Comparative mutational analysis of SARS-CoV-2 isolates from Pakistan and structural-functional implications using...

Area of Science:

• Virology
• Genomics
• Molecular Biology

Background:

• Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) exhibits high mutation rates globally.
• Genomic surveillance in Pakistan has yielded varied results, necessitating a comprehensive analysis.
• Understanding viral mutations is crucial for developing effective therapeutic strategies.

Purpose of the Study:

• To explore the mutation landscape of 250 Pakistani SARS-CoV-2 isolates.
• To assess genome diversity and the impact of mutations on protein stability and pathogenesis.
• To compare Pakistani isolates with global variants and a reference sequence.

Main Methods:

• Genomic sequencing of 250 Pakistani SARS-CoV-2 isolates.
• Bioinformatic analysis of mutation patterns in viral proteins.
• Molecular docking, dissociation constant (KD), and MM/GBSA simulations.
• Analysis of protein stability and binding affinity with ACE2.

Main Results:

• Structural proteins, especially nucleocapsid, showed significant mutations in Pakistani isolates.
• Nsp12 was the most mutated non-structural protein (NSP) in Pakistan and globally.
• Mutations in the spike protein, such as D614G, enhanced binding affinity to ACE2, increasing infectivity.
• Certain genes (E, M, ORF6, ORF7A, ORF7B, ORF10) demonstrated high stability.

Conclusions:

• Mutations in SARS-CoV-2 Pakistani isolates alter protein stability and biological pathways.
• Spike protein mutations significantly increase viral infectivity by enhancing ACE2 binding.
• Stable coding genes present potential targets for future vaccine and drug development.