Phylogenomic proximity and comparative proteomic analysis of SARS-CoV-2

Prathiviraj, R.; Kiran, George Seghal; Selvin, Joseph

doi:10.1016/j.genrep.2020.100777

Cited by 12 publications

(9 citation statements)

References 19 publications

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“…Characterization studies: Studying the structural details of the virus with its genes and proteins ( Li et al, 2020 ; Yoshimoto, 2020 ; Emameh et al, 2020 ; Shah et al, 2020 ) 3. Comparison of SARS-CoV-2 with other viruses in this family like SARS and MERS-CoV ( Li et al, 2020 ; Li et al, 2020 ; Tai et al, 2020 ; Prathiviraj et al, 2020 ) 4. Studying the mutations in SARS-CoV-2 ( Center for Disease Control and Prevention (CDC), n.d. ; Saha et al, 2020 ; Dorp et al, 2020 ; Khailany et al, 2020 ; Junejo et al, 2020 ) 5.…”

Section: Background and Related Workmentioning

confidence: 99%

Analysis and comparison of genetic variants and mutations of the novel coronavirus SARS-CoV-2

Almubaid

Al-Mubaid

2021

Gene Reports

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We present an analysis and comparison study of genetic variants and mutations of about 1200 genomes of SARS-CoV-2 virus sampled across the first seven months of 2020. The study includes 12 sets of about 100 genomes each collected between January and September . We analyzed the mutations, mutation frequency and count trends over time, and genomes trends over time from January through September. We show that certain mutations in the SARS-CoV-2 genome are not occurring randomly as it has been commonly believed. This finding is in agreement with other recently published research in this domain. Therefore, this validates other findings in this direction. This study includes approximately 1000 genomes and was able to identify over 35 different mutations most of which are common to almost all genomes groups. Some mutations' ratios (frequency percentage) fluctuate over time to adapt the virus to various environmental factors, climate, and populations. One of the interesting findings in this paper is that the coding region, at the nucleotide level for NSP13 protein is relatively conserved compared with other protein regions in the ORF1ab gene which makes this protein a good candidate for developing drug targets and treatment for the COVID-19 disease. Although this outcome was already reported by other researchers, we corroborated their result with our work in a different approach and another experimental setting with almost one thousand complete genome sequences. We presented and discussed all these results and findings with tables of results and illustrating figures.

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Section: Background and Related Workmentioning

confidence: 99%

Analysis and comparison of genetic variants and mutations of the novel coronavirus SARS-CoV-2

Almubaid

Al-Mubaid

2021

Gene Reports

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“…It has the potential to change its morphology corresponding to varying environmental conditions [ 4 ]. The size of the SARS-CoV-2 genome is around 30 kb, enclosed with 5′-cap and 3′-poly(A) tail and the structure is comprised of spike, envelope, membrane and nucleocapsid proteins [ 5 ]. Currently, there is no specific antiviral drug available for the treatment of COVID-19 and the infected patients are primarily treated only by supportive therapy [ 6 ].…”

Section: Introductionmentioning

confidence: 99%

Targeting COVID-19 (SARS-CoV-2) main protease through active phytocompounds of ayurvedic medicinal plants – Emblica officinalis (Amla), Phyllanthus niruri Linn. (Bhumi Amla) and Tinospora cordifolia (Giloy) – A molecular docking and simulation study

Murugesan

Kottekad

Crasta

et al. 2021

Computers in Biology and Medicine

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Coronavirus Disease-2019 (COVID-19), a viral disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was declared a global pandemic by WHO in 2020. In this scenario, SARS-CoV-2 main protease (COVID-19 M pro ), an enzyme mainly involved in viral replication and transcription is identified as a crucial target for drug discovery. Traditionally used medicinal plants contain a large amount of bioactives and pave a new path to develop drugs and medications for COVID-19. The present study was aimed to examine the potential of Emblica officinalis (amla), Phyllanthus niruri Linn. (bhumi amla) and Tinospora cordifolia (giloy) bioactive compounds to inhibit the enzymatic activity of COVID-19 M pro . In total, 96 bioactive compounds were selected and docked with COVID-19 M pro and further validated by molecular dynamics study. From the docking and molecular dynamics study, it was revealed that the bioactives namely amritoside, apigenin-6-C-glucosyl7-O-glucoside, pectolinarin and astragalin showed better binding affinities with COVID-19 M pro . Drug-likeness, ADEMT and bioactivity score prediction of best drug candidates were evaluated by DruLiTo, pkCSM and Molinspiration servers, respectively. Overall, the in silico results confirmed that the validated bioactives could be exploited as promising COVID-19 M pro inhibitors.

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“…The mean G+C content was found to be low (<38%) while comparing to the A+T disparity index. It determines that some divergence may occur during the evolutionary transmittance of this genome (Prathiviraj et al, 2020). From the result of the phylogenomic analysis, we found that the tree was separated into two major clades.…”

Section: Analysis Of Evolutionary Footprintmentioning

confidence: 92%

Identification of Genotypic Variants and its Proteomic mutations of Brazilian SARS-CoV-2 Isolates

Prathiviraj

Chellapandi

Kiran

et al. 2021

Preprint

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The second wave of COVID-19, which is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is rapidly spreading over the world. The mechanism behind the escaping from current antivirals is still not clear, due to the occurrence of continuous variants in SARS-CoV-2 genomes. Brazil is the world’s second most COVID-19-affected country. In the present study, we identified the genomic and proteomic variants of Brazilian SARS-CoV-2 isolates. We identified 16 different genotypic variants were found among the 27 isolates. The genotypes of three isolates such as Bra/1236/2021 (G15), Bra/MASP2C844R2/2020 (G11), and Bra/RJ-DCVN5/2020 (G9) have a unique mutant in NSP4 (S184N), 2’O-Mutase (R216N), membrane protein (A2V) and Envelope protein (V5A). A mutation in RdRp of SARS-CoV-2, particularly the change of Pro to Leu at 323 resulted in the stabilization of the structure in BRA/CD1739-P4/2020. NSP4, NSP5 protein mutants are more virulent in Genotype 15 and 16. A fast protein folding rate changes the structural stability and leads to escape for current antivirals. Thus, our findings help researchers to develop the best potent antivirals based on the new mutant of Brazilian isolates.

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Phylogenomic proximity and comparative proteomic analysis of SARS-CoV-2

Cited by 12 publications

References 19 publications

Analysis and comparison of genetic variants and mutations of the novel coronavirus SARS-CoV-2

Analysis and comparison of genetic variants and mutations of the novel coronavirus SARS-CoV-2

Targeting COVID-19 (SARS-CoV-2) main protease through active phytocompounds of ayurvedic medicinal plants – Emblica officinalis (Amla), Phyllanthus niruri Linn. (Bhumi Amla) and Tinospora cordifolia (Giloy) – A molecular docking and simulation study

Identification of Genotypic Variants and its Proteomic mutations of Brazilian SARS-CoV-2 Isolates

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