Genomic epidemiology of mpox virus during the 2022 outbreak in New York City
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.
Authors
- Mindy Leelawong (ORCID: https://orcid.org/0000-0002-3702-2938)
- Jade Wang
- Enoma Omoregie
- Marcia Wong (ORCID: https://orcid.org/0000-0001-9239-9570)
- Erik J. Kopping (ORCID: https://orcid.org/0000-0002-0367-1251)
- Saymon Akther (ORCID: https://orcid.org/0000-0002-9084-9379)
- Aaron Olsen
- Jennifer L. Havens (ORCID: https://orcid.org/0000-0003-3095-5900)
- Victoria Ruiz (ORCID: https://orcid.org/0000-0002-0121-4727)
- Michelle Su (ORCID: https://orcid.org/0000-0002-3212-2120)
- Julia Latash (ORCID: https://orcid.org/0000-0001-7606-2812)
- Helly Amin
- Tetyana I. Vasylyeva (ORCID: https://orcid.org/0000-0002-9736-7022)
- Jonathan E. Pekar (ORCID: https://orcid.org/0000-0003-0977-2886)
- Jennifer Baumgartner (ORCID: https://orcid.org/0009-0009-1791-4021)
- Joel O. Wertheim (ORCID: https://orcid.org/0000-0003-4882-5856)
- Randal C. Fowler (ORCID: https://orcid.org/0000-0002-6703-0488)
- Scott Hughes
- Faten Taki
- Moinuddin A. Chowdhury
- Kimberly Johnson (ORCID: https://orcid.org/0000-0002-7835-5288)
- Tyler Clabby
- Nelson De La Cruz
Institutions
- New York City Department of Health and Mental Hygiene (US)
- University of California, Irvine (US)
- University of California San Diego (US)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-09-24
- DOI
- https://doi.org/10.1038/s41467-025-60486-x
- Citations
- 1
- Primary Topic
- Poxvirus research and outbreaks
- Type
- article
- Field-Weighted Citation Impact
- 1.04
Funders
- U.S. Department of Health and Human Services
- Yale University
- Association of Public Health Laboratories
- Centers for Disease Control and Prevention