SARS-CoV 2 spike protein S1 subunit as an ideal target for stable vaccines: A bioinformatic study

Antivirals for Broader Coverage against Human Coronaviruses

Coronaviruses (CoVs) are enveloped positive-sense single-stranded RNA viruses with a genome that is 27-31 kbases in length. Critical genes include the spike (S), envelope (E), membrane (M), nucleocapsid (N) and nine accessory open reading frames encoding for non-structural proteins (NSPs) that have multiple roles in the replication cycle and immune evasion (1). There are seven known human CoVs that most likely appeared after zoonotic transfer, the most recent being SARS-CoV-2, responsible for the COVID-19 pandemic. Antivirals that have been approved by the FDA for use against COVID-19 such as Paxlovid can target and successfully inhibit the main protease (MPro) activity of multiple human CoVs; however, alternative proteomes encoded by CoV genomes have a closer genetic similarity to each other, suggesting that antivirals could be developed now that target future CoVs. New zoonotic introductions of CoVs to humans are inevitable and unpredictable. Therefore, new antivirals are required to control not only the next human CoV outbreak but also the four common human CoVs (229E, OC43, NL63, HKU1) that circulate frequently and to contain sporadic outbreaks of the severe human CoVs (SARS-CoV, MERS and SARS-CoV-2). The current study found that emerging antiviral drugs, such as Paxlovid, could target other CoVs, but only SARS-CoV-2 is known to be targeted in vivo. Other drugs which have the potential to target other human CoVs are still within clinical trials and are not yet available for public use. Monoclonal antibody (mAb) treatment and vaccines for SARS-CoV-2 can reduce mortality and hospitalisation rates; however, they target the Spike protein whose sequence mutates frequently and drifts. Spike is also not applicable for targeting other HCoVs as these are not well-conserved sequences among human CoVs. Thus, there is a need for readily available treatments globally that target all seven human CoVs and improve the preparedness for inevitable future outbreaks. Here, we discuss antiviral research, contributing to the control of common and severe CoV replication and transmission, including the current SARS-CoV-2 outbreak. The aim was to identify common features of CoVs for antivirals, biologics and vaccines that could reduce the scientific, political, economic and public health strain caused by CoV outbreaks now and in the future.

Performance of the SureScreen Diagnostics COVID-19 antibody rapid test in comparison with three automated immunoassays

Lateral flow immunoassays (LFIA) for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies are used for population surveillance and potentially individual risk assessment. The performance of the SureScreen Diagnostics LFIA targeting the spike protein was evaluated in comparison with 3 automated assays (Abbott Alinity-i SARS-CoV-2 IgG, DiaSorin Liaison® SARS-CoV-2 S1/S2 IgG, Wantai SARS-CoV-2 Ab ELISA). We assessed sensitivity using 110 serum samples from PCR confirmed COVID-19 infected patients. Specificity was evaluated using 120 prepandemic samples, including potential cross-reactive antibodies samples. Sensitivity ranged between 93.3% and 98.7% on samples collected >14 days postsymptom onset. All assays achieved a specificity >98%. Moreover, its performance seems not to be affected by Alpha, Beta or Delta variants over a wide range of antibody titers. The latter showed a very good agreement with the Wantai and the Abbott assays and a substantial agreement with the DiaSorin assay. Our data demonstrate the good clinical performance of the SureScreen Diagnostics LFIA for SARS-CoV-2 seroprevalence screening.

SARS-CoV-2: An Updated Review Highlighting Its Evolution and Treatments

Since the SARS-CoV-2 outbreak, pharmaceutical companies and researchers worldwide have worked hard to develop vaccines and drugs to end the SARS-CoV-2 pandemic. The potential pathogen responsible for Coronavirus Disease 2019 (COVID-19), SARS-CoV-2, belongs to a novel lineage of beta coronaviruses in the subgenus arbovirus. Antiviral drugs, convalescent plasma, monoclonal antibodies, and vaccines are effective treatments for SARS-CoV-2 and are beneficial in preventing infection. Numerous studies have already been conducted using the genome sequence of SARS-CoV-2 in comparison with that of other SARS-like viruses, and numerous treatments/prevention measures are currently undergoing or have already undergone clinical trials. We summarize these studies in depth in the hopes of highlighting some key details that will help us to better understand the viral origin, epidemiology, and treatments of the virus.

