2021 Project: University of Pennsylvania

Whole-genome sequencing to define SARS-CoV-2 variant populations during vaccine rollout in the Philadelphia metropolitan region

What to know

Awarded in 2021, this project sought to define how SARS-CoV-2 variant populations clustered geographically across Philadelphia and how the variants in this area changed over time as people were vaccinated. Using these data sets, researchers developed a model to predict the impact of vaccination campaigns on evolving variants to better inform public health interventions related to vaccines.

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

Findings on SARS-CoV-2 surveillance and investigations

This project:

  • Described the identification of a mutation in the SARS-CoV-2 genome as a marker of the then emerging variant Omicron BA.2.12.1, which suggested that the variant could be tracked using nucleic acid amplification tests.1
  • The model used to identify the mutation was made publicly available.
  • Described a likely transmission event between human SARS-CoV-2 cases and a domestic cat. Also described a protocol for isolation of SARS-CoV-2 RNA and whole-genome sequencing from fecal specimens. 2
  • Compared SARS-CoV-2 sequences in deer and humans in Pennsylvania and showed the Alpha variant persisted in deer even after it was displaced by Delta in humans and that Alpha variants had a different evolutionary trajectory in deer and in humans. 3
  • Analyzed variants among vaccine breakthrough samples compared to the general surveillance population using a novel modeling approach. Also, found the B.1.617.2 variant to be more common in vaccine breakthrough infections.4
  • Described how SARS-CoV-2 variant populations clustered geographically and changed over time across the Philadelphia metropolitan region. 5
  • Described the benefits of collaboration between clinical microbiology laboratories and academic laboratories to support SARS-CoV-2 sequencing and highlighted how the infrastructure established for this project can serve as a model for future work. 5

New SARS-CoV-2 dashboards and websites

This project resulted in a dashboard, The SARS-CoV-2 Variants Circulating in the Delaware River Valley Tracked by Surveillance Sequencing.

Print
Content Source:
National Center for Emerging and Zoonotic Infectious Diseases (NCEZID)
  1. Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1, J Clin Microbiol, 2022.
  2. SARS-CoV-2 Delta Variant (AY.3) in the Feces of a Domestic Cat, Viruses, 2022.
  3. Multiple Introductions of SARS-CoV-2 Alpha and Delta Variants into White-Tailed Deer in Pennsylvania, mBio, 2022.
  4. SARS-CoV-2 variants associated with vaccine breakthrough in the Delaware Valley through summer 2021, medRxiv, 2021.
  5. Collaboration between Clinical and Academic Laboratories for Sequencing SARS-CoV-2 Genomes, J Clin Microbiol, 2022.