tetano
Editor, Senior Moderator
J Med Virol
. 2020 Sep 24.
doi: 10.1002/jmv.26548. Online ahead of print.
Genomic and Proteomic Mutation Landscapes of SARS-CoV-2
Christian Luke D C Badua[SUP] 1 [/SUP], Karol Ann T Baldo[SUP] 1 [/SUP], Paul Mark B Medina[SUP] 1 [/SUP]
Affiliations
Abstract
The ongoing pandemic caused by a novel coronavirus, SARS-CoV-2, affects thousands of people every day worldwide. Hence, drugs and vaccines effective against all variants of SARS-CoV-2 are crucial today. Viral genome mutations are commonly existent which may impact the encoded proteins, possibly resulting to varied effectivity of detection tools and disease treatment. Thus, this study surveyed the SARS-CoV-2 genome and proteome and evaluated its mutation characteristics. Phylogenetic analyses of SARS-CoV-2 genes and proteins show three major clades and one minor clade (P6810S; ORF1ab). The overall frequency and densities of mutations in the genes and proteins of SARS-CoV-2 were observed Nucleocapsid exhibited the highest mutation density among the structural proteins while the Spike D614G was the most common, occurring mostly in genomes outside China and USA. ORF8 protein had the highest mutation density across all geographical areas. Moreover, mutation hotspots neighboring and at the catalytic site of RNA-dependent-RNA-polymerase were found that might challenge the binding and effectivity of remdesivir. Mutation coldspots may present as conserved diagnostic and therapeutic targets were found in ORF7b, ORF9b and ORF14. These findings suggest that the virion's genotype and phenotype in a specific population should be considered in developing diagnostic tools, and treatment options. This article is protected by copyright. All rights reserved.
Keywords: SARS-CoV-2; mutation hotspot; virus bioinformatics; Coronavirus; Genetic Variability; Mutation; coldspot.
. 2020 Sep 24.
doi: 10.1002/jmv.26548. Online ahead of print.
Genomic and Proteomic Mutation Landscapes of SARS-CoV-2
Christian Luke D C Badua[SUP] 1 [/SUP], Karol Ann T Baldo[SUP] 1 [/SUP], Paul Mark B Medina[SUP] 1 [/SUP]
Affiliations
- PMID: 32970329
- DOI: 10.1002/jmv.26548
Abstract
The ongoing pandemic caused by a novel coronavirus, SARS-CoV-2, affects thousands of people every day worldwide. Hence, drugs and vaccines effective against all variants of SARS-CoV-2 are crucial today. Viral genome mutations are commonly existent which may impact the encoded proteins, possibly resulting to varied effectivity of detection tools and disease treatment. Thus, this study surveyed the SARS-CoV-2 genome and proteome and evaluated its mutation characteristics. Phylogenetic analyses of SARS-CoV-2 genes and proteins show three major clades and one minor clade (P6810S; ORF1ab). The overall frequency and densities of mutations in the genes and proteins of SARS-CoV-2 were observed Nucleocapsid exhibited the highest mutation density among the structural proteins while the Spike D614G was the most common, occurring mostly in genomes outside China and USA. ORF8 protein had the highest mutation density across all geographical areas. Moreover, mutation hotspots neighboring and at the catalytic site of RNA-dependent-RNA-polymerase were found that might challenge the binding and effectivity of remdesivir. Mutation coldspots may present as conserved diagnostic and therapeutic targets were found in ORF7b, ORF9b and ORF14. These findings suggest that the virion's genotype and phenotype in a specific population should be considered in developing diagnostic tools, and treatment options. This article is protected by copyright. All rights reserved.
Keywords: SARS-CoV-2; mutation hotspot; virus bioinformatics; Coronavirus; Genetic Variability; Mutation; coldspot.