Gastrointestinal microbiota: A predictor of COVID-19 severity?

Coronavirus disease 2019 (COVID-19), caused by a severe acute respiratory syndrome coronavirus 2 infection, has raised serious concerns worldwide over the past 3 years. The severity and clinical course of COVID-19 depends on many factors (e.g., associated comorbidities, age, etc) and may have various clinical and imaging findings, which raises management concerns. Gut microbiota composition is known to influence respiratory disease, and respiratory viral infection can also influence gut microbiota. Gut and lung microbiota and their relationship (gut-lung axis) can act as modulators of inflammation. Modulating the intestinal microbiota, by improving its composition and diversity through nutraceutical agents, can have a positive impact in the prophylaxis/treatment of COVID-19.

Molecular Epidemiology of the Norwegian SARS-CoV-2 Delta Lineage AY.63

Extensive genomic surveillance has given great insights into the evolution of the SARS-CoV-2 virus and emerging variants. During the summer months of 2021, Norway was dominated by the Pango lineage AY.63 which is a sub-lineage of the highly transmissible Delta variant. Strikingly, AY.63 did not spread in other countries to any significant extent. AY.63 carried a key mutation, A222V, in the spike protein, as well as the deletion of three residues in nsp1. Although these mutations are close to functionally important areas, we did not find any evidence that they induced higher fitness compared to other Delta lineages. This variant was introduced to Norway at a time when there were low levels of SARS-CoV-2 and contact-reducing measures were relaxed, which probably explains why the lineage rose so quickly. Furthermore, we found that the lack of imports of AY.63 from other countries probably led to the eventual demise of the lineage in Norway.

In Silico Protein Folding Prediction of COVID-19 Mutations and Variants

With its fast-paced mutagenesis, the SARS-CoV-2 Omicron variant has threatened many societies worldwide. Strategies for predicting mutagenesis such as the computational prediction of SARS-CoV-2 structural diversity and its interaction with the human receptor will greatly benefit our understanding of the virus and help develop therapeutics against it. We aim to use protein structure prediction algorithms along with molecular docking to study the effects of various mutations in the Receptor Binding Domain (RBD) of the SARS-CoV-2 and its key interactions with the angiotensin-converting enzyme 2 (ACE-2) receptor. The RBD structures of the naturally occurring variants of SARS-CoV-2 were generated from the WUHAN-Hu-1 using the trRosetta algorithm. Docking (HADDOCK) and binding analysis (PRODIGY) between the predicted RBD sequences and ACE-2 highlighted key interactions at the Receptor-Binding Motif (RBM). Further mutagenesis at conserved residues in the Original, Delta, and Omicron variants (P499S and T500R) demonstrated stronger binding and interactions with the ACE-2 receptor. The predicted T500R mutation underwent some preliminary tests in vitro for its binding and transmissibility in cells; the results correlate with the in-silico analysis. In summary, we suggest conserved residues P499 and T500 as potential mutation sites that could increase the binding affinity and yet do not exist in nature. This work demonstrates the use of the trRosetta algorithm to predict protein structure and future mutations at the RBM of SARS-CoV-2, followed by experimental testing for further efficacy verification. It is important to understand the protein structure and folding to help develop potential therapeutics.

Immunoglobulin Y Specific for SARS-CoV-2 Spike Protein Subunits Effectively Neutralizes SARS-CoV-2 Infectivity and Ameliorates Disease Manifestations In Vivo

