Coronavirus disease (COVID-19): a scoping review

ProteinReDiff: Complex-based ligand-binding proteins redesign by equivariant diffusion-based generative models

Proteins, serving as the fundamental architects of biological processes, interact with ligands to perform a myriad of functions essential for life. Designing functional ligand-binding proteins is pivotal for advancing drug development and enhancing therapeutic efficacy. In this study, we introduce ProteinReDiff, an diffusion framework targeting the redesign of ligand-binding proteins. Using equivariant diffusion-based generative models, ProteinReDiff enables the creation of high-affinity ligand-binding proteins without the need for detailed structural information, leveraging instead the potential of initial protein sequences and ligand SMILES strings. Our evaluations across sequence diversity, structural preservation, and ligand binding affinity underscore ProteinReDiff's potential to advance computational drug discovery and protein engineering.

In Silico Evaluation of HIV Protease and RNA Polymerase Inhibitors as Potential COVID-19 Therapeutics

BACKGROUND

The COVID-19 coronavirus, also known as the acute respiratory syndrome coronavirus, emerged as a significant global health concern. First identified in Wuhan, China, in December 2019, the virus rapidly spread to over 187 countries due to its high transmissibility. Until an effective treatment or vaccine is developed, preventive measures remain the only mandatory strategy to curb person-to-person transmission.

AIMS AND OBJECTIVES

The study aimed to explore potential therapeutic options for COVID-19 by repurposing existing drugs. Specifically, the objective was to evaluate a library of clinically approved or investigational antiviral compounds through docking studies to identify candidates with high binding affinity to COVID-19 proteins.

MATERIALS AND METHODS

The study employed molecular docking techniques using the Maestro interface (Schrodinger Suite, LLC, NY) to assess the interaction of selected compounds with various COVID-19 protein targets. A total of 15 compounds were analyzed for their binding potential to multiple forms of the virus's proteins.

RESULTS

The docking studies revealed that several compounds, particularly HIV protease inhibitors and RNA-dependent RNA polymerase inhibitors, demonstrated strong binding affinities to key COVID-19 enzymes. These interactions suggest their potential as therapeutic candidates for COVID-19 treatment.

CONCLUSION

The findings from this drug repurposing study highlight the potential of certain existing antiviral agents in the treatment of COVID-19. The identified compounds could serve as promising candidates for further investigation in the ongoing battle against the coronavirus pandemic.

Impact of the COVID-19 pandemic on the conduct of non-COVID-19 clinical trials: protocol for a scoping review

INTRODUCTION

The COVID-19 pandemic posed a detrimental impact on the conduct of non-COVID-19 related clinical trials, raising concerns about the completeness of these studies and waste of resources. While several measures and strategies have been suggested to address these issues, a thorough and timely summarisation is still lacking. Therefore, our aim is to conduct a scoping review to summarise the negative effects of COVID-19 on non-COVID-19 clinical trials, outline the effective measures for mitigating these impacts, and provide insights for future pandemics.

METHODS AND ANALYSIS

This scoping review will be conducted in line with the Joanna Briggs Institute's scoping review methodological framework, and the results will be reported following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews. Relevant articles will be searched in PubMed, Embase and the Cochrane Library from 1 December 2019 to 1 July 2023. We will also screen the reference lists of the included studies manually to identify more potentially relevant articles. Articles focusing on the adverse impacts of COVID-19 on non-COVID-19 clinical trials and effective measures for mitigating them will be included. Two investigators will perform study selection and data extraction independently. A narrative summary as well as a descriptive analysis of the basic characteristics and key results of the included studies will be performed.

ETHICS AND DISSEMINATION

Ethical approval is not required, as this scoping review will be completed based only on published literature. The findings of this scoping review will be disseminated through a peer-reviewed publication and/or conference presentations.

Deep Drug Discovery of Mac Domain of SARS-CoV-2 (WT) Spike Inhibitors: Using Experimental ACE2 Inhibition TR-FRET Assay, Screening, Molecular Dynamic Simulations and Free Energy Calculations

SARS-CoV-2 exploits the homotrimer transmembrane Spike glycoproteins (S protein) during host cell invasion. The Omicron XBB subvariant, delta, and prototype SARS-CoV-2 receptor-binding domain show similar binding strength to hACE2 (human Angiotensin-Converting Enzyme 2). Here we utilized multiligand virtual screening to identify small molecule inhibitors for their efficacy against SARS-CoV-2 virus using QPLD, pseudovirus ACE2 Inhibition -Time Resolved Forster/Fluorescence energy transfer (TR-FRET) Assay Screening, and Molecular Dynamics simulations (MDS). Three hundred and fifty thousand compounds were screened against the macrodomain of the nonstructural protein 3 of SARS-CoV-2. Using TR-FRET Assay, we filtered out two of 10 compounds that had no reported activity in in vitro screen against Spike S1: ACE2 binding assay. The percentage inhibition at 30 µM was found to be 79% for "Compound F1877-0839" and 69% for "Compound F0470-0003". This first of its kind study identified "FILLY" pocket in macrodomains. Our 200 ns MDS revealed stable binding poses of both leads. They can be used for further development of preclinical candidates.

The reorganisation of emergency general surgery services during the COVID-19 pandemic in the UK: outcomes of delayed presentation, socio-economic deprivation and Black, Asian and Minority Ethnic patients

INTRODUCTION

The COVID-19 pandemic is a global public health emergency. Lockdown restrictions and the reconfiguration of healthcare systems to accommodate an increase in critical care capacity have had an impact on 'non-COVID' specialties. This study characterises the utilisation of emergency general surgery (EGS) services during the UK lockdown period at a university teaching hospital with a catchment population that represents one of the most deprived and ethnically diverse areas in the UK.

METHODS

EGS admissions during the UK lockdown period (March to May 2020) were compared with the same period in 2019. Patient demographics were recorded together with clinical presentation, hospital stay and treatment outcomes, and readmission data.

RESULTS

The study included 645 patients, comprising 223 in the COVID-19 period and 422 in the non-COVID-19 period. There was no difference in age, sex, comorbidity or socio-economic status. A lower proportion of patients of Black, Asian and Minority Ethnicity (BAME) were admitted during the pandemic (20.6% vs 35.4%, p < 0.05). The duration of symptoms prior to presentation was longer, and admission clinical parameters and serum inflammatory markers. More patients presented with an acute kidney injury (9.9% vs 4.7%, p = 0.012). There was no difference in perioperative outcomes or 30-day mortality, but more patients were readmitted following conservative management (10.6% vs 4.7%, p = 0.023).

CONCLUSIONS

The reorganisation of EGS to a senior-led model has been successful in terms of outcomes and access to treatment despite a more unwell population. There was a significantly lower proportion of BAME admissions suggesting additional barriers to healthcare access under pandemic lockdown conditions.

Agent-based modeling and simulation of pandemic propagation in a school environment

Spatial behavior is a principal aspect for architects to consider. Unfortunately, it is sometimes hard to predict, as users of space seldom follow a standard routine. However, predicting user behavior in a space can potentially illuminate the entire design process. Moreover, it is a key factor in fighting the recent COVID-19 pandemic. Until most of the public gets their vaccine, health officials recommend social distancing as the primary means of fighting the pandemic. This paper uses an agent-based modeling and simulation (ABMS) approach to reproduce, analyze, and predict spatial behavior during the pandemic in a school environment and its impact on disease propagation. The simulation reproduces the behavior of teachers and students at a sample elementary school. By manipulating parameters that simulate the school officials' response to the pandemic, stakeholders can assess the most effective preventive measures. As a result of running multiple scenarios, the study demonstrates how varying starting conditions and alternate spatial behaviors could lead to different results, providing insight to stakeholders on how to handle disease spread in school environments.

