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Background: With the rapid development of the genomic sequence data for the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants Delta (B.1.617.2) and Omicron (B.1.1.529), it is vital to successfully identify mutations within the genome., Objective: The main objective of the study is to investigate the full-length genome mutation analysis of 157 SARS-CoV-2 and its variant Delta and Omicron isolates. This study also provides possible effects at the structural level to understand the role of mutations and new insights into the evolution of COVID-19 and evaluates the differential level analysis in viral genome sequence among different nations. We have also tried to offer a mutation snapshot for these differences that could help in vaccine formulation. This study utilizes a unique and efficient method of targeting the stable genes for the drug discovery approach., Methods: Complete genome sequence information of SARS-CoV-2, Delta, and Omicron from online resources were used to predict structure domain identification, data mining, and screening; employing different bioinformatics tools. BioEdit software was used to perform their genomic alignments across countries and a phylogenetic tree as per the confidence of 500 bootstrapping values was constructed. Heterozygosity ratios were determined in-silico. A minimum spanning network (MSN) of selected populations was determined by Bruvo's distance role-based framework., Results: Out of all 157 different strains of SARS-CoV-2 and its variants, and their complete genome sequences from different countries, Corona nucleoca and DUF5515 were observed to be the most conserved domains. All genomes obtained changes in comparison to the Wuhan-Hu-1 strain, mainly in the TRS region (CUAAAC or ACGAAC). We discovered 596 mutations in all genes, with the highest number (321) found in ORF1ab (QHD43415.1), or TRS site mutations found only in ORF7a (1) and ORF10 (2). The Omicron variant has 30 mutations in the Spike protein and has a higher alpha-helix shape (23.46%) than the Delta version (22.03%). T478 was also discovered to be a prevalent polymorphism in Delta and Omicron variations, as well as genomic gaps ranging from 45 to 65aa. All 157 sequences contained variations and conformed to Nei's Genetic distance. We discovered heterozygosity (Hs) 0.01, mean anticipated Hs 0.32, the genetic diversity index (GDI) 0.01943989, and GD within population 0.01266951. The Hedrick value was 0.52324978, the GD coefficient was 0.52324978, the average Hs was 0.01371452, and the GD coefficient was 0.52324978. Among other countries, Brazil has the highest standard error (SE) rate (1.398), whereas Japan has the highest ratio of Nei's gene diversity (0.01)., Conclusions: The study's findings will assist in comprehending the shape and kind of complete genome, their streaming genomic sequences, and mutations in various additions of SARS-CoV-2, as well as its different variant strains like Omicron. These results will provide a scientific basis to design the vaccines and understand the genomic study of these viruses., Competing Interests: Declaration of Competing Interest We have no conflict of interest to declare., (Copyright © 2022 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Corona Virus (COVID-19) outbreak has threatened the world, since it has become pandemic and spread all over the world. The causative agent SARS-COV2 has proved lethal caused serious public health concern worldwide. Our aims were to describe the SARS-COV-2 genetic connections and check for recombination of all genome. The recombination was investigated by RDP5 and conflicting phylogenetic clustering in individual genomic fragments was established by phylogenetic study by maximum likelihood and Bayesian methods. Our analysis suggests that the available sequences from currently genomes of various strain were retrieved from different countries including Japan, French Republic, Spain, Peru, China, Vietnam, Taiwan, Brazil, U.S.A., South Korea, Sweden, Australia, Nepal, India, Iran, and Italy. The phylogeny of SARS-COV-2 observed the largest number of genome is Vietnam 29891-bp, while France is the smallest member identified with 29679-bp. Using Recombination Detection program5 (RDP5) the china strains was taken as parental strain but there were no recombination in the all strains. In our study we identified the mutation in Pakistani strains in high conserved region of Corona nucleoca super family domain at the nucleotide position (394: C replace with T, Position: 858: C replace with T and Position: 997 G replace A).

The newly emerged severe acute respiratory syndrome corona virus-2 (SARS-CoV-2), the causative agent of corona virus disease 2019 (COVID-19), has deteriorated the global order economically, socially and politically. As an emergency of global concern, the disease continuously spread havoc with its dreadful health manifestations with no regard for any race, religion and region. The mortality rates in different countries are surprisingly variable and there is debate about population-wise differential response to virus. Different countries have imposed lock-down to reduce the spread of virus; however, the positive outcomes of lock-down in terms of reducing mortality rate and transmission of virus are still questioned. Further, public accusations and debate of world powers regarding the origin of virus has created regional hate sentiments and political chaos which could result is serious repercussions following miscalculation of actual facts. Scientific communities are struggling to cope with the disease by developing potential vaccines against the S protein of SARS-CoV-2 and were testing the already marketed drugs against this coronavirus. Therefore, several medicinal plants and various vaccinations have been used against Covid-19. This review highlights the origin, virulence, vaccination but most importantly the plants extracts used against the causative agent of COVID-19. [ABSTRACT FROM AUTHOR]

SARS-CoV-2, a new world coronavirus belonging to class Nidovirales of Coronaviridae family causes COVID-19 infection which is the leading cause of death worldwide. Currently there are no approved drugs and vaccines available for the prevention of COVID-19 infection, although couples of immunizations are being tested in clinical trials. However, the present efforts are focused on computational vaccination technique for evaluating candidates to design multi-epitope-based vaccine against pathogenic mechanism of novel SARS-COV-2. Based on recent published evidence, we recognized spike glycoprotein and envelope small membrane protein are the potential targets to combat the pathogenic mechanism of SARS-CoV-2. Similarly, in the present study we identified epitope of both B and T cell associated with these proteins. Extremely antigenic, conserve, immunogenic and nontoxic epitope of B and T cell of Spike protein are WPWYVWLGFI, SRVKNLNSSEGVPDLLV whereas the CWCARPTCIK and YCCNIVNVSL are associated with envelope small membrane protein were selected as potential candidate for vaccine designing. These epitopes show virtuous interaction with HLAA0201 during molecular docking analysis. Under simulation protocol the predicted vaccine candidates show stability. Collectively, this work provides novel potential candidates for epitope-based vaccine designing against COVID-19 infection. [ABSTRACT FROM AUTHOR]