Peptide Based Viral Detection Systems for Effective Diagnosis of Common Viral Infections in India

Mohanraj, Ushanandini; Chander, Suresh; Chavan, Yashwant

doi:10.2174/1389203717666160724205226

Cited by 5 publications

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“…Facilitated by high mutation rates, traditional vaccines based on antibody-mediated protection are often poor inducers of T-cell responses and can have limited success (Rosendahl Huber et al, 2014). Peptidebased sensitive and rapid diagnostic kits are considered a better alternative to the conventional serological tests, including whole antigenic protein (Mohanraj et al, 2017). In our study, we predicted both B-cell and T-cell epitopes for conferring immunity in different ways.…”

Section: Resultsmentioning

confidence: 98%

“…As the situation worsens, there is a growing need for the development of suitable therapeutics, vaccines, and other diagnostics against SARS-CoV-2 for effective disease management strategies. Vaccines and diagnostic assays based on peptides have become increasingly substantial and indispensable for their advantages over conventional methods (Li et al, 2014;Mohanraj et al, 2017 aimed to locate appropriate epitopes within a particular protein antigen that can elicit an immune response and could be selected for the synthesis of an immunogenic peptide. Using a computational approach, the S glycoprotein of SARS-CoV-2 was explored to identify various immunodominant epitopes for the development of diagnostics and vaccines.…”

Section: Introductionmentioning

confidence: 99%

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Understanding the B and T cell epitopes of spike protein of severe acute respiratory syndrome coronavirus-2: A computational way to predict the immunogens

Vashi

Jagrit

Kumar

2020

Infection, Genetics and Evolution

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The 2019 novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) outbreak has caused a large number of deaths, with thousands of confirmed cases worldwide. The present study followed computational approaches to identify Band T-cell epitopes for the spike (S) glycoprotein of SARS-CoV-2 by its interactions with the human leukocyte antigen alleles. We identified 24 peptide stretches on the SARS-CoV-2 S protein that are well conserved among the reported strains. The S protein structure further validated the presence of predicted peptides on the surface, of which 20 are surface exposed and predicted to have reasonable epitope binding efficiency. The work could be useful for understanding the immunodominant regions in the surface protein of SARS-CoV-2 and could potentially help in designing some peptide-based diagnostics. Also, identified T-cell epitopes might be considered for incorporation in vaccine designs.

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Section: Resultsmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

Understanding the B and T cell epitopes of spike protein of severe acute respiratory syndrome coronavirus-2: A computational way to predict the immunogens

Vashi

Jagrit

Kumar

2020

Infection, Genetics and Evolution

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“…We speculate that the identified epitopes with considerably good epitope binding efficiency have the potential to be an immunodominant peptide. Peptide-based sensitive and rapid diagnostic kits are considered as a better alternative to the conventional serological tests including whole antigenic protein 13 . The study could help us to use the predicted peptide as an immunogen for the development of diagnostics against SARS-CoV-2.…”

Section: Resultsmentioning

confidence: 99%

“…As the situation worsens, there is a growing need for the development of suitable therapeutics and alternate diagnostics against SARS-CoV-2 for effective disease management strategies. Diagnostic assays based on peptides have become increasingly substantial and indispensable for its advantages over conventional methods 13 . The present study aimed to locate appropriate epitopes within a particular protein antigen, which can elicit an immune response that could be selected for the synthesis of the immunogenic peptide.…”

Section: Introductionmentioning

confidence: 99%

Understanding the B and T cells epitopes of spike protein of severe respiratory syndrome coronavirus-2: A computational way to predict the immunogens

