A Case Study of Applying Metagenomic Sequencing in Precise Epidemiology for the COVID-19 Pandemic — Sichuan Province, China, 2020

Abstract

Introduction: Determining the transmission chain of a virus in its incipient stages is extremely time consuming in traditional approaches that rely mainly on case incidence and interview-based contact data. With the development of high-throughput sequencing technology, genome-based epidemiology approach is showing promise in detecting viral transmission. However, there is still insufficient evidence for the relationship between the viral genetic variations and real viral transmission. Methods: To explore the possible relationship between transmission chains and viral genetic variations, we combined both epidemiological data and viral genomes of COVID-19 virus collected from Sichuan Province. A phylogenetic approach was used to infer the transmission chain, which was then compared to the transmission chain that came from epidemiological data. Results: We found that the putative transmission chains were highly concordant to the true transmission chains from epidemiological data, suggesting a strong correlation between viral genetic variations and the viral transmission chain. Discussion: Our results showed advantages of viral genomic sequencing in tracking and perceiving pathogen transmission, which allowed for potential improvements in the design and implementation of population-level public health interventions.