Accession Number:



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

Descriptive Note:

Technical Report

Corporate Author:

59th MDW San Antonio United States

Report Date:


Pagination or Media Count:



The outbreak of SARS-CoV-2 has created a global pandemic resulting in over 1 million deaths worldwide. Rapid estimations of transmission and mutational patterns of virus outbreaks can be accomplished using whole genome viral sequencing. Here we report the development of a local pipeline for molecular epidemiological surveillance enabling DoD public health officials to track viral evolution and outbreaks. Sequencing of clinical specimens revealed that by June 2020, SAR-CoV-2 strains carrying the 614G mutation were the predominant cause of COVID-19 infections at JBSALackland. Furthermore, we identified and mapped six additional spike protein amino acid changes, information which could potentially aid vaccine design. The sequencing and phylogenetic workflow described in this paper will enable local officials to track and better understand virus transmission events. Overall, this work could improve long-term readiness efforts by providing a mechanism for analyzing the current SARS-CoV-2 pandemic as well as future disease outbreaks.

Subject Categories:

  • Medicine and Medical Research
  • Microbiology

Distribution Statement: