Distribution and Functional Analyses of Mutations in Spike Protein and Phylogenic Diversity of SARS-CoV-2 Variants Emerged during the Year 2021 in India

Introduction

Prolonged COVID-19 pandemic accelerates the emergence and transmissibility of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants through the accumulation of adaptive mutations. Particularly, adaptive mutations in spike (S) protein of SARS-CoV-2 leads to increased viral infectivity, severe morbidity and mortality, and immune evasion. This study focuses on the phylodynamic distribution of SARS-CoV-2 variants during the year 2021 in India besides analyzing the functional significance of mutations in S-protein of SARS-CoV-2 variants.

Methods

Whole genome of SARS-CoV-2 sequences (n = 87957) from the various parts of India over the period of January to December 2021 was retrieved from Global Initiative on Sharing All Influenza Data. All the S-protein sequences were subjected to clade analysis, variant calling, protein stability, immune escape potential, structural divergence, Furin cleavage efficiency, and phylogenetic analysis using various in silico tools.

Results

Delta variant belonging to 21A, 21I, and 21J clades was found to be predominant throughout the year 2021 though many variants were also present. A total of 4639 amino acid mutations were found in S-protein. D614G was the most predominant mutation in the S-protein followed by P681R, L452R, T19R, T478K, and D950N. The highest number of mutations was found in the N-terminal domain of S-protein. Mutations in the crucial sites of S-protein impacting pathogenicity, immunogenicity, and fusogenicity were identified. Intralineage diversity analysis showed that certain variants of SARS-CoV-2 possess high diversification.

Conclusions

The study has disclosed the distribution of various variants including the Delta, the predominant variant, in India throughout the year 2021. The study has identified mutations in S-protein of each SARS-CoV-2 variant that can significantly impact the virulence, immune evasion, increased transmissibility, high morbidity, and mortality. In addition, it is found that mutations acquired during each viral replication cycle introduce new sub-lineages as studied by intralineage diversity analysis.

Serum levels of matrix metalloproteinases as prognostic markers for severe dengue with plasma leakage

BACKGROUND

Plasma leakage is a major pathogenic manifestation of severe dengue and is a precursor of life-threatening complications associated with dengue. Accumulating evidence indicates the role of Matrix Metalloproteinases (MMPs) in mediating vascular permeability and plasma leakage following induction by the dengue virus. This study aims to investigate the utility of MMP-2, MMP-3, and MMP-9 in predicting the severity of dengue infection and further explore the relationship of these markers with the pathogenic factors associated with plasma leakage.

METHODS

The dengue-positive subjects were classified into mild and severe dengue groups based on the manifestation of warning signs. The samples in each group and healthy controls were quantified for basic laboratory characteristics. The levels of MMP-2, MMP-3, MMP-9, and Macrophage migration inhibitory factor (MIF) were estimated in all serum samples using a multiplex bead-based assay.

RESULTS

MMP-2 and MMP-9 were markedly elevated in severe dengue patients compared to mild dengue patients and healthy controls. No alteration in the circulating levels of MMP-3 was observed between the study groups. ROC curve analysis indicated that MMP-2 and MMP-9 exhibited good potential for predicting severe dengue. Notably, an increase in MMP-9 was associated with increased MIF and Hematocrit levels in severe dengue patients.

CONCLUSION

MMP-2 and MMP-9 could serve as prognostic biomarkers for severe dengue. These findings also identify the association of MMP-9 with markers of plasma leakage, thereby encouraging further studies to explore the therapeutic potential of targeting MMP-9 in managing plasma leakage in severe dengue.

Epitope identification and designing a potent multi-epitope vaccine construct against SARS-CoV-2 including the emerging variants

Introduction:

The emergence of a novel coronavirus in China has turned into a SARS-CoV-2 pandemic with high fatality. As vaccines are developed through various strategies, their immunogenic potential may drastically vary and thus pose several challenges in offering immune responses against the virus.

Methods:

In this study, we adopted an immunoinformatics-aided approach for developing a new multi-epitope vaccine construct (MEVC). In silico approach was taken for the identification of B-cell and T-cell epitopes in the Spike protein, for MEVC various cytotoxic T-lymphocyte, helper T-lymphocyte, and B-cell epitopes with the highest affinity for the respective HLA alleles were assembled and joined by linkers.

Results:

The computational data suggest that the MEVC is nontoxic, nonallergenic and thermostable and elicit both humoral and cell-mediated immune responses. Subsequently, the biological activity of MEVC was assessed by bioinformatic tools using the interaction between the vaccine candidate and the innate immune system receptors TLR3 and TLR4. The epitopes of the construct were analyzed with that of the strains belonging to various clades including the emerging variants having multiple unique mutations in S protein.

Conclusions:

Due to the advantageous features, the MEVC can be tested in vitro for more practical validation and the study offers immense scope for developing a potential vaccine candidate against SARS-CoV-2 in view of the public health emergency associated with COVID-19 disease caused by SARS-CoV-2.

Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-Temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India

Introduction:

The COVID-19 pandemic is associated with high morbidity and mortality, with the emergence of numerous variants. The dynamics of SARS-CoV-2 with respect to clade distribution is uneven, unpredictable and fast changing.

Methods:

Retrieving the complete genomes of SARS-CoV-2 from India and subjecting them to analysis on phylogenetic clade diversity, Spike (S) protein mutations and their functional consequences such as immune escape features and impact on infectivity. Whole genome of SARS-CoV-2 isolates (n = 4,326) deposited from India during the period from January 2020 to December 2020 is retrieved from Global Initiative on Sharing All Influenza Data (GISAID) and various analyses performed using in silico tools.

Results:

Notable clade dynamicity is observed indicating the emergence of diverse SARS-CoV-2 variants across the country. GR clade is predominant over the other clades and the distribution pattern of clades is uneven. D614G is the commonest and predominant mutation found among the S-protein followed by L54F. Mutation score prediction analyses reveal that there are several mutations in S-protein including the RBD and NTD regions that can influence the virulence of virus. Besides, mutations having immune escape features as well as impacting the immunogenicity and virulence through changes in the glycosylation patterns are identified.

Conclusions:

The study has revealed emergence of variants with shifting of clade dynamics within a year in India. It is shown uneven distribution of clades across the nation requiring timely deposition of SARS-CoV-2 sequences. Functional evaluation of mutations in S-protein reveals their significance in virulence, immune escape features and disease severity besides impacting therapeutics and prophylaxis.

Synthesis and Characterization of Calcium Phosphate Ceramic/(Poly(vinyl alcohol)-Polycaprolactone) Bilayer Nanocomposites-A Bone Tissue Regeneration Scaffold

β Tricalcium phosphate ceramic was used to reinforce nanofibers in composite mats produced via electrospinning of poly(vinyl alcohol) (PVA), polycaprolactone (PCL) and (PVA: PCL) bilayers. The role of TCP ceramic on morphology of nanocomposites, crystalline structure, functional groups and thermal behaviour of nanocomposites were characterized by SEM, EDAX, XRD, FTIR and DSC analysis. Ultrathin cross-sections of the obtained nanocomposites were morphologically investigated with SEM and all fabricated composites consisted of fibers with average fiber diameter (AFD) around 100 nm except PCL-TCP fibers having AFD in the range of 608 nm. XRD profile presented the main peaks of β-TCP (JCPDS 090169 and JCPDS 70-2065). The characteristic absorption bands of TCP were also identified by FTIR in all the composites. The thermal stability was enhanced after adding TCP filler particles in all the polymer composites. The porosity of PCL-TCP was found around 63% and (PVA-PCL: TCP) composite was found to be 58%. The biocompatibility of the (PVA-PCL: TCP) composite scaffold has also been investigated by culturing MG-63 osteoblast cells on it; primary results showed that the cells adhered and proliferated well on the composite scaffold.

Single crystalline TiO2 nanorods as effective fillers for lithium ion conducting PVdF-HFP based composite polymer electrolytes

PVdF-HFP based composite electrolytes were prepared with single crystalline TiO₂ nanorods (PT) and commercial TiO₂ submicrons (PTC) as fillers. The effect of size/shape of the fillers on the properties of polymer electrolytes were investigated.

Enhanced photocatalytic efficacy of hetropolyacid pillared TiO2 nanocomposites

The removal of dye from industrial effluents is prime important, photo-catalysis is a finest method to combat dye from effluents. This study concerns about the investigation of photocatalytic activity of TiO2-HPAs (Hetropolyacids) nanocomposite namely TiO2-Phosphomolybdic nanocomposite [TiO2-HMA] and TiO2-Phosphotungstic nanocomposite [TiO2-HWA] which were prepared by Sol-gel method and the same were characterized by using XRD, SEM-EDAX. The photocatalytic activity of prepared photo-catalysts were evaluated and compared by the degradation of Methylene Blue dye in water solution under UV irradiation. In that TiO2-HMA nanocomposite showed superior photocatalytic activity than TiO2-HWA.

Assessment of nurse-led screening of pigmented lesions using SIAscope

The incidence of malignant melanoma in the UK is rising. Increased awareness of melanoma has led to an increase in patients presenting with pigmented lesions to their general practitioner (GP) and to pigmented lesion clinics. The sensitivity and specificity of the general practitioner in diagnosing melanoma remains poor.

OBJECTIVES

A trial was conducted to establish the effectiveness of SIAscope in triaging patients referred by GPs on suspicion of melanoma.

MATERIALS AND METHODS

After Ethical Committee approval, all consenting patients attending the Pigmented Lesion Clinic at Frenchay Hospital were scanned with the SIAscope. The consultant then examined all the patients and all suspicious lesions were excised and examined.

RESULTS

Eight hundred and eighty-six patients were included in the trial. The SIAscope had a sensitivity of 94.4% with a false negative rate of 3.7% for malignant melanoma.

CONCLUSIONS

The SIAscope could be useful in reducing the number of benign lesions seen by the consultant while still identifying most melanomas.