Fine-scale Spatial and Social Patterns of SARS-CoV-2 Transmission from Identical Pathogen Sequences

Overview

Journal medRxiv

Date 2024 Jun 3

PMID 38826243

Authors

Cecile Tran-Kiem

Miguel I Paredes

Amanda C Perofsky

Lauren A Frisbie

Hong Xie

Kevin Kong

Amelia Weixler

Alexander L Greninger

Pavitra Roychoudhury

JohnAric M Peterson

Andrew Delgado

Holly Halstead

Drew MacKellar

Philip Dykema

Luis Gamboa

Chris D Frazar

Erica Ryke

Jeremy Stone

David Reinhart

Lea Starita

Allison Thibodeau

Cory Yun

Frank Aragona

Allison Black

Cecile Viboud

Trevor Bedford

Affiliations

Soon will be listed here.

Abstract

Pathogen genomics can provide insights into underlying infectious disease transmission patterns, but new methods are needed to handle modern large-scale pathogen genome datasets and realize this full potential. In particular, genetically proximal viruses should be highly informative about transmission events as genetic proximity indicates epidemiological linkage. Here, we leverage pairs of identical sequences to characterise fine-scale transmission patterns using 114,298 SARS-CoV-2 genomes collected through Washington State (USA) genomic sentinel surveillance with associated age and residence location information between March 2021 and December 2022. This corresponds to 59,660 sequences with another identical sequence in the dataset. We find that the location of pairs of identical sequences is highly consistent with expectations from mobility and social contact data. Outliers in the relationship between genetic and mobility data can be explained by SARS-CoV-2 transmission between postal codes with male prisons, consistent with transmission between prison facilities. We find that transmission patterns between age groups vary across spatial scales. Finally, we use the timing of sequence collection to understand the age groups driving transmission. Overall, this work improves our ability to leverage large pathogen genome datasets to understand the determinants of infectious disease spread.

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