Identification of genotypic variants and its proteomic mutations of Brazilian SARS-CoV-2 isolates

• Published in: Virus research Vol. 307; p. 198618
• Main Authors: Prathiviraj, Ragothaman, Chellapandi, Paulchamy, Begum, Ajima, Kiran, George Seghal, Selvin, Joseph
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 02-01-2022
• Subjects: Brazil; Brazilian isolates; Coronavirus 3C Proteases - genetics; Coronavirus Nucleocapsid Proteins - genetics; Coronavirus RNA-Dependent RNA Polymerase - genetics; COVID-19 - pathology; Genetic Variation - genetics; Genome, Viral - genetics; Genotypic variants; Humans; Phosphoproteins - genetics; Phylogenomic study; Protein Folding; Protein mutations; SARS-CoV-2; SARS-CoV-2 - genetics; SARS-CoV-2 - isolation & purification; Spike Glycoprotein, Coronavirus - genetics; Viral Nonstructural Proteins - genetics; Virulence - genetics; Brazil; COVID-19; SARS-CoV-2; Phylogenomic study; Brazilian isolates; RdRp; Protein mutations; NSP; Genotypic variants; hACE2
• ISSN: 0168-1702; 1872-7492; 1872-7492
• DOI: 10.1016/j.virusres.2021.198618

•We identified 16 genotypic variants among the Brazilian isolates.•The genotype G9, G11 and G15 have a unique mutant at NSP4, 2′O-Mutase, membrane, and envelope protein.•The mutants identified in NSP4, NSP5 are becoming more virulent in genotype 15 and 16.
The second wave of COVID-19 caused by severe acute respiratory syndrome virus (SARS-CoV-2) is rapidly spreading over the world. Mechanisms behind the flee from current antivirals are still unclear due to the continuous occurrence of SARS-CoV-2 genetic variants. 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.