apart from this, different technical issues related to the COVID-19 pandemic including use of masks and other socio-economic problems associated with the pandemic have also been summarized. Additionally, we have reviewed various aspects of patient management strategies including mechanism of action, available diagnostic tools, etc., and also discussed different strategies for the development of effective vaccines and therapeutic combinations to deal with this viral outbreak. Overall, by the inclusion of various references, this review covers, in detail, the most important aspects of the COVID-19 pandemic.

In silico trial to test COVID-19 candidate vaccines: a case study with UISS platform

Background

SARS-CoV-2 is a severe respiratory infection that infects humans. Its outburst entitled it as a pandemic emergence. To get a grip on this outbreak, specific preventive and therapeutic interventions are urgently needed. It must be said that, until now, there are no existing vaccines for coronaviruses. To promptly and rapidly respond to pandemic events, the application of in silico trials can be used for designing and testing medicines against SARS-CoV-2 and speed-up the vaccine discovery pipeline, predicting any therapeutic failure and minimizing undesired effects.

Results

We present an in silico platform that showed to be in very good agreement with the latest literature in predicting SARS-CoV-2 dynamics and related immune system host response. Moreover, it has been used to predict the outcome of one of the latest suggested approach to design an effective vaccine, based on monoclonal antibody. Universal Immune System Simulator (UISS) in silico platform is potentially ready to be used as an in silico trial platform to predict the outcome of vaccination strategy against SARS-CoV-2.

Conclusions

In silico trials are showing to be powerful weapons in predicting immune responses of potential candidate vaccines. Here, UISS has been extended to be used as an in silico trial platform to speed-up and drive the discovery pipeline of vaccine against SARS-CoV-2.

Novel automated sample-to-result SARS-CoV-2 laboratory-developed RT-PCR assay for high-throughput testing using LabTurbo AIO 48 system

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LabTurbo AIO 48 can accurately identify SARS-CoV-2 infection.

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LabTurbo AIO 48 can reduce by ~ 47.9% the sample-to-result time.

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LabTurbo AIO 48 is more sensitive than the reference detection assay.

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LabTurbo AIO 48 can provide high-throughput and reliable SARS-CoV-2 diagnostic results.

Background and aims

Immediate detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for preventing the spread of coronavirus disease 2019 (COVID-19). The LabTurbo AIO 48 system is an automated platform that allows nucleic acid extraction and sample analysis on the same instrument, producing faster results without affecting their accuracy. We aimed to independently evaluate the LabTurbo AIO 48 (all-in-one system) for SARS-CoV-2 detection.

Materials and methods

Comparative limit of detection (LOD) was assessed on both the LabTurbo AIO 48 and current standard detection system based on real-time reverse transcriptase polymerase chain reaction (RT-PCR), using SARS-CoV-2 RNA control. Additional 125 primary clinical samples were assessed using both the protocols in parallel.

Results

The turnaround time from sample to results for 48 samples analyzed on LabTurbo AIO 48 was approximately 2.5 h, whereas that analyzed using the in-house RT-PCR protocol was 4.8 h. LabTurbo AIO 48 also demonstrated higher sensitivity than our reference RT-PCR assay, with a LOD of 9.4 copies/reaction. The overall percentage agreement between both the methods for 125 samples was 100%.

Conclusion

LabTurbo AIO 48 is a robust detection option for SARS-CoV-2, allowing faster results and, consequently, aiding in better control and prevention of COVID-19.

False-negative results of initial RT-PCR assays for COVID-19: A systematic review

BACKGROUND

A false-negative case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is defined as a person with suspected infection and an initial negative result by reverse transcription-polymerase chain reaction (RT-PCR) test, with a positive result on a subsequent test. False-negative cases have important implications for isolation and risk of transmission of infected people and for the management of coronavirus disease 2019 (COVID-19). We aimed to review and critically appraise evidence about the rate of RT-PCR false-negatives at initial testing for COVID-19.

METHODS

We searched MEDLINE, EMBASE, LILACS, as well as COVID-19 repositories, including the EPPI-Centre living systematic map of evidence about COVID-19 and the Coronavirus Open Access Project living evidence database. Two authors independently screened and selected studies according to the eligibility criteria and collected data from the included studies. The risk of bias was assessed using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. We calculated the proportion of false-negative test results using a multilevel mixed-effect logistic regression model. The certainty of the evidence about false-negative cases was rated using the GRADE approach for tests and strategies. All information in this article is current up to July 17, 2020.

RESULTS

We included 34 studies enrolling 12,057 COVID-19 confirmed cases. All studies were affected by several risks of bias and applicability concerns. The pooled estimate of false-negative proportion was highly affected by unexplained heterogeneity (tau-squared = 1.39; 90% prediction interval from 0.02 to 0.54). The certainty of the evidence was judged as very low due to the risk of bias, indirectness, and inconsistency issues.

