Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2 etiologic agent of global pandemic COVID-19: an<i>in silico</i>approach

Rahman, M. Shaminur; Hoque, M. Nazmul; Islam, M. Rafiul; Akter, Salma; Rubayet-Ul-Alam, A.S.M.; Siddique, Mohammad Anwar; Saha, Otun; Sultana, Munawar; Hossain, Md. Anwar

doi:10.1101/2020.03.30.015164

Cited by 28 publications

(60 citation statements)

References 66 publications

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“…However, the ongoing rapid transmission and global spread of SARS-CoV-2 have raised critical questions about the evolution and adaptation of the viral population driven by mutations, deletions and/or recombination as it spreads across the world encountering diverse host immune systems and various counter-measures 6 . Initial phylogenomic analysis of three super-clades (S, V, and G) isolated from the outbreaks of distinct geographic locations (China, USA and Europe) within SARS-CoV-2 showed little evidence of local/regional adaptation, suggesting instead that viral evolution is mainly driven by genetic drift and founder events 7 .…”

Section: Introductionmentioning

confidence: 99%

Genome Wide Analysis of Severe Acute Respiratory Syndrome Coronavirus-2 Implicates World-Wide Circulatory Virus Strains Heterogeneity

Islam¹,

Hoque²,

Rahman³

et al. 2020

Preprint

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Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), a novel evolutionarily divergent RNA virus etiological agent of COVID-19, is responsible for present devastating pandemic respiratory illness. To explore the genomic signatures, we comprehensively analyzed 2,492 complete and/or near-complete genome sequences of SARS-CoV-2 strains reported from across the globe to the GISAID database up to 30 March 2020. Genome-wide annotations revealed 1,407 nucleotide-level mutations at different positions throughout the entire genome of SARS-CoV-2. Moreover, nucleotide deletion analysis found nine deletions throughout the genome, including in polyprotein (n=6), ORF10 (n=1) and 3´-UTR (n=2). Evidence from the systematic gene-level mutational and protein profile analyses revealed a large number of amino acid (aa) substitutions (n=722), making the viral proteins heterogeneous. Notably, residues of receptor-binding domain (RBD) having crucial interactions with angiotensin-converting enzyme 2 (ACE2), and cross-reacting neutralizing antibody were found to be conserved among the analyzed SARS-CoV-2 strains, except for replacement of Lysine with Arginine at 378 position of the cryptic epitope of a Shanghai isolate, hCoV-19/Shanghai/SH0007/2020 (EPI_ISL_416320). Our method of genome annotation is a promising tool for monitoring and tracking the epidemic, the associated genetic variants, and their implications for the development of effective control and prophylaxis strategy.

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Section: Introductionmentioning

confidence: 99%

Genome Wide Analysis of Severe Acute Respiratory Syndrome Coronavirus-2 Implicates World-Wide Circulatory Virus Strains Heterogeneity

Islam¹,

Hoque²,

Rahman³

et al. 2020

Preprint

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“…These ORFs encode for different proteins such as the replicase polyprotein, the spike (S) glycoprotein, envelope (E), membrane (M), nucleocapsid (N) proteins, accessory proteins, and other non-structural proteins (nsp) (Ahmed et al, 2020;Islam et al, 2020;Phan, 2020;Walls et al, 2020). The genome of this RNA virus is approximately 30 kilobases (between 26,000 and 32,000 bases) in length (Abdelmageed et al, 2020;Rahman et al, 2020). It encodes for multiple structural and nonstructural proteins (Ahmed et al, 2020;Rahman et al, 2020) that possess many unique features.…”

Section: Introductionmentioning

confidence: 99%

“…The genome of this RNA virus is approximately 30 kilobases (between 26,000 and 32,000 bases) in length (Abdelmageed et al, 2020;Rahman et al, 2020). It encodes for multiple structural and nonstructural proteins (Ahmed et al, 2020;Rahman et al, 2020) that possess many unique features.…”

Section: Introductionmentioning

confidence: 99%

“…Due to the practice of open science, the research on SARS-CoV-2 is the fastest moving subject in the human history. In about four months, thousands of reports and data on genomics, origin, genome evolution, molecular diagnosis and vaccine or therapeutics of COVID-19 have been published (Clover B, 2020;Geo-Vax, 2020;Islam et al, 2020;Phan, 2020;Rahman et al, 2020;Shereen et al, 2020;Shanmugaraj et al, 2020;Walls et al, 2020;Zhang et al, 2020a).…”

