Analysis of Worldwide Real-time Recovery and Death Ratio of COVID-19 Pandemic

Covid-19 is a fast-spreading viral disease that not only infects humans but also animals. The daily lives of people, their health, and a country's economy are all impacted by this devastating virus. Unfortunately, India again got hit with the second wave of COVID-19, and this time the double mutant virus is much stronger than the one involved in the first wave of Pandemic. According to the scientists, the double mutant virus is 70% more deadly than the previous one that makes the situation even more alarming. This study shows that COVID-19 infected patients mostly suffer from lung infections after coming in contact with the virus. To perform the analysis, the data was collected from the Kaggle repository. This method only focuses on various trends and analyses of COVID-19 infected patients. This paper aims at performing exploratory Data Analysis to retrieve various kinds of important insights from the extracted data that involves the positivity rate of the top 10 countries around the world, positivity ratio of different states of India, death ratio of various states, and also the positivity rate based on gender is retrieved that is further important in claiming this virus' susceptibility towards a particular gender. The result of this analysis shows the man is at a greater risk of encountering the COVID-19 virus due to lack in presence of certain hormone that is only found in women. © 2022 American Institute of Physics Inc.. All rights reserved.

Elucidating the enhanced binding affinity of a double mutant SP-D with trimannose on the influenza A virus using molecular dynamics.

Surfactant protein D (SP-D) is an essential component of the human pulmonary surfactant system, which is crucial in the innate immune response against glycan-containing pathogens, including Influenza A viruses (IAV) and SARS-CoV-2. Previous studies have shown that wild-type (WT) SP-D can bind IAV but exhibits poor antiviral activities. However, a double mutant (DM) SP-D consisting of two point mutations (Asp325Ala and Arg343Val) inhibits IAV more potently. Presently, the structural mechanisms behind the point mutations' effects on SP-D's binding affinity with viral surface glycans are not fully understood. Here we use microsecond-scale, full-atomistic molecular dynamics (MD) simulations to understand the molecular mechanism of mutation-induced SP-D's higher antiviral activity. We find that the Asp325Ala mutation promotes a trimannose conformational change to a more stable state. Arg343Val increases the binding with trimannose by increasing the hydrogen bonding interaction with Glu333. Free energy perturbation (FEP) binding free energy calculations indicate that the Arg343Val mutation contributes more to the increase of SP-D's binding affinity with trimannose than Asp325Ala. This study provides a molecular-level exploration of how the two mutations increase SP-D binding affinity with trimannose, which is vital for further developing preventative strategies for related diseases.

Biochemical Characterization of SARS-CoV-2 Spike RBD Mutations and Their Impact on ACE2 Receptor Binding.

Infection of mammalian cells by SARS-CoV-2 coronavirus requires primary interaction between the receptor binding domain (RBD) of the viral spike protein and the host cell surface receptor angiotensin-converting enzyme 2 (ACE2) glycoprotein. Several mutations in the RBD of SARS-CoV-2 spike protein have been reported for several variants and resulted in wide spread of the COVID pandemic. For instance, the double mutations L452R and E484Q present in the Indian B.1.617 variant have been suggested to cause evasion of the host immune response. The common RBD mutations N501Y and E484K were found to enhance the interaction with the ACE2 receptor. In the current study, we analyzed the biosynthesis and secretion of the RBD double mutants L452R and E484Q in comparison to the wild-type RBD and the individual mutations N501 and E484K in mammalian cells. Moreover, we evaluated the interaction of these variants with ACE2 by means of expression of the S protein and co-immunoprecipitation with ACE2. Our results revealed that the double RBD mutations L452R and E484Q resulted in a higher expression level and secretion of spike S1 protein than other mutations. In addition, an increased interaction of these mutant forms with ACE2 in Calu3 cells was observed. Altogether, our findings highlight the impact of continuous S1 mutations on the pathogenicity of SARS-CoV-2 and provide further biochemical evidence for the dominance and high transmissibility of the double Indian mutations.

Effect of Double Mutation (L452R and E484Q) in RBD of Spike Protein on its Interaction with ACE2 Receptor Protein

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) caused coronavirus disease 2019 (COVID-19) pandemic has become a global health issue. Recently, the SARS-CoV-2 strain (B.1.617 double mutant variant) has raised alarms in India and other nations. B.1.617 variant was found to contain two key mutations (L452R and E484Q) in the RBD region of the spike protein. In this work, we have focussed on the effect of the double mutations in spike protein on its binding to the host cell receptor protein, angiotensin-converting enzyme 2 (ACE2). From the molecular dynamics simulation, we observed that the L452R and E484Q double mutant (DM) in spike protein utilizes unique strategies to achieve stable binding to ACE2 compared to the spike protein's wild type (WT). Using MM-GBSA/MM-PBSA algorithms, we found that the binding affinity between spike protein-containing DM and ACE2 is high (GBTOT =-47.09 kcal mol-1, PBTOT=-19.93 kcal mol-1) in comparison with spike protein WT and ACE2 (GBTOT =-31.79 kcal mol-1, PBTOT=-6.33 kcal mol-1). Stable binding of spike protein to ACE2 is essential for virus entry. They should understand interactions between them while designing drugs and treatment modalities to target or disrupt this interface. © 2022 by the authors.