(Background) The coronavirus disease 2019 (COVID-19) that is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) carries high infectivity and mortality. Efficient intervention strategies are urgently needed. Avian immunoglobulin Y (IgY) showed efficacy against viral infection whereas the in vivo efficacy remains unclear. (Methods) We immunized laying hens with S1, S1 receptor-binding domain (S1-RBD), or S2 subunits of the SARS-CoV-2 spike (S) protein. After immunization, IgYs were collected and extracted from the egg yolks. The neutralization potential of IgYs was examined by the plaque reduction neutralization test (PRNT). The bioutility of IgYs was examined in Syrian hamsters in vivo. (Results) IgYs exhibited typical banding patterns in SDS-PAGE and Western blot and were immunoreactive against S1, S1-RBD, and S2 subunits. The plaque reduction neutralization test (PRNT) showed that all purified IgYs potently neutralized different SARS-CoV-2 strains in vitro. In Syrian hamsters, the combination of IgYs for S1-RBD and S2 subunits administered before or after SARS-CoV-2 infection effectively restored body weight loss and reduced intrapulmonary lesions and the amount of immunoreactive N protein-positive cells, which were caused by SARS-CoV-2 infection. (Conclusions) Collectively, IgYs specific for S protein subunits effectively neutralized SARS-CoV-2 in vitro and in vivo and may serve as prophylactic or therapeutic antibodies in the prevention or treatment of COVID-19.

Comparative study of effective antibiofilm activity of beneficial microbes-mediated zirconia nanoparticles

In the present study, beneficial microbes-mediated zirconia nanoparticles were prepared using endophytic bacteria isolated from the seed of Terminalia chebula which were evaluated on inhibition of bacterial adherence and promotion to exhibit antibiofilm properties. The structure and distribution of the zirconia nanoparticles were examined through SEM (Scanning Electron Microscopy), EDS (Energy-Dispersive X-Ray spectroscopy), and XRD (X-ray diffraction analysis), which reveal the distribution of the particles. The morphology of biogenic zirconia nanoparticles was monoclinic and cubic. The formation of zirconia particle was confirmed using UV spectrum and the functional groups were intensified in FTIR (Fourier-transform infrared spectroscopy). The antibiofilm activity of the synthesized nanoparticles was tested in oral pathogens that cause biofilm by membrane integrity and leads to periodontal associated disease. The results showed that the particles had a significant effect on biofilm removal caused by oral pathogens. For determined concentration, the cytotoxicity of the endophytic bacterial facilitated zirconia nanoparticle (Zr NPs) was examined in HGF (Human gingival fibroblast cell line).

Low SARS-CoV-2 viral load among vaccinated individuals infected with Delta B.1.617.2 and Omicron BA.1.1.529 but not with Omicron BA.1.1 and BA.2 variants

The rapid spread of SARS-CoV-2 variants in the global population is indicative of the development of selective advantages in emerging virus strains. Here, we performed a case-control investigation of the clinical and demographic characteristics, clinical history, and virological markers to predict disease progression in hospitalized adults for COVID-19 between December 2021 and January 2022 in Chennai, India. COVID-19 diagnosis was made by a commercial TaqPath COVID-19 RT-PCR, and WGS was performed with the Ion Torrent Next Generation Sequencing System. High-quality (<5% of N) complete sequences of 73 Omicron B.1.1.529 variants were randomly selected for phylogenetic analysis. SARS-CoV-2 viral load, number of comorbidities, and severe disease presentation were independently associated with a shorter time-to-death. Strikingly, this was observed among individuals infected with Omicron BA.2 but not among those with the BA.1.1.529, BA.1.1, or the Delta B.1.617.2 variants. Phylogenetic analysis revealed severe cases predominantly clustering under the BA.2 lineage. Sequence analyses showed 30 mutation sites in BA.1.1.529 and 33 in BA.1.1. The mutations unique to BA.2 were T19I, L24S, P25del, P26del, A27S, V213G, T376A, D405N and R408S. Low SARS-CoV-2 viral load among vaccinated individuals infected with Delta B.1.617.2 and the Omicron BA.1.1.529 variant but not with Omicron BA.1.1 or BA.2 suggests that the newer strains are largely immune escape variants. The number of vaccine doses received was independently associated with increased odds of developing asymptomatic disease or recovery. We propose that the novel mutations reported herein could likely bear a significant impact on the clinical characteristics, disease progression, and epidemiological aspects of COVID-19. Surging rates of mutations and the emergence of eclectic variants of SARS-CoV-2 appear to impact disease dynamics.