Guidance on the Conduct of Clinical Research within OECD Countries during the Early Stages of the COVID-19 Pandemic: A Systematic Review

BACKGROUND

In response to the COVID-19 pandemic, member countries of the Organisation for Economic Co-operation and Development (OECD) rapidly published guidance regarding the conduct of clinical research. A systematic review was conducted to explore the recommendations issued in relation to the commencement, continuation and termination of clinical research during the early phases of the pandemic.

METHODS

Searches consisting of the terms "COVID-19", "clinical research", and "guidance", were conducted in PubMed, Embase, MEDLINE, Trip, Guidelines International Network, and Google in April-May 2021 (up to 4 May 2021). Data were extracted from guidance published from OECD member countries and mapped to inductively-developed categories.

RESULTS

9419 references were systematically screened, resulting in the inclusion of 46 publications from 27 OECD countries. Thirty-three sources made recommendations regarding monitoring, risk-benefit assessments and information technology. There was limited specific recommendations made in relation to personal protective equipment (PPE) in the included guidance. Findings demonstrate that guidance differed by publication date demonstrating the rapidly evolving environment within which research was conducted. Importantly, many organisations opted to endorse existing guidance published by the United States' Food and Drug Administration and the European Medicines Agency rather than develop their own recommendations.

CONCLUSIONS

Given the rapidly evolving nature of the pandemic, particularly in the early stages, findings demonstrate the global response in relation to clinical research conduct, thereby providing important insights for future public health emergencies.

Space-Distributed Traffic-Enhanced LSTM-Based Machine Learning Model for COVID-19 Incidence Forecasting

The COVID-19 virus continues to generate waves of infections around the world. With major areas in developing countries still lagging behind in vaccination campaigns, the risk of new variants that can cause re-infections worldwide makes the monitoring and forecasting of the evolution of the virus a high priority. Having accurate models able to forecast the incidence of the spread of the virus provides help to policymakers and health professionals in managing the scarce resources in an optimal way. In this paper, a new machine learning model is proposed to forecast the spread of the virus one-week ahead in a geographic area which combines mobility and COVID-19 incidence data. The area is divided into zones or districts according to the location of the COVID-19 measuring points. A traffic-driven mobility estimate among adjacent districts is proposed to capture the spatial spread of the virus. Traffic-driven mobility in adjacent districts will be used together with COVID-19 incidence data to feed a new deep learning LSTM-based model which will extract patterns from mobility-modulated COVID-19 incidence spatiotemporal data in order to optimize one-week ahead estimations. The model is trained and validated with open data available for the city of Madrid (Spain) for 3 different validation scenarios. A baseline model based on previous literature able to extract temporal patterns in COVID-19 incidence time series is also trained with the same dataset. The results show that the proposed model, based on the combination of traffic and COVID-19 incidence data, is able to outperform the baseline model in all the validation scenarios.

Impact of COVID-19 on glaucoma management: A review

Glaucoma is the leading cause of irreversible vision loss and the second leading cause of blindness worldwide. The rapid transmission of SARS-CoV-2virus compelled governments to concentrate their efforts on emergency units to treat the large number of cases that arose due to the Covid-19 outbreak. As a result, many chronically ill patients were left without access to medical care. The progression of glaucoma in previously diagnosed cases has been accelerated; due to this, some have lost their vision. Evaluation of Covid-19's effect on glaucoma treatment was one goal of this study. We used search phrases like "COVID-19," "telemedicine," and "glaucoma" to find published papers on COVID-19 and glaucoma. Artificial Intelligence (AI) may be the answer to the unanswered questions that arose due to this pandemic crisis. The benefits and drawbacks of AI in the context of teliglaucoma have been thoroughly examined. These AI-related ideas have been floating around for some time. We hope that Covid-19's enormous revisions will provide them with the motivation to move forward and significantly improve services. Despite the devastation the pandemic has caused, we are hopeful that eye care services will be better prepared and better equipped to avoid the loss of sight due to glaucoma in future.

Ongoing Positive Selection Drives the Evolution of SARS-CoV-2 Genomes

SARS-CoV-2 is a new RNA virus affecting humans and spreads extensively through world populations since its first outbreak in December, 2019. Whether the transmissibility and pathogenicity of SARS-CoV-2 in humans after zoonotic transfer are actively evolving, and driven by adaptation to the new host and environments is still under debate. Understanding the evolutionary mechanism underlying epidemiological and pathological characteristics of COVID-19 is essential for predicting the epidemic trend, and providing guidance for disease control and treatments. Interrogating novel strategies for identifying natural selection using within-species polymorphisms and 3,674,076 SARS-CoV-2 genome sequences of 169 countries as of December 30, 2021, we demonstrate with population genetic evidence that during the course of SARS-CoV-2 pandemic in humans, 1) SARS-CoV-2 genomes are overall conserved under purifying selection, especially for the 14 genes related to viral RNA replication, transcription, and assembly; 2) ongoing positive selection is actively driving the evolution of 6 genes (e.g., S, ORF3a, and N) that play critical roles in molecular processes involving pathogen-host interactions, including viral invasion into and egress from host cells, and viral inhibition and evasion of host immune response, possibly leading to high transmissibility and mild symptom in SARS-CoV-2 evolution. According to an established haplotype phylogenetic relationship of 138 viral clusters, a spatial and temporal landscape of 556 critical mutations is constructed based on their divergence among viral haplotype clusters or repeatedly increase in frequency within at least 2 clusters, of which multiple mutations potentially conferring alterations in viral transmissibility, pathogenicity, and virulence of SARS-CoV-2 are highlighted, warranting attentions.

Methodology and experiences of rapid advice guideline development for children with COVID-19: responding to the COVID-19 outbreak quickly and efficiently

BACKGROUND

Rapid Advice Guidelines (RAG) provide decision makers with guidance to respond to public health emergencies by developing evidence-based recommendations in a short period of time with a scientific and standardized approach. However, the experience from the development process of a RAG has so far not been systematically summarized. Therefore, our working group will take the experience of the development of the RAG for children with COVID-19 as an example to systematically explore the methodology, advantages, and challenges in the development of the RAG. We shall propose suggestions and reflections for future research, in order to provide a more detailed reference for future development of RAGs.

RESULT

The development of the RAG by a group of 67 researchers from 11 countries took 50 days from the official commencement of the work (January 28, 2020) to submission (March 17, 2020). A total of 21 meetings were held with a total duration of 48 h (average 2.3 h per meeting) and an average of 16.5 participants attending. Only two of the ten recommendations were fully supported by direct evidence for COVID-19, three recommendations were supported by indirect evidence only, and the proportion of COVID-19 studies among the body of evidence in the remaining five recommendations ranged between 10 and 83%. Six of the ten recommendations used COVID-19 preprints as evidence support, and up to 50% of the studies with direct evidence on COVID-19 were preprints.

CONCLUSIONS

In order to respond to public health emergencies, the development of RAG also requires a clear and transparent formulation process, usually using a large amount of indirect and non-peer-reviewed evidence to support the formation of recommendations. Strict following of the WHO RAG handbook does not only enhance the transparency and clarity of the guideline, but also can speed up the guideline development process, thereby saving time and labor costs.