Insights into the structure and dynamics of SARS-CoV-2 spike glycoprotein double mutant L452R-E484Q.

The Receptor Binding Domain (RBD) of SARS-CoV-2, located on the S1 subunit, plays a vital role in the virus binding and its entry into the host cell through angiotensin-converting enzyme 2 (ACE2) receptor. Therefore, understanding the dynamic effects of mutants on the SARS-CoV-2 RBD is essential for discovering drugs to inhibit the virus binding and disrupt its entry into the host cells. A recent study reported a double mutant of SARS-CoV-2, L452R-E484Q, located in the RBD region. Thus, this study employed various computational algorithms and methods to understand the structural impact of both individual variants L452R, E484Q, and the double mutant L452R-E484Q on the native RBD of spike glycoprotein. The effects of the mutations on native RBD structure were predicted by in silico algorithms, which predicted changes in the protein structure and function upon the mutations. Subsequently, molecular dynamics (MD) simulations were employed to understand the conformational stability and functional changes on the RBD upon the mutations. The comparative results of MD simulation parameters displayed that the double mutant induces significant conformational changes in the spike glycoprotein RBD, which may alter its biological functions. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03151-0.

Vaccine Candidate Double Mutant Variants of Enterotoxigenic Escherichia coli Heat-Stable Toxin.

Heat-stable enterotoxin (ST) producing enterotoxigenic Escherichia coli (ETEC) strains are among the top four enteropathogens associated with moderate-to-severe diarrhea in children under five years in low-to-middle income countries, thus making ST a target for an ETEC vaccine. However, ST must be mutated to abolish its enterotoxicity and to prevent a potential immunological cross-reaction due to its structural resemblance to the human peptides uroguanylin and guanylin. To reduce the risk of eliciting cross-reacting antibodies with our lead STh-A14T toxoid, L9 was chosen as an additional mutational target. A double mutant vaccine candidate immunogen, STh-L9A/A14T, was constructed by conjugation to the synthetic virus-like mi3 nanoparticle using the SpyTag/SpyCatcher technology. This immunogen elicited STh neutralizing antibodies in mice, but with less consistency than STh-A14T peptide control immunogens. Moreover, individual sera from mice immunized with both single and double mutant variants displayed varying levels of unwanted cross-reacting antibodies. The lowest levels of cross-reacting antibodies were observed with STh-L9K/A14T control immunogens, suggesting that it is indeed possible to reduce the risk of eliciting cross-reacting antibodies by mutation. However, mutant-specific antibodies were observed for most double mutant immunogens, demonstrating the delicate balancing act between disrupting cross-reacting epitopes, keeping protective ones, and avoiding the formation of neoepitopes.

Impact of the Double Mutants on Spike Protein of SARS-CoV-2 B.1.617 Lineage on the Human ACE2 Receptor Binding: A Structural Insight.

The recent emergence of novel SARS-CoV-2 variants has threatened the efforts to contain the COVID-19 pandemic. The emergence of these "variants of concern" has increased immune escape and has supplanted the ancestral strains. The novel variants harbored by the B.1.617 lineage (kappa and delta) carry mutations within the receptor-binding domain of spike (S) protein (L452R + E484Q and L452R + T478K), the region binding to the host receptor. The double mutations carried by these novel variants are primarily responsible for an upsurge number of COVID-19 cases in India. In this study, we thoroughly investigated the impact of these double mutations on the binding capability to the human host receptor. We performed several structural analyses and found that the studied double mutations increase the binding affinity of the spike protein to the human host receptor (ACE2). Furthermore, our study showed that these double mutants might be a dominant contributor enhancing the receptor-binding affinity of SARS-CoV-2 and consequently making it more stable. We also investigated the impact of these mutations on the binding affinity of two monoclonal antibodies (Abs) (2-15 and LY-CoV555) and found that the presence of the double mutations also hinders its binding with the studied Abs. The principal component analysis, free energy landscape, intermolecular interaction, and other investigations provided a deeper structural insight to better understand the molecular mechanism responsible for increased viral transmissibility of these variants.

False-Negative RT-PCR Findings and Double Mutant Variant as Factors of an Overwhelming Second Wave of COVID-19 in India: an Emerging Global Health Disaster.

