The far-reaching effects of the SARS-CoV-2 pandemic have crippled the progress of the world today. With the introduction of newer and newer mutated variants of the virus, it has become necessary to have a vaccine that remains useful against all the mutated strains of SARS-CoV-2. In this regard, peptide vaccines turn out to be a cheap alternative to the traditionally designed vaccines owing to their much quicker and computationally easier, and more robust design procedures. Here, in this article, we hypothesize that there are three possible peptide vaccine regions that can be targeted to prevent the surge of SARS-CoV-2. The candidates that were selected, were surface-exposed and were not sequestered by any neighbouring amino acids. They were also found to be capable of generating both B-cell and T-cell immune responses. Most importantly, none of them contains any spike protein mutation of the currently prevailing variants of SARS-CoV-2. From these findings, we have therefore concluded that these three regions can be used in wet labs for peptide vaccine design against the upcoming strains of SARS-CoV-2.

BACKGROUNDCoronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has become a worldwide pandemic and created an utmost crisis across the globe. To mitigate the crisis, the design of vaccines is a crucial solution. The frequent mutation of the virus demands generalized vaccine candidates, which would be effective for all mutated strains at present and for the strains that would evolve due to further new mutations in the virus.OBJECTIVEThe objective of this study is to identify more frequently occurring mutated variants of SARS-CoV-2 and to suggest peptide vaccine candidates effective in common against the viral strains considered.METHODIn this study, we have identified all currently prevailing mutated strains of SARS-CoV-2 through 2D Polar plot and Quotient Radius〖(q〗_R) characterization descriptor. Then, by considering the top eight mutation strains, which are significant due to their frequency of occurrence, peptide regions suitable for vaccine design have been identified with the help of a mathematical model - 2D Polygon Representation, followed by the evaluation of epitope potential and ensuring that there is no case of any autoimmune threat. Lastly, in order to verify whether this entire approach is applicable for vaccine design against any other virus in general, we have made a comparative study between the peptide vaccine candidates prescribed for the Zika virus using the current approach and a list of potential vaccine candidates for the same already established in the past.RESULTSWe have finally suggested three generalized peptide regions which would be suitable as sustainable peptide vaccine candidates against SARS-CoV-2 irrespective of its currently prevailing strains as well any other variant of the same that may appear in the future. We also observed that during the comparative study using the case of E protein of Zika virus, the peptide regions suggested using the new approach matched with the already established results.CONCLUSIONThe study, therefore, illustrates an approach that would help in developing peptide vaccine against SARS-CoV-2 by suggesting those peptide regions which can be targeted irrespective of any mutated form of this virus. The consistency with which this entire approach was also able to figure out similar vaccine candidates for Zika virus with utmost accuracy proves that this protocol can be extended for peptide vaccine design against any other virus in the future.

: From December 2019 till now, the coronavirus disease pandemic has exposed the whole world to a new challenge where the survival of human beings faces an alarming phase. The human with its utmost intelligence is trying to find out the key to unlock the lock made by SARS-CoV-2, the causative virus of COVID-19. We, here briefly summarize the possible remedies so far introduced worldwide to combat the deadly pathogenic virus. The article includes the information of varieties of drugs applied globally: allopathic, homeopathic, Ayurveda, nanoparticle implicated protections and vaccinations trials along with other biotechnical applications in different countries. Our review work may be useful to scientists involved in researches in this field to know the global remedial aspects so far developed and also to create awareness among people to the present pandemic preventive mechanisms.

The currently surging SARS-COV-2 (or CoVID-19) is challenging the public health authorities worldwide. As of now there is no approved vaccine or drug available for the control of the viral disease. Therefore, non-pharmaceutical interventions (NPIs) are being used around the world to manage the spread of CoVID-19. In this article we used a computer-assisted vaccine design (CAVD) approach to develop a set of most probable peptide vaccine candidates which can be tested for their efficacy by wet lab experiments.

We consider a novel approach to mathematically define a graphing method to represent amino acid sequences of proteins in two-dimensional plane and characterize them numerically. The amino acids are represented by their relative magnitude of their hydrophobicity. Each amino acid is compared with a vector and moves in relative direction which generates a graph. Applications are shown in Zaire Ebola Virus to conclude how this plotting can be more useful than base sequence plotting. Also, superimposition graph of SARS and SARS-CoV-2 shows that these sequences are strongly related and Various other applications are shown too to explain it's fruitfulness.

SARS-CoV-2 pandemic starting from Wuhan, China has now been spreading worldwide making the infection count more than 41 million. Within a short time span, many mutations are continuously occurring in the viral genome, be it point mutation or frameshift mutation. Scientists have been suggesting that, one of those numerous point mutations is becoming prevalent by replacing all the initial Wuhan strains of SARS-CoV-2. In this work, we have conducted a rigorous bio-informatic analyses and compared the properties of wild and mutant strains to find out the changes. Eventually, it is considered to be a more pathogenic and infective strain by our theoretical reports with a change in amino acid position number 614, which coincidentally converges with one or few publications mentioning emergence of new pathogenic D614G strain. Here we describe our approach to arrive at the conclusion.

