SARS-CoV-2 Genomic Variation in Space and Time in Hospitalized Patients in Philadelphia

Area of Science:

• Virology
• Epidemiology
• Genomics

Background:

• The severe acute respiratory coronavirus 2 (SARS-CoV-2) caused the COVID-19 pandemic.
• Philadelphia experienced a significant increase in COVID-19 cases in spring 2020.

Purpose of the Study:

• To investigate the origins and within-host diversity of SARS-CoV-2 during the first wave in Philadelphia.
• To analyze the genetic relatedness of viral samples to understand transmission patterns.

Main Methods:

• Full-genome sequencing of 52 SARS-CoV-2 samples from 27 hospitalized patients.
• Analysis of viral sequences collected between March and July 2020.
• Comparison of Philadelphia viral genomes with global and regional databases.

Main Results:

• Most Philadelphia SARS-CoV-2 sequences resembled those from New York, indicating primary introduction from that location.
• Evidence of local transmission within Philadelphia was observed.
• Some patients harbored diverse viral populations within different body sites or over time.
• No correlation was found between viral lineage and disease outcome.

Conclusions:

• The initial SARS-CoV-2 epidemic in Philadelphia was largely driven by introductions from New York, supplemented by local spread.
• Intra-patient viral diversity exists and warrants further investigation.
• Disease severity in COVID-19 appears independent of the specific SARS-CoV-2 lineage, highlighting host factors.