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Bioinformatics pipeline unveils genetic variability to synthetic vaccine design for Indian SARS-CoV-2 genomes.
Ghosh, Nimisha; Saha, Indrajit; Sharma, Nikhil; Nandi, Suman.
  • Ghosh N; Department of Computer Science and Information Technology, Institute of Technical Education and Research, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India.
  • Saha I; Department of Computer Science and Engineering, National Institute of Technical Teachers' Training and Research, Kolkata, West Bengal, India. Electronic address: indrajit@nitttrkol.ac.in.
  • Sharma N; Department of Electronics and Communication Engineering, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India.
  • Nandi S; Department of Computer Science and Engineering, National Institute of Technical Teachers' Training and Research, Kolkata, West Bengal, India.
Int Immunopharmacol ; 112: 109224, 2022 Nov.
Artículo en Inglés | MEDLINE | ID: covidwho-2076214
ABSTRACT
In the worrisome scenarios of various waves of SARS-CoV-2 pandemic, a comprehensive bioinformatics pipeline is essential to analyse the virus genomes in order to understand its evolution, thereby identifying mutations as signature SNPs, conserved regions and subsequently to design epitope based synthetic vaccine. We have thus performed multiple sequence alignment of 4996 Indian SARS-CoV-2 genomes as a case study using MAFFT followed by phylogenetic analysis using Nextstrain to identify virus clades. Furthermore, based on the entropy of each genomic coordinate of the aligned sequences, conserved regions are identified. After refinement of the conserved regions, based on its length, one conserved region is identified for which the primers and probes are reported for virus detection. The refined conserved regions are also used to identify T-cell and B-cell epitopes along with their immunogenic and antigenic scores. Such scores are used for selecting the most immunogenic and antigenic epitopes. By executing this pipeline, 40 unique signature SNPs are identified resulting in 23 non-synonymous signature SNPs which provide 28 amino acid changes in protein. On the other hand, 12 conserved regions are selected based on refinement criteria out of which one is selected as the potential target for virus detection. Additionally, 22 MHC-I and 21 MHC-II restricted T-cell epitopes with 10 unique HLA alleles each and 17 B-cell epitopes are obtained for 12 conserved regions. All the results are validated both quantitatively and qualitatively which show that from genetic variability to synthetic vaccine design, the proposed pipeline can be used effectively to combat SARS-CoV-2.
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Texto completo: Disponible Colección: Bases de datos internacionales Base de datos: MEDLINE Asunto principal: Vacunas Virales / COVID-19 Tipo de estudio: Estudio observacional / Estudio pronóstico / Investigación cualitativa / Ensayo controlado aleatorizado Tópicos: Vacunas Límite: Humanos Idioma: Inglés Revista: Int Immunopharmacol Asunto de la revista: Alergia e Inmunología / Farmacología Año: 2022 Tipo del documento: Artículo País de afiliación: J.intimp.2022.109224

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Texto completo: Disponible Colección: Bases de datos internacionales Base de datos: MEDLINE Asunto principal: Vacunas Virales / COVID-19 Tipo de estudio: Estudio observacional / Estudio pronóstico / Investigación cualitativa / Ensayo controlado aleatorizado Tópicos: Vacunas Límite: Humanos Idioma: Inglés Revista: Int Immunopharmacol Asunto de la revista: Alergia e Inmunología / Farmacología Año: 2022 Tipo del documento: Artículo País de afiliación: J.intimp.2022.109224