Vashi

Jagrit

Kumar

2020

Preprint

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24The 2019 novel severe respiratory syndrome coronavirus-2 (SARS-CoV-2) outbreak 25 has caused a large number of deaths with thousands of confirmed cases worldwide. The present 26 study followed computational approaches to identify B-and T-cell epitopes for spike 27 glycoprotein of SARS-CoV-2 by its interactions with the human leukocyte antigen alleles. We 28 identified twenty-four peptide stretches on the SARS-CoV-2 spike protein that are well 29 conserved among the reported strains. The S protein structure further validated the presence of 30 predicted peptides on the surface. Out of which twenty are surface exposed and predicted to 31 have reasonable epitope binding efficiency. The work could be useful for understanding the 32 immunodominant regions in the surface protein of SARS-CoV-2 and could potentially help in 33 designing some peptide-based diagnostics. 34 35 36 37 38 39 40 41 42 43 44 45 46 47Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a recent 51 pandemic and declared as a public health emergency by World Health Organization (WHO) 1 . 52The disease rapidly spread across the globe and caused havoc to humanity 2 . By the end of 53 March, SARS-CoV-2 had spread to 200 countries and infected over 4,50,000 people 3 . The 54 WHO is continuously monitoring and updating the health-related plans to curtail the disease 55 spread. The absence of specific treatment and vaccine worsen the situation and threat the world. 56 International Committee on Taxonomy of Viruses (ICTV), classified SARS-CoV-2 57 under family coronaviridae of order nidovirales. The genomic sequence of SARS-CoV-2 58 isolated from the bronchoalveolar lavage fluid of a patient from the Wuhan, China showed a 59 length of 29,903 nucleotides (GenBank accession number NC_045512) 4 . The SARS-CoV-2 60 contains a positive single-stranded RNA with 5ˊ and 3ˊ UTR. The genome codes for ORF1a, 61 ORF1b, Spike (S), ORF3a, ORF3b, Envelope (E), Membrane (M), ORF6, ORF7a, ORF7b, 62ORF8, ORF9b, ORF14, Nucleocapsid (N), and ORF10 from 5ˊ to 3ˊ 4,5 . 63The S glycoprotein forms homotrimers and represents a potential target for therapeutic 64 and vaccine design as it mediates viral entry into host cells 6,7 . S glycoprotein comprises of two 65 functional subunits. Whereas the S1 subunit is responsible for binding to the host cell receptor, 66 the S2 subunit is responsible for the fusion of the viral with the cell membrane. Usually, in 67 CoVs, S is cleaved at the boundary between the S1 and S2 subunits, which remain non-68 covalently bound in the prefusion conformation, to activate the protein for membrane fusion 69 via extensive irreversible conformational changes [8][9][10] . Setting apart from other SARS-CoVs, it 70 is found that S glycoprotein of SARS-CoV-2 harbors a furin cleavage site at the boundary 71 between the S1/S2 subunits 11 . By now, it is evident that SARS-CoV-2 S uses angiotensin-72 converting enzyme 2 (ACE2) receptor-mediated entry into cells. It is found that the receptor-73 was not certified by peer review) is th...

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“…The ability to identify epitope is vital to combat the infection through antibody-mediated immunity and also essential in several biomedical applications like rational vaccine design, disease diagnostic, and immune-therapeutics [ 14 , 15 ]. As a growing need for the development of suitable therapeutics against SARS-CoV-2 for effective disease management, the diagnostic assays based on peptides have become indispensable for their advantages over conventional methods [ 16 , 17 ]. Identification of appropriate epitopes within a particular protein antigen can elicit an immune response and could have been used for the synthesis of an immunogenic peptide.…”

mentioning

confidence: 99%

Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants

Gupta

Chakrabarti

Mandal

2020

Microbes and Infection

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The non-synonymous mutations of SARS-CoV-2 isolated from across the world have been identified during the last few months. The surface glycoprotein spike of SARS-CoV-2 forms the most important hotspot for amino acid alterations followed by the ORF1a/ORF1ab poly-proteins. It is evident that the D614G mutation in spike glycoprotein and P4715L in RdRp is the important determinant of SARS-CoV-2 evolution since its emergence. P4715L in RdRp, G251V in ORF3a and S1498F of Nsp3 is associated with the epitope loss that may influence pathogenesis caused by antibody escape variants. The phylogenomics distinguished the ancestral viral samples from China and most part of Asia, isolated since the initial outbreak and the later evolved variants isolated from Europe and Americas. The evolved variants have been found to predominant globally with the loss of epitopes from its proteins. These have implications for SARS-CoV-2 transmission, pathogenesis and immune interventions.

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Peptide Based Viral Detection Systems for Effective Diagnosis of Common Viral Infections in India

Abstract: The finding of this review uncovers the importance of a peptide based diagnostic system for rapid detection of viral infections. Even though, in recent times, peptide based assays have intrigued researchers, further work in this domain is entailed.

Cited by 5 publications

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Understanding the B and T cell epitopes of spike protein of severe acute respiratory syndrome coronavirus-2: A computational way to predict the immunogens

Understanding the B and T cell epitopes of spike protein of severe acute respiratory syndrome coronavirus-2: A computational way to predict the immunogens

Understanding the B and T cells epitopes of spike protein of severe respiratory syndrome coronavirus-2: A computational way to predict the immunogens

Non-synonymous mutations of SARS-CoV-2 leads epitope loss and segregates its variants

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