Whole-genome Sequencing of SARS-CoV-2: Using Phylogeny and Structural Modeling to Contextualize Local Viral Evolution

Area of Science:

• Virology
• Genomics
• Bioinformatics

Background:

• The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has caused significant global mortality and infections within the Department of Defense (DoD).
• Whole-genome viral sequencing is crucial for estimating transmission and mutation patterns during outbreaks.

Purpose of the Study:

• To develop and present a streamlined sequencing and bioinformatics workflow for molecular epidemiological surveillance of SARS-CoV-2.
• To enable near real-time evaluation of viral evolution and support public health readiness efforts within the DoD.

Main Methods:

• Utilized excess clinical specimens for SARS-CoV-2 surveillance under an IRB-exempt protocol.
• Workflow involved RNA isolation, viral load quantification, tiling-based next-generation sequencing, and bioinformatics analysis.
• Data visualization included phylogenetic trees and protein mapping to interpret sequence data.

Main Results:

• Identified the 614G mutation as predominant in local infections by June 2020.
• Detected 109 nucleotide changes leading to 63 unique amino acid mutations, plus UTR mutations.
• Mapped six additional spike protein amino acid changes with potential implications for vaccine design.

Conclusions:

• The presented workflow facilitates DoD public health officials in tracking viral evolution and assessing outbreaks in near real-time.
• Molecular epidemiological data generation is vital for developing disease intervention strategies, particularly vaccine design.
• This methodology enhances long-term readiness efforts within the DoD through improved outbreak response capabilities.