ArticleInfection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases2020
Genome-wide analysis of Indian SARS-CoV-2 genomes for the identification of genetic mutation and SNP.
Article in Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Predicting the spread of SARS-CoV-2 variants: An artificial intelligence enabled early detection.PNAS nexus · 2024Article
- Clinical and laboratory features of SARS-CoV-2 variants across multiple rounds of pandemic waves in hospitalized children in an Iranian referral hospital.BMC pediatrics · 2023Article
- L-shaped distribution of the relative substitution rate (c/μ) observed for SARS-COV-2's genome, inconsistent with the selectionist theory, the neutral theory and the nearly neutral theory but a near-neutral balanced selection theory: Implication on "neutralist-selectionist" debate.Computers in biology and medicine · 2023Article
- Identification of potent compounds against SARs-CoV-2: An in-silico based drug searching against Mpro.Computers in biology and medicine · 2022Article
- Online Predictor Using Machine Learning to Predict Novel Coronavirus and Other Pathogenic Viruses.ACS omega · 2022Article
- Characterisation of SARS-CoV-2 clades based on signature SNPs unveils continuous evolution.Methods (San Diego, Calif.) · 2022Article
- Visualization of copper nanoclusters for SARS-CoV-2 Delta variant detection based on rational primers design.Talanta · 2022Article
- From delta to Omicron: S1-RBD/S2 mutation/deletion equilibrium in SARS-CoV-2 defined variants.Gene · 2022Review
- Article
- Characterizing genomic variants and mutations in SARS-CoV-2 proteins from Indian isolates.Gene reports · 2021Article
- A Global Mutational Profile of SARS-CoV-2: A Systematic Review and Meta-Analysis of 368,316 COVID-19 Patients.Life (Basel, Switzerland) · 2021Review
- Global SNP analysis of 11,183 SARS-CoV-2 strains reveals high genetic diversity.Transboundary and emerging diseases · 2021Article
- SARS-CoV-2 surveillance in Italy through phylogenomic inferences based on Hamming distances derived from pan-SNPs, -MNPs and -InDels.BMC genomics · 2021Article
- Genome interaction of the virus and the host genes and non-coding RNAs in SARS-CoV-2 infection.Immunobiology · 2021Review
- Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism.Virus research · 2021Article
- Different SARS-CoV-2 haplotypes associate with geographic origin and case fatality rates of COVID-19 patients.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2021Article
- Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6.Briefings in bioinformatics · 2021Article
- Topological Analysis for Sequence Variability: Case Study on more than 2K SARS-CoV-2 sequences of COVID-19 infected 54 countries in comparison with SARS-CoV-1 and MERS-CoV.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2021Review
- Genome-wide analysis of Indian SARS-CoV-2 genomes to identify T-cell and B-cell epitopes from conserved regions based on immunogenicity and antigenicity.International immunopharmacology · 2021Article
- COVID-19: The question of genetic diversity and therapeutic intervention approaches.Genetics and molecular biology · 2021Article
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6 authors.
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Abstract
The wave of COVID-19 is a big threat to the human population. Presently, the world is going through different phases of lock down in order to stop this wave of pandemic; India being no exception. We have also started the lock down on 23rd March 2020. In this current situation, apart from social distancing only a vaccine can be the proper solution to serve the population of human being. Thus it is important for all the nations to perform the genome-wide analysis in order to identify the genetic variation in Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) so that proper vaccine can be designed. This fast motivated us to analyze publicly available 566 Indian complete or near complete SARS-CoV-2 genomes to find the mutation points as substitution, deletion and insertion. In this regard, we have performed the multiple sequence alignment in presence of reference sequence from NCBI. After the alignment, a consensus sequence is built to analyze each genome in order to identify the mutation points. As a consequence, we have found 933 substitutions, 2449 deletions and 2 insertions, in total 3384 unique mutation points, in 566 genomes across 29.9 K bp. Further, it has been classified into three groups as 100 clusters of mutations (mostly deletions), 1609 point mutations as substitution, deletion and insertion and 64 SNPs. These outcomes are visualized using BioCircos and bar plots as well as plotting entropy value of each genomic location. Moreover, phylogenetic analysis has also been performed to see the evolution of SARS-CoV-2 virus in India. It also shows the wide variation in tree which indeed vivid in genomic analysis. Finally, these SNPs can be the useful target for virus classification, designing and defining the effective dose of vaccine for the heterogeneous population.
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