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.
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
- 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
- , J Clin Microbiol, 2022.
- , Viruses, 2022.
- , mBio, 2022.
- , medRxiv, 2021.
- , J Clin Microbiol, 2022.