Viral epidemics have posed a problem for quick development of drugs and vaccines to control the menace. A case in point is the Ebola viral disease with high fatality ratio in Africa. It is making a comeback in the Democratic Republic of Congo (DRC), after its rampage in West Africa in 2014-16 that has spawned fears of leading to a pandemic. Vaccines such as the experimental rVSV-ZEBOV has provided protection in 70-80% of the cases, but such vaccines are in short supply and doubts exist of its availability and sustainability in pandemic cases. Peptide vaccines promise to amend this lacuna as a chemical construct that can be scaled up to requirement in manufacturing set-up, are easy to produce in pure form and store as well as transport much more easily and economically than traditional vaccines. Although no peptide vaccines have been licensed yet for human use, the rapid growth of applications of in silico approaches to peptide vaccine design and application to a myriad of virus infections, and subsequent follow-up experimental work, have led to expectations of licensures in the near future. We have proposed a protocol to automate the search procedure using mathematical and computational modelling approaches to generate peptide libraries that promote long life of such vaccines even in the face of rapid mutational changes in the viral sequences. In this paper, we outline the mathematical model we have used and the recent improvements in the techniques to ensure the best recommendations for peptide vaccine libraries, especially against the Ebola virus that threatens to spill over the Congo border and cause epidemics and pandemics in a globalized world.

Human civilization has always been combating different pathogens that have caused epidemics or pandemics at various points of time, which has ultimately taken away millions of lives worldwide. Among all the disease-causing pathogens, viruses are notably pathogenic. Their relatively smaller size and comparatively higher rate of mutation make them more problematic than others. Vaccines turn out to be the best tool against viruses, but designing efficient vaccines against them is a difficult and time-consuming task; moreover, the efficiency of a classical vaccine can deteriorate as the virus mutates to newer strains. In this situation, peptide vaccines may appear as the need of the hour since they can be designed and developed relatively easily and quickly with the help of novel computational tools and chemical technology. Peptide vaccines have the potential to be rapidly manufactured and deployed to confront sudden disease outbreaks. These alternative vaccines are now also being tested against tumors and hence it can be expected that in the near future they can provide a cure for or protection against cancer too. Designing peptide vaccines comprises a careful analysis of the protein sequences, identification of epitopes, screening out of autoimmune threats, and so on. To make researchers aware of these aspects, in this chapter we briefly discuss various novel techniques that are being developed to assist in this task.

The ongoing rapid spread of COVID-19 disease from its first detection in Wuhan, China in late 2019 was declared a pandemic by World Health Organization on 11th March, 2020. It is believed that to combat this deadly virus, now designated as SARS-CoV-2, designing and developing a proper vaccine is the best solution. For developing a sustainable vaccine against this virus, one should have a proper understanding of the mutational changes occurring constantly in its genome and also about the variations that may arise in different communities. Here, we report an algorithm to identify and characterize the mutational changes in the COVID-19 sequences isolated from different countries. The patterns in mutation along with the demographic analysis shown here can be very effective for community specific vaccine designing in the future.

SARS-CoV-2 infection has become a worldwide pandemic and is spreading rapidly to people across the globe. To combat the situation, vaccine design is the essential solution. Mutation in the virus genome plays an important role in limiting the working life of a vaccine. In this study, we have identified several mutated clusters in the structural proteins of the virus through our novel 2D Polar plot and qR characterization descriptor. We have also studied several biochemical properties of the proteins to explore the dynamics of evolution of these mutations. This study would be helpful to understand further new mutations in the virus and would facilitate the process of designing a sustainable vaccine against the deadly virus.

The Ebola viral disease with high fatality ratio is making a comeback in the Democratic Republic of Congo (DRC), after its rampage in West Africa in2014-16, that has spawned fears of leading to a pandemic. Vaccines such as the experimental rVSV-ZEBOV has provided protection in 70-80% of the cases, but such vaccines are in short supply and doubts exist of its availability and sustainability in pandemic cases. Peptide vaccines promise to amend this lacunae as a chemical construct that can be scaled up to requirement in manufacturing set-up, are easy to produce in pure form and store as well as transport much more easily and economically than traditional vaccines. Although no peptide vaccines have been licensed yet for human use, the rapid growth of applications of in silica approaches to peptide vaccine design and application to a myriad of virus infections, and subsequent follow-up experimental work, have led to expectations to licensures in the near future. We have proposed a protocol to automate the search procedure for suitable vaccines using mathematical and computational modelling approaches that ensure long life of such vaccines even in the face of rapid mutational changes in viral sequences. In this paper we outline the mathematical model we have used and the recent improvements in the techniques to ensure the best recommendations for peptide vaccine libraries, especially against the Ebola virus that threatens to spill over the Congo border and cause epidemic and pandemics in a globalized world.