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Monkeypox Virus Partial-Genome Amplicon Sequencing for Improvement of Genomic Surveillance during Mpox Outbreaks

by Li, Yu , Haddock, Luis A. , Hutson, Christina L. , Mbala-Kingebeni, Placide , Rabeneck, Demi B. , Gigante, Crystal , Madden, Joseph , McGrath, Daisy , Deng, Jiusheng , Wilkins, Kimberly , Amuri-Aziza, Adrienne , Wawina-Bokalanga, Tony , Wicker, Vaughn , Davidson, Whitni

in amplicon / antimicrobial resistance / Bar codes / Causes of / Disease Outbreaks / DNA / DNA sequencing / DNA viruses / Drug resistance / Epidemics / Genetic aspects / Genetic testing / genome sequencing / Genome, Viral / Genomes / Genomics / Genomics - methods / Health surveillance / High-Throughput Nucleotide Sequencing / Human monkeypox / Humans / Identification and classification / Infectious diseases / Laboratories / Methods / monkeypox virus / Monkeypox virus - classification / Monkeypox virus - genetics / Monkeypox Virus Partial-Genome Amplicon Sequencing for Improvement of Genomic Surveillance during Mpox Outbreaks / Mpox / Mpox, Monkeypox - epidemiology / Mpox, Monkeypox - virology / Nucleotide sequencing / Outbreaks / Performance evaluation / Phylogenetics / Phylogeny / Sentinel health events / United States / viruses / Whole Genome Sequencing

2025

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Monkeypox Virus Partial-Genome Amplicon Sequencing for Improvement of Genomic Surveillance during Mpox Outbreaks

2025

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Monkeypox Virus Partial-Genome Amplicon Sequencing for Improvement of Genomic Surveillance during Mpox Outbreaks

2025

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Journal Article

Monkeypox Virus Partial-Genome Amplicon Sequencing for Improvement of Genomic Surveillance during Mpox Outbreaks

Li, Yu,

Haddock, Luis A.,

Hutson, Christina L.,

Mbala-Kingebeni, Placide,

Rabeneck, Demi B.,

Gigante, Crystal,

Madden, Joseph,

McGrath, Daisy,

Deng, Jiusheng,

Wilkins, Kimberly,

Amuri-Aziza, Adrienne,

Wawina-Bokalanga, Tony,

Wicker, Vaughn,

Davidson, Whitni

2025

Overview

Mpox is a reemerging infectious disease caused by monkeypox virus (MPXV). Whole-genome sequencing provides comprehensive surveillance of MPXV but is challenging in resource-limited outbreak settings and on clinical samples with low viral load. We developed a low-cost, high-throughput partial-genome sequencing strategy and a freeware Nextflow pipeline for MPXV genomic surveillance. We targeted 2 genomic regions of MPXV by using short overlapping amplicons. This amplicon-based approach generated high-quality sequences over the 2 genomic regions from clinical specimens, including samples with low viral DNA and from formalin-fixed tissues. This partial-genome sequencing approach can determine MPXV subclades and offers an attractive strategy to lower cost and improve MPXV surveillance during outbreaks in mpox-endemic and -nonendemic countries.

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Publisher

U.S. National Center for Infectious Diseases,Centers for Disease Control and Prevention

Subject

amplicon

/ antimicrobial resistance

/ DNA