Interventional research to tackle antimicrobial resistance in Low Middle Income Countries in the era of the COVID-19 pandemic: lessons in resilience from an international consortium

This article summarizes the consequences of the COVID-19 pandemic, on an international project to tackle antimicrobial resistance (AMR). The research leadership and process, the access to data, and stakeholders were deeply disrupted by the national and international response to the pandemic, including the interruption of healthcare delivery, lockdowns, and quarantines. The key principles to deliver the research through the pandemic were mainly the high degree of interdisciplinary engagement with integrated teams, and equitable partnership across sites with capacity building and leadership training. The level of preexisting collaboration and partnership were also keys to sustaining connections and involvements throughout the pandemic. The pandemic offered opportunities for realigning research priorities. Flexibility in funding timelines and projects inputs are required to accommodate variance introduced by external factors. The current models for research collaboration and funding need to be critically evaluated and redesigned to retain the innovation that was shown to be successful through this pandemic.

Analysis of Glycosylation and Disulfide Bonding of Wild-Type SARS-CoV-2 Spike Glycoprotein

The SARS-CoV-2 coronavirus, the etiologic agent of COVID-19, uses its spike (S) glycoprotein anchored in the viral membrane to enter host cells. The S glycoprotein is the major target for neutralizing antibodies elicited by natural infection and by vaccines. Approximately 35% of the SARS-CoV-2 S glycoprotein consists of carbohydrate, which can influence virus infectivity and susceptibility to antibody inhibition. We found that virus-like particles produced by coexpression of SARS-CoV-2 S, M, E, and N proteins contained spike glycoproteins that were extensively modified by complex carbohydrates. We used a fucose-selective lectin to purify the Golgi-modified fraction of a wild-type SARS-CoV-2 S glycoprotein trimer and determined its glycosylation and disulfide bond profile. Compared with soluble or solubilized S glycoproteins modified to prevent proteolytic cleavage and to retain a prefusion conformation, more of the wild-type S glycoprotein N-linked glycans are processed to complex forms. Even Asn 234, a significant percentage of which is decorated by high-mannose glycans on other characterized S trimer preparations, is predominantly modified in the Golgi compartment by processed glycans. Three incompletely occupied sites of O-linked glycosylation were detected. Viruses pseudotyped with natural variants of the serine/threonine residues implicated in O-linked glycosylation were generally infectious and exhibited sensitivity to neutralization by soluble ACE2 and convalescent antisera comparable to that of the wild-type virus. Unlike other natural cysteine variants, a Cys15Phe (C15F) mutant retained partial, but unstable, infectivity. These findings enhance our understanding of the Golgi processing of the native SARS-CoV-2 S glycoprotein carbohydrates and could assist the design of interventions. IMPORTANCE The SARS-CoV-2 coronavirus, which causes COVID-19, uses its spike glycoprotein to enter host cells. The viral spike glycoprotein is the main target of host neutralizing antibodies that help to control SARS-CoV-2 infection and are important for the protection provided by vaccines. The SARS-CoV-2 spike glycoprotein consists of a trimer of two subunits covered with a coat of carbohydrates (sugars). Here, we describe the disulfide bonds that assist the SARS-CoV-2 spike glycoprotein to assume the correct shape and the composition of the sugar moieties on the glycoprotein surface. We also evaluate the consequences of natural virus variation in O-linked sugar addition and in the cysteine residues involved in disulfide bond formation. This information can expedite the improvement of vaccines and therapies for COVID-19.

Growth, Antigenicity, and Immunogenicity of SARS-CoV-2 Spike Variants Revealed by a Live rVSV-SARS-CoV-2 Virus

SARS-CoV-2 is an emerging coronavirus threatening human health and the economy worldwide. As an RNA virus, variants emerge during the pandemic and potentially influence the efficacy of the anti-viral drugs and vaccines. Eight spike variants harboring highly recurrent mutations were selected and introduced into a replication-competent recombinant VSV in place of the original G protein (rVSV-SARS-CoV-2). The resulting mutant viruses displayed similar growth curves in vitro as the wild-type virus and could be neutralized by sera from convalescent COVID-19 patients. Several variants, especially Beta strain, showed resistance to human neutralizing monoclonal antibodies targeting the receptor-binding domain (RBD). A single dose of rVSV-SARS-CoV-2 Beta variant could elicit enhanced and broad-spectrum neutralizing antibody responses in human ACE2 knock-in mice and golden Syrian hamsters, while other mutants generated antibody levels comparable to the wild-type. Therefore, our results will be of value to the development of next-generation vaccines and therapeutic antibodies.

Trombosis y COVID-19: revisión de alcance

La enfermedad por coronavirus COVID-19 ha generado la mayor crisis de salud pública de la era moderna. Se considera que el estado protrombótico inducido por la infección tiene una relación directa y de importancia sustancial con el daño agudo en el pulmón y con las complicaciones de la infección, incluida la muerte. Esta revisión de alcance (scoping review) resume y evalúa críticamente la evidencia sobre la relación entre la trombosis y la COVID-19, y se basa en una búsqueda bibliográfica sistemática de todos los artículos publicados hasta el 5 de mayo de 2020 e incluidos en las bases de datos PubMed, Scopus, Cochrane y Clinicaltrials.gov. Hemos incluido 26 artículos en la revisión, y hemos evaluado su calidad empleando la guía STROBE. Los principales síntomas que presentan los pacientes diagnosticados con COVID-19 son disnea, fiebre, tos, diarrea y vómitos. A nivel analítico destaca, en esta enfermedad, un aumento de dímero-D, fibrinógeno, tiempo de protrombina y linfopenia. En cuanto a las pruebas radiológicas, las técnicas más usadas para el diagnóstico de tromboembolismo pulmonar, trombosis venosa profunda y otros fenómenos trombóticos fueron la ecografía y la tomografía computarizada. Como conclusión, en la actualidad existe escasa evidencia científica con respecto a la COVID-19 y sus complicaciones trombóticas. Esta revisión resume este cuerpo de evidencia, evalúa su calidad, y ofrece conclusiones que orientan los siguientes pasos a dar en este área de investigación de enorme relevancia y crecimiento exponencial.

AI-based Power Screening Solution for SARS-CoV2 Infection: A Sociodemographic Survey and COVID-19 Cough Detector

Globally, the confirmed coronavirus (SARS-CoV2) cases are being increasing day by day. Coronavirus (COVID-19) causes an acute infection in the respiratory tract that started spreading in late 2019. Huge datasets of SARS-CoV2 patients can be incorporated and analyzed by machine learning strategies for understanding the pattern of pathological spread and helps to analyze the accuracy and speed of novel therapeutic methodologies, also detect the susceptible people depends on their physiological and genetic aspects. To identify the possible cases faster and rapidly, we propose the Artificial Intelligence (AI) power screening solution for SARS- CoV2 infection that can be deployable through the mobile application. It collects the details of the travel history, symptoms, common signs, gender, age and diagnosis of the cough sound. To examine the sharpness of pathomorphological variations in respiratory tracts induced by SARS-CoV2, that compared to other respiratory illnesses to address this issue. To overcome the shortage of SARS-CoV2 datasets, we apply the transfer learning technique. Multipronged mediator for risk-averse Artificial Intelligence Architecture is induced for minimizing the false diagnosis of risk-stemming from the problem of complex dimensionality. This proposed application provides early detection and prior screening for SARS-CoV2 cases. Huge data points can be processed through AI framework that can examine the users and classify them into "Probably COVID", "Probably not COVID" and "Result indeterminate".

