Development and validation of HIV SMRTcap for the characterization of HIV-1 reservoirs across tissues and subtypes

• Ghazal Sadri ,

  Contributed equally to this work with: Ghazal Sadri, Steven T. Nadakal, David Sachs, Eric Rouchka, Melissa L. Smith

  Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Project administration, Software, Validation, Visualization, Writing – original draft, Writing – review & editing

  Affiliation Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America

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• Steven T. Nadakal ,

  Contributed equally to this work with: Ghazal Sadri, Steven T. Nadakal, David Sachs, Eric Rouchka, Melissa L. Smith

  Roles Data curation, Formal analysis, Investigation, Methodology, Resources, Software, Validation, Visualization, Writing – original draft, Writing – review & editing

  Affiliation Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America

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• William Lauer,

  Roles Formal analysis, Investigation, Methodology, Writing – review & editing

  Affiliation Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America

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• Justin Kos,

  Roles Formal analysis, Investigation, Methodology

  Affiliation Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America

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• Parmit K. Singh,

  Roles Data curation, Formal analysis, Investigation, Methodology, Project administration, Writing – review & editing

  Affiliations Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America, Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America

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• Erin Elliott,

  Roles Formal analysis, Investigation, Methodology, Validation, Writing – review & editing

  Affiliation Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America

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• Catherine W. Kaiser,

  Roles Formal analysis, Investigation, Methodology, Writing – review & editing

  Affiliation Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America

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• Easton E. Ford,

  Roles Formal analysis, Investigation, Methodology, Project administration, Validation, Writing – review & editing

  Affiliation Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America

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• Nadia Richardson,

  Roles Investigation, Methodology, Visualization, Writing – review & editing

  Affiliation Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America

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• Kaitlyn M. Shields,

  Roles Data curation, Methodology

  Affiliation Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America

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• Elizabeth Hudson,

  Roles Investigation, Methodology, Resources, Writing – review & editing

  Affiliation Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America

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• Noemi L. Linden,

  Roles Investigation, Methodology, Resources, Writing – review & editing

  Affiliations Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, United States of America, Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York, United States of America, Weill Cornell Medicine, Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, New York, United States of America

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• Ali Danesh,

  Roles Investigation, Methodology, Resources

  Affiliations Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York, United States of America, Weill Cornell Medicine, Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, New York, United States of America

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• James Powell,

  Roles Conceptualization, Investigation, Methodology

  Affiliation Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America

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• Peter Warburton,

  Roles Conceptualization, Investigation, Methodology, Writing – review & editing

  Affiliation Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America

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• Juan Soto,

  Roles Investigation, Methodology

  Affiliation Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America

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• Matthew Emery,

  Roles Investigation, Methodology, Validation

  Affiliation Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America

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• Gintaras Deikus,

  Roles Conceptualization, Investigation, Methodology, Validation

  Affiliations Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America, Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America

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• Guinevere Q. Lee,

  Roles Methodology, Resources, Validation

  Affiliation Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, United States of America

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• Susanna L. Lamers,

  Roles Resources, Software, Visualization

  Affiliation BioinfoExperts, LLC., Thibodaux, Louisiana, United States of America

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• Steven J. Reynolds,

  Roles Project administration, Resources, Supervision, Writing – review & editing

  Affiliations Rakai Health Sciences Program, Kalisizo, Uganda, Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland, United States of America, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America

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• Ronald Galiwango,

  Roles Project administration, Resources, Supervision, Validation

  Affiliation Rakai Health Sciences Program, Kalisizo, Uganda

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• Jessica L. Prodger,

  Roles Formal analysis, Methodology, Project administration, Resources, Supervision, Visualization, Writing – review & editing

  Affiliations Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada, Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada

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• Stephen Tomusange,

  Roles Resources, Writing – review & editing

  Affiliation Rakai Health Sciences Program, Kalisizo, Uganda

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• Taddeo Kityamuweesi,

  Roles Project administration, Resources, Writing – review & editing

  Affiliation Rakai Health Sciences Program, Kalisizo, Uganda

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• Tina Han,

  Roles Conceptualization, Investigation, Methodology, Writing – review & editing

  Affiliation Twist Bioscience Corp., San Francisco, California, United States of America

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• R. Brad Jones,

  Roles Data curation, Formal analysis, Project administration, Resources, Supervision, Visualization, Writing – review & editing

  Affiliations Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York, United States of America, Weill Cornell Medicine, Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, New York, United States of America

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• Aaron A. R. Tobian,

  Roles Conceptualization, Formal analysis, Funding acquisition, Project administration, Resources, Supervision, Visualization, Writing – review & editing

  Affiliation Department of Pathology, Johns Hopkins University, Baltimore, Maryland, United States of America

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• Alan N. Engelman,

  Roles Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Writing – review & editing

  Affiliations Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America, Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America

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• Robert Sebra,

  Roles Conceptualization, Funding acquisition, Investigation, Methodology, Project administration, Resources, Supervision, Visualization, Writing – review & editing

  Affiliations Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America, Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America

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• Susan Morgello,

  Roles Conceptualization, Data curation, Investigation, Methodology, Project administration, Resources, Visualization, Writing – review & editing

  Affiliation Division of Neuro-Infectious Diseases, Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America

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• Andrew D. Redd,

  Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Project administration, Resources, Validation, Visualization, Writing – original draft

  Affiliations Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, Maryland, United States of America, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa

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• David Sachs ,

  Contributed equally to this work with: Ghazal Sadri, Steven T. Nadakal, David Sachs, Eric Rouchka, Melissa L. Smith

  Roles Conceptualization, Formal analysis, Funding acquisition, Methodology, Software, Validation, Writing – original draft

  Affiliations Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America, Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America

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• Eric Rouchka ,

  Contributed equally to this work with: Ghazal Sadri, Steven T. Nadakal, David Sachs, Eric Rouchka, Melissa L. Smith

  Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing

  Affiliations Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America, Kentucky Biomedical Research Infrastructure Network Data Science Core, University of Louisville, Louisville, Kentucky, United States of America

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•  [ ... ],
• Melissa L. Smith

  Contributed equally to this work with: Ghazal Sadri, Steven T. Nadakal, David Sachs, Eric Rouchka, Melissa L. Smith

  Roles Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing

  * E-mail: ml.smith@louisville.edu

  Affiliation Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America

  https://orcid.org/0000-0001-7151-3207

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