Latest updates on SARS-CoV-2 genomic characterization, drug, and vaccine development; a comprehensive bioinformatics review

Sakr, Masarra M.; Elsayed, Noha S.; El-Housseiny, Ghadir S.

doi:10.1016/j.micpath.2021.104809

Cited by 7 publications

(7 citation statements)

References 160 publications

(258 reference statements)

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“…The selected core genes were ADM, ARRB1, AVPR2, CCR1, MTNR1A, PTH, and S1PR2. ADM significantly alleviates renal fibrosis by inhibiting oxidative stress, gene transfer blocking renal tubular cell inflammation, and inhibiting epithelial-mesenchymal transition (EMT) (33). ADM-induced HO-1 is a potential target for the prevention and treatment of renal fibrosis in patients with CKD.…”

Section: Discussionmentioning

confidence: 99%

Bioinformatics analysis of the potential regulatory mechanisms of renal fibrosis and the screening and identification of factors related to human renal fibrosis

Wang¹,

Wu²,

Li³

et al. 2022

Transl Androl Urol

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Background: This paper aimed to identify the key genes and potential mechanisms of renal fibrosis, and provide methods of evaluation and new ideas for the early diagnosis and treatment of renal fibrosis. Methods:The GSE102515 dataset was searched from the Gene Expression Omnibus (GEO) database was searched, the differential genes were screened out, and the down-regulated and up-regulated genes were identified. Enrichment analysis of differential genes in the development of renal fibrosis was carried out using the DAVID database, differential genes were analyzed using the STRING database, and Cytoscape software was used for visual processing.Results: Eighteen up-regulated genes and ten down-regulated genes were screened. Differential genes are mainly involved in the integrin-mediated signaling pathway and mitotic sister chromatid binding, etc. We found that the molecular functions (MFs) of the differential genes are phospholipid binding and regulatory region DNA binding, etc. Moreover, the cellular components (CCs) of the differential genes are mainly related to low-density lipoprotein (LDL) particles and nuclei. Screening revealed that ADM, ARRB1, AVPR2, CCR1, MTNR1A, PTH, and S1PR2 were core genes in the interaction network of renal fibrosis riskrelated proteins.Conclusions: In this study, the differential genes in the occurrence of renal fibrosis were screened out via dataset analysis. It was found that ADM, ARRB1, AVPR2, CCR1, MTNR1A, PTH, and S1PR2 may be important participants in the development of renal fibrosis, which provides analytical support for the identification of valuable markers of renal fibrosis.

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Section: Discussionmentioning

confidence: 99%

Bioinformatics analysis of the potential regulatory mechanisms of renal fibrosis and the screening and identification of factors related to human renal fibrosis

Wang¹,

Wu²,

Li³

et al. 2022

Transl Androl Urol

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“…In addition to the four structural proteins, the rest of the genome encodes six accessory proteins, ORF3a, ORF6, ORF7a, ORF7b, ORF8, and ORF10, respectively. The envelope has a coronal spike composed of the first three structural proteins [22]. One study examined 10,022 complete SARS-CoV-2 genome sequences in four databases and aligned these sequences with reference genomes, and the results indicated 5775 distinct genomic variants, and the most common variants being synonymous 3037C > T (6334 samples), P4715L in ORF1ab (6319 samples) and D614G in spike protein (6294 samples) [16].…”

Section: Structure Of Sars-cov-2mentioning

confidence: 99%

SARS-CoV-2: next generation sequencing and analysis

Yuan

2022

International Conference on Biomedical and Intelligent Systems (IC-BIS 2022)

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Sars-cov-2 is the causative agent responsible for the global pandemic of COVID-19. Bioinformatics tools are used to sequence the viral genome, identify SARS-CoV-2 from all host genomes, and detect its variants. There is no all-in-one tool that can automatically analyse complete sequences, so different bioinformatics resources are needed to work together for detection and characterisation. This paper discusses the use of next-generation sequencing for virus definition and characterization.

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“…Several studies about the COVID 19 vaccine have been launched since 2020. There are 2 mRNA vaccines on the market and several protein vaccines [13][14][15][16][17]. These vaccines are developed on the basis of S protein and present a great protection.…”

Section: Introductionmentioning

confidence: 99%

A New Vaccine Targeting the S1 of the S Protein Induce Mice Immune Response against COVID-19

ZW¹,

Lin²,

WH³

et al. 2022

Int J Vaccine Immunizat

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Coronavirus disease 2019 is pandemic across the world since the severe acute respiratory coronavirus-2 emerged in December 2019. The most efficient method to defend COVID 19 is vaccine. Here, we used HEK293 cell line to produce the recombinant protein and compared several vaccine candidates’ efficiency. The structures of the candidates were designed based on the S1 protein and RBD region. After three doses, the vaccines induced SARS-CoV-2 specific neutralizing antibodies in mice which presented high titers. The maximum neutralization activity could reach more than 90% without inflammation suggesting the great neutralizing ability against SARS-CoV-2. Significance statement: The COVID-19 has threatened human beings since 2019. This paper reveals a new recombinant protein vaccine that could induce mice immunity against the coronavirus. It compared the efficacy of different potential vaccines expressed by human embryonic kidney 293 cell. It showed the difference of them and helps people learn more about the COVID-19 subunit vaccines.

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Latest updates on SARS-CoV-2 genomic characterization, drug, and vaccine development; a comprehensive bioinformatics review

Cited by 7 publications

References 160 publications

Bioinformatics analysis of the potential regulatory mechanisms of renal fibrosis and the screening and identification of factors related to human renal fibrosis

Bioinformatics analysis of the potential regulatory mechanisms of renal fibrosis and the screening and identification of factors related to human renal fibrosis

SARS-CoV-2: next generation sequencing and analysis

A New Vaccine Targeting the S1 of the S Protein Induce Mice Immune Response against COVID-19

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