Characterization of SARS-CoV-2 Variants N501Y.V1 and N501Y.V2 Spike on Viral Infectivity

SARS-coronavirus 2 (SARS-CoV-2), pathogen of coronavirus disease 2019 (COVID-19), is constantly evolving to adapt to the host and evade antiviral immunity. The newly emerging variants N501Y.V1 (B.1.1.7) and N501Y.V2 (B.1.351), first reported in the United Kingdom and South Africa respectively, raised concerns due to the unusually rapid global spread. The mutations in spike (S) protein may contribute to the rapid spread of these variants. Here, with a vesicular stomatitis virus (VSV)-based pseudotype system, we demonstrated that the pseudovirus bearing N501Y.V2 S protein has higher infection efficiency than pseudovirus with wildtype (WT) and D614G S protein. Moreover, pseudovirus with N501Y.V1 or N501Y.V2 S protein has better thermal stability than WT and D614G, suggesting these mutations of variants may increase the stability of SARS-CoV-2 S protein and virion. However, the pseudovirus bearing N501Y.V1 or N501Y.V2 S protein has similar sensitivity to inhibitors of protease and endocytosis with WT and D614G. These findings could be of value in preventing the spread of virus and developing drugs for emerging SARS-CoV-2 variants.

Scoping reviews: reinforcing and advancing the methodology and application

Scoping reviews are an increasingly common approach to evidence synthesis with a growing suite of methodological guidance and resources to assist review authors with their planning, conduct and reporting. The latest guidance for scoping reviews includes the JBI methodology and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses-Extension for Scoping Reviews. This paper provides readers with a brief update regarding ongoing work to enhance and improve the conduct and reporting of scoping reviews as well as information regarding the future steps in scoping review methods development. The purpose of this paper is to provide readers with a concise source of information regarding the difference between scoping reviews and other review types, the reasons for undertaking scoping reviews, and an update on methodological guidance for the conduct and reporting of scoping reviews.Despite available guidance, some publications use the term 'scoping review' without clear consideration of available reporting and methodological tools. Selection of the most appropriate review type for the stated research objectives or questions, standardised use of methodological approaches and terminology in scoping reviews, clarity and consistency of reporting and ensuring that the reporting and presentation of the results clearly addresses the review's objective(s) and question(s) are critical components for improving the rigour of scoping reviews.Rigourous, high-quality scoping reviews should clearly follow up to date methodological guidance and reporting criteria. Stakeholder engagement is one area where further work could occur to enhance integration of consultation with the results of evidence syntheses and to support effective knowledge translation. Scoping review methodology is evolving as a policy and decision-making tool. Ensuring the integrity of scoping reviews by adherence to up-to-date reporting standards is integral to supporting well-informed decision-making.

Social support through religion and psychological well-being: COVID-19 and coping strategies in Indonesia

The Coronavirus pandemic (COVID-19) originated in China at the end of 2019, the virus festered there for four months before spreading globally. Impacting the developed and developing world including Indonesia. It has transformed social, economic and political practices social life, everyday habits and government policies, with multi-dimensional consequences on human life. The present study endeavours to explore the relationship between religiosity, social capital, and psychological well-being of the general public, particularly in terms of coping with the pandemic. In addition to this, the study aims to highlight the importance of public awareness regarding social distancing, use of religion as a coping mechanism, and living a healthy lifestyle during pandemic. For knowing the perception of the masses, an online survey by using a self-administered questionnaire was carried out among coronavirus patients, the general public, social media activists, students, and professionals across Indonesia. The findings indicate that the pandemic has altered the lifestyle of the masses in different ways and that people have varied perceptions towards this virus regarding its spread and preventive measures. The study also reveals that, social capital (β = .418, p < .001), psychological well-being (β = .343, p < .001), and religious coping (β = .145, p <. 01) have a significant amount of the variance of coronavirus situational stress (F =  69.77, p < .001, R2 = 0.485). Lastly, the study suggests that, adopting preventative measures, standard operating procedures that are sustainable and healthy forms of coping with the pandemic will be equally as important as medical care in order to contain and eventually eradicate the virus.

Comparative phylogenetic analysis of SARS-CoV-2 spike protein-possibility effect on virus spillover

Coronavirus disease 2019 has developed into a dramatic pandemic with tremendous global impact. The receptor-binding motif (RBM) region of the causative virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), binds to host angiotensin-converting enzyme 2 (ACE2) receptors for infection. As ACE2 receptors are highly conserved within vertebrate species, SARS-CoV-2 can infect significant animal species as well as human populations. An analysis of SARS-CoV-2 genotypes isolated from human and significant animal species was conducted to compare and identify mutation and adaptation patterns across different animal species. The phylogenetic data revealed seven distinct phylogenetic clades with no significant relationship between the clades and geographical locations. A high rate of variation within SARS-CoV-2 mink isolates implies that mink populations were infected before human populations. Positions of most single-nucleotide polymorphisms (SNPs) within the spike (S) protein of SARS-CoV-2 genotypes from the different hosts are mostly accumulated in the RBM region and highlight the pronounced accumulation of variants with mutations in the RBM region in comparison with other variants. These SNPs play a crucial role in viral transmission and pathogenicity and are keys in identifying other animal species as potential intermediate hosts of SARS-CoV-2. The possible roles in the emergence of new viral strains and the possible implications of these changes, in compromising vaccine effectiveness, deserve urgent considerations.

Deciphering the impact of novel coronavirus pandemic on agricultural sustainability, food security, and socio-economic sectors-a review

The Spanish flu, Asian flu, Hong Kong flu, HIV/AIDS, SARS, Ebola, and Swine flu, among others, have had a significant impact on agriculture, education, the economy, and human activities, including leisureliness, shipping, healthiness, fisheries, mining, industry, and trade. Currently, manhood is dealing with a new epidemic, the infection of the latest coronavirus (2019-nCoV), which causes a deadly disease named COVID-19. This article aims to examine COVID-19's effect on agriculture, education, and the economy. There are existing estimates to conclude that the COVID-19 pandemic has a significant influence on agriculture and the food supply chain, mostly influencing food demand and, as a result, food security, with a disproportionate impact on the most disadvantaged. To overcome spread of COVID-19, a non-contact food delivery system has been used by utilizing drown for this purpose. This epidemic crisis also introduced a digital education system that is challenging for students and teachers who are not educated in it. Weak infrastructure, such as electricity, poor access to the Internet connection, and a lack of technology literacy, has hampered the online education system. Coronavirus has an undesirable influence on the global economy by affecting tourism, the financial market, commerce, shipping, manufacturing, and the service sector. The exchange market was also down during the COVID-19 pandemic. In conclusion, we should strictly follow SOP's to improve our agriculture, education, economy, and other ways of normal life. We should also be vaccinated to fulfill our all losses in different fields.

Analysis of COVID-19 Guideline Quality and Change of Recommendations: A Systematic Review

Background

Hundreds of coronavirus disease 2019 (COVID-19) clinical practice guidelines (CPGs) and expert consensus statements have been developed and published since the outbreak of the epidemic. However, these CPGs are of widely variable quality. So, this review is aimed at systematically evaluating the methodological and reporting qualities of COVID-19 CPGs, exploring factors that may influence their quality, and analyzing the change of recommendations in CPGs with evidence published.

