Characterizing SARS-CoV-2 mutations in the United States

Area of Science:

• Virology
• Genomics
• Computational Biology

Background:

• Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has undergone significant mutation since its emergence.
• Understanding SARS-CoV-2 evolution within the United States is critical due to the high number of infections.

Approach:

• Utilized genotyping, sequence alignment, time-evolution analysis, k-means clustering, protein stability, algebraic topology, and network theory.
• Analyzed mutations on the spike protein and identified distinct SARS-CoV-2 substrains and their properties.

Key Points:

• Identified four SARS-CoV-2 substrains circulating in the US.
• Discovered that five top mutations were initially detected outside the US, while three were first identified domestically.
• Revealed a prevalent group of five concurrent mutations and a fading group of three, with one mutation (27964C>T-(S24L) on ORF8) exhibiting strong gender dependence.
• Found that three of the four US SARS-CoV-2 substrains exhibit increased infectiousness.

Conclusions:

• The study reveals complex mutation patterns and substrain evolution of SARS-CoV-2 in the US.
• Findings underscore the need for targeted viral control and containment strategies within the United States.