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Long-Read Deep Sequencing Reveals High Rates of Multilineage Transmission and Rapid Viral Population Changes in Acute HIV Infection.

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Title: Long-Read Deep Sequencing Reveals High Rates of Multilineage Transmission and Rapid Viral Population Changes in Acute HIV Infection.
Authors: Mullins JI; Department of Microbiology, University of Washington, Seattle, WA, US., Deng W; Department of Microbiology, University of Washington, Seattle, WA, US., Giorgi EE; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US., Magaret CA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US., Rolland M; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, US.; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, US., Bhattacharya T; Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, US.; Santa Fe Institute, Santa Fe, NM, US., Westfall DH; Department of Microbiology, University of Washington, Seattle, WA, US., Yssel AEJ; Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town, Cape Town, ZA., Bumgarner RE; Department of Microbiology, University of Washington, Seattle, WA, US., Murrell B; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE., Ndung'u T; African Health Research Institute, University of KwaZulu Natal, Durban, ZA.; HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, ZA.; Ragon Institute of Mass General Brigham, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, US.; Division of Infection and Immunity, University College London, London, UK., Robb ML; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, US., Rossenkhan R; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US., Edlefsen PT; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US., Dong KL; Ragon Institute of Mass General Brigham, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, US., Chen L; Department of Microbiology, University of Washington, Seattle, WA, US., Gwashu-Nyangiri A; Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town, Cape Town, ZA., Zhao H; Department of Microbiology, University of Washington, Seattle, WA, US., Thebus R; Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town, Cape Town, ZA., Sawe F; Kenya Medical Research Institute, Walter Reed Army Institute of Research-Africa, Nairobi, KE.; Henry M. Jackson Foundation Medical Research International, Nairobi, KE., Nitayaphan S; Armed Forces Research Institute of Medical Sciences, Bangkok, TH., York T; Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town, Cape Town, ZA., Matten D; Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town, Cape Town, ZA., Murrell H; Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town, Cape Town, ZA., Pankow AP; Department of Microbiology, University of Washington, Seattle, WA, US., Juraska M; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US., Ludwig J; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US., Hural J; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US., Cohen MS; University of North Carolina, Chapel Hill, NC, US., Corey L; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US., McElrath MJ; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US., Gilbert PB; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US., Williamson C; Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town, Cape Town, ZA.; National Health Laboratory Services, ZA.
Source: BioRxiv : the preprint server for biology [bioRxiv] 2025 Oct 15. Date of Electronic Publication: 2025 Oct 15.
Publication Type: Journal Article; Preprint
Journal Info: Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE
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  Data: Long-Read Deep Sequencing Reveals High Rates of Multilineage Transmission and Rapid Viral Population Changes in Acute HIV Infection.
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  Data: <searchLink fieldCode="AU" term="%22Mullins+JI%22">Mullins JI</searchLink>; Department of Microbiology, University of Washington, Seattle, WA, US.<br /><searchLink fieldCode="AU" term="%22Deng+W%22">Deng W</searchLink>; Department of Microbiology, University of Washington, Seattle, WA, US.<br /><searchLink fieldCode="AU" term="%22Giorgi+EE%22">Giorgi EE</searchLink>; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US.<br /><searchLink fieldCode="AU" term="%22Magaret+CA%22">Magaret CA</searchLink>; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US.<br /><searchLink fieldCode="AU" term="%22Rolland+M%22">Rolland M</searchLink>; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, US.; U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, US.