2021 Project: Arizona State University

SARS-CoV-2 genomic surveillance in Arizona

What to know

Arizona State University conducted next-generation sequencing and developed tools to track SARS-CoV-2 in Arizona. Awarded in 2021, this project sequenced 2,000 positive samples over 12 months. Sample criteria included reinfection cases, routine surveillance of low-population counties, and vaccinated individuals. The university developed a tool for researchers to upload sequences and analyze the data for emerging variant trends.

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

Findings on SARS-CoV-2 surveillance and investigations

  • This project contributed sequencing data to SARS-CoV-2 baseline surveillance in Arizona.12

Findings on SARS-CoV-2 variant characteristics

This project:

  • Used software developed to analyze the spike protein of SARS-CoV-2 to analyze mutations in the vaccine antigenic site of respiratory syncytial virus (RSV).3
  • Contributed sequencing data to characterization of SARS-CoV-2 illness due to the BA.2 variant in a university-associated cohort.4
  • Contributed sequencing data to characterization of SARS-CoV-2 mutations that reduce diagnostic assay detection.5

New and improved sequencing software tools

This project developed a mutation analysis tool to analyze large sequencing datasets with code publicly available and adapted the mutation analysis tool to identify mutations in RSV F protein involved in vaccine immunity.

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Content Source:
National Center for Emerging and Zoonotic Infectious Diseases (NCEZID)
  1. Baseline Sequencing Surveillance of Public Clinical Testing, Hospitals, and Community Wastewater Reveals Rapid Emergence of SARS-CoV-2 Omicron Variant of Concern in Arizona, USA. mBio, 2023
  2. Seasonality of Respiratory, Enteric and Urinary Viruses Revealed by Wastewater Genomic Surveillance. medRxiv, 2024
  3. Holland LA, Holland SC, Smith MF, et al. Genomic Sequencing Surveillance to Identify Respiratory Syncytial Virus Mutations, Arizona, USA. Emerg Infect Dis. 2023;29(11):2380-2382. doi:10.3201/eid2911.230836
  4. University-Associated SARS-CoV-2 Omicron BA.2 Infections, Maricopa County, Arizona, USA, 2022. Emerging Infectious Diseases, 2022.
  5. SARS-CoV-2 Delta Variant N Gene Mutations Reduce Sensitivity to the TaqPath COVID-19 Multiplex Molecular Diagnostic Assay. Viruses, 2022.