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Sequential intrahost evolution and onward transmission of SARS-CoV-2 variants

Author

Listed:
  • Ana S. Gonzalez-Reiche

    (Icahn School of Medicine at Mount Sinai)

  • Hala Alshammary

    (Icahn School of Medicine at Mount Sinai
    Icahn School of Medicine at Mount Sinai)

  • Sarah Schaefer

    (Icahn School of Medicine at Mount Sinai)

  • Gopi Patel

    (Icahn School of Medicine at Mount Sinai)

  • Jose Polanco

    (Icahn School of Medicine at Mount Sinai
    Icahn School of Medicine at Mount Sinai)

  • Juan Manuel Carreño

    (Icahn School of Medicine at Mount Sinai
    Icahn School of Medicine at Mount Sinai)

  • Angela A. Amoako

    (Icahn School of Medicine at Mount Sinai
    Icahn School of Medicine at Mount Sinai)

  • Aria Rooker

    (Icahn School of Medicine at Mount Sinai
    Icahn School of Medicine at Mount Sinai)

  • Christian Cognigni

    (Icahn School of Medicine at Mount Sinai
    Icahn School of Medicine at Mount Sinai)

  • Daniel Floda

    (Icahn School of Medicine at Mount Sinai)

  • Adriana Guchte

    (Icahn School of Medicine at Mount Sinai)

  • Zain Khalil

    (Icahn School of Medicine at Mount Sinai)

  • Keith Farrugia

    (Icahn School of Medicine at Mount Sinai)

  • Nima Assad

    (Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai)

  • Jian Zhang

    (Icahn School of Medicine at Mount Sinai)

  • Bremy Alburquerque

    (Icahn School of Medicine at Mount Sinai
    Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai)

  • Levy A. Sominsky

    (Icahn School of Medicine at Mount Sinai
    Icahn School of Medicine at Mount Sinai)

  • Charles Gleason

    (Icahn School of Medicine at Mount Sinai
    Icahn School of Medicine at Mount Sinai)

  • Komal Srivastava

    (Icahn School of Medicine at Mount Sinai
    Icahn School of Medicine at Mount Sinai)

  • Robert Sebra

    (Icahn School of Medicine at Mount Sinai
    Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai
    Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai
    The Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai)

  • Juan David Ramirez

    (Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai
    Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario)

  • Radhika Banu

    (Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai)

  • Paras Shrestha

    (Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai)

  • Florian Krammer

    (Icahn School of Medicine at Mount Sinai
    Icahn School of Medicine at Mount Sinai
    Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai)

  • Alberto Paniz-Mondolfi

    (Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai)

  • Emilia Mia Sordillo

    (Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai)

  • Viviana Simon

    (Icahn School of Medicine at Mount Sinai
    Icahn School of Medicine at Mount Sinai
    Icahn School of Medicine at Mount Sinai
    Molecular, and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai)

  • Harm Bakel

    (Icahn School of Medicine at Mount Sinai
    Icahn School of Medicine at Mount Sinai
    Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai)

Abstract

Persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have been reported in immune-compromised individuals and people undergoing immune-modulatory treatments. Although intrahost evolution has been documented, direct evidence of subsequent transmission and continued stepwise adaptation is lacking. Here we describe sequential persistent SARS-CoV-2 infections in three individuals that led to the emergence, forward transmission, and continued evolution of a new Omicron sublineage, BA.1.23, over an eight-month period. The initially transmitted BA.1.23 variant encoded seven additional amino acid substitutions within the spike protein (E96D, R346T, L455W, K458M, A484V, H681R, A688V), and displayed substantial resistance to neutralization by sera from boosted and/or Omicron BA.1-infected study participants. Subsequent continued BA.1.23 replication resulted in additional substitutions in the spike protein (S254F, N448S, F456L, M458K, F981L, S982L) as well as in five other virus proteins. Our findings demonstrate not only that the Omicron BA.1 lineage can diverge further from its already exceptionally mutated genome but also that patients with persistent infections can transmit these viral variants. Thus, there is, an urgent need to implement strategies to prevent prolonged SARS-CoV-2 replication and to limit the spread of newly emerging, neutralization-resistant variants in vulnerable patients.

Suggested Citation

  • Ana S. Gonzalez-Reiche & Hala Alshammary & Sarah Schaefer & Gopi Patel & Jose Polanco & Juan Manuel Carreño & Angela A. Amoako & Aria Rooker & Christian Cognigni & Daniel Floda & Adriana Guchte & Zain, 2023. "Sequential intrahost evolution and onward transmission of SARS-CoV-2 variants," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-38867-x
    DOI: 10.1038/s41467-023-38867-x
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