Methods

We searched five electronic databases and five websites from 1 January to 31 December 2020 to retrieve all COVID-19 CPGs. The assessment of the methodological and reporting qualities of CPGs was performed using the AGREE II instrument and RIGHT checklist. Recommendations and evidence used to make recommendations in the CPGs regarding some treatments for COVID-19 (remdesivir, glucocorticoids, hydroxychloroquine/chloroquine, interferon, and lopinavir-ritonavir) were also systematically assessed. And the statistical inference was performed to identify factors associated with the quality of CPGs.

Results

We included a total of 92 COVID-19 CPGs developed by 19 countries. Overall, the RIGHT checklist reporting rate of COVID-19 CPGs was 33.0%, and the AGREE II domain score was 30.4%. The overall methodological and reporting qualities of COVID-19 CPGs gradually improved during the year 2020. Factors associated with high methodological and reporting qualities included the evidence-based development process, management of conflicts of interest, and use of established rating systems to assess the quality of evidence and strength of recommendations. The recommendations of only seven (7.6%) CPGs were informed by a systematic review of evidence, and these seven CPGs have relatively high methodological and reporting qualities, in which six of them fully meet the Institute of Medicine (IOM) criteria of guidelines. Besides, a rapid advice CPG developed by the World Health Organization (WHO) of the seven CPGs got the highest overall scores in methodological (72.8%) and reporting qualities (83.8%). Many CPGs covered the same clinical questions (it refers to the clinical questions on the effectiveness of treatments of remdesivir, glucocorticoids, hydroxychloroquine/chloroquine, interferon, and lopinavir-ritonavir in COVID-19 patients) and were published by different countries or organizations. Although randomized controlled trials and systematic reviews on the effectiveness of treatments of remdesivir, glucocorticoids, hydroxychloroquine/chloroquine, interferon, and lopinavir-ritonavir for patients with COVID-19 have been published, the recommendations on those treatments still varied greatly across COVID-19 CPGs published in different countries or regions, which may suggest that the CPGs do not make sufficient use of the latest evidence.

Conclusions

Both the methodological and reporting qualities of COVID-19 CPGs increased over time, but there is still room for further improvement. The lack of effective use of available evidence and management of conflicts of interest were the main reasons for the low quality of the CPGs. The use of formal rating systems for the quality of evidence and strength of recommendations may help to improve the quality of CPGs in the context of the COVID-19 pandemic. During the pandemic, we suggest developing a living guideline of which recommendations are supported by a systematic review for it can facilitate the timely translation of the latest research findings to clinical practice. We also suggest that CPG developers should register the guidelines in a registration platform at the beginning for it can reduce duplication development of guidelines on the same clinical question, increase the transparency of the development process, and promote cooperation among guideline developers all over the world. Since the International Practice Guideline Registry Platform has been created, developers could register guidelines prospectively and internationally on this platform.

Bioinformatics Analysis Unveils Certain Mutations Implicated in Spike Structure Damage and Ligand-Binding Site of Severe Acute Respiratory Syndrome Coronavirus 2

There are certain mutations related to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In addition to these known mutations, other new mutations have been found across regions in this study. Based on the results, in which 4,326 SARS-CoV-2 whole sequences were used, some mutations are found to be peculiar with certain regions, while some other mutations are found in all regions. In Asia, mutations (3 different mutations in QLA46612 isolated from South Korea) were found in the same sequence. Although huge number of mutations are detected (more than 70 in Asia) by regions, according to bioinformatics tools, some of them which are G75V (isolated from North America), T95I (isolated from South Korea), G143V (isolated from North America), M177I (isolated from Asia), L293M (isolated from Asia), P295H (isolated from Asia), T393P (isolated from Europe), P507S (isolated from Asia), and D614G (isolated from all regions) (These color used only make correct) predicted a damage to spike' protein structure. Furthermore, this study also aimed to reveal how binding sites of ligands change if the spike protein structure is damaged, and whether more than one mutation affects ligand binding. Mutations that were predicted to damage the structure did not affect the ligand-binding sites, whereas ligands' binding sites were affected in those with multiple mutations. It is thought that this study will give a different perspective to both the vaccine SARS-CoV studies and the change in the structure of the spike protein belonging to this virus against mutations.

Clinical Research Redirection and Optimization During a Pandemic

The COVID-19 pandemic has seen many hurdles to crucial research processes, in particular those that depend on personnel interactions, in providing safeguards against the incipient infectious disease. At the same time, there was a rapid redirection of research, driven by popular and social media and demand for pandemic-related content, to the detriment of non-COVID-19 research and perhaps to COVID-19 research itself. This article provides historical context to research redirection and discusses approaches to optimizing research methodology in the setting of COVID-19 pandemic.

Comparative immunogenicity analysis of intradermal versus intramuscular administration of SARS-CoV-2 RBD epitope peptide-based immunogen In vivo

COVID-19 pandemic has caused severe disruption of global health and devastated the socio-economic conditions all over the world. The disease is caused by SARS-CoV-2 virus that belongs to the family of Coronaviruses which are known to cause a wide spectrum of diseases both in humans and animals. One of the characteristic features of the SARS-CoV-2 virus is the high reproductive rate (R0) that results in high transmissibility of the virus among humans. Vaccines are the best option to prevent and control this disease. Though, the traditional intramuscular (IM) route of vaccine administration is one of the effective methods for induction of antibody response, a needle-free self-administrative intradermal (ID) immunization will be easier for SARS-CoV-2 infection containment, as vaccine administration method will limit human contacts. Here, we have assessed the humoral and cellular responses of a RBD-based peptide immunogen when administered intradermally in BALB/c mice and side-by-side compared with the intramuscular immunization route. The results demonstrate that ID vaccination is well tolerated and triggered a significant magnitude of humoral antibody responses as similar to IM vaccination. Additionally, the ID immunization resulted in higher production of IFN-γ and IL-2 suggesting superior cellular response as compared to IM route. Overall, our data indicates immunization through ID route provides a promising alternative approach for the development of self-administrative SARS-CoV-2 vaccine candidates.

Analysis of glycosylation and disulfide bonding of wild-type SARS-CoV-2 spike glycoprotein

The SARS-CoV-2 coronavirus, the etiologic agent of COVID-19, uses its spike (S) glycoprotein anchored in the viral membrane to enter host cells. The S glycoprotein is the major target for neutralizing antibodies elicited by natural infection and by vaccines. Approximately 35% of the SARS-CoV-2 S glycoprotein consists of carbohydrate, which can influence virus infectivity and susceptibility to antibody inhibition. We found that virus-like particles produced by coexpression of SARS-CoV-2 S, M, E and N proteins contained spike glycoproteins that were extensively modified by complex carbohydrates. We used a fucose-selective lectin to enrich the Golgi-resident fraction of a wild-type SARS-CoV-2 S glycoprotein trimer, and determined its glycosylation and disulfide bond profile. Compared with soluble or solubilized S glycoproteins modified to prevent proteolytic cleavage and to retain a prefusion conformation, more of the wild-type S glycoprotein N-linked glycans are processed to complex forms. Even Asn 234, a significant percentage of which is decorated by high-mannose glycans on soluble and virion S trimers, is predominantly modified in the Golgi by processed glycans. Three incompletely occupied sites of O-linked glycosylation were detected. Viruses pseudotyped with natural variants of the serine/threonine residues implicated in O-linked glycosylation were generally infectious and exhibited sensitivity to neutralization by soluble ACE2 and convalescent antisera comparable to that of the wild-type virus. Unlike other natural cysteine variants, a Cys15Phe (C15F) mutant retained partial, but unstable, infectivity. These findings enhance our understanding of the Golgi processing of the native SARS-CoV-2 S glycoprotein carbohydrates and could assist the design of interventions.