<br /><searchLink fieldCode="AU" term="%22Bhattacharya+T%22">Bhattacharya T</searchLink>; Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, US.; Santa Fe Institute, Santa Fe, NM, US.<br /><searchLink fieldCode="AU" term="%22Westfall+DH%22">Westfall DH</searchLink>; Department of Microbiology, University of Washington, Seattle, WA, US.<br /><searchLink fieldCode="AU" term="%22Yssel+AEJ%22">Yssel AEJ</searchLink>; Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town, Cape Town, ZA.<br /><searchLink fieldCode="AU" term="%22Bumgarner+RE%22">Bumgarner RE</searchLink>; Department of Microbiology, University of Washington, Seattle, WA, US.<br /><searchLink fieldCode="AU" term="%22Murrell+B%22">Murrell B</searchLink>; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE.<br /><searchLink fieldCode="AU" term="%22Ndung'u+T%22">Ndung'u T</searchLink>; African Health Research Institute, University of KwaZulu Natal, Durban, ZA.; HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, ZA.; Ragon Institute of Mass General Brigham, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, US.; Division of Infection and Immunity, University College London, London, UK.<br /><searchLink fieldCode="AU" term="%22Robb+ML%22">Robb ML</searchLink>; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, US.<br /><searchLink fieldCode="AU" term="%22Rossenkhan+R%22">Rossenkhan R</searchLink>; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US.<br /><searchLink fieldCode="AU" term="%22Edlefsen+PT%22">Edlefsen PT</searchLink>; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US.<br /><searchLink fieldCode="AU" term="%22Dong+KL%22">Dong KL</searchLink>; Ragon Institute of Mass General Brigham, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, US.<br /><searchLink fieldCode="AU" term="%22Chen+L%22">Chen L</searchLink>; Department of Microbiology, University of Washington, Seattle, WA, US.<br /><searchLink fieldCode="AU" term="%22Gwashu-Nyangiri+A%22">Gwashu-Nyangiri A</searchLink>; Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town, Cape Town, ZA.<br /><searchLink fieldCode="AU" term="%22Zhao+H%22">Zhao H</searchLink>; Department of Microbiology, University of Washington, Seattle, WA, US.<br /><searchLink fieldCode="AU" term="%22Thebus+R%22">Thebus R</searchLink>; Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town, Cape Town, ZA.<br /><searchLink fieldCode="AU" term="%22Sawe+F%22">Sawe F</searchLink>; Kenya Medical Research Institute, Walter Reed Army Institute of Research-Africa, Nairobi, KE.; Henry M. Jackson Foundation Medical Research International, Nairobi, KE.<br /><searchLink fieldCode="AU" term="%22Nitayaphan+S%22">Nitayaphan S</searchLink>; Armed Forces Research Institute of Medical Sciences, Bangkok, TH.<br /><searchLink fieldCode="AU" term="%22York+T%22">York T</searchLink>; Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town, Cape Town, ZA.<br /><searchLink fieldCode="AU" term="%22Matten+D%22">Matten D</searchLink>; Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town, Cape Town, ZA.<br /><searchLink fieldCode="AU" term="%22Murrell+H%22">Murrell H</searchLink>; Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town, Cape Town, ZA.<br /><searchLink fieldCode="AU" term="%22Pankow+AP%22">Pankow AP</searchLink>; Department of Microbiology, University of Washington, Seattle, WA, US.<br /><searchLink fieldCode="AU" term="%22Juraska+M%22">Juraska M</searchLink>; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US.<br /><searchLink fieldCode="AU" term="%22Ludwig+J%22">Ludwig J</searchLink>; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US.<br /><searchLink fieldCode="AU" term="%22Hural+J%22">Hural J</searchLink>; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US.<br /><searchLink fieldCode="AU" term="%22Cohen+MS%22">Cohen MS</searchLink>; University of North Carolina, Chapel Hill, NC, US.<br /><searchLink fieldCode="AU" term="%22Corey+L%22">Corey L</searchLink>; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US.<br /><searchLink fieldCode="AU" term="%22McElrath+MJ%22">McElrath MJ</searchLink>; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US.<br /><searchLink fieldCode="AU" term="%22Gilbert+PB%22">Gilbert PB</searchLink>; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, US.<br /><searchLink fieldCode="AU" term="%22Williamson+C%22">Williamson C</searchLink>; Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town, Cape Town, ZA.; National Health Laboratory Services, ZA.
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