2021 Project: University of Washington

Viral genome sequencing and open-source software development to support genetic epidemiology in Washington State

What to know

The University of Washington provided whole-genome sequencing and phylogenetic analyses of SARS-CoV-2 for the state of Washington and the surrounding region. Awarded in 2021, this project performed sequencing on an additional 4,400 SARS-CoV-2 virus genomes and analyzed their diversity and development. Based on this analysis, the team reported on variants in the area, detected emerging variants, and determined how the variant proportions changed as more of the population were vaccinated.

Decorative image with words "2021" and "SARS-CoV-2"

Findings on SARS-CoV-2 Variant Characteristics

This project found that infection with Alpha, Gamma, or Delta variants resulted in a higher hospitalization risk than ancestral lineages of SARS-CoV-2.1 The project also found that vaccination decreased risk of hospitalization.

New and improved sequencing software tools

This project:

  • Continued development of phylodynamic visualization software for SARS-CoV-2 to accommodate large amounts of SARS-CoV-2 for genomic epidemiology analysis.
  • Continued development of , an open-source data warehouse.

New SARS-CoV-2 dashboards and websites

This project:

  • Used Nexstrain phylogenetic visualization SARS-CoV-2 analyses using publicly available data.
  • showing the percent of specimens with positive results for different pathogens among samples collected as part of the Seattle Flu Alliance.
Print
Content Source:
National Center for Emerging and Zoonotic Infectious Diseases (NCEZID)
  1. Clin Infect Dis, 2022.