As SARS-CoV-2 grows, the virus occasionally makes mistakes copying its genetic material, and so introduces heritable changes. As the virus spreads in people, chance changes that increase replication in humans may lead to new variants that spread preferentially. It is important to track these variants in order to understand their possible influences on the effectiveness of vaccines and therapies. Researchers at Penn Medicine with collaborators at the City of Philadelphia Department of Public Health, Jefferson Hospital and CHOP are carrying out systematic viral whole genome sequencing to track the nature and spread of viral variants in the Delaware Valley. Samples primarily originate from southeastern Pennsylvania and southwestern New Jersey, providing an overview of the dynamics in the Delaware Valley. Below that are summaries of all genomes sequenced, and reports on each genome individually.

The output of the sequencing effort to date is:
Most recent sequencing run: 2023-05-16
Total number of sequenced samples: 7,977
Sequenced samples with ≥ 95% genome coverage (≥ 5 reads per position): 7,538
Sequenced lineages | Mutation tables | Mutant positions | Run stats | Report archive (1.7 GB) | Code base





SARS-CoV-2 variants of interest and variants of concern are described in detail by the Centers for Disease Control and Prevention (here).

Methods: Samples are sequenced primarily using the Polar Protocol and ARTIC primers, essentially as described in Everett et al. (mBio 2021). Variant lineages are called using PANGO lineage.





The display above shows the Delaware Valley baseline surveillance by week for the most recently sequenced samples.


The display below shows all samples acquired. These include surveillance samples, hospitalized cases, vaccine breakthroughs,
asymptomatics and S drop outs. The later group are selected based on a specific failure of an amplicon targeting the spike coding
region, which is disrupted by a mutation found in B.1.1.7.






The graphs below track the distribution of mutations in randomly sampled subjects. Mutations are dislayed for the S gene (spike protein), N gene (nucleoprotein), M gene (membrane protein), and ORF1ab.





The table below describes all completed genomes including links to sequence analysis reports which provide additional analyses including variant grids and read coverage visualizations.




Resource for Clinical Interpretations
Susceptibility data - Stanford Coronavirus Antiviral & Resistance Database (CoVDB)

Contributing authors
John K. Everett, Kyle Rodino, Andrew D. Marques, Young Hwang, Shantan Reddy, Aoife M. Roche,
Scott Sherrill-Mix, Samantha A. Whiteside, Jevon Graham-Wooten, Lisa Mattei, Paige Fenn, Madelyne Om, Ayannah S. Fitzgerald, Abigail Glascock, Pascha Hokama, Ahmed Moustafa, Nitika Badjatia, Zi-Xuan Wang, Paul Planet, Mike Feldman,
Brendan Kelly, Ronald G. Collman, and Frederic Bushman


Surveillance Performed by the City of Philadelphia Department of Public Health Genomic surveillance data collected by the City of Philadelphia Department of Public Health is submitted publicly as consensus sequences. This publicly submitted data is collected and displayed on this dashboard. These consensus sequences are do not contain sequencing quality information, therefore, reports will be missing these data.

Funding graciously provided by University of Pennsylvania Health System
Perelman School of Medicine
Dept. of Pathology and Laboratory Medicine
Peter Quinn clinical philanthropy
Penn Cares COVID-19 Response Program
Penn Center for Research on Coronaviruses and Other Emerging Pathogens
Center of Excellence for Influenza Research and Response
Centers for Disease Control and Prevention


Media contact
Kelsey Odorczyk Senior Medical Communications Officer
Perelman School of Medicine
Kelsey.Odorczyk@Pennmedicine.upenn.edu


References
Everett, John et al. “SARS-CoV-2 Genomic Variation in Space and Time in Hospitalized Patients in Philadelphia.”
mBio vol. 12,1 e03456-20. 19 Jan. 2021, doi:10.1128/mBio.03456-20