RT-PCR is considered to be the standard gold diagnostic test for detecting COVID-19 causing SARS-CoV-2. Recent reports and recent pieces of evidence from scientific literature, however, tell a different story. There have been speculations of SARS-CoV-2 escaping the RT-PCR because of the series of mutations it has gone through. It is possible that host-dependent RNA editing and high person-to-person transmission have equipped the virus with mutations enabling it to spread faster and even evade the RT-PCR. Added to this is burnout among healthcare workers and technicians handling the RT-PCR machines and sampling. All of these factors may be working in unison to result in the deluge of false-negative cases India is facing during the second COVID-19 wave. The mutant strains are spreading to other parts, posing challenges to the whole world. These circumstances warrant supplementary diagnostic tests such as serological and radiological findings to deal with cases of high clinical suspicion. Even one misdiagnosed COVID-19 patient poses a risk to hundreds of others in the vicinity. Healthcare workers' burnout also has to be dealt with. Erroneous staff should be re-trained.

Review of COVID-19 Variants and COVID-19 Vaccine Efficacy: What the Clinician Should Know?

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a beta coronavirus that belongs to the Coronaviridae family. SARS-CoV-2 is an enveloped spherical-shaped virus. The ribonucleic acid (RNA) is oriented in a 5'-3'direction which makes it a positive sense RNA virus, and the RNA can be read directly as a messenger RNA. The nonstructural protein 14 (nsp14) has proofreading activity which allows the rate of mutations to stay low. A change in the genetic sequence is called a mutation. Genomes that differ from each other in genetic sequence are called variants. Variants are the result of mutations but differ from each other by one or more mutations. When a phenotypic difference is demonstrated among the variants, they are called strains. Viruses constantly change in two different ways, antigenic drift and antigenic shift. SARS-CoV-2 genome is also prone to various mutations that led to antigenic drift resulting in escape from immune recognition. The Center of Disease Control and Prevention (CDC) updates the variant strains in the different classes. The classes are variant of interest, variant of concern and variant of high consequence. The current variants included in the variant of interest by the USA are: B.1.526, B.1.525, and P.2; and those included in the variant of concern by the USA are B.1.1.7, P.1, B.1.351, B.1.427, and B.1.429. The double and triple mutant variants first reported in India have resulted in a massive increase in the number of cases. Emerging variants not only result in increased transmissibility, morbidity and mortality, but also have the ability to evade detection by existing or currently available diagnostic tests, which can potentially delay the diagnosis and treatment, exhibit decreased susceptibility to treatment including antivirals, monoclonal antibodies and convalescent plasma, possess the ability to cause reinfection in previously infected and recovered individuals, and vaccine breakthrough cases in fully vaccinated individuals. Hence, continuation of precautionary measures, genomic surveillance and vaccination plays an important role in the prevention of spread, early identification of variants, prevention of mutations and viral replication, respectively.

Discovery of Taroxaz-104: The first potent antidote of SARS-CoV-2 VOC-202012/01 strain.

Polyhydroxyphenols and nitrogenous heterocyclics are two of the most powerful active species of molecules in pharmaceutical chemistry, as each of them is renowned for its various bioactivities for humans. One of their outstanding actions is the antiviral activities, which clearly appear if the principal functional entities of both classes meet into one compound. The recent COVID-19 pandemic pushed us to computationally sift and assess our small library of synthetic 2-(3,4,5-trihydroxyphenyl)-1,3,4-oxadiazoles against the main coronaviral protein/enzymatic targets. Surprisingly, few ligands exhibited interesting low binding energies (strong inhibitory affinities) with some SARS-CoV-2 proteins, mainly the pivotal enzyme RNA-dependent RNA polymerase (nCoV-RdRp). One of these compounds was Taroxaz-104 (5,5'-{5,5'-[(1R,2R)-1,2-dihydroxyethane-1,2-diyl]bis(1,3,4-oxadiazole-5,2-diyl)}dibenzene-1,2,3-triol), which presented lower binding free energies of about -10.60 and -9.10 kcal/mol (as compared to the reference agent, GS-443902, which presented about -9.20 and -7.90 kcal/mol) with nCoV-RdRp-RNA and nCoV-RdRp alone, respectively. Extensive molecular modeling examination disclosed the potent Taroxaz-104 inhibition of one of the possible active/allosteric sites of nCoV-RdRp, since Taroxaz-104 molecule interacts with at least seven main amino acids of the presumed pocket/cavity of this nCoV-RdRp active site. The effective repurposing of Taroxaz-104 molecule was attained after the satisfactorily interesting results of the anti-COVID-19 bioassay were secured, since these data demonstrated that Taroxaz-104 showed very efficient anti-COVID-19 actions (anti-SARS-CoV-2 EC50 = 0.42 µM) with specific promising efficacy against the new SARS-CoV-2 strains. Additional research studies for the progress of Taroxaz-104 and other related polyphenolic 2,5-disubstituted-1,3,4-oxadiazole analogs as successful anti-SARS-CoV-2 medications, via, e.g., preclinical/clinical trials, are pressingly required.