ArticleVaccines2023
In Silico Analysis of SARS-CoV-2 Spike Proteins of Different Field Variants.
Article in Vaccines, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
3 citing papers in PubMed, 6 citations in OpenAlex.
- APathogens (Basel, Switzerland) · 2025Article
- The Possible Mechanistic Basis of Individual Susceptibility to Spike Protein Injury.Advances in virology · 2025Review
- Human and animal exposure to newly discovered sand fly viruses, China.Frontiers in cellular and infection microbiology · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Coronaviruses belong to the group of RNA family of viruses that trigger diseases in birds, humans, and mammals, which can cause respiratory tract infections. The COVID-19 pandemic has badly affected every part of the world. Our study aimed to explore the genome of SARS-CoV-2, followed by in silico analysis of its proteins. Different nucleotide and protein variants of SARS-CoV-2 were retrieved from NCBI. Contigs and consensus sequences were developed to identify these variants using SnapGene. Data of the variants that significantly differed from each other was run through Predict Protein software to understand the changes produced in the protein structure. The SOPMA web server was used to predict the secondary structure of the proteins. Tertiary structure details of the selected proteins were analyzed using the web server SWISS-MODEL. Sequencing results showed numerous single nucleotide polymorphisms in the surface glycoprotein, nucleocapsid, ORF1a, and ORF1ab polyprotein while the envelope, membrane, ORF3a, ORF6, ORF7a, ORF8, and ORF10 genes had no or few SNPs. Contigs were used to identify variations in the Alpha and Delta variants of SARS-CoV-2 with the reference strain (Wuhan). Some of the secondary structures of the SARS-CoV-2 proteins were predicted by using Sopma software and were further compared with reference strains of SARS-CoV-2 (Wuhan) proteins. The tertiary structure details of only spike proteins were analyzed through the SWISS-MODEL and Ramachandran plots. Through the Swiss-model, a comparison of the tertiary structure model of the SARS-CoV-2 spike protein of the Alpha and Delta variants was made with the reference strain (Wuhan). Alpha and Delta variants of the SARS-CoV-2 isolates submitted in GISAID from Pakistan with changes in structural and nonstructural proteins were compared with the reference strain, and 3D structure mapping of the spike glycoprotein and mutations in the amino acids were seen. The surprisingly increased rate of SARS-CoV-2 transmission has forced numerous countries to impose a total lockdown due to an unusual occurrence. In this research, we employed in silico computational tools to analyze the SARS-CoV-2 genomes worldwide to detect vital variations in structural proteins and dynamic changes in all SARS-CoV-2 proteins, mainly spike proteins, produced due to many mutations. Our analysis revealed substantial differences in the functionality, immunological, physicochemical, and structural variations in the SARS-CoV-2 isolates. However, the real impact of these SNPs can only be determined further by experiments. Our results can aid in vivo and in vitro experiments in the future.
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Registered trials
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