CONCLUSIONS

There is substantial and largely unexplained heterogeneity in the proportion of false-negative RT-PCR results. The collected evidence has several limitations, including risk of bias issues, high heterogeneity, and concerns about its applicability. Nonetheless, our findings reinforce the need for repeated testing in patients with suspicion of SARS-Cov-2 infection given that up to 54% of COVID-19 patients may have an initial false-negative RT-PCR (very low certainty of evidence).

SYSTEMATIC REVIEW REGISTRATION

Protocol available on the OSF website: https://tinyurl.com/vvbgqya.

False-negative results of initial RT-PCR assays for COVID-19: A systematic review

BACKGROUND

A false-negative case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is defined as a person with suspected infection and an initial negative result by reverse transcription-polymerase chain reaction (RT-PCR) test, with a positive result on a subsequent test. False-negative cases have important implications for isolation and risk of transmission of infected people and for the management of coronavirus disease 2019 (COVID-19). We aimed to review and critically appraise evidence about the rate of RT-PCR false-negatives at initial testing for COVID-19.

METHODS

We searched MEDLINE, EMBASE, LILACS, as well as COVID-19 repositories, including the EPPI-Centre living systematic map of evidence about COVID-19 and the Coronavirus Open Access Project living evidence database. Two authors independently screened and selected studies according to the eligibility criteria and collected data from the included studies. The risk of bias was assessed using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. We calculated the proportion of false-negative test results using a multilevel mixed-effect logistic regression model. The certainty of the evidence about false-negative cases was rated using the GRADE approach for tests and strategies. All information in this article is current up to July 17, 2020.

RESULTS

We included 34 studies enrolling 12,057 COVID-19 confirmed cases. All studies were affected by several risks of bias and applicability concerns. The pooled estimate of false-negative proportion was highly affected by unexplained heterogeneity (tau-squared = 1.39; 90% prediction interval from 0.02 to 0.54). The certainty of the evidence was judged as very low due to the risk of bias, indirectness, and inconsistency issues.

CONCLUSIONS

There is substantial and largely unexplained heterogeneity in the proportion of false-negative RT-PCR results. The collected evidence has several limitations, including risk of bias issues, high heterogeneity, and concerns about its applicability. Nonetheless, our findings reinforce the need for repeated testing in patients with suspicion of SARS-Cov-2 infection given that up to 54% of COVID-19 patients may have an initial false-negative RT-PCR (very low certainty of evidence).

SYSTEMATIC REVIEW REGISTRATION

Protocol available on the OSF website: https://tinyurl.com/vvbgqya.

A CT-based radiomics nomogram for predicting prognosis of coronavirus disease 2019 (COVID-19) radiomics nomogram predicting COVID-19

Objectives:

To identify the value of radiomics method derived from CT images to predict prognosis in patients with COVID-19.

Methods:

A total of 40 patients with COVID-19 were enrolled in the study. Baseline clinical data, CT images, and laboratory testing results were collected from all patients. We defined that ROIs in the absorption group decreased in the density and scope in GGO, and ROIs in the progress group progressed to consolidation. A total of 180 ROIs from absorption group (n = 118) and consolidation group (n = 62) were randomly divided into a training set (n = 145) and a validation set (n = 35) (8:2). Radiomics features were extracted from CT images, and the radiomics-based models were built with three classifiers. A radiomics score (Rad-score) was calculated by a linear combination of selected features. The Rad-score and clinical factors were incorporated into the radiomics nomogram construction. The prediction performance of the clinical factors model and the radiomics nomogram for prognosis was estimated.

Results:

A total of 15 radiomics features with respective coefficients were calculated. The AUC values of radiomics models (kNN, SVM, and LR) were 0.88, 0.88, and 0.84, respectively, showing a good performance. The C-index of the clinical factors model was 0.82 [95% CI (0.75–0.88)] in the training set and 0.77 [95% CI (0.59–0.90)] in the validation set. The radiomics nomogram showed optimal prediction performance. In the training set, the C-index was 0.91 [95% CI (0.85–0.95)], and in the validation set, the C-index was 0.85 [95% CI (0.69–0.95)]. For the training set, the C-index of the radiomics nomogram was significantly higher than the clinical factors model (p = 0.0021). Decision curve analysis showed that radiomics nomogram outperformed the clinical model in terms of clinical usefulness.

Conclusions:

The radiomics nomogram based on CT images showed favorable prediction performance in the prognosis of COVID-19. The radiomics nomogram could be used as a potential biomarker for more accurate categorization of patients into different stages for clinical decision-making process.

Advances in knowledge:

Radiomics features based on chest CT images help clinicians to categorize the patients of COVID-19 into different stages. Radiomics nomogram based on CT images has favorable predictive performance in the prognosis of COVID-19. Radiomics act as a potential modality to supplement conventional medical examinations.