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Review
. 2025;12(1):10.
doi: 10.1007/s40588-025-00247-y. Epub 2025 May 15.

Long-Read Sequencing for the Rapid Response to Infectious Diseases Outbreaks

Josephine B Oehler  1   2 , Kaitlin Burns  2   3 , Jeffrey Warner  2   3 , Ulf Schmitz  1   4   5
Affiliations
Review

Long-Read Sequencing for the Rapid Response to Infectious Diseases Outbreaks

Josephine B Oehler et al. Curr Clin Microbiol Rep. 2025.

Abstract

Purpose of review: Long-read sequencing (LRS) has revolutionized pathogen surveillance by enabling real-time, high-fidelity genomic analysis critical for outbreak response. This review synthesizes recent breakthroughs in LRS, evaluating its impact on genomic epidemiology, metagenomics, and public health decision-making while addressing limitations and prospects for integrating LRS into global outbreak surveillance.

Recent findings: Unlike short-read sequencing, LRS-pioneered by Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio)-resolves complex genomic structures, antimicrobial resistance determinants, and transmission dynamics with unprecedented accuracy. The portability of some LRS devices has facilitated rapid pathogen identification in field settings, notably during the Ebola and COVID-19 pandemics. Despite advancements in basecalling algorithms and target enrichment, challenges including sequencing errors, computational bottlenecks, and cost barriers remain.

Summary: By critically evaluating recent findings and discussing future directions, this review highlights the importance of leveraging LRS for outbreak preparedness and response, equipping researchers and public health professionals with the knowledge necessary to navigate the complexities of modern infectious disease challenges.

Keywords: Genomic epidemiology antimicrobial resistance profiling; Metagenomics; Pathogen identification; Real-time surveillance; Third-generation sequencing.

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Conflict of interest statement

Conflicts of interestThe authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Evolution of sequencing technologies in outbreak response (Pre-2010 to Present)
See this image and copyright information in PMC

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