Section: Introductionmentioning

confidence: 99%

“…They evaluated several drugs or therapies namely, penciclovir, ribavirin, nitazoxanide, remdesivir (GS-5734), nafamostat, favipiravir (T-750) or Avigan, EIDD-2801, hydroxychloroquine, chloroquine, and convalescent plasma (CP) therapy against the infection of SARS-CoV-2 (Duan et al, 2020;Liu et al, 2020;Martinez, 2020;Wang et al, 2020b). Furthermore, the fast evolution and high genomic disparity of RNA viruses, mutations on the receptor-binding domain (RBD) may help the new strains to get away neutralization mechanism by RBD-targeting antibodies (Rahman et al, 2020). Therefore, non-RBD functional regions of the S glycoprotein could efficiently be selected for developing effective therapeutic and prophylactic interventions against the infection of SARS-CoV-2.…”

Section: Introductionmentioning

confidence: 99%

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Genomic Diversity and Evolution, Diagnosis, Prevention, and Therapeutics of the Pandemic COVID-19 Disease

Hoque¹,

Chaudhury²,

Akanda³

et al. 2020

Preprint

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A novel coronavirus COVID-19 was first emerged in Wuhan city of Hubei Province in China in December 2019. The COVID-19, since then spreads to 213 countries and territories, and has become a pandemic. Genomic analyses have indicated that the virus, popularly named as corona, originated through a natural process and is probably not a purposefully manipulated laboratory construct. However, currently available data are not sufficient to precisely conclude the origin of this fearsome virus. Genome-wide annotation of thousands of genomes revealed that more than 1,407 nucleotide mutations and 722 amino acids replacements occurred at different positions of the SARS-CoV-2. The spike (S) glycoprotein of SARS-CoV-2 possesses a functional polybasic (furin) cleavage site at the S1-S2 boundary through the insertion of 12 nucleotides. It leads to the predicted acquisition of 3-O-linked glycan around the cleavage site. Although real-time RT-PCR methods targeting specific gene(s) have widely been used to diagnose the COVID-19 patients, however, recently developed more convenient, rapid, and specific diagnostic tools targeting IgM/IgG or newly developed plug and play methods should be available for resource-poor developing countries. Some drugs, vaccines and therapies have shown great promise in early trials, however, these candidates of preventive or therapeutic agents have to pass a long path of trials before being released for the practical application against COVID-19. This review updates current knowledge on origin, genomic evolution, development of the diagnostic tools and the preventive or therapeutic remedies of the COVID-19, and discusses on scopes for further research and effective management and surveillance of COVID-19.

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Physicochemical properties of SARS‐CoV‐2 for drug targeting, virus inactivation and attenuation, vaccine formulation and quality control

et al. 2020

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The material properties of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its proteins are discussed. We review the viral structure, size, rigidity, lipophilicity, isoelectric point, buoyant density and centrifugation conditions, stability against pH, temperature, UV light, gamma radiation, and susceptibility to various chemical agents including solvents and detergents. Possible inactivation, downstream, and formulation conditions are given including suitable buffers and some first ideas for quality-control methods. This information supports vaccine development and discussion with competent authorities during vaccine approval and is certainly related to drug-targeting strategies and hygienics. Several instructive tables are given, including the pI and grand average of hydropathicity (GRAVY) of SARS-CoV-1 and-2 proteins in comparison. SARS-CoV-1 and SARS-CoV-2 are similar in many regards, so information can often be derived. Both are unusually stable, but sensitive at their lipophilic membranes. However, since seemingly small differences can have strong effects, for example, on immunologically relevant epitope settings, unevaluated knowledge transfer from SARS-CoV-1 to SARS-CoV-2 cannot be advised. Published knowledge regarding downstream processes, formulations and quality assuring methods is, as yet, limited. However, standard approaches employed for other viruses and vaccines seem to be feasible including virus inactivation, centrifugation conditions, and the use of adjuvants.

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Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2 etiologic agent of global pandemic COVID-19: anin silicoapproach

Abstract: 33

Cited by 28 publications

References 66 publications

Genome Wide Analysis of Severe Acute Respiratory Syndrome Coronavirus-2 Implicates World-Wide Circulatory Virus Strains Heterogeneity

Genome Wide Analysis of Severe Acute Respiratory Syndrome Coronavirus-2 Implicates World-Wide Circulatory Virus Strains Heterogeneity

Genomic Diversity and Evolution, Diagnosis, Prevention, and Therapeutics of the Pandemic COVID-19 Disease

Physicochemical properties of SARS‐CoV‐2 for drug targeting, virus inactivation and attenuation, vaccine formulation and quality control

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