Deficiencies in Planning Interventional Trial Registration of COVID-19 in China

Background: The coronavirus disease 2019 (COVID-19) pandemic has affected the world since late 2019. The efforts to control the spread of the virus need to be supported by credible evidence. Therefore, we analyzed the rationality of the timeline and geographic distribution of COVID-19 trial registration in mainland China. Methods: We searched the Chinese Clinical Trial Registry (ChiCTR, http://www.chictr.org.cn/) and International Clinical Trials Registry Platform (ICTRP, https://www.who.int/ictrp/en/) using keywords including novel coronavirus, coronavirus pneumonia, 2019-nCoV, COVID-19, and SARS-COV-2 from 1 December 2019 to 27 April 2020 and included interventional randomized and non-randomized trials including patients with confirmed cases of COVID-19 in mainland China. The registered trials were reviewed, and data were independently extracted by two reviewers based on the inclusion criteria. Results: A total of 263 registered interventional trials were included in the study. We defined the sample size index (SI) as the total number of patients needed by the trials divided by the total number of patients diagnosed with COVID-19. A total of 84,341 patients had been diagnosed with COVID-19 in China as of 26 April 2020, and the included trials had a combined sample size of 31,156 patients (SI: 0.37). After control of the COVID-19 epidemic was achieved in China (February 18, 2020), the SI was 1.54, suggesting that the number of patients needed by the trials was greater than the number of newly diagnosed patients. The SIs in 8 out of 26 provinces in mainland China were >1. Conclusions: Our results suggested a clear over registration of COVID-19 trials in China, especially after control of the pandemic was achieved, preventing the generation of high-quality evidence.

Spike glycoprotein and host cell determinants of SARS-CoV-2 entry and cytopathic effects

SARS-CoV-2, a betacoronavirus, is the cause of the COVID-19 pandemic. The SARS-CoV-2 spike (S) glycoprotein trimer mediates virus entry into host cells and cytopathic effects (syncytium formation). We studied the contribution of several S glycoprotein features to these functions, focusing on those that differ among related coronaviruses. Acquisition of the furin cleavage site by the SARS-CoV-2 S glycoprotein decreased virus stability and infectivity, but greatly enhanced syncytium-forming ability. Notably, the D614G change found in globally predominant SARS-CoV-2 strains increased infectivity, modestly enhanced responsiveness to the ACE2 receptor and susceptibility to neutralizing sera, and tightened association of the S1 subunit with the trimer. Apparently, these two features of the SARS-CoV-2 S glycoprotein, the furin cleavage site and D614G, have evolved to balance virus infectivity, stability, cytopathicity and antibody vulnerability. Although the endodomain (cytoplasmic tail) of the S2 subunit was not absolutely required for virus entry or syncytium formation, alteration of palmitoylated cysteine residues in the cytoplasmic tail decreased the efficiency of these processes. As proteolytic cleavage contributes to the activation of the SARS-CoV-2 S glycoprotein, we evaluated the ability of protease inhibitors to suppress S glycoprotein function. Matrix metalloprotease inhibitors suppressed S-mediated cell-cell fusion, but not virus entry. Synergy between inhibitors of matrix metalloproteases and TMPRSS2 suggests that both host proteases can activate the S glycoprotein during the process of syncytium formation. These results provide insights into SARS-CoV-2 S glycoprotein-host cell interactions that likely contribute to the transmission and pathogenicity of this pandemic agent.IMPORTANCE The development of an effective and durable SARS-CoV-2 vaccine is essential for combating the growing COVID-19 pandemic. The SARS-CoV-2 spike (S) glycoprotein is the main target of neutralizing antibodies elicited during virus infection or following vaccination. Knowledge of the spike glycoprotein evolution, function and interactions with host factors will help researchers to develop effective vaccine immunogens and treatments. Here we identify key features of the spike glycoprotein, including the furin cleavage site and the D614G natural mutation, that modulate viral cytopathic effects, infectivity and sensitivity to inhibition. We also identify two inhibitors of host metalloproteases that block S-mediated cell-cell fusion, a process that contributes to the destruction of the virus-infected cell.

Spike S2 Subunit: The Dark Horse in the Race for Prophylactic and Therapeutic Interventions against SARS-CoV-2

In the midst of the unceasing COVID-19 pandemic, the identification of immunogenic epitopes in the SARS-CoV-2 spike (S) glycoprotein plays a vital role in the advancement and development of intervention strategies. S is expressed on the exterior of the SARS-CoV-2 virion and contains two subunits, namely the N-terminal S1 and C-terminal S2. It is the key element for mediating viral entry as well as a crucial antigenic determinant capable of stimulating protective immune response through elicitation of anti-SARS-CoV-2 antibodies and activation of CD4+ and CD8+ cells in COVID-19 patients. Given that S2 is highly conserved in comparison to the S1, here, we provide a review of the latest findings on the SARS-CoV-2 S2 subunit and further discuss its potential as an attractive and promising target for the development of prophylactic vaccines and therapeutic agents against COVID-19.

Electrochemical Biosensors for the Detection of SARS-CoV-2 and Other Viruses

The last few decades have been plagued by viral outbreaks that present some of the biggest challenges to public safety. The current coronavirus (COVID-19) disease pandemic has exponentiated these concerns. Increased research on diagnostic tools is currently being implemented in order to assist with rapid identification of the virus, as mass diagnosis and containment is the best way to prevent the outbreak of the virus. Accordingly, there is a growing urgency to establish a point-of-care device for the rapid detection of coronavirus to prevent subsequent spread. This device needs to be sensitive, selective, and exhibit rapid diagnostic capabilities. Electrochemical biosensors have demonstrated these traits and, hence, serve as promising candidates for the detection of viruses. This review summarizes the designs and features of electrochemical biosensors developed for some past and current pandemic or epidemic viruses, including influenza, HIV, Ebola, and Zika. Alongside the design, this review also discusses the detection principles, fabrication techniques, and applications of the biosensors. Finally, research and perspective of biosensors as potential detection tools for the rapid identification of SARS-CoV-2 is discussed.

Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains

This study aims to highlight SARS-COV-2 mutations which are associated with increased or decreased viral virulence. We utilize genetic data from all strains available from GISAID and countries' regional information, such as deaths and cases per million, as well as COVID-19-related public health austerity measure response times. Initial indications of selective advantage of specific mutations can be obtained from calculating their frequencies across viral strains. By applying modelling approaches, we provide additional information that is not evident from standard statistics or mutation frequencies alone. We therefore, propose a more precise way of selecting informative mutations. We highlight two interesting mutations found in genes N (P13L) and ORF3a (Q57H). The former appears to be significantly associated with decreased deaths and cases per million according to our models, while the latter shows an opposing association with decreased deaths and increased cases per million. Moreover, protein structure prediction tools show that the mutations infer conformational changes to the protein that significantly alter its structure when compared to the reference protein.

