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

Author

Listed:
  • 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
    University of California San Diego)

  • 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
    University of California Irvine)

  • Joel O. Wertheim

    (University of California San Diego)

  • Scott Hughes

    (Department of Health and Mental Hygiene)

  • Enoma Omoregie

    (Department of Health and Mental Hygiene)

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.

Suggested Citation

  • 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 Jo, 2025. "Genomic epidemiology of mpox virus during the 2022 outbreak in New York City," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-60486-x
    DOI: 10.1038/s41467-025-60486-x
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