Isolating SARS-CoV-2 Strains From Countries in the Same Meridian: Genome Evolutionary Analysis

Area of Science:

• Virology
• Genomics
• Molecular Biology

Background:

• COVID-19, caused by SARS-CoV-2, is a global health threat with significant mortality.
• SARS-CoV-2 strains exhibit geographic and genomic specificity, with potential variations in clinical features.
• Previous genomic comparisons identified distinct clades in Europe, Asia, and North America.

Purpose of the Study:

• To compare SARS-CoV-2 genomes from Italy, Sweden, Congo, and Brazil.
• To analyze evolutionary pressure signatures in viral genomes across different geographical and climatic conditions.
• To investigate potential differences in SARS-CoV-2 evolution.

Main Methods:

• Genome data acquisition from GISAID.
• Phylogenetic and evolutionary analyses using HyPhy (genetic algorithm recombination detection, mixed effects model of evolution).
• Secondary structure prediction, disorder, transmembrane analyses, and ab initio protein structure prediction.

Main Results:

• Codon 9628 identified as under episodic selective pressure across all analyzed SARS-CoV-2 strains.
• Mutation at codon 9628 affects the secondary structure of the P0DTD3 protein, influencing helical modification.
• The mutation enhances protein binding probability and may be involved in viral attachment.

Conclusions:

• A specific mutation (codon 9628) impacts SARS-CoV-2 RNA secondary structure and protein function.
• Amino acid changes (T to G, G to D) may enhance viral binding to human cells.
• Findings support the development of targeted in vitro experiments, vaccines, and antiviral therapies.