Identifying Transcriptomic Signatures and Rules for SARS-CoV-2 Infection

The world-wide Coronavirus Disease 2019 (COVID-19) pandemic was triggered by the widespread of a new strain of coronavirus named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Multiple studies on the pathogenesis of SARS-CoV-2 have been conducted immediately after the spread of the disease. However, the molecular pathogenesis of the virus and related diseases has still not been fully revealed. In this study, we attempted to identify new transcriptomic signatures as candidate diagnostic models for clinical testing or as therapeutic targets for vaccine design. Using the recently reported transcriptomics data of upper airway tissue with acute respiratory illnesses, we integrated multiple machine learning methods to identify effective qualitative biomarkers and quantitative rules for the distinction of SARS-CoV-2 infection from other infectious diseases. The transcriptomics data was first analyzed by Boruta so that important features were selected, which were further evaluated by the minimum redundancy maximum relevance method. A feature list was produced. This list was fed into the incremental feature selection, incorporating some classification algorithms, to extract qualitative biomarker genes and construct quantitative rules. Also, an efficient classifier was built to identify patients infected with SARS-COV-2. The findings reported in this study may help in revealing the potential pathogenic mechanisms of COVID-19 and finding new targets for vaccine design.

A Systematic Review and Meta-Analysis of Clinical Characteristics and Outcomes in Patients With Lung Cancer with Coronavirus Disease 2019

Cancer is considered to be an independent risk factor for severe illness and higher mortality in patients with coronavirus disease 2019 (COVID-19). These adverse outcomes have been suspected to be more severe in patients with lung cancer. The objective of this systematic review and meta-analysis is to outline patient characteristics, challenges in diagnosis and treatment, and outcomes of patients with lung cancer with COVID-19. A comprehensive search was conducted using EMBASE and PubMed databases using the terms “COVID” and “cancer.” Studies that reported clinical characteristics or outcomes of patients with lung cancer with COVID-19 were then systematically identified. Meta-analysis for COVID-19 related mortality associated with lung cancer compared with other cancer types was conducted. The results were reported as OR and confidence intervals using the mixed-effects logistic regression model. The most frequently reported clinical findings in patients with lung cancer with COVID-19 were fever and cough, with 68% and 61%, respectively. Laboratory and radiographic findings were consistent with broadly reported data. The meta-analysis noted a statistically significant increase in mortality rate in patients with lung cancer compared with other patients with cancer, with an OR of 1.62 (95% confidence interval: 1.06–2.48). Patients with lung cancer with COVID-19 also reflected greater severity of illness and higher rates of intensive care unit admissions and mechanical ventilation. COVID-19 in patients with lung cancer is associated with severe disease and increased mortality relative to patients with other malignancies and the general population. There is conflicting evidence on the effect of specific lung cancer treatments on outcomes. Until more definitive data is available, lung cancer–directed treatment should be continued or restarted as early as possible in mild to moderate cases to prevent worsening and cancer-related mortality.

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Patients with lung cancer and coronavirus disease 2019 infection have higher mortality rates compared with patients with other cancer types.

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Rates of severe illness, intensive care unit admissions, and mechanical ventilation are also higher in patients with lung cancer.

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Clinical, laboratory, and radiographic characteristics are similar to reports in the general population.

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There is conflicting data regarding the effect of specific lung cancer treatments on outcomes.

Genetic analysis of the 2019 coronavirus pandemic with from real-time reverse transcriptase polymerase chain reaction

Corona viruses (CoV) are known to cause extreme pandemics in the globe. The year 2020 will be a pandemic with the spread of the novel coronavirus (SARS-CoV-2) across the globe. Coronavirus 2019 (COVID-19) has been a part of our scary life for more than a quarter of a year in 2020. The Wuhan market and China have been the most commonly used terms in the world for at least a quarter of 2020. A zoonotic coronavirus has entered organisms to affect organisms for the third season in several centuries. CoV is a global pandemic prompted a drastic and rapid reconfiguration of society. CoV have extraordinary broad genomes of about 30 kilobases of RNA. There is no genetic relationship between the SARS-CoV, MERS and SARS-CoV-2. For health care strategies and for anticipating and preventing potential outbreaks, adequate description of the international spread of COVID-19 virus is imperative. The WHO has declared COVID-19 as endemic to pandemic in the first trimester of 2020. The biggest issues for diagnosis COVID-19 is not established apart from Real-time reverse transcriptase polymerase chain reaction (RT-PCR). In order to monitor the COVID-19 pandemic, testing of active SARS-CoV-2 infections is a fundamental public health method. The vast use of SARS-CoV-2 RT-PCR tests around the world has led to increased availability of test kits, which is also a major bottleneck. The technique RT-PCR was generally agreed in the present scenario to detect SARS-CoV-2 in the human body. This review discusses about the importance of molecular technique for diagnosing the pandemic disease of 2019. In conclusion, RT-PCR was found to be an apt technique for identification of SARS-CoV-2.

A retrospective comparison of drugs against COVID-19

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Hydroxychloroquine is an efficient candidate drug against COVID-19.

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Oseltamivir can be prudently considered in combination therapy.

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Drug repurposing is a promising way to combat SARS-CoV-2 infection.

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Comparison of drug effects against COVID-19 is instructive in the pandemic.

Coronavirus disease 19 (COVID-19) has posed serious threats to the general population. To relieve the crisis, a comparison of drug effects against COVID-19 is instructive. Between January 27, 2020 and March 21, 2020, a total of 333 patients treated with arbidol, corticosteroids, hydroxychloroquine, lopinavir/ritonavir, or oseltamivir monotherapy, having definite outcomes and serological antibody detection results, were retrospectively analyzed. The hydroxychloroquine group had a significantly reduced duration of hospital stay than the arbidol and corticosteroids groups. The oseltamivir group had a significantly shorter length of hospital stay than the arbidol, corticosteroids, and lopinavir/ritonavir groups. The hydroxychloroquine group had a significantly higher IgM titer than the other four groups and exhibited significantly higher IgG levels than the arbidol, lopinavir/ritonavir, and oseltamivir groups. Our findings indicated that hydroxychloroquine might have the potential for efficient COVID-19 management, while oseltamivir should be prudently considered in combination therapy.

Multiscale Feedback Loops in SARS-CoV-2 Viral Evolution

COVID-19 is an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The viral genome is considered to be relatively stable and the mutations that have been observed and reported thus far are mainly focused on the coding region. This article provides evidence that macrolevel pandemic dynamics, such as social distancing, modulate the genomic evolution of SARS-CoV-2. This view complements the prevalent paradigm that microlevel observables control macrolevel parameters such as death rates and infection patterns. First, we observe differences in mutational signals for geospatially separated populations such as the prevalence of A23404G in CA versus NY and WA. We show that the feedback between macrolevel dynamics and the viral population can be captured employing a transfer entropy framework. Second, we observe complex interactions within mutational clades. Namely, when C14408T first appeared in the viral population, the frequency of A23404G spiked in the subsequent week. Third, we identify a noncoding mutation, G29540A, within the segment between the coding gene of the N protein and the ORF10 gene, which is largely confined to NY (>95%). These observations indicate that macrolevel sociobehavioral measures have an impact on the viral genomics and may be useful for the dashboard-like tracking of its evolution. Finally, despite the fact that SARS-CoV-2 is a genetically robust organism, our findings suggest that we are dealing with a high degree of adaptability. Owing to its ample spread, mutations of unusual form are observed and a high complexity of mutational interaction is exhibited.

Help-Seeking Behavior of Returning to Work in Healthcare Workers and its Influencing Factors During COVID-19 Subsiding

OBJECTIVES

To explore the level and influencing factors of help-seeking behavior of returning to work in healthcare workers (HCWs).

METHODS

A total of 861 HCWs were surveyed. A structured self-administered questionnaire was used to collect data. Multivariable logistic regression was performed to examine the influencing factors of help-seeking behavior.

