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Fine-scale patterns of SARS-CoV-2 spread from identical pathogen sequences

Cécile Tran-Kiem1, Miguel I Paredes2,3, Amanda C Perofsky4,5

  • 1Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA. ctrankie@fredhutch.org.

Nature
|March 5, 2025
PubMed

Insights

Analyzing identical SARS-CoV-2 genomes reveals fine-scale transmission patterns. This genomic surveillance approach identified transmission links, including between correctional facilities, and highlighted age-related spatial transmission dynamics.

Area of Science:

  • Genomic epidemiology
  • Infectious disease surveillance
  • Computational biology

Background:

  • Pathogen genomics offers insights into infectious disease transmission dynamics.
  • Large-scale genomic datasets require advanced analytical methods for full potential realization.
  • Genetically similar pathogen sequences often indicate direct epidemiological linkage.

Purpose of the Study:

  • To develop and apply novel methods for analyzing large-scale pathogen genome datasets.
  • To characterize fine-scale transmission patterns of SARS-CoV-2 using genomic data.
  • To investigate the relationship between genetic proximity, mobility, and transmission.

Main Methods:

  • Utilized 114,298 SARS-CoV-2 genomes from Washington State (March 2021-December 2022).
  • Analyzed pairs of identical sequences to identify transmission events and patterns.
  • Integrated genomic data with demographic (age) and geographic (residence location) information.

Main Results:

  • Identified high consistency between the geographic locations of identical sequence pairs and mobility data.
  • Detected SARS-CoV-2 transmission between correctional facilities, explaining deviations from expected mobility patterns.
  • Observed varying transmission patterns between age groups across different spatial scales and identified age groups driving transmission.

Conclusions:

  • Pairs of identical pathogen sequences are valuable for fine-scale transmission analysis.
  • Genomic surveillance effectively identifies transmission hotspots and links, such as within correctional facilities.
  • Understanding age-related and spatially stratified transmission is crucial for controlling infectious disease spread.

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