Genomic epidemiology of mpox virus during the 2022 outbreak in New York City

Saymon Akther (), Michelle Su, Jade C. Wang, Helly Amin, Faten Taki, Nelson Cruz, Moinuddin Chowdhury, Tyler Clabby, Erik Kopping, Victoria E. Ruiz, Mindy Leelawong, Julia Latash, Kimberly Johnson, Jennifer Baumgartner, Marcia Wong, Aaron Olsen, Randal C. Fowler, Jonathan E. Pekar, Jennifer L. Havens, Tetyana I. Vasylyeva, Joel O. Wertheim, Scott Hughes and Enoma Omoregie
Additional contact information
Saymon Akther: Department of Health and Mental Hygiene
Michelle Su: Department of Health and Mental Hygiene
Jade C. Wang: Department of Health and Mental Hygiene
Helly Amin: Department of Health and Mental Hygiene
Faten Taki: Department of Health and Mental Hygiene
Nelson Cruz: Department of Health and Mental Hygiene
Moinuddin Chowdhury: Department of Health and Mental Hygiene
Tyler Clabby: Department of Health and Mental Hygiene
Erik Kopping: Department of Health and Mental Hygiene
Victoria E. Ruiz: Department of Health and Mental Hygiene
Mindy Leelawong: Department of Health and Mental Hygiene
Julia Latash: Department of Health and Mental Hygiene
Kimberly Johnson: Department of Health and Mental Hygiene
Jennifer Baumgartner: Department of Health and Mental Hygiene
Marcia Wong: Department of Health and Mental Hygiene
Aaron Olsen: Department of Health and Mental Hygiene
Randal C. Fowler: Department of Health and Mental Hygiene
Jonathan E. Pekar: University of California San Diego
Jennifer L. Havens: University of California San Diego
Tetyana I. Vasylyeva: University of California San Diego
Joel O. Wertheim: University of California San Diego
Scott Hughes: Department of Health and Mental Hygiene
Enoma Omoregie: Department of Health and Mental Hygiene

Nature Communications, 2025, vol. 16, issue 1, 1-14

Abstract: Abstract New York City (NYC) was a major hotspot during the 2022 multi-country Mpox virus (MPXV) outbreak in the U.S. To investigate the genomic characteristics of MPXV in NYC, we sequenced 1138 specimens from 758 individuals using PrimalSeq and Illumina technology and performed phylogenomic analyses alongside 2967 global MPXV sequences. Nextclade lineage assignment revealed a NYC-specific B.1.12 lineage, with phylogenetic analysis showing unique clusters in NYC and North America. MPXV lineage B-specific mutations were predominantly driven by APOBEC3 activity (53/58 mutations). APOBEC3-associated mutations were significantly higher in 2022 outbreak sequences compared to those before 2022. Intra-host genome diversity was investigated in individuals with multiple specimens (n = 360). This analysis showed that 6.4% of these individuals had distinct genomic profiles, with 4.2% likely due to co-infections with distinct MPXV strains. This study identified unique MPXV genomic profiles in NYC, estimated concurrent infections with multiple MPXV strains and emphasized the need for enhanced surveillance and public health strategies to address co-infections, especially through collaboration with labs, clinics, and community groups.

Date: 2025
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-025-60486-x Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-60486-x

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-025-60486-x

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().