RESULTS

HCWs sought help with respect to COVID-19-diagnosized problem most. Help-seeking intention, problems encountered after return, test for return, work condition during COVID-19, relatives or friends diagnosed or suspected as COVID-19, and socio-demographic characteristics such as occupation, education, title, and marriage status are predictors of help-seeking behavior.

CONCLUSIONS

Education and intervention should lay particular stress on HCWs featured rest at home before return, doctor, lower education and lower title to ensure the safety, accuracy, and quality of work after they return to work for a better occupational environment.

Transmission Dynamics of the COVID-19 Epidemic at the District Level in India: Prospective Observational Study

BACKGROUND

On March 9, 2020, the first COVID-19 case was reported in Jodhpur, Rajasthan, in the northwestern part of India. Understanding the epidemiology of COVID-19 at a local level is becoming increasingly important to guide measures to control the pandemic.

OBJECTIVE

The aim of this study was to estimate the serial interval and basic reproduction number (R0) to understand the transmission dynamics of the COVID-19 outbreak at a district level. We used standard mathematical modeling approaches to assess the utility of these factors in determining the effectiveness of COVID-19 responses and projecting the size of the epidemic.

METHODS

Contact tracing of individuals infected with SARS-CoV-2 was performed to obtain the serial intervals. The median and 95th percentile values of the SARS-CoV-2 serial interval were obtained from the best fits with the weibull, log-normal, log-logistic, gamma, and generalized gamma distributions. Aggregate and instantaneous R0 values were derived with different methods using the EarlyR and EpiEstim packages in R software.

RESULTS

The median and 95th percentile values of the serial interval were 5.23 days (95% CI 4.72-5.79) and 13.20 days (95% CI 10.90-18.18), respectively. R0 during the first 30 days of the outbreak was 1.62 (95% CI 1.07-2.17), which subsequently decreased to 1.15 (95% CI 1.09-1.21). The peak instantaneous R0 values obtained using a Poisson process developed by Jombert et al were 6.53 (95% CI 2.12-13.38) and 3.43 (95% CI 1.71-5.74) for sliding time windows of 7 and 14 days, respectively. The peak R0 values obtained using the method by Wallinga and Teunis were 2.96 (95% CI 2.52-3.36) and 2.92 (95% CI 2.65-3.22) for sliding time windows of 7 and 14 days, respectively. R0 values of 1.21 (95% CI 1.09-1.34) and 1.12 (95% CI 1.03-1.21) for the 7- and 14-day sliding time windows, respectively, were obtained on July 6, 2020, using method by Jombert et al. Using the method by Wallinga and Teunis, values of 0.32 (95% CI 0.27-0.36) and 0.61 (95% CI 0.58-0.63) were obtained for the 7- and 14-day sliding time windows, respectively. The projection of cases over the next month was 2131 (95% CI 1799-2462). Reductions of transmission by 25% and 50% corresponding to reasonable and aggressive control measures could lead to 58.7% and 84.0% reductions in epidemic size, respectively.

CONCLUSIONS

The projected transmission reductions indicate that strengthening control measures could lead to proportionate reductions of the size of the COVID-19 epidemic. Time-dependent instantaneous R0 estimation based on the process by Jombart et al was found to be better suited for guiding COVID-19 response at the district level than overall R0 or instantaneous R0 estimation by the Wallinga and Teunis method. A data-driven approach at the local level is proposed to be useful in guiding public health strategy and surge capacity planning.

Characteristics of academic publications, preprints, and registered clinical trials on the COVID-19 pandemic

The COVID-19 pandemic has unleashed a deluge of publications. For this cross-sectional study we compared the amount and reporting characteristics of COVID-19-related academic articles and preprints and the number of ongoing clinical trials and systematic reviews. To do this, we searched the PubMed database of citations and abstracts for published life science journals by using appropriate combinations of medical subject headings (MeSH terms), and the COVID-19 section of the MedRxiv and BioRxiv archives up to 20 May 2020 (21 weeks). In addition, we searched Clinicaltrial.gov, Chinese Clinical Trial Registry, EU Clinical Trials Register, and 15 other trial registers, as well as PROSPERO, the international prospective register of systematic reviews. The characteristics of each publication were extracted. Regression analyses and Z tests were used to detect publication trends and their relative proportions. A total of 3635 academic publications and 3805 preprints were retrieved. Only 8.6% (n = 329) of the preprints were already published in indexed journals. The number of academic and preprint publications increased significantly over time (p<0.001). Case reports (6% academic vs 0.9% preprints; p<0.001) and letters (17.4% academic vs 0.5% preprints; p<0.001) accounted for a greater share of academic compared to preprint publications. Differently, randomized controlled trials (0.22% vs 0.63%; p<0.001) and systematic reviews (0.08% vs 5%) made up a greater share of the preprints. The relative proportion of clinical studies registered at Clinicaltrials.gov, Chinese Clinical Trial Registry, and EU Clinical Trials Register was 57.9%, 49.5%, and 98.9%, respectively, most of which were still “recruiting”. PROSPERO listed 962 systematic review protocols. Preprints were slightly more prevalent than academic articles but both were increasing in number. The void left by the lack of primary studies was filled by an outpour of immediate opinions (i.e., letters to the editor) published in PubMed-indexed journals. Summarizing, preprints have gained traction as a publishing response to the demand for prompt access to empirical, albeit not peer-reviewed, findings during the present pandemic.

The Impact of Mutations in SARS-CoV-2 Spike on Viral Infectivity and Antigenicity

The spike protein of SARS-CoV-2 has been undergoing mutations and is highly glycosylated. It is critically important to investigate the biological significance of these mutations. Here, we investigated 80 variants and 26 glycosylation site modifications for the infectivity and reactivity to a panel of neutralizing antibodies and sera from convalescent patients. D614G, along with several variants containing both D614G and another amino acid change, were significantly more infectious. Most variants with amino acid change at receptor binding domain were less infectious, but variants including A475V, L452R, V483A, and F490L became resistant to some neutralizing antibodies. Moreover, the majority of glycosylation deletions were less infectious, whereas deletion of both N331 and N343 glycosylation drastically reduced infectivity, revealing the importance of glycosylation for viral infectivity. Interestingly, N234Q was markedly resistant to neutralizing antibodies, whereas N165Q became more sensitive. These findings could be of value in the development of vaccine and therapeutic antibodies.

Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus

A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional, and municipal. The shift occurred even in local epidemics where the original D614 form was well established prior to introduction of the G614 variant. The consistency of this pattern was highly statistically significant, suggesting that the G614 variant may have a fitness advantage. We found that the G614 variant grows to a higher titer as pseudotyped virions. In infected individuals, G614 is associated with lower RT-PCR cycle thresholds, suggestive of higher upper respiratory tract viral loads, but not with increased disease severity. These findings illuminate changes important for a mechanistic understanding of the virus and support continuing surveillance of Spike mutations to aid with development of immunological interventions.

Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus

A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional, and municipal. The shift occurred even in local epidemics where the original D614 form was well established prior to introduction of the G614 variant. The consistency of this pattern was highly statistically significant, suggesting that the G614 variant may have a fitness advantage. We found that the G614 variant grows to a higher titer as pseudotyped virions. In infected individuals, G614 is associated with lower RT-PCR cycle thresholds, suggestive of higher upper respiratory tract viral loads, but not with increased disease severity. These findings illuminate changes important for a mechanistic understanding of the virus and support continuing surveillance of Spike mutations to aid with development of immunological interventions.